=============================================================================== About this build: this rebuild has been done as part of reproduce.debian.net where we aim to reproduce Debian binary packages distributed via ftp.debian.org, by rebuilding using the exact same packages as the original build on the buildds, as described in the relevant .buildinfo file from buildinfos.debian.net. For more information please go to https://reproduce.debian.net or join #debian-reproducible on irc.debian.org =============================================================================== Preparing download of sources for /srv/rebuilderd/tmp/rebuilderdJmxW9F/inputs/salmon_1.10.2+ds1-1+b5_amd64.buildinfo Source: salmon Version: 1.10.2+ds1-1 rebuilderd-worker node: osuosl4-amd64 +------------------------------------------------------------------------------+ | Downloading sources Mon, 23 Jun 2025 03:19:22 +0000 | +------------------------------------------------------------------------------+ Get:1 https://deb.debian.org/debian trixie InRelease [166 kB] Get:2 https://deb.debian.org/debian sid InRelease [208 kB] Get:3 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:4 https://deb.debian.org/debian sid/main Sources [11.0 MB] Fetched 21.9 MB in 2s (10.2 MB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/s/salmon/salmon_1.10.2%2bds1-1.dsc' salmon_1.10.2+ds1-1.dsc 2558 SHA256:b5097bef9c0f5f1af3d1811e7de794f2eec2d1d5c59e2cc85badd3a4a2ab72ab 'https://deb.debian.org/debian/pool/main/s/salmon/salmon_1.10.2%2bds1.orig.tar.xz' salmon_1.10.2+ds1.orig.tar.xz 5718424 SHA256:895840bed22f93cb8c02ff00b9007473e291ef06b753a950ec2b75373d78219c 'https://deb.debian.org/debian/pool/main/s/salmon/salmon_1.10.2%2bds1-1.debian.tar.xz' salmon_1.10.2+ds1-1.debian.tar.xz 1893940 SHA256:6d296a4cb41e4068975b0ff8592d700cd525a2f961c7fc10ba54cdc69cfe2456 895840bed22f93cb8c02ff00b9007473e291ef06b753a950ec2b75373d78219c salmon_1.10.2+ds1.orig.tar.xz 6d296a4cb41e4068975b0ff8592d700cd525a2f961c7fc10ba54cdc69cfe2456 salmon_1.10.2+ds1-1.debian.tar.xz b5097bef9c0f5f1af3d1811e7de794f2eec2d1d5c59e2cc85badd3a4a2ab72ab salmon_1.10.2+ds1-1.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Mon, 23 Jun 2025 03:19:26 +0000 | +------------------------------------------------------------------------------+ + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdJmxW9F/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdJmxW9F/inputs/salmon_1.10.2+ds1-1+b5_amd64.buildinfo Rebuilding salmon=1.10.2+ds1-1 in /srv/rebuilderd/tmp/rebuilderdJmxW9F/inputs now. /srv/rebuilderd/tmp/rebuilderdJmxW9F/inputs/salmon_1.10.2+ds1-1+b5_amd64.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/salmon-1.10.2+ds1 I: verifying dsc... successful! Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid InRelease [205 kB] Get:2 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 Packages [10.1 MB] Fetched 10.3 MB in 1s (8755 kB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20250403T143652Z/dists/sid/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3.13-doc all 3.13.2-3 [15.3 MB] Fetched 15.3 MB in 0s (77.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7o4jtzmo/python3.13-doc_3.13.2-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libattr1 amd64 1:2.5.2-3 [22.9 kB] Fetched 22.9 kB in 0s (2064 kB/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpabbwy5xa/libattr1_2.5.2-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Fetched 30.5 kB in 0s (1562 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt_m1u9mi/libjs-sphinxdoc_8.1.3-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 icu-devtools amd64 76.1-3 [215 kB] Fetched 215 kB in 0s (7670 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8htoxpea/icu-devtools_76.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libstdc++-14-dev amd64 14.2.0-19 [2376 kB] Fetched 2376 kB in 0s (85.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj_6193b_/libstdc++-14-dev_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Fetched 349 kB in 0s (11.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3j21ajve/libarchive13t64_3.7.4-1.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libpam-modules-bin amd64 1.7.0-3 [48.9 kB] Fetched 48.9 kB in 0s (3663 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5j05448r/libpam-modules-bin_1.7.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB] Fetched 698 kB in 0s (14.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcwn6xhqm/libxml2_2.12.7+dfsg+really2.9.14-0.4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Fetched 6050 kB in 0s (40.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnw_i0po_/python-babel-localedata_2.17.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 nodejs amd64 20.19.0+dfsg-1 [350 kB] Fetched 350 kB in 0s (8170 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdqskztnc/nodejs_20.19.0+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-4.2 [254 kB] Fetched 254 kB in 0s (5518 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvamvju3a/libboost-iostreams1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 findutils amd64 4.10.0-3 [700 kB] Fetched 700 kB in 0s (45.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcaywra_t/findutils_4.10.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-regex1.83.0 amd64 1.83.0-4.2 [330 kB] Fetched 330 kB in 0s (10.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmy7w7yog/libboost-regex1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 help2man amd64 1.49.3 [198 kB] Fetched 198 kB in 0s (6424 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpainp32_7/help2man_1.49.3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Fetched 403 kB in 0s (30.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq49i9dwz/python3-docutils_0.21.2+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 autopoint all 0.23.1-1 [770 kB] Fetched 770 kB in 0s (55.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc5q_z4bz/autopoint_0.23.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1 [1200 B] Fetched 1200 B in 0s (0 B/s) dpkg-name: info: moved 'g++-x86-64-linux-gnu_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpux0fe1v6/g++-x86-64-linux-gnu_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Fetched 138 kB in 0s (12.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpni_c1yvg/libgssapi-krb5-2_1.21.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-docs-theme all 2025.2-1 [19.4 kB] Fetched 19.4 kB in 0s (741 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppa3fvfdj/python3-docs-theme_2025.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libdivsufsort-dev amd64 2.0.1-6+b1 [19.1 kB] Fetched 19.1 kB in 0s (894 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppu564l1k/libdivsufsort-dev_2.0.1-6+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libc6-dev amd64 2.41-6 [1988 kB] Fetched 1988 kB in 0s (34.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3z9n5fkv/libc6-dev_2.41-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libtbb-dev amd64 2022.1.0-1 [201 kB] Fetched 201 kB in 0s (6321 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi5ag1n19/libtbb-dev_2022.1.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Fetched 1041 kB in 0s (24.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi6kaohpj/libeigen3-dev_3.4.0-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Fetched 81.5 kB in 0s (8030 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaj22kwyk/libk5crypto3_1.21.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libidn2-dev amd64 2.3.8-2 [103 kB] Fetched 103 kB in 0s (9512 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjguprw6_/libidn2-dev_2.3.8-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 bsdextrautils amd64 2.41-3 [94.4 kB] Fetched 94.4 kB in 0s (4755 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzjwt28p5/bsdextrautils_2.41-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Fetched 108 kB in 0s (1650 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpviiqkb1q/python3-chardet_5.2.0+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-timer-dev amd64 1.83.0.2+b2 [3716 B] Fetched 3716 B in 0s (306 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvkl3pxk4/libboost-timer-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libubsan1 amd64 14.2.0-19 [1074 kB] Fetched 1074 kB in 0s (59.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvyv5y8z2/libubsan1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Fetched 128 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7uvo0yeh/docutils-common_0.21.2+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Fetched 3628 B in 0s (211 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw7zjef52/libboost-filesystem-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Fetched 9652 B in 0s (721 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu1jdn07q/python3-certifi_2025.1.31+ds-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Fetched 63.3 kB in 0s (6172 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4dktdy0i/rpcsvc-proto_1.4.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Fetched 326 kB in 0s (26.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpykr_4598/libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Fetched 1318 kB in 0s (28.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsz52a1xq/nettle-dev_3.10.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libdpkg-perl all 1.22.18 [649 kB] Fetched 649 kB in 0s (17.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcll6on3b/libdpkg-perl_1.22.18_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 perl-modules-5.40 all 5.40.1-2 [3017 kB] Fetched 3017 kB in 0s (89.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0uwzsrxb/perl-modules-5.40_5.40.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 m4 amd64 1.4.19-7 [294 kB] Fetched 294 kB in 0s (9968 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpor4xih1w/m4_1.4.19-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libpython3.13-minimal amd64 3.13.2-3 [861 kB] Fetched 861 kB in 0s (20.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw95gd5ct/libpython3.13-minimal_3.13.2-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 sensible-utils all 0.0.24 [24.8 kB] Fetched 24.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfipiokkr/sensible-utils_0.0.24_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 util-linux amd64 2.41-3 [1231 kB] Fetched 1231 kB in 0s (29.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkqzvu0lo/util-linux_2.41-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-urllib3 all 2.3.0-2 [114 kB] Fetched 114 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbqxcgcjp/python3-urllib3_2.3.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-doc all 3.13.2-2 [10.3 kB] Fetched 10.3 kB in 0s (688 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphmmj_cbd/python3-doc_3.13.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Fetched 75.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbi1e0nv8/libgdbm6t64_1.24-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libdebconfclient0 amd64 0.278 [10.5 kB] Fetched 10.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_3br1342/libdebconfclient0_0.278_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 gzip amd64 1.13-1 [138 kB] Fetched 138 kB in 0s (12.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5pipg9zg/gzip_1.13-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 liblz4-1 amd64 1.10.0-4 [63.9 kB] Fetched 63.9 kB in 0s (3389 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp001d8luq/liblz4-1_1.10.0-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libmpc3 amd64 1.3.1-1+b3 [52.2 kB] Fetched 52.2 kB in 0s (3810 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3f4ap3q1/libmpc3_1.3.1-1+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 autotools-dev all 20240727.1 [60.2 kB] Fetched 60.2 kB in 0s (4091 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwe2w8l65/autotools-dev_20240727.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 media-types all 13.0.0 [29.3 kB] Fetched 29.3 kB in 0s (1985 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoygyat8l/media-types_13.0.0_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 ca-certificates all 20241223 [164 kB] Fetched 164 kB in 0s (14.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph3azious/ca-certificates_20241223_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-system1.83.0 amd64 1.83.0-4.2 [231 kB] Fetched 231 kB in 0s (5830 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqq_u0lzf/libboost-system1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB] Fetched 29.7 kB in 0s (1462 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd8xqt7dz/python3-sphinx-rtd-theme_3.0.2+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 mawk amd64 1.3.4.20250131-1 [141 kB] Fetched 141 kB in 0s (9745 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphdcfkc7l/mawk_1.3.4.20250131-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 debconf all 1.5.91 [121 kB] Fetched 121 kB in 0s (7887 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk0rv8dnb/debconf_1.5.91_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 dpkg-dev all 1.22.18 [1338 kB] Fetched 1338 kB in 0s (72.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9z0qmxgs/dpkg-dev_1.22.18_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libatomic1 amd64 14.2.0-19 [9308 B] Fetched 9308 B in 0s (803 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj9yjp8qq/libatomic1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libxxhash0 amd64 0.8.3-2 [27.1 kB] Fetched 27.1 kB in 0s (1369 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmiwdzhas/libxxhash0_0.8.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Fetched 14.0 kB in 0s (97.9 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzjettata/pkg-config_1.8.1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-system1.83-dev amd64 1.83.0-4.2 [232 kB] Fetched 232 kB in 0s (9087 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprzrcbowz/libboost-system1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libsystemd0 amd64 257.4-9 [452 kB] Fetched 452 kB in 0s (13.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc5bbl9cz/libsystemd0_257.4-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libbz2-1.0 amd64 1.0.8-6 [37.9 kB] Fetched 37.9 kB in 0s (3623 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5uhbuh_e/libbz2-1.0_1.0.8-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Fetched 316 kB in 0s (19.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5t3y7uie/libbrotli-dev_1.1.0-2+b7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Fetched 154 kB in 0s (13.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv7aqm9xh/libuv1t64_1.50.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 sphinx-common all 8.1.3-5 [617 kB] Fetched 617 kB in 0s (19.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprouknecr/sphinx-common_8.1.3-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Fetched 127 kB in 0s (6945 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvy4ya3na/libfmt10_10.1.1+ds1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 automake all 1:1.17-4 [862 kB] Fetched 862 kB in 0s (53.5 MB/s) dpkg-name: info: moved 'automake_1%3a1.17-4_all.deb' to '/srv/rebuilderd/tmp/tmpciyw6u01/automake_1.17-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-timer1.83.0 amd64 1.83.0-4.2 [235 kB] Fetched 235 kB in 0s (7120 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0va0e326/libboost-timer1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 gcc-14-base amd64 14.2.0-19 [49.4 kB] Fetched 49.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfzkvb0p8/gcc-14-base_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libbwa-dev amd64 0.7.18-1 [156 kB] Fetched 156 kB in 0s (8186 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcwl13b6t/libbwa-dev_0.7.18-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libjemalloc2 amd64 5.3.0-3 [274 kB] Fetched 274 kB in 0s (6731 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph80nlwnh/libjemalloc2_5.3.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Fetched 43.4 kB in 0s (3868 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7pwgidz9/python3-defusedxml_0.7.1-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3 [1014 kB] Fetched 1014 kB in 0s (66.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1hsgamyu/binutils-x86-64-linux-gnu_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 hostname amd64 3.25 [11.0 kB] Fetched 11.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5lp5jtlb/hostname_3.25_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 node-speech-rule-engine all 4.0.7+~0.1.31-2 [532 kB] Fetched 532 kB in 0s (13.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpix9x_f3n/node-speech-rule-engine_4.0.7+~0.1.31-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libhwasan0 amd64 14.2.0-19 [1488 kB] Fetched 1488 kB in 0s (76.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvcozfvho/libhwasan0_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 liblzma5 amd64 5.6.4-1 [280 kB] Fetched 280 kB in 0s (23.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqggywl9z/liblzma5_5.6.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B] Fetched 3736 B in 0s (164 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwmx8d1uu/libboost-system-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 xz-utils amd64 5.6.4-1 [554 kB] Fetched 554 kB in 0s (39.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx5u3zl_n/xz-utils_5.6.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libcares2 amd64 1.34.4-2.1 [97.9 kB] Fetched 97.9 kB in 0s (3547 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1ie1ipq2/libcares2_1.34.4-2.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Fetched 455 kB in 0s (15.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxgvt0pib/libgnutls-openssl27t64_3.8.9-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB] Fetched 125 kB in 0s (11.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp65egun6d/python3-charset-normalizer_3.4.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 gettext amd64 0.23.1-1 [1680 kB] Fetched 1680 kB in 0s (50.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7d9zatzt/gettext_0.23.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libicu76 amd64 76.1-3 [9721 kB] Fetched 9721 kB in 0s (20.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdyjq6azj/libicu76_76.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 rapmap-dev all 0.15.0+dfsg-4 [193 kB] Fetched 193 kB in 0s (6219 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpevei72zv/rapmap-dev_0.15.0+dfsg-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 node-commander all 9.4.1-1 [65.3 kB] Fetched 65.3 kB in 0s (1438 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy3051wuy/node-commander_9.4.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 patch amd64 2.7.6-7 [128 kB] Fetched 128 kB in 0s (10.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpev_8t0vn/patch_2.7.6-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libjemalloc-dev amd64 5.3.0-3 [490 kB] Fetched 490 kB in 0s (6081 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn6zkv7tz/libjemalloc-dev_5.3.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 liblsan0 amd64 14.2.0-19 [1204 kB] Fetched 1204 kB in 0s (73.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsk6smf8n/liblsan0_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 sgml-base all 1.31 [15.4 kB] Fetched 15.4 kB in 0s (812 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5dokyiug/sgml-base_1.31_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-thread1.83.0 amd64 1.83.0-4.2 [270 kB] Fetched 270 kB in 0s (7024 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpydp88gu0/libboost-thread1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Fetched 68.0 kB in 0s (2834 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcynt84jt/librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-4.2 [261 kB] Fetched 261 kB in 0s (4277 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyi6oknp4/libboost-iostreams1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Fetched 75.5 kB in 0s (5962 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp24bpwtl3/libnghttp2-14_1.64.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libpam-modules amd64 1.7.0-3 [177 kB] Fetched 177 kB in 0s (15.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe3irtiem/libpam-modules_1.7.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 g++ amd64 4:14.2.0-1 [1344 B] Fetched 1344 B in 0s (0 B/s) dpkg-name: info: moved 'g++_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpm1nx3kh4/g++_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-4.2 [282 kB] Fetched 282 kB in 0s (570 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc1umnqin/libboost-filesystem1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Fetched 91.3 kB in 0s (520 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpenbjzrfh/libnghttp3-dev_1.8.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Fetched 76.8 kB in 0s (2010 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnoiffbg5/libsparsehash-dev_2.0.3-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Fetched 517 kB in 0s (41.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgwumd7z4/fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libquadmath0 amd64 14.2.0-19 [145 kB] Fetched 145 kB in 0s (14.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfzztwar7/libquadmath0_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 openssl amd64 3.4.1-1 [1427 kB] Fetched 1427 kB in 0s (49.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsovb4lnz/openssl_3.4.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-date-time1.83.0 amd64 1.83.0-4.2 [230 kB] Fetched 230 kB in 0s (7350 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwq6o7422/libboost-date-time1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgff-dev amd64 2.0.0-3 [154 kB] Fetched 154 kB in 0s (4246 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7664uk_v/libgff-dev_2.0.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libbinutils amd64 2.44-3 [534 kB] Fetched 534 kB in 0s (31.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuqv80nj8/libbinutils_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libldap-dev amd64 2.6.9+dfsg-2 [311 kB] Fetched 311 kB in 0s (9916 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6mwjf4hd/libldap-dev_2.6.9+dfsg-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 base-files amd64 13.7 [73.0 kB] Fetched 73.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnrtzpk56/base-files_13.7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libtclap-dev amd64 1.2.5-1+b2 [3359 kB] Fetched 3359 kB in 0s (41.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_dn9rxum/libtclap-dev_1.2.5-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 bsdutils amd64 1:2.41-3 [110 kB] Fetched 110 kB in 0s (486 kB/s) dpkg-name: info: moved 'bsdutils_1%3a2.41-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp454n_0hr/bsdutils_2.41-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgprofng0 amd64 2.44-3 [808 kB] Fetched 808 kB in 0s (58.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppr9zpovf/libgprofng0_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Fetched 87.5 kB in 0s (4166 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz61zlzbf/libjson-perl_4.10000-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Fetched 245 kB in 0s (21.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk6qcfs4m/libssh2-1t64_1.11.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 node-mathjax-full all 3.2.2+~cs4.2.1-4 [3660 kB] Fetched 3660 kB in 0s (13.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5ubkprsp/node-mathjax-full_3.2.2+~cs4.2.1-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Fetched 30.2 kB in 0s (2441 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphdikap_4/pkgconf-bin_1.8.1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB] Fetched 1023 kB in 0s (8022 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeiw9l0fa/sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libhtscodecs-dev amd64 1.6.1-2 [3000 kB] Fetched 3000 kB in 0s (40.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptn8a9vf9/libhtscodecs-dev_1.6.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Fetched 19.7 kB in 0s (1886 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpww2w7rx_/libfile-stripnondeterminism-perl_1.14.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Fetched 137 kB in 0s (13.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkutgb4qx/libgomp1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-requests all 2.32.3+dfsg-5 [72.2 kB] Fetched 72.2 kB in 0s (3686 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp46ixwn4/python3-requests_2.32.3+dfsg-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 cmake-data all 3.31.6-2 [2268 kB] Fetched 2268 kB in 0s (25.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp04yc14ll/cmake-data_3.31.6-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libc-bin amd64 2.41-6 [635 kB] Fetched 635 kB in 0s (36.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8qguxobi/libc-bin_2.41-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Fetched 126 kB in 0s (11.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgrzpiwdl/krb5-multidev_1.21.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 grep amd64 3.11-4 [431 kB] Fetched 431 kB in 0s (20.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx4ejl58c/grep_3.11-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (8845 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph93cltct/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1 [4840 B] Fetched 4840 B in 0s (457 kB/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpjsekhh9a/cpp-x86-64-linux-gnu_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libsframe1 amd64 2.44-3 [78.4 kB] Fetched 78.4 kB in 0s (6692 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx5vuhaia/libsframe1_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libctf-nobfd0 amd64 2.44-3 [156 kB] Fetched 156 kB in 0s (11.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxijhsfvh/libctf-nobfd0_2.44-3_amd64.deb' Downloading dependency 1 of 348: python3.13-doc:amd64=3.13.2-3 Downloading dependency 2 of 348: libattr1:amd64=1:2.5.2-3 Downloading dependency 3 of 348: libjs-sphinxdoc:amd64=8.1.3-5 Downloading dependency 4 of 348: icu-devtools:amd64=76.1-3 Downloading dependency 5 of 348: libstdc++-14-dev:amd64=14.2.0-19 Downloading dependency 6 of 348: libarchive13t64:amd64=3.7.4-1.1 Downloading dependency 7 of 348: libpam-modules-bin:amd64=1.7.0-3 Downloading dependency 8 of 348: libxml2:amd64=2.12.7+dfsg+really2.9.14-0.4 Downloading dependency 9 of 348: python-babel-localedata:amd64=2.17.0-1 Downloading dependency 10 of 348: nodejs:amd64=20.19.0+dfsg-1 Downloading 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bsdextrautils:amd64=2.41-3 Downloading dependency 27 of 348: python3-chardet:amd64=5.2.0+dfsg-2 Downloading dependency 28 of 348: libboost-timer-dev:amd64=1.83.0.2+b2 Downloading dependency 29 of 348: libubsan1:amd64=14.2.0-19 Downloading dependency 30 of 348: docutils-common:amd64=0.21.2+dfsg-2 Downloading dependency 31 of 348: libboost-filesystem-dev:amd64=1.83.0.2+b2 Downloading dependency 32 of 348: python3-certifi:amd64=2025.1.31+ds-1 Downloading dependency 33 of 348: rpcsvc-proto:amd64=1.4.3-1 Downloading dependency 34 of 348: libjs-jquery:amd64=3.6.1+dfsg+~3.5.14-1 Downloading dependency 35 of 348: nettle-dev:amd64=3.10.1-1 Downloading dependency 36 of 348: libdpkg-perl:amd64=1.22.18 Downloading dependency 37 of 348: perl-modules-5.40:amd64=5.40.1-2 Downloading dependency 38 of 348: m4:amd64=1.4.19-7 Downloading dependency 39 of 348: libpython3.13-minimal:amd64=3.13.2-3 Downloading dependency 40 of 348: sensible-utils:amd64=0.0.24 Downloading dependency 41 of 348: 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libatomic1:amd64=14.2.0-19 Downloading dependency 58 of 348: libxxhash0:amd64=0.8.3-2 Downloading dependency 59 of 348: pkg-config:amd64=1.8.1-4 Downloading dependency 60 of 348: libboost-system1.83-dev:amd64=1.83.0-4.2 Downloading dependency 61 of 348: libsystemd0:amd64=257.4-9 Downloading dependency 62 of 348: libbz2-1.0:amd64=1.0.8-6 Downloading dependency 63 of 348: libbrotli-dev:amd64=1.1.0-2+b7 Downloading dependency 64 of 348: libuv1t64:amd64=1.50.0-2 Downloading dependency 65 of 348: sphinx-common:amd64=8.1.3-5 Downloading dependency 66 of 348: libfmt10:amd64=10.1.1+ds1-4 Downloading dependency 67 of 348: automake:amd64=1:1.17-4 Downloading dependency 68 of 348: libboost-timer1.83.0:amd64=1.83.0-4.2 Downloading dependency 69 of 348: gcc-14-base:amd64=14.2.0-19 Downloading dependency 70 of 348: libbwa-dev:amd64=0.7.18-1 Downloading dependency 71 of 348: libjemalloc2:amd64=5.3.0-3 Downloading dependency 72 of 348: python3-defusedxml:amd64=0.7.1-3 Downloading dependency 73 of 348: 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dependency 89 of 348: liblsan0:amd64=14.2.0-19 Downloading dependency 90 of 348: sgml-base:amd64=1.31 Downloading dependency 91 of 348: libboost-thread1.83.0:amd64=1.83.0-4.2 Downloading dependency 92 of 348: librtmp-dev:amd64=2.4+20151223.gitfa8646d.1-2+b5 Downloading dependency 93 of 348: libboost-iostreams1.83-dev:amd64=1.83.0-4.2 Downloading dependency 94 of 348: libnghttp2-14:amd64=1.64.0-1 Downloading dependency 95 of 348: libpam-modules:amd64=1.7.0-3 Downloading dependency 96 of 348: g++:amd64=4:14.2.0-1 Downloading dependency 97 of 348: libboost-filesystem1.83.0:amd64=1.83.0-4.2 Downloading dependency 98 of 348: libnghttp3-dev:amd64=1.8.0-1 Downloading dependency 99 of 348: libsparsehash-dev:amd64=2.0.3-2 Downloading dependency 100 of 348: fonts-font-awesome:amd64=5.0.10+really4.7.0~dfsg-4.1 Downloading dependency 101 of 348: libquadmath0:amd64=14.2.0-19 Downloading dependency 102 of 348: openssl:amd64=3.4.1-1 Downloading dependency 103 of 348: libboost-date-time1.83.0:amd64=1.83.0-4.2 Downloading dependency 104 of 348: libgff-dev:amd64=2.0.0-3 Downloading dependency 105 of 348: libbinutils:amd64=2.44-3 Downloading dependency 106 of 348: libldap-dev:amd64=2.6.9+dfsg-2 Downloading dependency 107 of 348: base-files:amd64=13.7 Downloading dependency 108 of 348: libtclap-dev:amd64=1.2.5-1+b2 Downloading dependency 109 of 348: bsdutils:amd64=1:2.41-3 Downloading dependency 110 of 348: libgprofng0:amd64=2.44-3 Downloading dependency 111 of 348: libjson-perl:amd64=4.10000-1 Downloading dependency 112 of 348: libssh2-1t64:amd64=1.11.1-1 Downloading dependency 113 of 348: node-mathjax-full:amd64=3.2.2+~cs4.2.1-4 Downloading dependency 114 of 348: pkgconf-bin:amd64=1.8.1-4 Downloading dependency 115 of 348: sphinx-rtd-theme-common:amd64=3.0.2+dfsg-2 Downloading dependency 116 of 348: libhtscodecs-dev:amd64=1.6.1-2 Downloading dependency 117 of 348: libfile-stripnondeterminism-perl:amd64=1.14.1-2 Downloading dependency 118 of 348: libgomp1:amd64=14.2.0-19 Downloading dependency 119 of 348: python3-requests:amd64=2.32.3+dfsg-5 Downloading dependency 120 of 348: cmake-data:amd64=3.31.6-2 Downloading dependency 121 of 348: libc-bin:amd64=2.41-6 Downloading dependency 122 of 348: krb5-multidev:amd64=1.21.3-5 Downloading dependency 123 of 348: grep:amd64=3.11-4 Downloading dependency 124 of 348: libarchive-zip-perl:amd64=1.68-1 Downloading dependency 125 of 348: cpp-x86-64-linux-gnu:amd64=4:14.2.0-1 Downloading dependency 126 of 348: libsframe1:amd64=2.44-3 Downloading dependency 127 of 348: libctf-nobfd0:amd64=2.44-3 Downloading dependency 128 of 348: comerr-dev:amd64=2.1-1.47.2-1+b1Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 comerr-dev amd64 2.1-1.47.2-1+b1 [56.0 kB] Fetched 56.0 kB in 0s (1296 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxurx7mo2/comerr-dev_2.1-1.47.2-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libspdlog1.15 amd64 1:1.15.1+ds-1 [108 kB] Fetched 108 kB in 0s (1260 kB/s) dpkg-name: info: moved 'libspdlog1.15_1%3a1.15.1+ds-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpzch0k6cs/libspdlog1.15_1.15.1+ds-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost1.83-dev amd64 1.83.0-4.2 [10.6 MB] Fetched 10.6 MB in 4s (2371 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0cvnq3ur/libboost1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libzstd1 amd64 1.5.7+dfsg-1 [304 kB] Fetched 304 kB in 0s (25.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg5qza4pz/libzstd1_1.5.7+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libjellyfish-2.0-2 amd64 2.3.1-4+b1 [67.3 kB] Fetched 67.3 kB in 0s (3561 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpswe8uod3/libjellyfish-2.0-2_2.3.1-4+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libssl3t64 amd64 3.4.1-1 [2304 kB] Fetched 2304 kB in 0s (96.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfz5s1d9a/libssl3t64_3.4.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libpython3.13-stdlib amd64 3.13.2-3 [1952 kB] Fetched 1952 kB in 0s (7239 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp207gxkv9/libpython3.13-stdlib_3.13.2-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 liblastlog2-2 amd64 2.41-3 [28.3 kB] Fetched 28.3 kB in 0s (516 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp99y9oohi/liblastlog2-2_2.41-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libmagic-mgc amd64 1:5.46-4 [337 kB] Fetched 337 kB in 0s (3398 kB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.46-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpmbka47bg/libmagic-mgc_5.46-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Fetched 27.9 kB in 0s (1644 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjjkgjavu/python3-alabaster_0.7.16-0.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libcurl4t64 amd64 8.13.0-1 [381 kB] Fetched 381 kB in 0s (7835 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp49fi3s75/libcurl4t64_8.13.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 node-undici all 7.3.0+dfsg1+~cs24.12.11-1 [333 kB] Fetched 333 kB in 0s (2691 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgv9zh235/node-undici_7.3.0+dfsg1+~cs24.12.11-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libspdlog-dev amd64 1:1.15.1+ds-1 [90.8 kB] Fetched 90.8 kB in 0s (3412 kB/s) dpkg-name: info: moved 'libspdlog-dev_1%3a1.15.1+ds-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpv6vt4uvw/libspdlog-dev_1.15.1+ds-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-19 [21.4 MB] Fetched 21.4 MB in 0s (48.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp15m8p6t7/gcc-14-x86-64-linux-gnu_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libsmartcols1 amd64 2.41-3 [142 kB] Fetched 142 kB in 0s (2599 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx1zp6u2_/libsmartcols1_2.41-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 ncurses-bin amd64 6.5+20250216-2 [438 kB] Fetched 438 kB in 0s (31.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprdw3u0qe/ncurses-bin_6.5+20250216-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libstaden-read14t64 amd64 1.15.0-1.1+b2 [268 kB] Fetched 268 kB in 0s (4976 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph7f6wmgk/libstaden-read14t64_1.15.0-1.1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 readline-common all 8.2-6 [69.4 kB] Fetched 69.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7yjb4kwu/readline-common_8.2-6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Fetched 1401 kB in 0s (35.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfvt814qu/libgnutls28-dev_3.8.9-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-4.2 [240 kB] Fetched 240 kB in 0s (4862 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjqot3aiw/libboost-chrono1.83.0t64_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 sphinx-doc all 8.1.3-5 [3487 kB] Fetched 3487 kB in 0s (16.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpju2cdtk2/sphinx-doc_8.1.3-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 bzip2 amd64 1.0.8-6 [40.5 kB] Fetched 40.5 kB in 0s (4025 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxzla3f4e/bzip2_1.0.8-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Fetched 42.5 kB in 0s (3869 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp512qsijw/libkadm5clnt-mit12_1.21.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Fetched 108 kB in 0s (7313 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk63nlbf7/libexpat1_2.7.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 docutils-doc all 0.21.2+dfsg-2 [1122 kB] Fetched 1122 kB in 0s (2928 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4p96sqqx/docutils-doc_0.21.2+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 coreutils amd64 9.5-1+b1 [2922 kB] Fetched 2922 kB in 0s (96.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe2db6ya3/coreutils_9.5-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Fetched 189 kB in 0s (12.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp73trhuni/libelf1t64_0.192-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Fetched 31.4 kB in 0s (3006 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyeqqilgp/libbz2-dev_1.0.8-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.2 [347 kB] Fetched 347 kB in 0s (6586 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgees9yw7/libboost-program-options1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libhwloc15 amd64 2.12.0-1 [164 kB] Fetched 164 kB in 0s (571 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1i9lni9v/libhwloc15_2.12.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-program-options1.83-dev amd64 1.83.0-4.2 [375 kB] Fetched 375 kB in 0s (3473 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdp76e7oq/libboost-program-options1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3.13-minimal amd64 3.13.2-3 [2212 kB] Fetched 2212 kB in 1s (1824 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpovxrm05y/python3.13-minimal_3.13.2-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Fetched 19.8 kB in 0s (1197 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkx_0e1dj/libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libaudit-common all 1:4.0.2-2 [12.7 kB] Fetched 12.7 kB in 0s (444 kB/s) dpkg-name: info: moved 'libaudit-common_1%3a4.0.2-2_all.deb' to '/srv/rebuilderd/tmp/tmpyjnz2p0b/libaudit-common_4.0.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Fetched 131 kB in 0s (5493 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7meqye6q/libngtcp2-16_1.11.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Fetched 58.0 kB in 0s (2454 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpejpdq8zs/python3-snowballstemmer_2.2.0-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-4.2 [297 kB] Fetched 297 kB in 0s (6328 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbevmrkqi/libboost-filesystem1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Fetched 68.9 kB in 0s (3221 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf7xl2k83/libuchardet0_0.0.8-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Fetched 598 kB in 0s (13.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvjnjyixl/libunbound8_1.22.0-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Fetched 8620 B in 0s (687 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbq1eg6kp/dh-strip-nondeterminism_1.14.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libnode115 amd64 20.19.0+dfsg-1 [12.1 MB] Fetched 12.1 MB in 0s (27.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpurq1eg7r/libnode115_20.19.0+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Fetched 42.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6x6metpd/libpipeline1_1.5.8-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-babel all 2.17.0-1 [117 kB] Fetched 117 kB in 0s (7641 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6w9kzrh9/python3-babel_2.17.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-jinja2 all 3.1.6-1 [107 kB] Fetched 107 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqk6bizyg/python3-jinja2_3.1.6-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Fetched 50.3 kB in 0s (5008 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphhdc2ur8/libgdbm-compat4t64_1.24-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 cpp-14 amd64 14.2.0-19 [1280 B] Fetched 1280 B in 0s (68.8 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu141tcsg/cpp-14_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Fetched 54.2 kB in 0s (192 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwt3j5etx/libkadm5srv-mit12_1.21.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 dash amd64 0.5.12-12 [98.5 kB] Fetched 98.5 kB in 0s (1233 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdy344z_p/dash_0.5.12-12_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-timer1.83-dev amd64 1.83.0-4.2 [237 kB] Fetched 237 kB in 0s (5190 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdml3diln/libboost-timer1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-roman all 5.0-1 [10.6 kB] Fetched 10.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmjelqn68/python3-roman_5.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 procps amd64 2:4.0.4-7 [878 kB] Fetched 878 kB in 0s (9862 kB/s) dpkg-name: info: moved 'procps_2%3a4.0.4-7_amd64.deb' to '/srv/rebuilderd/tmp/tmpxzgu3bnm/procps_4.0.4-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Fetched 3624 B in 0s (122 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi14ij27f/libboost-thread-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 liblzma-dev amd64 5.6.4-1 [323 kB] Fetched 323 kB in 0s (21.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf37lv3ph/liblzma-dev_5.6.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Fetched 307 kB in 0s (14.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2neewbdt/libbrotli1_1.1.0-2+b7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Fetched 132 kB in 0s (3364 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu0wx6fkv/librhash1_1.4.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libcereal-dev amd64 1.3.2+dfsg-5 [221 kB] Fetched 221 kB in 0s (6617 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp00zjcvzm/libcereal-dev_1.3.2+dfsg-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Fetched 248 kB in 0s (21.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppkss1o8e/po-debconf_1.0.21+nmu1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libtbbbind-2-5 amd64 2022.1.0-1 [14.0 kB] Fetched 14.0 kB in 0s (1107 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp38t2v4rb/libtbbbind-2-5_2022.1.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libtbbmalloc2 amd64 2022.1.0-1 [50.2 kB] Fetched 50.2 kB in 0s (423 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm8lz58mx/libtbbmalloc2_2022.1.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 cmake amd64 3.31.6-2 [12.0 MB] Fetched 12.0 MB in 0s (50.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoy3ksmeg/cmake_3.31.6-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libmd0 amd64 1.1.0-2+b1 [36.3 kB] Fetched 36.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7if8y3k5/libmd0_1.1.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 perl amd64 5.40.1-2 [267 kB] Fetched 267 kB in 0s (19.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0w5mosuw/perl_5.40.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 netbase all 6.5 [12.4 kB] Fetched 12.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptqguh3tr/netbase_6.5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libmagic1t64 amd64 1:5.46-4 [109 kB] Fetched 109 kB in 0s (7521 kB/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.46-4_amd64.deb' to '/srv/rebuilderd/tmp/tmp202q7zn6/libmagic1t64_5.46-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libcrypt-dev amd64 1:4.4.38-1 [119 kB] Fetched 119 kB in 0s (11.7 MB/s) dpkg-name: info: moved 'libcrypt-dev_1%3a4.4.38-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp47_xfhs3/libcrypt-dev_4.4.38-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 diffutils amd64 1:3.10-3 [385 kB] Fetched 385 kB in 0s (19.1 MB/s) dpkg-name: info: moved 'diffutils_1%3a3.10-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpv3vfo7pb/diffutils_3.10-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libcrypt1 amd64 1:4.4.38-1 [90.1 kB] Fetched 90.1 kB in 0s (0 B/s) dpkg-name: info: moved 'libcrypt1_1%3a4.4.38-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp1ru9pb65/libcrypt1_4.4.38-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Fetched 81.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0bc_0sla/libjsoncpp26_1.9.6-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Fetched 16.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph905mt0h/libkrb5-dev_1.21.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Fetched 34.0 kB in 0s (2216 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr72asht7/libngtcp2-crypto-gnutls-dev_1.11.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Fetched 208 kB in 0s (6168 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpleeo66qm/libp11-kit-dev_0.25.5-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libisl23 amd64 0.27-1 [659 kB] Fetched 659 kB in 0s (22.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe80ybdar/libisl23_0.27-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Fetched 29.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpykhwzvr0/libngtcp2-crypto-gnutls8_1.11.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 node-mj-context-menu all 0.9.1+ds-2 [69.9 kB] Fetched 69.9 kB in 0s (1787 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7srs67c9/node-mj-context-menu_0.9.1+ds-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libstdc++6 amd64 14.2.0-19 [714 kB] Fetched 714 kB in 0s (54.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmkt5v70o/libstdc++6_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 node-balanced-match all 2.0.0-1 [4872 B] Fetched 4872 B in 0s (368 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_qxh3p1j/node-balanced-match_2.0.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-19 [11.0 MB] Fetched 11.0 MB in 1s (18.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphpeo55v1/cpp-14-x86-64-linux-gnu_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-regex1.83-dev amd64 1.83.0-4.2 [346 kB] Fetched 346 kB in 1s (401 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl0kx8__k/libboost-regex1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libc-dev-bin amd64 2.41-6 [57.0 kB] Fetched 57.0 kB in 0s (1347 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprhc43216/libc-dev-bin_2.41-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libmount1 amd64 2.41-3 [208 kB] Fetched 208 kB in 1s (350 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9i7yc9hh/libmount1_2.41-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgcc-s1 amd64 14.2.0-19 [72.8 kB] Fetched 72.8 kB in 0s (1544 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzhzb_w_z/libgcc-s1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Fetched 90.9 kB in 0s (1758 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdjbq_r_k/libdebhelper-perl_13.24.2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Fetched 98.0 kB in 0s (863 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4yuma6mf/rapidjson-dev_1.1.0+dfsg2-7.3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 fonts-lato all 2.015-1 [2780 kB] Fetched 2780 kB in 1s (5438 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp46a1frtz/fonts-lato_2.015-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (1297 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpytpvb9q2/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-atomic1.83.0 amd64 1.83.0-4.2 [234 kB] Fetched 234 kB in 0s (845 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd6gnrluv/libboost-atomic1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-sphinx all 8.1.3-5 [468 kB] Fetched 468 kB in 0s (3737 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpegw78tz7/python3-sphinx_8.1.3-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-serialization1.83.0 amd64 1.83.0-4.2 [333 kB] Fetched 333 kB in 1s (571 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9z3itxg8/libboost-serialization1.83.0_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Fetched 467 kB in 1s (511 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuz3k2gaw/libsimde-dev_0.8.2-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libcc1-0 amd64 14.2.0-19 [42.8 kB] Fetched 42.8 kB in 0s (4175 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9utbyrnc/libcc1-0_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libcap-ng0 amd64 0.8.5-4+b1 [17.6 kB] Fetched 17.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvnwzmavw/libcap-ng0_0.8.5-4+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libsqlite3-0 amd64 3.46.1-2 [913 kB] Fetched 913 kB in 0s (57.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcneg6omm/libsqlite3-0_3.46.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 bash amd64 5.2.37-1.1+b2 [1500 kB] Fetched 1500 kB in 0s (27.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf2t9q8ra/bash_5.2.37-1.1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-packaging all 24.2-1 [55.3 kB] Fetched 55.3 kB in 0s (5233 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyypk4zpc/python3-packaging_24.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 man-db amd64 2.13.0-1 [1420 kB] Fetched 1420 kB in 0s (40.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxpnnpvpi/man-db_2.13.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 openssl-provider-legacy amd64 3.4.1-1 [302 kB] Fetched 302 kB in 0s (2377 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8hbpwusn/openssl-provider-legacy_3.4.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 ncurses-base all 6.5+20250216-2 [273 kB] Fetched 273 kB in 0s (16.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnttyoh47/ncurses-base_6.5+20250216-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Fetched 26.2 kB in 0s (2583 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbzzowh8j/pkgconf_1.8.1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libaudit1 amd64 1:4.0.2-2+b2 [55.1 kB] Fetched 55.1 kB in 0s (5111 kB/s) dpkg-name: info: moved 'libaudit1_1%3a4.0.2-2+b2_amd64.deb' to '/srv/rebuilderd/tmp/tmp0no34r_q/libaudit1_4.0.2-2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Fetched 329 kB in 0s (26.5 MB/s) dpkg-name: info: moved 'libgmpxx4ldbl_2%3a6.3.0+dfsg-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp54nm6vc0/libgmpxx4ldbl_6.3.0+dfsg-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-idna all 3.10-1 [42.0 kB] Fetched 42.0 kB in 0s (2922 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmbj5p976/python3-idna_3.10-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Fetched 3612 B in 0s (97.3 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplixvu3mc/libboost-program-options-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 node-xtend all 4.0.2-3 [3932 B] Fetched 3932 B in 0s (44.4 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi_v8vpdh/node-xtend_4.0.2-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 sed amd64 4.9-2 [329 kB] Fetched 329 kB in 0s (12.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplu6l78k8/sed_4.9-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-9 [704 kB] Fetched 704 kB in 0s (27.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptoywafq4/libdb5.3t64_5.3.28+dfsg2-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-3 [560 kB] Fetched 560 kB in 0s (11.2 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpnwuxwl2p/libgmp10_6.3.0+dfsg-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-serialization1.83-dev amd64 1.83.0-4.2 [373 kB] Fetched 373 kB in 0s (1102 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplb4uejgr/libboost-serialization1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libnettle8t64 amd64 3.10.1-1 [305 kB] Fetched 305 kB in 0s (24.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3br7y9wx/libnettle8t64_3.10.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 cpp amd64 4:14.2.0-1 [1568 B] Fetched 1568 B in 0s (0 B/s) dpkg-name: info: moved 'cpp_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpdqso146z/cpp_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 g++-14 amd64 14.2.0-19 [22.5 kB] Fetched 22.5 kB in 0s (2205 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf6r_zi_8/g++-14_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1+b1 [88.9 kB] Fetched 88.9 kB in 0s (7628 kB/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp3ehpum3l/zlib1g_1.3.dfsg+really1.3.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Fetched 116 kB in 0s (426 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8581f8m8/libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Fetched 455 kB in 0s (1658 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzpdpkdsb/libgnutls-dane0t64_3.8.9-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 node-acorn all 8.8.1+ds+~cs25.17.7-2 [128 kB] Fetched 128 kB in 0s (5948 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9w500lu6/node-acorn_8.8.1+ds+~cs25.17.7-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 tzdata all 2025b-1 [259 kB] Fetched 259 kB in 0s (14.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq4u1w34s/tzdata_2025b-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 file amd64 1:5.46-4 [43.5 kB] Fetched 43.5 kB in 0s (3228 kB/s) dpkg-name: info: moved 'file_1%3a5.46-4_amd64.deb' to '/srv/rebuilderd/tmp/tmpb57yxzeb/file_5.46-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libtinfo6 amd64 6.5+20250216-2 [348 kB] Fetched 348 kB in 0s (28.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbuo_ddbk/libtinfo6_6.5+20250216-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Fetched 1464 kB in 0s (4262 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp219zjgkt/libgnutls30t64_3.8.9-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Fetched 109 kB in 0s (2072 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6omnv4wv/libidn2-0_2.3.8-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libtsan2 amd64 14.2.0-19 [2460 kB] Fetched 2460 kB in 0s (50.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjjwqzh0x/libtsan2_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Fetched 45.9 kB in 0s (329 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaxmxbids/libdivsufsort3_2.0.1-6+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Fetched 115 kB in 0s (1034 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3n0y0cb3/libnghttp2-dev_1.64.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 sysvinit-utils amd64 3.14-4 [34.1 kB] Fetched 34.1 kB in 0s (3216 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq_nlxtjg/sysvinit-utils_3.14-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 node-cjs-module-lexer all 1.2.3+dfsg-1 [30.6 kB] Fetched 30.6 kB in 0s (814 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl3t6sg5s/node-cjs-module-lexer_1.2.3+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 base-passwd amd64 3.6.7 [53.7 kB] Fetched 53.7 kB in 0s (4916 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp33xef3j3/base-passwd_3.6.7_amd64.deb' Downloading dependency 129 of 348: libspdlog1.15:amd64=1:1.15.1+ds-1 Downloading dependency 130 of 348: libboost1.83-dev:amd64=1.83.0-4.2 Downloading dependency 131 of 348: libzstd1:amd64=1.5.7+dfsg-1 Downloading dependency 132 of 348: libjellyfish-2.0-2:amd64=2.3.1-4+b1 Downloading dependency 133 of 348: libssl3t64:amd64=3.4.1-1 Downloading dependency 134 of 348: libpython3.13-stdlib:amd64=3.13.2-3 Downloading dependency 135 of 348: liblastlog2-2:amd64=2.41-3 Downloading dependency 136 of 348: libmagic-mgc:amd64=1:5.46-4 Downloading dependency 137 of 348: python3-alabaster:amd64=0.7.16-0.1 Downloading dependency 138 of 348: libcurl4t64:amd64=8.13.0-1 Downloading dependency 139 of 348: node-undici:amd64=7.3.0+dfsg1+~cs24.12.11-1 Downloading dependency 140 of 348: libspdlog-dev:amd64=1:1.15.1+ds-1 Downloading dependency 141 of 348: gcc-14-x86-64-linux-gnu:amd64=14.2.0-19 Downloading dependency 142 of 348: libsmartcols1:amd64=2.41-3 Downloading dependency 143 of 348: ncurses-bin:amd64=6.5+20250216-2 Downloading dependency 144 of 348: libstaden-read14t64:amd64=1.15.0-1.1+b2 Downloading dependency 145 of 348: readline-common:amd64=8.2-6 Downloading dependency 146 of 348: libgnutls28-dev:amd64=3.8.9-2 Downloading dependency 147 of 348: libboost-chrono1.83.0t64:amd64=1.83.0-4.2 Downloading dependency 148 of 348: sphinx-doc:amd64=8.1.3-5 Downloading dependency 149 of 348: bzip2:amd64=1.0.8-6 Downloading dependency 150 of 348: libkadm5clnt-mit12:amd64=1.21.3-5 Downloading dependency 151 of 348: libexpat1:amd64=2.7.1-1 Downloading dependency 152 of 348: docutils-doc:amd64=0.21.2+dfsg-2 Downloading dependency 153 of 348: coreutils:amd64=9.5-1+b1 Downloading dependency 154 of 348: libelf1t64:amd64=0.192-4 Downloading dependency 155 of 348: libbz2-dev:amd64=1.0.8-6 Downloading dependency 156 of 348: libboost-program-options1.83.0:amd64=1.83.0-4.2 Downloading dependency 157 of 348: libhwloc15:amd64=2.12.0-1 Downloading dependency 158 of 348: libboost-program-options1.83-dev:amd64=1.83.0-4.2 Downloading dependency 159 of 348: python3.13-minimal:amd64=3.13.2-3 Downloading dependency 160 of 348: libsasl2-modules-db:amd64=2.1.28+dfsg1-9 Downloading dependency 161 of 348: libaudit-common:amd64=1:4.0.2-2 Downloading dependency 162 of 348: libngtcp2-16:amd64=1.11.0-1 Downloading dependency 163 of 348: python3-snowballstemmer:amd64=2.2.0-4 Downloading dependency 164 of 348: libboost-filesystem1.83-dev:amd64=1.83.0-4.2 Downloading dependency 165 of 348: libuchardet0:amd64=0.0.8-1+b2 Downloading dependency 166 of 348: libunbound8:amd64=1.22.0-1+b1 Downloading dependency 167 of 348: dh-strip-nondeterminism:amd64=1.14.1-2 Downloading dependency 168 of 348: libnode115:amd64=20.19.0+dfsg-1 Downloading dependency 169 of 348: libpipeline1:amd64=1.5.8-1 Downloading dependency 170 of 348: python3-babel:amd64=2.17.0-1 Downloading dependency 171 of 348: python3-jinja2:amd64=3.1.6-1 Downloading dependency 172 of 348: libgdbm-compat4t64:amd64=1.24-2 Downloading dependency 173 of 348: cpp-14:amd64=14.2.0-19 Downloading dependency 174 of 348: libkadm5srv-mit12:amd64=1.21.3-5 Downloading dependency 175 of 348: dash:amd64=0.5.12-12 Downloading dependency 176 of 348: libboost-timer1.83-dev:amd64=1.83.0-4.2 Downloading dependency 177 of 348: python3-roman:amd64=5.0-1 Downloading dependency 178 of 348: procps:amd64=2:4.0.4-7 Downloading dependency 179 of 348: libboost-thread-dev:amd64=1.83.0.2+b2 Downloading dependency 180 of 348: liblzma-dev:amd64=5.6.4-1 Downloading dependency 181 of 348: libbrotli1:amd64=1.1.0-2+b7 Downloading dependency 182 of 348: librhash1:amd64=1.4.5-1 Downloading dependency 183 of 348: libcereal-dev:amd64=1.3.2+dfsg-5 Downloading dependency 184 of 348: po-debconf:amd64=1.0.21+nmu1 Downloading dependency 185 of 348: libtbbbind-2-5:amd64=2022.1.0-1 Downloading dependency 186 of 348: libtbbmalloc2:amd64=2022.1.0-1 Downloading dependency 187 of 348: cmake:amd64=3.31.6-2 Downloading dependency 188 of 348: libmd0:amd64=1.1.0-2+b1 Downloading dependency 189 of 348: perl:amd64=5.40.1-2 Downloading dependency 190 of 348: netbase:amd64=6.5 Downloading dependency 191 of 348: libmagic1t64:amd64=1:5.46-4 Downloading dependency 192 of 348: libcrypt-dev:amd64=1:4.4.38-1 Downloading dependency 193 of 348: diffutils:amd64=1:3.10-3 Downloading dependency 194 of 348: libcrypt1:amd64=1:4.4.38-1 Downloading dependency 195 of 348: libjsoncpp26:amd64=1.9.6-3 Downloading dependency 196 of 348: libkrb5-dev:amd64=1.21.3-5 Downloading dependency 197 of 348: libngtcp2-crypto-gnutls-dev:amd64=1.11.0-1 Downloading dependency 198 of 348: libp11-kit-dev:amd64=0.25.5-3 Downloading dependency 199 of 348: libisl23:amd64=0.27-1 Downloading dependency 200 of 348: libngtcp2-crypto-gnutls8:amd64=1.11.0-1 Downloading dependency 201 of 348: node-mj-context-menu:amd64=0.9.1+ds-2 Downloading dependency 202 of 348: libstdc++6:amd64=14.2.0-19 Downloading dependency 203 of 348: node-balanced-match:amd64=2.0.0-1 Downloading dependency 204 of 348: cpp-14-x86-64-linux-gnu:amd64=14.2.0-19 Downloading dependency 205 of 348: libboost-regex1.83-dev:amd64=1.83.0-4.2 Downloading dependency 206 of 348: libc-dev-bin:amd64=2.41-6 Downloading dependency 207 of 348: libmount1:amd64=2.41-3 Downloading dependency 208 of 348: libgcc-s1:amd64=14.2.0-19 Downloading dependency 209 of 348: libdebhelper-perl:amd64=13.24.2 Downloading dependency 210 of 348: rapidjson-dev:amd64=1.1.0+dfsg2-7.3 Downloading dependency 211 of 348: fonts-lato:amd64=2.015-1 Downloading dependency 212 of 348: intltool-debian:amd64=0.35.0+20060710.6 Downloading dependency 213 of 348: libboost-atomic1.83.0:amd64=1.83.0-4.2 Downloading dependency 214 of 348: python3-sphinx:amd64=8.1.3-5 Downloading dependency 215 of 348: libboost-serialization1.83.0:amd64=1.83.0-4.2 Downloading dependency 216 of 348: libsimde-dev:amd64=0.8.2-3 Downloading dependency 217 of 348: libcc1-0:amd64=14.2.0-19 Downloading dependency 218 of 348: libcap-ng0:amd64=0.8.5-4+b1 Downloading dependency 219 of 348: libsqlite3-0:amd64=3.46.1-2 Downloading dependency 220 of 348: bash:amd64=5.2.37-1.1+b2 Downloading dependency 221 of 348: python3-packaging:amd64=24.2-1 Downloading dependency 222 of 348: man-db:amd64=2.13.0-1 Downloading dependency 223 of 348: openssl-provider-legacy:amd64=3.4.1-1 Downloading dependency 224 of 348: ncurses-base:amd64=6.5+20250216-2 Downloading dependency 225 of 348: pkgconf:amd64=1.8.1-4 Downloading dependency 226 of 348: libaudit1:amd64=1:4.0.2-2+b2 Downloading dependency 227 of 348: libgmpxx4ldbl:amd64=2:6.3.0+dfsg-3 Downloading dependency 228 of 348: python3-idna:amd64=3.10-1 Downloading dependency 229 of 348: libboost-program-options-dev:amd64=1.83.0.2+b2 Downloading dependency 230 of 348: node-xtend:amd64=4.0.2-3 Downloading dependency 231 of 348: sed:amd64=4.9-2 Downloading dependency 232 of 348: libdb5.3t64:amd64=5.3.28+dfsg2-9 Downloading dependency 233 of 348: libgmp10:amd64=2:6.3.0+dfsg-3 Downloading dependency 234 of 348: libboost-serialization1.83-dev:amd64=1.83.0-4.2 Downloading dependency 235 of 348: libnettle8t64:amd64=3.10.1-1 Downloading dependency 236 of 348: cpp:amd64=4:14.2.0-1 Downloading dependency 237 of 348: g++-14:amd64=14.2.0-19 Downloading dependency 238 of 348: zlib1g:amd64=1:1.3.dfsg+really1.3.1-1+b1 Downloading dependency 239 of 348: libjs-underscore:amd64=1.13.4~dfsg+~1.11.4-3 Downloading dependency 240 of 348: libgnutls-dane0t64:amd64=3.8.9-2 Downloading dependency 241 of 348: node-acorn:amd64=8.8.1+ds+~cs25.17.7-2 Downloading dependency 242 of 348: tzdata:amd64=2025b-1 Downloading dependency 243 of 348: file:amd64=1:5.46-4 Downloading dependency 244 of 348: libtinfo6:amd64=6.5+20250216-2 Downloading dependency 245 of 348: libgnutls30t64:amd64=3.8.9-2 Downloading dependency 246 of 348: libidn2-0:amd64=2.3.8-2 Downloading dependency 247 of 348: libtsan2:amd64=14.2.0-19 Downloading dependency 248 of 348: libdivsufsort3:amd64=2.0.1-6+b1 Downloading dependency 249 of 348: libnghttp2-dev:amd64=1.64.0-1 Downloading dependency 250 of 348: sysvinit-utils:amd64=3.14-4 Downloading dependency 251 of 348: node-cjs-module-lexer:amd64=1.2.3+dfsg-1 Downloading dependency 252 of 348: base-passwd:amd64=3.6.7 Downloading dependency 253 of 348: dpkg:amd64=1.22.18Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 dpkg amd64 1.22.18 [1545 kB] Fetched 1545 kB in 0s (81.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0d2g9050/dpkg_1.22.18_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 debianutils amd64 5.21 [92.1 kB] Fetched 92.1 kB in 0s (8741 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg5gj604z/debianutils_5.21_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Fetched 179 kB in 0s (3607 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6qje22jk/libngtcp2-dev_1.11.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libblkid1 amd64 2.41-3 [171 kB] Fetched 171 kB in 0s (5876 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphr6xdzgm/libblkid1_2.41-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 tar amd64 1.35+dfsg-3.1 [815 kB] Fetched 815 kB in 0s (53.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxpxte1ol/tar_1.35+dfsg-3.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-atomic1.83-dev amd64 1.83.0-4.2 [236 kB] Fetched 236 kB in 0s (1291 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3uo4rq2t/libboost-atomic1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libacl1 amd64 2.3.2-2+b1 [32.9 kB] Fetched 32.9 kB in 0s (359 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_baqjlq_/libacl1_2.3.2-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Fetched 7348 B in 0s (331 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjykgku31/python3-sphinxcontrib.jquery_4.1-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libc6 amd64 2.41-6 [2843 kB] Fetched 2843 kB in 0s (13.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpioocwqob/libc6_2.41-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Fetched 9092 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcybouir5/libkeyutils1_1.6.3-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Fetched 60.0 kB in 0s (5573 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbu8qxkzy/libgssrpc4t64_1.21.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Fetched 33.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjqyo0kn4/libkrb5support0_1.21.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Fetched 169 kB in 0s (14.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpndz8_zde/libreadline8t64_8.2-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB] Fetched 27.1 kB in 0s (2606 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe_xc2323/python3-minimal_3.13.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Fetched 836 kB in 0s (40.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2k4206ty/python3-pygments_2.18.0+dfsg-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libperl5.40 amd64 5.40.1-2 [4315 kB] Fetched 4315 kB in 0s (106 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1tyia0mm/libperl5.40_5.40.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libseccomp2 amd64 2.6.0-2 [51.7 kB] Fetched 51.7 kB in 0s (4915 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvl2y4ked/libseccomp2_2.6.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Fetched 14.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjpv2tzuw/python3-markupsafe_2.1.5-1+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libpam0g amd64 1.7.0-3 [69.7 kB] Fetched 69.7 kB in 0s (6396 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy8vno0wl/libpam0g_1.7.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Fetched 23.9 kB in 0s (2063 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1mclpyel/libffi8_3.4.7-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Fetched 57.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnm96t18_/libpsl5t64_0.21.2-1.1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libpam-runtime all 1.7.0-3 [248 kB] Fetched 248 kB in 0s (23.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuai_b_da/libpam-runtime_1.7.0-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB] Fetched 10.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3h209o1x/libpython3-stdlib_3.13.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB] Fetched 194 kB in 0s (2567 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7so4pjeg/libldap2_2.6.9+dfsg-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 gcc-14 amd64 14.2.0-19 [540 kB] Fetched 540 kB in 0s (7161 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp126i_36m/gcc-14_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3 amd64 3.13.2-2 [28.1 kB] Fetched 28.1 kB in 0s (85.9 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp30xm57y0/python3_3.13.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgcc-14-dev amd64 14.2.0-19 [2672 kB] Fetched 2672 kB in 0s (18.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpub86zwyu/libgcc-14-dev_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libselinux1 amd64 3.8.1-1 [84.7 kB] Fetched 84.7 kB in 0s (254 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplxdisfvs/libselinux1_3.8.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Fetched 58.8 kB in 0s (631 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpelvgmrcg/librtmp1_2.4+20151223.gitfa8646d.1-2+b5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libudev1 amd64 257.4-9 [151 kB] Fetched 151 kB in 0s (875 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa5cmn5m_/libudev1_257.4-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Fetched 182 kB in 0s (15.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9emo3zha/libevent-2.1-7t64_2.1.12-stable-10+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Fetched 95.8 kB in 0s (6537 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd2sdr8mf/libhtscodecs2_1.6.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Fetched 642 kB in 0s (11.5 MB/s) dpkg-name: info: moved 'libgmp-dev_2%3a6.3.0+dfsg-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp90wgw_ih/libgmp-dev_6.3.0+dfsg-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Fetched 243 kB in 0s (17.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphtti6hk6/gettext-base_0.23.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 debhelper all 13.24.2 [919 kB] Fetched 919 kB in 0s (44.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvd0txmsk/debhelper_13.24.2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Fetched 57.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp56a3azsq/libsasl2-2_2.1.28+dfsg1-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libunistring5 amd64 1.3-2 [477 kB] Fetched 477 kB in 0s (34.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjueyi4yt/libunistring5_1.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-date-time1.83-dev amd64 1.83.0-4.2 [239 kB] Fetched 239 kB in 0s (6900 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqdhxsp43/libboost-date-time1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Fetched 36.4 kB in 0s (3369 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnqbxlvp_/libpkgconf3_1.8.1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libuuid1 amd64 2.41-3 [37.5 kB] Fetched 37.5 kB in 0s (211 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmperl1i1di/libuuid1_2.41-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 build-essential amd64 12.12 [4624 B] Fetched 4624 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu8ntm0se/build-essential_12.12_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 node-brace-expansion all 2.0.1+~1.1.0-1 [7912 B] Fetched 7912 B in 0s (271 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw6fq9d25/node-brace-expansion_2.0.1+~1.1.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB] Fetched 24.3 kB in 0s (1816 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbyq638xc/libcom-err2_1.47.2-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Fetched 99.2 kB in 0s (4526 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxnoafoq5/libtasn1-6-dev_4.20.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 binutils amd64 2.44-3 [265 kB] Fetched 265 kB in 0s (20.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoiixqzal/binutils_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Fetched 15.3 kB in 0s (1051 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzbjxxvky/liblocale-gettext-perl_1.07-7+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libjansson4 amd64 2.14-2+b3 [39.8 kB] Fetched 39.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0x1gppkv/libjansson4_2.14-2+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 dwz amd64 0.15-1+b1 [110 kB] Fetched 110 kB in 0s (9692 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj91zuo6f/dwz_0.15-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 xml-core all 0.19 [20.1 kB] Fetched 20.1 kB in 0s (2004 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv3ef24j9/xml-core_0.19_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libitm1 amd64 14.2.0-19 [26.0 kB] Fetched 26.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpejacbj1e/libitm1_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 920 kB in 0s (43.2 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp_9afwwqc/zlib1g-dev_1.3.dfsg+really1.3.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 node-minimatch all 9.0.3-5 [76.7 kB] Fetched 76.7 kB in 0s (1073 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp46gpjf28/node-minimatch_9.0.3-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libtbb12 amd64 2022.1.0-1 [91.7 kB] Fetched 91.7 kB in 0s (390 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp08mcxcah/libtbb12_2022.1.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python-requests-doc all 2.32.3+dfsg-5 [196 kB] Fetched 196 kB in 0s (6544 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzcm27ccy/python-requests-doc_2.32.3+dfsg-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-chrono1.83-dev amd64 1.83.0-4.2 [246 kB] Fetched 246 kB in 0s (3470 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps3dt0vl0/libboost-chrono1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Fetched 42.6 kB in 1s (72.1 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn5on8_46/libkdb5-10t64_1.21.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libtool all 2.5.4-4 [539 kB] Fetched 539 kB in 0s (44.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7kq3_b94/libtool_2.5.4-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Fetched 425 kB in 0s (29.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3eqa7dwb/libp11-kit0_0.25.5-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-19 [12.1 MB] Fetched 12.1 MB in 0s (30.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpaue7ce59/g++-14-x86-64-linux-gnu_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Fetched 135 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwsdyqp0o/libncursesw6_6.5+20250216-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libpcre2-8-0 amd64 10.45-1 [298 kB] Fetched 298 kB in 0s (20.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpknc13gg6/libpcre2-8-0_10.45-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libstaden-read-dev amd64 1.15.0-1.1+b2 [347 kB] Fetched 347 kB in 0s (1361 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw94mgr5s/libstaden-read-dev_1.15.0-1.1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Fetched 49.9 kB in 0s (2367 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7j5jh3hx/libtasn1-6_4.20.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Fetched 3580 B in 0s (31.4 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmulwlqnc/libboost-iostreams-dev_1.83.0.2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libboost-thread1.83-dev amd64 1.83.0-4.2 [277 kB] Fetched 277 kB in 1s (437 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptniqay3_/libboost-thread1.83-dev_1.83.0-4.2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libmpfr6 amd64 4.2.2-1 [729 kB] Fetched 729 kB in 0s (48.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbesbmby_/libmpfr6_4.2.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Fetched 64.9 kB in 0s (4455 kB/s) dpkg-name: info: moved 'libproc2-0_2%3a4.0.4-7_amd64.deb' to '/srv/rebuilderd/tmp/tmp9ar0v5_q/libproc2-0_4.0.4-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1 [1436 B] Fetched 1436 B in 0s (143 kB/s) dpkg-name: info: moved 'gcc-x86-64-linux-gnu_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpvnnqjaow/gcc-x86-64-linux-gnu_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3.13 amd64 3.13.2-3 [746 kB] Fetched 746 kB in 0s (15.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcgd5ecbk/python3.13_3.13.2-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libcurl3t64-gnutls amd64 8.13.0-1 [374 kB] Fetched 374 kB in 0s (2314 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyibzo1l9/libcurl3t64-gnutls_8.13.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libasan8 amd64 14.2.0-19 [2725 kB] Fetched 2725 kB in 0s (100 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmc4yxeu2/libasan8_14.2.0-19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Fetched 67.7 kB in 0s (6489 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprn5_zjpb/libnghttp3-9_1.8.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 init-system-helpers all 1.68 [38.7 kB] Fetched 38.7 kB in 0s (1542 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdjgh6rdh/init-system-helpers_1.68_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 gcc amd64 4:14.2.0-1 [5136 B] Fetched 5136 B in 0s (372 kB/s) dpkg-name: info: moved 'gcc_4%3a14.2.0-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpty1o57je/gcc_14.2.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Fetched 1185 kB in 0s (61.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzeij92pg/groff-base_1.23.0-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 node-corepack all 0.24.0-4 [704 kB] Fetched 704 kB in 0s (14.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwtwrw5g5/node-corepack_0.24.0-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Fetched 77.6 kB in 0s (808 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2l0hg3vp/libpsl-dev_0.21.2-1.1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libcurl4-gnutls-dev amd64 8.13.0-1 [492 kB] Fetched 492 kB in 0s (15.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb16lutx_/libcurl4-gnutls-dev_8.13.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 make amd64 4.4.1-1 [463 kB] Fetched 463 kB in 0s (34.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphdmnv_a7/make_4.4.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libhogweed6t64 amd64 3.10.1-1 [335 kB] Fetched 335 kB in 0s (24.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcrt6xliz/libhogweed6t64_3.10.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 perl-base amd64 5.40.1-2 [1665 kB] Fetched 1665 kB in 0s (66.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn99gdj83/perl-base_5.40.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 linux-libc-dev all 6.12.21-1 [2542 kB] Fetched 2542 kB in 0s (34.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkml2v_0u/linux-libc-dev_6.12.21-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 binutils-common amd64 2.44-3 [2509 kB] Fetched 2509 kB in 0s (94.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyd2je84y/binutils-common_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libcap2 amd64 1:2.75-4 [27.9 kB] Fetched 27.9 kB in 0s (2094 kB/s) dpkg-name: info: moved 'libcap2_1%3a2.75-4_amd64.deb' to '/srv/rebuilderd/tmp/tmppvy7orvr/libcap2_2.75-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 dh-autoreconf all 20 [17.1 kB] Fetched 17.1 kB in 0s (707 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpslk1h23s/dh-autoreconf_20_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libjellyfish-2.0-dev amd64 2.3.1-4+b1 [138 kB] Fetched 138 kB in 0s (737 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuf1jw99f/libjellyfish-2.0-dev_2.3.1-4+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Fetched 326 kB in 0s (15.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprs2yxq3q/libkrb5-3_1.21.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Fetched 371 kB in 0s (31.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv8xkih04/libzstd-dev_1.5.7+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libctf0 amd64 2.44-3 [88.6 kB] Fetched 88.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuokk_rhy/libctf0_2.44-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Fetched 393 kB in 0s (11.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps54ede2h/libssh2-1-dev_1.11.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libfmt-dev amd64 10.1.1+ds1-4 [177 kB] Fetched 177 kB in 0s (608 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph33m6v5l/libfmt-dev_10.1.1+ds1-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libicu-dev amd64 76.1-3 [10.8 MB] Fetched 10.8 MB in 0s (86.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9_wf6g9m/libicu-dev_76.1-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libpthread-stubs0-dev amd64 0.5-1 [5168 B] Fetched 5168 B in 0s (334 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprd54rada/libpthread-stubs0-dev_0.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 autoconf all 2.72-3 [493 kB] Fetched 493 kB in 0s (39.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk39c9r68/autoconf_2.72-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Fetched 6688 B in 0s (372 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd7uicm2f/python3-imagesize_1.4.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20250403T143652Z sid/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB] Fetched 2787 kB in 0s (106 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnwnp0tl6/libssl-dev_3.4.1-1_amd64.deb' dpkg-buildpackage: info: source package debootsnap-dummy dpkg-buildpackage: info: source version 1.0 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Equivs Dummy Package Generator dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/debootsnap-dummy/ dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'debootsnap-dummy' in '../debootsnap-dummy_1.0_all.deb'. dpkg-genbuildinfo --build=binary -O../debootsnap-dummy_1.0_amd64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) The package has been created. Attention, the package has been created in the /srv/rebuilderd/tmp/tmpkqd2z8of/cache directory, not in ".." as indicated by the message above! I: automatically chosen mode: unshare I: chroot architecture amd64 is equal to the host's architecture I: using /srv/rebuilderd/tmp/mmdebstrap.SdVR7RpOu4 as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.SdVR7RpOu4 127.0.0.1 - - [23/Jun/2025 03:22:20] code 404, message File not found 127.0.0.1 - - [23/Jun/2025 03:22:20] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:46015 ./ InRelease 127.0.0.1 - - [23/Jun/2025 03:22:20] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:46015 ./ Release [462 B] 127.0.0.1 - - [23/Jun/2025 03:22:20] code 404, message File not found 127.0.0.1 - - [23/Jun/2025 03:22:20] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:46015 ./ Release.gpg 127.0.0.1 - - [23/Jun/2025 03:22:20] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:46015 ./ Packages [446 kB] Fetched 447 kB in 0s (22.0 MB/s) Reading package lists... usr-is-merged found but not real -- not running merged-usr setup hook I: skipping apt-get update because it was already run I: downloading packages with apt... 127.0.0.1 - 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- [23/Jun/2025 03:22:21] "GET /./ncurses-base_6.5%2b20250216-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [23/Jun/2025 03:22:21] "GET /./sysvinit-utils_3.14-4_amd64.deb HTTP/1.1" 200 - I: extracting archives... I: running --extract-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/extract00.sh /srv/rebuilderd/tmp/mmdebstrap.SdVR7RpOu4 127.0.0.1 - - [23/Jun/2025 03:22:23] code 404, message File not found 127.0.0.1 - - [23/Jun/2025 03:22:23] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:46015 ./ InRelease 127.0.0.1 - - [23/Jun/2025 03:22:23] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:46015 ./ Release 127.0.0.1 - - [23/Jun/2025 03:22:23] code 404, message File not found 127.0.0.1 - - [23/Jun/2025 03:22:23] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:46015 ./ Release.gpg Reading package lists... usr-is-merged found but not real -- not running merged-usr extract hook I: installing essential packages... 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- [23/Jun/2025 03:22:44] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmpkqd2z8of/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.SdVR7RpOu4 Reading package lists... Building dependency tree... Reading state information... python3.13-doc is already the newest version (3.13.2-3). python3.13-doc set to manually installed. libattr1 is already the newest version (1:2.5.2-3). libjs-sphinxdoc is already the newest version (8.1.3-5). libjs-sphinxdoc set to manually installed. icu-devtools is already the newest version (76.1-3). icu-devtools set to manually installed. libstdc++-14-dev is already the newest version (14.2.0-19). libstdc++-14-dev set to manually installed. libarchive13t64 is already the newest version (3.7.4-1.1). libarchive13t64 set to manually installed. libpam-modules-bin is already the newest version (1.7.0-3). libxml2 is already the newest version (2.12.7+dfsg+really2.9.14-0.4). libxml2 set to manually installed. python-babel-localedata is already the newest version (2.17.0-1). python-babel-localedata set to manually installed. nodejs is already the newest version (20.19.0+dfsg-1). nodejs set to manually installed. libboost-iostreams1.83.0 is already the newest version (1.83.0-4.2). libboost-iostreams1.83.0 set to manually installed. findutils is already the newest version (4.10.0-3). libboost-regex1.83.0 is already the newest version (1.83.0-4.2). libboost-regex1.83.0 set to manually installed. help2man is already the newest version (1.49.3). help2man set to manually installed. python3-docutils is already the newest version (0.21.2+dfsg-2). python3-docutils set to manually installed. autopoint is already the newest version (0.23.1-1). autopoint set to manually installed. g++-x86-64-linux-gnu is already the newest version (4:14.2.0-1). g++-x86-64-linux-gnu set to manually installed. libgssapi-krb5-2 is already the newest version (1.21.3-5). libgssapi-krb5-2 set to manually installed. python3-docs-theme is already the newest version (2025.2-1). python3-docs-theme set to manually installed. libdivsufsort-dev is already the newest version (2.0.1-6+b1). libdivsufsort-dev set to manually installed. libc6-dev is already the newest version (2.41-6). libc6-dev set to manually installed. libtbb-dev is already the newest version (2022.1.0-1). libtbb-dev set to manually installed. libeigen3-dev is already the newest version (3.4.0-4). libeigen3-dev set to manually installed. libk5crypto3 is already the newest version (1.21.3-5). libk5crypto3 set to manually installed. libidn2-dev is already the newest version (2.3.8-2). libidn2-dev set to manually installed. bsdextrautils is already the newest version (2.41-3). bsdextrautils set to manually installed. python3-chardet is already the newest version (5.2.0+dfsg-2). python3-chardet set to manually installed. libboost-timer-dev is already the newest version (1.83.0.2+b2). libboost-timer-dev set to manually installed. libubsan1 is already the newest version (14.2.0-19). libubsan1 set to manually installed. docutils-common is already the newest version (0.21.2+dfsg-2). docutils-common set to manually installed. libboost-filesystem-dev is already the newest version (1.83.0.2+b2). libboost-filesystem-dev set to manually installed. python3-certifi is already the newest version (2025.1.31+ds-1). python3-certifi set to manually installed. rpcsvc-proto is already the newest version (1.4.3-1). rpcsvc-proto set to manually installed. libjs-jquery is already the newest version (3.6.1+dfsg+~3.5.14-1). libjs-jquery set to manually installed. nettle-dev is already the newest version (3.10.1-1). nettle-dev set to manually installed. libdpkg-perl is already the newest version (1.22.18). libdpkg-perl set to manually installed. perl-modules-5.40 is already the newest version (5.40.1-2). perl-modules-5.40 set to manually installed. m4 is already the newest version (1.4.19-7). m4 set to manually installed. libpython3.13-minimal is already the newest version (3.13.2-3). libpython3.13-minimal set to manually installed. sensible-utils is already the newest version (0.0.24). sensible-utils set to manually installed. util-linux is already the newest version (2.41-3). python3-urllib3 is already the newest version (2.3.0-2). python3-urllib3 set to manually installed. python3-doc is already the newest version (3.13.2-2). python3-doc set to manually installed. libgdbm6t64 is already the newest version (1.24-2). libgdbm6t64 set to manually installed. libdebconfclient0 is already the newest version (0.278). gzip is already the newest version (1.13-1). liblz4-1 is already the newest version (1.10.0-4). liblz4-1 set to manually installed. libmpc3 is already the newest version (1.3.1-1+b3). libmpc3 set to manually installed. autotools-dev is already the newest version (20240727.1). autotools-dev set to manually installed. media-types is already the newest version (13.0.0). media-types set to manually installed. ca-certificates is already the newest version (20241223). ca-certificates set to manually installed. libboost-system1.83.0 is already the newest version (1.83.0-4.2). libboost-system1.83.0 set to manually installed. python3-sphinx-rtd-theme is already the newest version (3.0.2+dfsg-2). python3-sphinx-rtd-theme set to manually installed. mawk is already the newest version (1.3.4.20250131-1). debconf is already the newest version (1.5.91). dpkg-dev is already the newest version (1.22.18). dpkg-dev set to manually installed. libatomic1 is already the newest version (14.2.0-19). libatomic1 set to manually installed. libxxhash0 is already the newest version (0.8.3-2). libxxhash0 set to manually installed. pkg-config is already the newest version (1.8.1-4). pkg-config set to manually installed. libboost-system1.83-dev is already the newest version (1.83.0-4.2). libboost-system1.83-dev set to manually installed. libsystemd0 is already the newest version (257.4-9). libbz2-1.0 is already the newest version (1.0.8-6). libbrotli-dev is already the newest version (1.1.0-2+b7). libbrotli-dev set to manually installed. libuv1t64 is already the newest version (1.50.0-2). libuv1t64 set to manually installed. sphinx-common is already the newest version 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libbrotli1 is already the newest version (1.1.0-2+b7). libbrotli1 set to manually installed. librhash1 is already the newest version (1.4.5-1). librhash1 set to manually installed. libcereal-dev is already the newest version (1.3.2+dfsg-5). libcereal-dev set to manually installed. po-debconf is already the newest version (1.0.21+nmu1). po-debconf set to manually installed. libtbbbind-2-5 is already the newest version (2022.1.0-1). libtbbbind-2-5 set to manually installed. libtbbmalloc2 is already the newest version (2022.1.0-1). libtbbmalloc2 set to manually installed. cmake is already the newest version (3.31.6-2). cmake set to manually installed. libmd0 is already the newest version (1.1.0-2+b1). perl is already the newest version (5.40.1-2). perl set to manually installed. netbase is already the newest version (6.5). netbase set to manually installed. libmagic1t64 is already the newest version (1:5.46-4). libmagic1t64 set to manually installed. libcrypt-dev is already the newest 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node-brace-expansion set to manually installed. libcom-err2 is already the newest version (1.47.2-1+b1). libcom-err2 set to manually installed. libtasn1-6-dev is already the newest version (4.20.0-2). libtasn1-6-dev set to manually installed. binutils is already the newest version (2.44-3). binutils set to manually installed. liblocale-gettext-perl is already the newest version (1.07-7+b1). liblocale-gettext-perl set to manually installed. libjansson4 is already the newest version (2.14-2+b3). libjansson4 set to manually installed. dwz is already the newest version (0.15-1+b1). dwz set to manually installed. xml-core is already the newest version (0.19). xml-core set to manually installed. libitm1 is already the newest version (14.2.0-19). libitm1 set to manually installed. zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.1-1+b1). zlib1g-dev set to manually installed. node-minimatch is already the newest version (9.0.3-5). node-minimatch set to manually installed. libtbb12 is already the newest version (2022.1.0-1). libtbb12 set to manually installed. python-requests-doc is already the newest version (2.32.3+dfsg-5). python-requests-doc set to manually installed. libboost-chrono1.83-dev is already the newest version (1.83.0-4.2). libboost-chrono1.83-dev set to manually installed. libkdb5-10t64 is already the newest version (1.21.3-5). libkdb5-10t64 set to manually installed. libtool is already the newest version (2.5.4-4). libtool set to manually installed. libp11-kit0 is already the newest version (0.25.5-3). libp11-kit0 set to manually installed. g++-14-x86-64-linux-gnu is already the newest version (14.2.0-19). g++-14-x86-64-linux-gnu set to manually installed. libncursesw6 is already the newest version (6.5+20250216-2). libncursesw6 set to manually installed. libpcre2-8-0 is already the newest version (10.45-1). libstaden-read-dev is already the newest version (1.15.0-1.1+b2). libstaden-read-dev set to manually installed. libtasn1-6 is already the newest version (4.20.0-2). libtasn1-6 set to manually installed. libboost-iostreams-dev is already the newest version (1.83.0.2+b2). libboost-iostreams-dev set to manually installed. libboost-thread1.83-dev is already the newest version (1.83.0-4.2). libboost-thread1.83-dev set to manually installed. libmpfr6 is already the newest version (4.2.2-1). libmpfr6 set to manually installed. libproc2-0 is already the newest version (2:4.0.4-7). libproc2-0 set to manually installed. gcc-x86-64-linux-gnu is already the newest version (4:14.2.0-1). gcc-x86-64-linux-gnu set to manually installed. python3.13 is already the newest version (3.13.2-3). python3.13 set to manually installed. libcurl3t64-gnutls is already the newest version (8.13.0-1). libcurl3t64-gnutls set to manually installed. libasan8 is already the newest version (14.2.0-19). libasan8 set to manually installed. libnghttp3-9 is already the newest version (1.8.0-1). libnghttp3-9 set to manually installed. init-system-helpers is already the newest version (1.68). gcc is already the newest version (4:14.2.0-1). gcc set to manually installed. groff-base is already the newest version (1.23.0-7). groff-base set to manually installed. node-corepack is already the newest version (0.24.0-4). node-corepack set to manually installed. libpsl-dev is already the newest version (0.21.2-1.1+b1). libpsl-dev set to manually installed. libcurl4-gnutls-dev is already the newest version (8.13.0-1). libcurl4-gnutls-dev set to manually installed. make is already the newest version (4.4.1-1). make set to manually installed. libhogweed6t64 is already the newest version (3.10.1-1). libhogweed6t64 set to manually installed. perl-base is already the newest version (5.40.1-2). linux-libc-dev is already the newest version (6.12.21-1). linux-libc-dev set to manually installed. binutils-common is already the newest version (2.44-3). binutils-common set to manually installed. libcap2 is already the newest version (1:2.75-4). dh-autoreconf is already the newest version (20). dh-autoreconf set to manually installed. libjellyfish-2.0-dev is already the newest version (2.3.1-4+b1). libjellyfish-2.0-dev set to manually installed. libkrb5-3 is already the newest version (1.21.3-5). libkrb5-3 set to manually installed. libzstd-dev is already the newest version (1.5.7+dfsg-1). libzstd-dev set to manually installed. libctf0 is already the newest version (2.44-3). libctf0 set to manually installed. libssh2-1-dev is already the newest version (1.11.1-1). libssh2-1-dev set to manually installed. libfmt-dev is already the newest version (10.1.1+ds1-4). libfmt-dev set to manually installed. libicu-dev is already the newest version (76.1-3). libicu-dev set to manually installed. libpthread-stubs0-dev is already the newest version (0.5-1). libpthread-stubs0-dev set to manually installed. autoconf is already the newest version (2.72-3). autoconf set to manually installed. python3-imagesize is already the newest version (1.4.1-1). python3-imagesize set to manually installed. libssl-dev is already the newest version (3.4.1-1). libssl-dev set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg -r debootsnap-dummy' exec /srv/rebuilderd/tmp/mmdebstrap.SdVR7RpOu4 (Reading database ... 52392 files and directories currently installed.) Removing debootsnap-dummy (1.0) ... I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg-query --showformat '${binary:Package}=${Version}\n' --show > "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.SdVR7RpOu4 I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.SdVR7RpOu4 I: running special hook: upload sources.list /etc/apt/sources.list I: waiting for background processes to finish... I: cleaning package lists and apt cache... I: skipping cleanup/reproducible as requested I: creating tarball... I: done I: removing tempdir /srv/rebuilderd/tmp/mmdebstrap.SdVR7RpOu4... I: success in 88.2900 seconds Downloading dependency 254 of 348: debianutils:amd64=5.21 Downloading dependency 255 of 348: libngtcp2-dev:amd64=1.11.0-1 Downloading dependency 256 of 348: libblkid1:amd64=2.41-3 Downloading dependency 257 of 348: tar:amd64=1.35+dfsg-3.1 Downloading dependency 258 of 348: libboost-atomic1.83-dev:amd64=1.83.0-4.2 Downloading dependency 259 of 348: libacl1:amd64=2.3.2-2+b1 Downloading dependency 260 of 348: python3-sphinxcontrib.jquery:amd64=4.1-5 Downloading dependency 261 of 348: libc6:amd64=2.41-6 Downloading dependency 262 of 348: libkeyutils1:amd64=1.6.3-4 Downloading dependency 263 of 348: libgssrpc4t64:amd64=1.21.3-5 Downloading dependency 264 of 348: libkrb5support0:amd64=1.21.3-5 Downloading dependency 265 of 348: libreadline8t64:amd64=8.2-6 Downloading dependency 266 of 348: python3-minimal:amd64=3.13.2-2 Downloading dependency 267 of 348: python3-pygments:amd64=2.18.0+dfsg-2 Downloading dependency 268 of 348: libperl5.40:amd64=5.40.1-2 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libstaden-read-dev:amd64=1.15.0-1.1+b2 Downloading dependency 315 of 348: libtasn1-6:amd64=4.20.0-2 Downloading dependency 316 of 348: libboost-iostreams-dev:amd64=1.83.0.2+b2 Downloading dependency 317 of 348: libboost-thread1.83-dev:amd64=1.83.0-4.2 Downloading dependency 318 of 348: libmpfr6:amd64=4.2.2-1 Downloading dependency 319 of 348: libproc2-0:amd64=2:4.0.4-7 Downloading dependency 320 of 348: gcc-x86-64-linux-gnu:amd64=4:14.2.0-1 Downloading dependency 321 of 348: python3.13:amd64=3.13.2-3 Downloading dependency 322 of 348: libcurl3t64-gnutls:amd64=8.13.0-1 Downloading dependency 323 of 348: libasan8:amd64=14.2.0-19 Downloading dependency 324 of 348: libnghttp3-9:amd64=1.8.0-1 Downloading dependency 325 of 348: init-system-helpers:amd64=1.68 Downloading dependency 326 of 348: gcc:amd64=4:14.2.0-1 Downloading dependency 327 of 348: groff-base:amd64=1.23.0-7 Downloading dependency 328 of 348: node-corepack:amd64=0.24.0-4 Downloading dependency 329 of 348: libpsl-dev:amd64=0.21.2-1.1+b1 Downloading dependency 330 of 348: libcurl4-gnutls-dev:amd64=8.13.0-1 Downloading dependency 331 of 348: make:amd64=4.4.1-1 Downloading dependency 332 of 348: libhogweed6t64:amd64=3.10.1-1 Downloading dependency 333 of 348: perl-base:amd64=5.40.1-2 Downloading dependency 334 of 348: linux-libc-dev:amd64=6.12.21-1 Downloading dependency 335 of 348: binutils-common:amd64=2.44-3 Downloading dependency 336 of 348: libcap2:amd64=1:2.75-4 Downloading dependency 337 of 348: dh-autoreconf:amd64=20 Downloading dependency 338 of 348: libjellyfish-2.0-dev:amd64=2.3.1-4+b1 Downloading dependency 339 of 348: libkrb5-3:amd64=1.21.3-5 Downloading dependency 340 of 348: libzstd-dev:amd64=1.5.7+dfsg-1 Downloading dependency 341 of 348: libctf0:amd64=2.44-3 Downloading dependency 342 of 348: libssh2-1-dev:amd64=1.11.1-1 Downloading dependency 343 of 348: libfmt-dev:amd64=10.1.1+ds1-4 Downloading dependency 344 of 348: libicu-dev:amd64=76.1-3 Downloading dependency 345 of 348: libpthread-stubs0-dev:amd64=0.5-1 Downloading dependency 346 of 348: autoconf:amd64=2.72-3 Downloading dependency 347 of 348: python3-imagesize:amd64=1.4.1-1 Downloading dependency 348 of 348: libssl-dev:amd64=3.4.1-1 env --chdir=/srv/rebuilderd/tmp/rebuilderdJmxW9F/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 SOURCE_DATE_EPOCH=1743660794 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildYD3bSU/debrebuild.sbuildrc.Amti9MHV2JzY sbuild --build=amd64 --host=amd64 --no-source --arch-any --no-arch-all --binNMU-changelog= salmon (1.10.2+ds1-1+b5) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for outdated Built-Using (sphinx/7.4.7-3) -- amd64 / i386 Build Daemon (x86-ubc-01) Thu, 03 Apr 2025 06:13:14 +0000 --chroot=/srv/rebuilderd/tmp/debrebuildYD3bSU/debrebuild.tar.V_yvsScGLu9I --chroot-mode=unshare --dist=unstable --no-run-lintian --no-run-piuparts --no-run-autopkgtest --no-apt-update --no-apt-upgrade --no-apt-distupgrade --verbose --nolog --bd-uninstallable-explainer= --build-path=/build/reproducible-path --dsc-dir=salmon-1.10.2+ds1 /srv/rebuilderd/tmp/rebuilderdJmxW9F/inputs/salmon_1.10.2+ds1-1.dsc I: consider moving your ~/.sbuildrc to /srv/rebuilderd/.config/sbuild/config.pl The Debian buildds switched to the "unshare" backend and sbuild will default to it in the future. To start using "unshare" add this to your `~/.config/sbuild/config.pl`: $chroot_mode = "unshare"; If you want to keep the old "schroot" mode even in the future, add the following to your `~/.config/sbuild/config.pl`: $chroot_mode = "schroot"; $schroot = "schroot"; sbuild: warning: descr(l1): found blank line where expected first heading sbuild (Debian sbuild) 0.89.3 (07 June 2025) on osuosl4-amd64.reproducible.osuosl.org +==============================================================================+ | salmon 1.10.2+ds1-1+b5 (amd64) Mon, 23 Jun 2025 03:23:49 +0000 | +==============================================================================+ Package: salmon Version: 1.10.2+ds1-1+b5 Source Version: 1.10.2+ds1-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuildYD3bSU/debrebuild.tar.V_yvsScGLu9I to /srv/rebuilderd/tmp/tmp.sbuild.rKvZ6dBVxW... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Mon, 23 Jun 2025 03:24:00 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdJmxW9F/inputs/salmon_1.10.2+ds1-1.dsc exists in /srv/rebuilderd/tmp/rebuilderdJmxW9F/inputs; copying to chroot sbuild: warning: descr(l1): found blank line where expected first heading +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 23 Jun 2025 03:24:02 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev, libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev (>> 2.0), libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, python3-docs-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev, libsimde-dev, build-essential Filtered Build-Depends: debhelper-compat (= 13), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev, libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev (>> 2.0), libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, python3-docs-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev, libsimde-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-Sk0Orf/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Mon, 23 Jun 2025 03:24:07 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any-amd64 arm64) +------------------------------------------------------------------------------+ | Build environment Mon, 23 Jun 2025 03:24:08 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.31-1 (2025-06-09) amd64 (x86_64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.18 g++-14_14.2.0-19 gcc-14_14.2.0-19 libc6-dev_2.41-6 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 linux-libc-dev_6.12.21-1 Package versions: autoconf_2.72-3 automake_1:1.17-4 autopoint_0.23.1-1 autotools-dev_20240727.1 base-files_13.7 base-passwd_3.6.7 bash_5.2.37-1.1+b2 binutils_2.44-3 binutils-common_2.44-3 binutils-x86-64-linux-gnu_2.44-3 bsdextrautils_2.41-3 bsdutils_1:2.41-3 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20241223 cmake_3.31.6-2 cmake-data_3.31.6-2 comerr-dev_2.1-1.47.2-1+b1 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-14_14.2.0-19 cpp-14-x86-64-linux-gnu_14.2.0-19 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.2 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-3 docutils-common_0.21.2+dfsg-2 docutils-doc_0.21.2+dfsg-2 dpkg_1.22.18 dpkg-dev_1.22.18 dwz_0.15-1+b1 file_1:5.46-4 findutils_4.10.0-3 fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1 fonts-lato_2.015-1 g++_4:14.2.0-1 g++-14_14.2.0-19 g++-14-x86-64-linux-gnu_14.2.0-19 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-19 gcc-14-base_14.2.0-19 gcc-14-x86-64-linux-gnu_14.2.0-19 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-1 gettext-base_0.23.1-1 grep_3.11-4 groff-base_1.23.0-7 gzip_1.13-1 help2man_1.49.3 hostname_3.25 icu-devtools_76.1-3 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.21.3-5 libacl1_2.3.2-2+b1 libarchive-zip-perl_1.68-1 libarchive13t64_3.7.4-1.1 libasan8_14.2.0-19 libatomic1_14.2.0-19 libattr1_1:2.5.2-3 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b2 libbinutils_2.44-3 libblkid1_2.41-3 libboost-atomic1.83-dev_1.83.0-4.2 libboost-atomic1.83.0_1.83.0-4.2 libboost-chrono1.83-dev_1.83.0-4.2 libboost-chrono1.83.0t64_1.83.0-4.2 libboost-date-time1.83-dev_1.83.0-4.2 libboost-date-time1.83.0_1.83.0-4.2 libboost-filesystem-dev_1.83.0.2+b2 libboost-filesystem1.83-dev_1.83.0-4.2 libboost-filesystem1.83.0_1.83.0-4.2 libboost-iostreams-dev_1.83.0.2+b2 libboost-iostreams1.83-dev_1.83.0-4.2 libboost-iostreams1.83.0_1.83.0-4.2 libboost-program-options-dev_1.83.0.2+b2 libboost-program-options1.83-dev_1.83.0-4.2 libboost-program-options1.83.0_1.83.0-4.2 libboost-regex1.83-dev_1.83.0-4.2 libboost-regex1.83.0_1.83.0-4.2 libboost-serialization1.83-dev_1.83.0-4.2 libboost-serialization1.83.0_1.83.0-4.2 libboost-system-dev_1.83.0.2+b2 libboost-system1.83-dev_1.83.0-4.2 libboost-system1.83.0_1.83.0-4.2 libboost-thread-dev_1.83.0.2+b2 libboost-thread1.83-dev_1.83.0-4.2 libboost-thread1.83.0_1.83.0-4.2 libboost-timer-dev_1.83.0.2+b2 libboost-timer1.83-dev_1.83.0-4.2 libboost-timer1.83.0_1.83.0-4.2 libboost1.83-dev_1.83.0-4.2 libbrotli-dev_1.1.0-2+b7 libbrotli1_1.1.0-2+b7 libbwa-dev_0.7.18-1 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.41-6 libc-dev-bin_2.41-6 libc6_2.41-6 libc6-dev_2.41-6 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-4 libcares2_1.34.4-2.1 libcc1-0_14.2.0-19 libcereal-dev_1.3.2+dfsg-5 libcom-err2_1.47.2-1+b1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libcurl3t64-gnutls_8.13.0-1 libcurl4-gnutls-dev_8.13.0-1 libcurl4t64_8.13.0-1 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.278 libdebhelper-perl_13.24.2 libdivsufsort-dev_2.0.1-6+b1 libdivsufsort3_2.0.1-6+b1 libdpkg-perl_1.22.18 libeigen3-dev_3.4.0-4 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libexpat1_2.7.1-1 libffi8_3.4.7-1 libfile-stripnondeterminism-perl_1.14.1-2 libfmt-dev_10.1.1+ds1-4 libfmt10_10.1.1+ds1-4 libgcc-14-dev_14.2.0-19 libgcc-s1_14.2.0-19 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgff-dev_2.0.0-3 libgmp-dev_2:6.3.0+dfsg-3 libgmp10_2:6.3.0+dfsg-3 libgmpxx4ldbl_2:6.3.0+dfsg-3 libgnutls-dane0t64_3.8.9-2 libgnutls-openssl27t64_3.8.9-2 libgnutls28-dev_3.8.9-2 libgnutls30t64_3.8.9-2 libgomp1_14.2.0-19 libgprofng0_2.44-3 libgssapi-krb5-2_1.21.3-5 libgssrpc4t64_1.21.3-5 libhogweed6t64_3.10.1-1 libhtscodecs-dev_1.6.1-2 libhtscodecs2_1.6.1-2 libhwasan0_14.2.0-19 libhwloc15_2.12.0-1 libicu-dev_76.1-3 libicu76_76.1-3 libidn2-0_2.3.8-2 libidn2-dev_2.3.8-2 libisl23_0.27-1 libitm1_14.2.0-19 libjansson4_2.14-2+b3 libjellyfish-2.0-2_2.3.1-4+b1 libjellyfish-2.0-dev_2.3.1-4+b1 libjemalloc-dev_5.3.0-3 libjemalloc2_5.3.0-3 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_8.1.3-5 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libjson-perl_4.10000-1 libjsoncpp26_1.9.6-3 libk5crypto3_1.21.3-5 libkadm5clnt-mit12_1.21.3-5 libkadm5srv-mit12_1.21.3-5 libkdb5-10t64_1.21.3-5 libkeyutils1_1.6.3-4 libkrb5-3_1.21.3-5 libkrb5-dev_1.21.3-5 libkrb5support0_1.21.3-5 liblastlog2-2_2.41-3 libldap-dev_2.6.9+dfsg-2 libldap2_2.6.9+dfsg-2 liblocale-gettext-perl_1.07-7+b1 liblsan0_14.2.0-19 liblz4-1_1.10.0-4 liblzma-dev_5.6.4-1 liblzma5_5.6.4-1 libmagic-mgc_1:5.46-4 libmagic1t64_1:5.46-4 libmd0_1.1.0-2+b1 libmount1_2.41-3 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnghttp2-14_1.64.0-1 libnghttp2-dev_1.64.0-1 libnghttp3-9_1.8.0-1 libnghttp3-dev_1.8.0-1 libngtcp2-16_1.11.0-1 libngtcp2-crypto-gnutls-dev_1.11.0-1 libngtcp2-crypto-gnutls8_1.11.0-1 libngtcp2-dev_1.11.0-1 libnode115_20.19.0+dfsg-1 libp11-kit-dev_0.25.5-3 libp11-kit0_0.25.5-3 libpam-modules_1.7.0-3 libpam-modules-bin_1.7.0-3 libpam-runtime_1.7.0-3 libpam0g_1.7.0-3 libpcre2-8-0_10.45-1 libperl5.40_5.40.1-2 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-4 libproc2-0_2:4.0.4-7 libpsl-dev_0.21.2-1.1+b1 libpsl5t64_0.21.2-1.1+b1 libpthread-stubs0-dev_0.5-1 libpython3-stdlib_3.13.2-2 libpython3.13-minimal_3.13.2-3 libpython3.13-stdlib_3.13.2-3 libquadmath0_14.2.0-19 libreadline8t64_8.2-6 librhash1_1.4.5-1 librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5 librtmp1_2.4+20151223.gitfa8646d.1-2+b5 libsasl2-2_2.1.28+dfsg1-9 libsasl2-modules-db_2.1.28+dfsg1-9 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsframe1_2.44-3 libsimde-dev_0.8.2-3 libsmartcols1_2.41-3 libsparsehash-dev_2.0.3-2 libspdlog-dev_1:1.15.1+ds-1 libspdlog1.15_1:1.15.1+ds-1 libsqlite3-0_3.46.1-2 libssh2-1-dev_1.11.1-1 libssh2-1t64_1.11.1-1 libssl-dev_3.4.1-1 libssl3t64_3.4.1-1 libstaden-read-dev_1.15.0-1.1+b2 libstaden-read14t64_1.15.0-1.1+b2 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 libsystemd0_257.4-9 libtasn1-6_4.20.0-2 libtasn1-6-dev_4.20.0-2 libtbb-dev_2022.1.0-1 libtbb12_2022.1.0-1 libtbbbind-2-5_2022.1.0-1 libtbbmalloc2_2022.1.0-1 libtclap-dev_1.2.5-1+b2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_14.2.0-19 libubsan1_14.2.0-19 libuchardet0_0.0.8-1+b2 libudev1_257.4-9 libunbound8_1.22.0-1+b1 libunistring5_1.3-2 libuuid1_2.41-3 libuv1t64_1.50.0-2 libxml2_2.12.7+dfsg+really2.9.14-0.4 libxxhash0_0.8.3-2 libzstd-dev_1.5.7+dfsg-1 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.21-1 m4_1.4.19-7 make_4.4.1-1 man-db_2.13.0-1 mawk_1.3.4.20250131-1 media-types_13.0.0 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 netbase_6.5 nettle-dev_3.10.1-1 node-acorn_8.8.1+ds+~cs25.17.7-2 node-balanced-match_2.0.0-1 node-brace-expansion_2.0.1+~1.1.0-1 node-cjs-module-lexer_1.2.3+dfsg-1 node-commander_9.4.1-1 node-corepack_0.24.0-4 node-mathjax-full_3.2.2+~cs4.2.1-4 node-minimatch_9.0.3-5 node-mj-context-menu_0.9.1+ds-2 node-speech-rule-engine_4.0.7+~0.1.31-2 node-undici_7.3.0+dfsg1+~cs24.12.11-1 node-xtend_4.0.2-3 nodejs_20.19.0+dfsg-1 openssl_3.4.1-1 openssl-provider-legacy_3.4.1-1 patch_2.7.6-7 perl_5.40.1-2 perl-base_5.40.1-2 perl-modules-5.40_5.40.1-2 pkg-config_1.8.1-4 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 procps_2:4.0.4-7 python-babel-localedata_2.17.0-1 python-requests-doc_2.32.3+dfsg-5 python3_3.13.2-2 python3-alabaster_0.7.16-0.1 python3-babel_2.17.0-1 python3-certifi_2025.1.31+ds-1 python3-chardet_5.2.0+dfsg-2 python3-charset-normalizer_3.4.1-1+b1 python3-defusedxml_0.7.1-3 python3-doc_3.13.2-2 python3-docs-theme_2025.2-1 python3-docutils_0.21.2+dfsg-2 python3-idna_3.10-1 python3-imagesize_1.4.1-1 python3-jinja2_3.1.6-1 python3-markupsafe_2.1.5-1+b3 python3-minimal_3.13.2-2 python3-packaging_24.2-1 python3-pygments_2.18.0+dfsg-2 python3-requests_2.32.3+dfsg-5 python3-roman_5.0-1 python3-snowballstemmer_2.2.0-4 python3-sphinx_8.1.3-5 python3-sphinx-rtd-theme_3.0.2+dfsg-2 python3-sphinxcontrib.jquery_4.1-5 python3-urllib3_2.3.0-2 python3.13_3.13.2-3 python3.13-doc_3.13.2-3 python3.13-minimal_3.13.2-3 rapidjson-dev_1.1.0+dfsg2-7.3 rapmap-dev_0.15.0+dfsg-4 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sed_4.9-2 sensible-utils_0.0.24 sgml-base_1.31 sphinx-common_8.1.3-5 sphinx-doc_8.1.3-5 sphinx-rtd-theme-common_3.0.2+dfsg-2 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 tzdata_2025b-1 util-linux_2.41-3 xml-core_0.19 xz-utils_5.6.4-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Mon, 23 Jun 2025 03:24:08 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: salmon Binary: salmon Architecture: any-amd64 arm64 Version: 1.10.2+ds1-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Kevin Murray Homepage: https://github.com/COMBINE-lab/salmon Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/salmon Vcs-Git: https://salsa.debian.org/med-team/salmon.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev, libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev (>> 2.0), libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, python3-docs-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev, libsimde-dev Package-List: salmon deb science optional arch=any-amd64,arm64 Checksums-Sha1: 8cb3bf45b7d8ffe9e3c8a72576541df2c0c547f2 5718424 salmon_1.10.2+ds1.orig.tar.xz 30674e13817eeb27ade3c0ee5073540e9cbda647 1893940 salmon_1.10.2+ds1-1.debian.tar.xz Checksums-Sha256: 895840bed22f93cb8c02ff00b9007473e291ef06b753a950ec2b75373d78219c 5718424 salmon_1.10.2+ds1.orig.tar.xz 6d296a4cb41e4068975b0ff8592d700cd525a2f961c7fc10ba54cdc69cfe2456 1893940 salmon_1.10.2+ds1-1.debian.tar.xz Files: 142f7da8a6cde566343ae6f3431d7a39 5718424 salmon_1.10.2+ds1.orig.tar.xz 07a9180c1b0c41c4dae2adb41ac2e605 1893940 salmon_1.10.2+ds1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmTcroMACgkQPCZ2P2xn 5uIu5w/+JPSxmuJiLVVlIZ7SjpjJMMgEiYMmna5OIZS+0BRh3/Y5fdXty8GHJ1ry bDntR1ondwWXHZoglZCykAtP6jWbx67/WfmnnmYqrKPP977KpbjyAJ9Grrt9nK9u VlENkkFxv0b1vLdlwuuX8dEZWz282kvJyquthYWB1oIXUIRYhBlaiuuEBQy95SS7 eEOrs6K6wxFfwFHZ4wEx8uAit/7EuFyH9uw0+WKtlfbUAEyowIAL8MwD/osP+0jd iaQo+0KOE+297HMV2gJTeAvP8kTvCBwb6NFPtUWS2zjGmipkU7lurV+gpMC0HNFw Fk/63W9Je9d6RJlpXa3grfCrwmfV2MvVjjTOBo4U/W4QvDfrqqQRQHQBxQCj9Joi O0CHb8KrH0flPsex71TREbYqZj35l9llT1AyMqJ0Q3eR2gBRgIW7nrnR/0/kTMLR oyn+ooaXEMhSLYIHmV1auVOQ4yAff/s8RiejlWCBTDuHHB1T/e4H70ZSyrCMqNyg 1l/MabEpZO6gEatn8VsehdqKDimyrunkou+VvDsvYigbIIGrgzYZNFvudXfEKRSo SDxiRAdvasN0neNqy01gepn7iSZSqKTVaTkuBKSwBpmiLEkSj/1rIYL5tGcSHBxR 7av8D94MGO6MQN5JvtR+exUKdseIMAq90NWqC9sq++WDRmeTGkM= =HBVp -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./salmon_1.10.2+ds1-1.dsc: unsupported subcommand dpkg-source: info: extracting salmon in /build/reproducible-path/salmon-1.10.2+ds1 dpkg-source: info: unpacking salmon_1.10.2+ds1.orig.tar.xz dpkg-source: info: unpacking salmon_1.10.2+ds1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying pufferfish dpkg-source: info: applying disable-version-check.patch dpkg-source: info: applying sphinx.patch Check disk space ---------------- Sufficient free space for build Hack binNMU version ------------------- Created changelog entry for binNMU version 1.10.2+ds1-1+b5 User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=6 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LC_COLLATE=C.UTF-8 LC_CTYPE=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh SOURCE_DATE_EPOCH=1743660794 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -B dpkg-buildpackage: info: source package salmon dpkg-buildpackage: info: source version 1.10.2+ds1-1+b5 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-ubc-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with sphinxdoc debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1' dh_auto_clean rm -rf external rm -f debian/*.1 rm -Rf sample_data cd doc && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/doc' rm -rf build/* make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/doc' rm -rf tests/unitTests make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1' dh_clean debian/rules binary-arch dh binary-arch --with sphinxdoc dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1' # See here # https://github.com/COMBINE-lab/salmon/issues/87 # for a discussion with upstream why it is necessary to include rapmap source mkdir -p /build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap cp -av /usr/share/rapmap/src/* /build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap '/usr/share/rapmap/src/HitManager.cpp' -> '/build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap/HitManager.cpp' '/usr/share/rapmap/src/RapMapFileSystem.cpp' -> '/build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap/RapMapFileSystem.cpp' '/usr/share/rapmap/src/RapMapSAIndex.cpp' -> '/build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap/RapMapSAIndex.cpp' '/usr/share/rapmap/src/RapMapSAIndexer.cpp' -> '/build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap/RapMapSAIndexer.cpp' '/usr/share/rapmap/src/RapMapUtils.cpp' -> '/build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap/RapMapUtils.cpp' '/usr/share/rapmap/src/bit_array.c' -> '/build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap/bit_array.c' '/usr/share/rapmap/src/rank9b.cpp' -> '/build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap/rank9b.cpp' dh_auto_configure -- -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE .. CC: gcc CC version: -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Detected non-ARM host. Setting USE_ARM to false. version: 1.10.2 -- CMAKE_BUILD_TYPE = Release -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE Building with CONDA_BUILD flag Making Release build setting -DHAVE_NUMERIC_LIMITS128 CMake Warning (dev) at CMakeLists.txt:314 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. running cd "/build/reproducible-path/salmon-1.10.2+ds1" && cp -r ./debian/external ./ 2>&1 -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Performing Test Iconv_IS_BUILT_IN -- Performing Test Iconv_IS_BUILT_IN - Success -- Found Iconv: built in to C library -- Found LibLZMA: lzma (found version "5.6.4") Found liblzma library: lzma =========================================== -- Found BZip2: -lbz2 (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found Found libbz2 library: -lbz2 =========================================== CMake Warning (dev) at CMakeLists.txt:429 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.59.0") found components: iostreams system filesystem timer chrono program_options BOOST_INCLUDEDIR = BOOST_LIBRARYDIR = Boost_FOUND = TRUE BOOST ROOT = BOOST INCLUDE DIR = /usr/include BOOST INCLUDE DIRS = /usr/include BOOST LIB DIR = /usr/lib/x86_64-linux-gnu BOOST LIBRARIES = Boost::iostreams;Boost::system;Boost::filesystem;Boost::timer;Boost::chrono;Boost::program_options -- Found cereal: /usr/include (found suitable version "1.3.2", minimum required is "1.3.2") -- cereal found (include: /usr/include) FOUND SUITABLE TBB VERSION : 2022.1.0 -- libgff ver. 2.0.0 found. -- include: /usr/include/ -- lib : /usr/lib/ -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "8.13.0") -- Found libstadenio: /usr/lib/x86_64-linux-gnu/libstaden-read.so (Required is at least version "1.14.15") -- Staden IOLib found (include: /usr/include) -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Found Jemalloc: /usr/lib/x86_64-linux-gnu/libjemalloc.so (found version "5.3.0-0-g54eaed1d8b56b1aa528be3bdd1877e59c56fa90c") Found Jemalloc library --- using this memory allocator CPACK_SOURCE_IGNORE_FILES = /src/PCA.cpp;/src/PCAUtils.cpp;/build/;/scripts/AggregateToGeneLevel.py;/scripts/ExpressionTools.py;/scripts/GenerateExpressionFiles.sh;/scripts/ParseSoftFile.py;/scripts/PlotCorrelation.py;/scripts/junk;/scripts/sfstrace.log;/scripts/SFPipeline.py;/bin/;/lib/;/sample_data/;PublishREADMEToWebsite.sh;/external/;/src/obsolete/;/include/obsolete/;WebsiteHeader.txt;/experimental_configs/;.git/ CC: /usr/bin/cc CC version: version: 1.0.0 Building basic pufferfish components for salmon setting -DHAVE_NUMERIC_LIMITS128 CMake Deprecation Warning at external/pufferfish/external/ntcard/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at external/pufferfish/external/twopaco/graphdump/CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- setting COMPACT_VECTOR_DIR for graphdump to be /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump CMake Deprecation Warning at external/pufferfish/external/twopaco/graphconstructor/CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. add library puffer : PufferfishIndexer.cpp;PufferfishBaseIndex.cpp;PufferfishIndex.cpp;PufferfishSparseIndex.cpp;PufferfishLossyIndex.cpp;edlib.cpp;Util.cpp;rank9sel.cpp;rank9b.cpp;PufferfishValidate.cpp;PufferfishStats.cpp;PufferfishTestLookup.cpp;PufferfishExamine.cpp;PufferfishKmerQuery.cpp;FastxParser.cpp;PufferfishBinaryGFAReader.cpp;PufferFS.cpp;xxhash.c;FixFasta.cpp;MemCollector.cpp;MemChainer.cpp;PuffAligner.cpp;PufferfishAligner.cpp;RefSeqConstructor.cpp;metro/metrohash64.cpp;/build/reproducible-path/salmon-1.10.2+ds1/src/LibraryFormat.cpp adding /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump to include path for libpuffer fetched path for compact_vector as [/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump] NO_IPO = FALSE TBB_LIBRARIES = TBB_LIB_INSTALL_DIR = TBBGLOBS = -- Configuring done (3.2s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED FETCHED_RAPMAP -- Build files have been written to: /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1' dh_auto_build cd obj-x86_64-linux-gnu && make -j6 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/salmon-1.10.2+ds1 -B/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend make -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend make -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 1%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o [ 2%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o [ 2%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c [ 3%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o -MF CMakeFiles/graphdump.dir/graphdump.cpp.o.d -o CMakeFiles/graphdump.dir/graphdump.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/graphdump.cpp cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -MF CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o.d -o CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common/SignalHandler.cpp cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c [ 4%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/kalloc.c [ 5%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -MF CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/dnachar.cpp [ 6%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extd.c [ 7%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o -MF CMakeFiles/twopaco.dir/constructor.cpp.o.d -o CMakeFiles/twopaco.dir/constructor.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp [ 8%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extz.c [ 9%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -MF CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o.d -o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common/Fcontrol.cpp [ 10%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o -MF CMakeFiles/ntcard.dir/nthll.cpp.o.d -o CMakeFiles/ntcard.dir/nthll.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/nthll.cpp [ 11%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c [ 12%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_gg.c [ 13%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c [ 14%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c [ 15%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2.c [ 16%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c [ 16%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2_sse.c make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 16%] Built target ksw2pp_sse2 make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 17%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndexer.cpp [ 18%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp [ 19%] Linking CXX static library libntcard.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -E cmake_link_script CMakeFiles/ntcard.dir/link.txt --verbose=1 /usr/bin/ar qc libntcard.a CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o CMakeFiles/ntcard.dir/nthll.cpp.o /usr/bin/ranlib libntcard.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 19%] Built target ntcard [ 20%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 20%] Built target ksw2pp_sse4 [ 21%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -MF CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o.d -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 21%] Built target ksw2pp_basic make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 22%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -MF CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o.d -o CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/jellyfish/mer_dna.cc In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBaseIndex.hpp:14, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 22%] Building CXX object src/CMakeFiles/salmon_core.dir/backtrace.cc.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/backtrace.cc.o -MF CMakeFiles/salmon_core.dir/backtrace.cc.o.d -o CMakeFiles/salmon_core.dir/backtrace.cc.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/backtrace.cc [ 23%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/xxhash.c.o -MF CMakeFiles/salmon_core.dir/xxhash.c.o.d -o CMakeFiles/salmon_core.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/xxhash.c cc1: warning: command-line option ‘-Wno-reorder’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-Wno-deprecated-copy’ is valid for C++/ObjC++ but not for C [ 24%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -MF CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o.d -o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/TranscriptGroup.cpp [ 25%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o -MF CMakeFiles/twopaco.dir/compressedstring.cpp.o.d -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp [ 26%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -MF CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o.d -o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/EffectiveLengthStats.cpp [ 27%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o -MF CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o.d -o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/dnachar.cpp [ 28%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndex.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]’ 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from ‘void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]’ 2817 | for (destructive_iterator it = ht.destructive_begin(); | ~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]’ 2948 | _move_from(mover, ht, min_buckets_wanted); | ^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from ‘bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]’ 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]’ 3278 | if (_resize_delta(1)) | ^~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here 161 | path[ref_cnt].resize(contigCntPerPath); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared ‘constexpr spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >&)’ is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because ‘spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >’ has user-provided ‘spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair > >; row_it = spp::sparsegroup > >, spp::libc_allocator > > > >*; col_it = std::pair > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator > > >]’ 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; value_type = std::pair > >; reference = std::pair > >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here 161 | path[ref_cnt].resize(contigCntPerPath); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup > >, spp::libc_allocator > > > >::value_type’ {aka ‘std::pair > >’} to ‘spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference’ {aka ‘std::pair > >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >; dest_it = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >]’ 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from ‘void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2817 | for (destructive_iterator it = ht.destructive_begin(); | ~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2948 | _move_from(mover, ht, min_buckets_wanted); | ^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from ‘bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3278 | if (_resize_delta(1)) | ^~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here 414 | eqID = eqMap[tlist]; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared ‘constexpr spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >&)’ is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because ‘spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >’ has user-provided ‘spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair, unsigned int>; row_it = spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*; col_it = std::pair, unsigned int>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator, unsigned int> >]’ 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here 414 | eqID = eqMap[tlist]; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; mutable_value_type = std::pair > >; reference = std::pair > >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here 161 | path[ref_cnt].resize(contigCntPerPath); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup > >, spp::libc_allocator > > > >::value_type’ {aka ‘std::pair > >’} to ‘spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference’ {aka ‘std::pair > >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here 414 | eqID = eqMap[tlist]; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishIndex.hpp:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndex.cpp:9: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 29%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -MF CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o.d -o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/LibraryFormat.cpp [ 30%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -MF CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o.d -o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/GenomicFeature.cpp [ 31%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o.d -o 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CMakeFiles/twopaco.dir/test.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp [ 33%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -MF CMakeFiles/salmon_core.dir/VersionChecker.cpp.o.d -o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/VersionChecker.cpp make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 34%] Building CXX object src/CMakeFiles/alevin_core.dir/edlib.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/edlib.cpp.o -MF CMakeFiles/alevin_core.dir/edlib.cpp.o.d -o CMakeFiles/alevin_core.dir/edlib.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/edlib.cpp [ 35%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -MF CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o.d -o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SingleCellProtocols.cpp [ 35%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o.d -o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinOpts.hpp:5, from /build/reproducible-path/salmon-1.10.2+ds1/include/SingleCellProtocols.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/src/SingleCellProtocols.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 36%] Linking CXX static library libgraphdump.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -P CMakeFiles/graphdump.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphdump.dir/link.txt --verbose=1 /usr/bin/ar qc libgraphdump.a CMakeFiles/graphdump.dir/graphdump.cpp.o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o /usr/bin/ranlib libgraphdump.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 36%] Built target graphdump [ 37%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SBModel.cpp.o -MF CMakeFiles/salmon_core.dir/SBModel.cpp.o.d -o CMakeFiles/salmon_core.dir/SBModel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SBModel.cpp [ 38%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -MF CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o.d -o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp [ 38%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -MF CMakeFiles/twopaco.dir/vertexenumerator.cpp.o.d -o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp [ 38%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o -MF CMakeFiles/salmon_core.dir/FastxParser.cpp.o.d -o CMakeFiles/salmon_core.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:27, from /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 39%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -MF CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp make -f src/CMakeFiles/UnitTestsMain.dir/build.make src/CMakeFiles/UnitTestsMain.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/UnitTestsMain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/UnitTestsMain.dir/build.make src/CMakeFiles/UnitTestsMain.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 39%] Building CXX object src/CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -MF CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o.d -o CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/tests/UnitTests.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, from /build/reproducible-path/salmon-1.10.2+ds1/include/UtilityFunctions.hpp:4, from /build/reproducible-path/salmon-1.10.2+ds1/include/SBModel.hpp:6, from /build/reproducible-path/salmon-1.10.2+ds1/src/SBModel.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 40%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp: In function ‘bool alevin::utils::extractBarcode(std::string&, std::string&, ProtocolT&, std::string&) [with ProtocolT = alevin::protocols::SciSeq3; std::string = std::__cxx11::basic_string]’: /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:350:104: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 350 | if (pt.anchorPos != std::string::npos && ( pt.anchorPos == pt.maxHairpinIndexLen || pt.anchorPos == pt.maxHairpinIndexLen -1) // only 2 possible values of pt.anchorPos | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishSparseIndex.hpp:13, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp:10: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; value_type = std::pair, std::vector >; reference = std::pair, std::vector >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; allocator_type = spp::libc_allocator, std::vector > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; pointer = std::pair, std::vector >*; allocator_type = spp::libc_allocator, std::vector > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; reference = std::pair, std::vector >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, std::vector >; Value = std::pair, std::vector >; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, std::vector >::SelectKey; SetKey = spp::sparse_hash_map, std::vector >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::vector > >; reference = std::pair, std::vector >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::vector >::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, std::vector >; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, std::vector >::SelectKey; SetKey = spp::sparse_hash_map, std::vector >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::vector > >; value_type = std::pair, std::vector >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = std::vector; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::vector > >; mapped_type = std::vector]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:620:34: required from here 620 | txpIdxMap[txpNames[i]].emplace_back(i); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, std::vector >, spp::libc_allocator, std::vector > > >::value_type’ {aka ‘std::pair, std::vector >’} to ‘spp::sparsegroup, std::vector >, spp::libc_allocator, std::vector > > >::mutable_reference’ {aka ‘std::pair, std::vector >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = std::vector; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = std::vector]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:643:33: required from here 643 | geneIdxMap[txpNames[i]] = i; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:644:25: required from here 644 | txpToGeneMap[i] = i; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; mutable_value_type = std::pair, std::vector >; reference = std::pair, std::vector >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; allocator_type = spp::libc_allocator, std::vector > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; allocator_type = spp::libc_allocator, std::vector > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; pointer = std::pair, std::vector >*; allocator_type = spp::libc_allocator, std::vector > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; reference = std::pair, std::vector >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, std::vector >; Value = std::pair, std::vector >; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, std::vector >::SelectKey; SetKey = spp::sparse_hash_map, std::vector >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::vector > >; reference = std::pair, std::vector >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::vector >::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, std::vector >; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, std::vector >::SelectKey; SetKey = spp::sparse_hash_map, std::vector >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::vector > >; value_type = std::pair, std::vector >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = std::vector; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::vector > >; mapped_type = std::vector]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:620:34: required from here 620 | txpIdxMap[txpNames[i]].emplace_back(i); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, std::vector >, spp::libc_allocator, std::vector > > >::value_type’ {aka ‘std::pair, std::vector >’} to ‘spp::sparsegroup, std::vector >, spp::libc_allocator, std::vector > > >::mutable_reference’ {aka ‘std::pair, std::vector >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = std::vector; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = std::vector]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:643:33: required from here 643 | geneIdxMap[txpNames[i]] = i; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:644:25: required from here 644 | txpToGeneMap[i] = i; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 41%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -MF CMakeFiles/salmon_core.dir/StadenUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/StadenUtils.cpp [ 42%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonUtils.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12, from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonUtils.cpp:18: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 43%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -MF CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/DistributionUtils.cpp [ 44%] Linking CXX static library libalevin_core.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-14" qc libalevin_core.a CMakeFiles/alevin_core.dir/edlib.cpp.o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o "/usr/bin/gcc-ranlib-14" libalevin_core.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 44%] Built target alevin_core [ 45%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonExceptions.cpp make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 46%] Linking CXX static library libksw2pp.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-14" qc libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o "/usr/bin/gcc-ranlib-14" libksw2pp.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 46%] Built target ksw2pp [ 47%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o -MF CMakeFiles/twopaco.dir/common.cpp.o.d -o CMakeFiles/twopaco.dir/common.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/common.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ [ 48%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonStringUtils.cpp /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 48%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishLossyIndex.cpp [ 49%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o -MF CMakeFiles/puffer.dir/edlib.cpp.o.d -o CMakeFiles/puffer.dir/edlib.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/edlib.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, from /build/reproducible-path/salmon-1.10.2+ds1/include/Transcript.hpp:8, from /build/reproducible-path/salmon-1.10.2+ds1/src/DistributionUtils.cpp:3: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishLossyIndex.hpp:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishLossyIndex.cpp:7: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 50%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o -MF CMakeFiles/puffer.dir/Util.cpp.o.d -o CMakeFiles/puffer.dir/Util.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/Util.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/Util.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 51%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -MF CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o.d -o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SimplePosBias.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SimplePosBias.hpp:4, from /build/reproducible-path/salmon-1.10.2+ds1/src/SimplePosBias.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 52%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o -MF CMakeFiles/puffer.dir/rank9sel.cpp.o.d -o CMakeFiles/puffer.dir/rank9sel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/rank9sel.cpp [ 53%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o -MF CMakeFiles/puffer.dir/rank9b.cpp.o.d -o CMakeFiles/puffer.dir/rank9b.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/rank9b.cpp [ 54%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -MF CMakeFiles/salmon_core.dir/SGSmooth.cpp.o.d -o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SGSmooth.cpp [ 54%] Building CXX object src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -MF CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o.d -o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/install/src/pufferfish/metro/metrohash64.cpp [ 55%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -MF CMakeFiles/puffer.dir/PufferfishValidate.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishValidate.cpp [ 56%] Linking CXX static library libsalmon_core.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-14" qc libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o CMakeFiles/salmon_core.dir/backtrace.cc.o CMakeFiles/salmon_core.dir/xxhash.c.o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o CMakeFiles/salmon_core.dir/SBModel.cpp.o CMakeFiles/salmon_core.dir/FastxParser.cpp.o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o "/usr/bin/gcc-ranlib-14" libsalmon_core.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 56%] Built target salmon_core [ 57%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o -MF CMakeFiles/puffer.dir/PufferfishStats.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishStats.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishStats.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishValidate.cpp:15: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishStats.cpp:16: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 58%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -MF CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp:14: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp: In function ‘std::vector get_kmers(const std::string&, uint32_t)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp:25:78: warning: unused parameter ‘k’ [-Wunused-parameter] 25 | std::vector get_kmers(const std::string& fasta_file, uint32_t k) { | ~~~~~~~~~^ [ 58%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -MF CMakeFiles/puffer.dir/PufferfishExamine.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishExamine.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PuffAligner.hpp:8, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishExamine.cpp:6: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 59%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -MF CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishKmerQuery.cpp [ 60%] Linking CXX static library libUnitTestsMain.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/UnitTestsMain.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/UnitTestsMain.dir/link.txt --verbose=1 /usr/bin/ar qc libUnitTestsMain.a CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o /usr/bin/ranlib libUnitTestsMain.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 60%] Built target UnitTestsMain make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/unitTests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 61%] Building CXX object src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishKmerQuery.cpp:13: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 62%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o -MF CMakeFiles/puffer.dir/FastxParser.cpp.o.d -o CMakeFiles/puffer.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FastxParser.cpp [ 63%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]’ 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from ‘void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]’ 2817 | for (destructive_iterator it = ht.destructive_begin(); | ~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]’ 2948 | _move_from(mover, ht, min_buckets_wanted); | ^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from ‘bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]’ 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]’ 3278 | if (_resize_delta(1)) | ^~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here 161 | path[ref_cnt].resize(contigCntPerPath); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared ‘constexpr spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >&)’ is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because ‘spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >’ has user-provided ‘spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair > >; row_it = spp::sparsegroup > >, spp::libc_allocator > > > >*; col_it = std::pair > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator > > >]’ 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; value_type = std::pair > >; reference = std::pair > >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here 161 | path[ref_cnt].resize(contigCntPerPath); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup > >, spp::libc_allocator > > > >::value_type’ {aka ‘std::pair > >’} to ‘spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference’ {aka ‘std::pair > >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >; dest_it = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >]’ 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from ‘void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2817 | for (destructive_iterator it = ht.destructive_begin(); | ~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2948 | _move_from(mover, ht, min_buckets_wanted); | ^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from ‘bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3278 | if (_resize_delta(1)) | ^~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here 414 | eqID = eqMap[tlist]; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared ‘constexpr spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >&)’ is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because ‘spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >’ has user-provided ‘spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair, unsigned int>; row_it = spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*; col_it = std::pair, unsigned int>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator, unsigned int> >]’ 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here 414 | eqID = eqMap[tlist]; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; mutable_value_type = std::pair > >; reference = std::pair > >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here 161 | path[ref_cnt].resize(contigCntPerPath); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup > >, spp::libc_allocator > > > >::value_type’ {aka ‘std::pair > >’} to ‘spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference’ {aka ‘std::pair > >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here 414 | eqID = eqMap[tlist]; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, from /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp:12: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 64%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o -MF CMakeFiles/puffer.dir/PufferFS.cpp.o.d -o CMakeFiles/puffer.dir/PufferFS.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferFS.cpp [ 65%] Building C object external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o -MF CMakeFiles/puffer.dir/xxhash.c.o.d -o CMakeFiles/puffer.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/xxhash.c cc1: warning: command-line option ‘-Wno-reorder’ is valid for C++/ObjC++ but not for C [ 66%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o -MF CMakeFiles/puffer.dir/FixFasta.cpp.o.d -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp [ 67%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o -MF CMakeFiles/puffer.dir/MemCollector.cpp.o.d -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemCollector.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:5: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishIndex.hpp:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/MemCollector.hpp:6, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemCollector.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 67%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o -MF CMakeFiles/puffer.dir/MemChainer.cpp.o.d -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemChainer.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishIndex.hpp:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/MemChainer.hpp:8, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemChainer.cpp:2: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:4: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]’ 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from ‘void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]’ 2817 | for (destructive_iterator it = ht.destructive_begin(); | ~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]’ 2948 | _move_from(mover, ht, min_buckets_wanted); | ^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from ‘bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; size_type = long unsigned int]’ 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]’ 3278 | if (_resize_delta(1)) | ^~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here 264 | duplicateNames[dupInfo.txId].push_back(processedName); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared ‘constexpr spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >&)’ is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because ‘spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >’ has user-provided ‘spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair > >; row_it = spp::sparsegroup > >, spp::libc_allocator > > > >*; col_it = std::pair > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator > > >]’ 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; value_type = std::pair > >; reference = std::pair > >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here 264 | duplicateNames[dupInfo.txId].push_back(processedName); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup > >, spp::libc_allocator > > > >::value_type’ {aka ‘std::pair > >’} to ‘spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference’ {aka ‘std::pair > >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >; dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >]’ 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from ‘void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; size_type = long unsigned int]’ 2817 | for (destructive_iterator it = ht.destructive_begin(); | ~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; size_type = long unsigned int]’ 2948 | _move_from(mover, ht, min_buckets_wanted); | ^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from ‘bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; size_type = long unsigned int]’ 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3234:9: required from ‘std::pair::ne_iterator, bool> spp::sparse_hashtable::insert(P&&) [with P = std::__cxx11::basic_string&; Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; typename spp::sparsetable::ne_iterator = spp::Two_d_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::bidirectional_iterator_tag>]’ 3234 | _resize_delta(1); // adding an object, grow if need be | ^~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:4225:73: required from ‘std::pair::Identity, spp::sparse_hash_set::SetKey, EqualKey, Alloc>::const_iterator, bool> spp::sparse_hash_set::insert(P&&) [with P = std::__cxx11::basic_string&; Value = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; typename spp::sparse_hashtable::const_iterator = spp::Two_d_iterator, const spp::sparsegroup, spp::libc_allocator > >*, const std::__cxx11::basic_string*, std::bidirectional_iterator_tag>]’ 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(obj)); } | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:490:26: required from here 490 | auto it = dset.insert(dname); | ~~~~~~~~~~~^~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared ‘constexpr spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >&)’ is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because ‘spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >’ has user-provided ‘spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::__cxx11::basic_string; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::__cxx11::basic_string*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]’ 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; mutable_value_type = std::pair > >; reference = std::pair > >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here 264 | duplicateNames[dupInfo.txId].push_back(processedName); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup > >, spp::libc_allocator > > > >::value_type’ {aka ‘std::pair > >’} to ‘spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference’ {aka ‘std::pair > >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 68%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -MF CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o.d -o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/install/src/pufferfish/rank9b.cpp [ 69%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o -MF CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o.d -o CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/tests/GCSampleTests.cpp [ 70%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -MF CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o.d -o CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/tests/LibraryTypeTests.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, from /build/reproducible-path/salmon-1.10.2+ds1/tests/LibraryTypeTests.cpp:6: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 71%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, from /build/reproducible-path/salmon-1.10.2+ds1/tests/GCSampleTests.cpp:6: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o -MF CMakeFiles/puffer.dir/PuffAligner.cpp.o.d -o CMakeFiles/puffer.dir/PuffAligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PuffAligner.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PuffAligner.hpp:8, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PuffAligner.cpp:2: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 72%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -MF CMakeFiles/puffer.dir/PufferfishAligner.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishAligner.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishAligner.cpp:35: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 73%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -MF CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o.d -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/sha2.hpp:9, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/digestpp.hpp:6, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:27: In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:537:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript ‘const long unsigned int[0]’ is partly outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/digestpp.hpp:5: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript ‘const unsigned int[0]’ is partly outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [1, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 4 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [2, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 8 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [3, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 12 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [4, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 16 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [5, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 20 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [6, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 24 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [7, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 28 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [8, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 32 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [9, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 36 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [10, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 40 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [11, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 44 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [12, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 48 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [13, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 52 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [14, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 56 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ In member function ‘void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’, inlined from ‘digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from ‘void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, inlined from ‘void digestpp::detail::sha2_provider::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23, inlined from ‘digestpp::hasher& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; Mixin = digestpp::mixin::null_mixin]’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from ‘bool extractFasta(std::string&, std::string&, uint32_t&)’ at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [15, 2305843009213693951] is outside array bounds of ‘unsigned char [1]’ [-Warray-bounds=] 208 | M[i] = byteswap(reinterpret_cast(data)[blk * 16 + i]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function ‘bool extractFasta(std::string&, std::string&, uint32_t&)’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 60 into object ‘byte’ of size 1 169 | unsigned char byte = *begin++; | ^~~~ [ 74%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -MF CMakeFiles/puffer.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/metro/metrohash64.cpp [ 75%] Linking CXX executable unitTests cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitTests.dir/link.txt --verbose=1 [ 76%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -MF CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o.d -o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/LibraryFormat.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/RefSeqConstructor.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/RefSeqConstructor.hpp:5: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >; dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from ‘spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]’ 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from ‘void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]’ 2817 | for (destructive_iterator it = ht.destructive_begin(); | ~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]’ 2948 | _move_from(mover, ht, min_buckets_wanted); | ^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from ‘bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]’ 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); | ^~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3278 | if (_resize_delta(1)) | ^~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from ‘Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]’ 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; | ~~~~~~~~~~~~~~~~~~^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here 466 | template class RefSeqConstructor; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared ‘constexpr spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >&)’ is deprecated [-Wdeprecated-copy] 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } | ^~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because ‘spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >’ has user-provided ‘spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::pair*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]’ 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from ‘Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]’ 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; | ~~~~~~~~~~~~~~~~~~^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here 466 | template class RefSeqConstructor; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = pufferfish::util::ContigBlock; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = pufferfish::util::ContigBlock]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from ‘Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]’ 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; | ~~~~~~~~~~~~~~~~~~^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here 466 | template class RefSeqConstructor; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = pufferfish::util::ContigBlock; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = pufferfish::util::ContigBlock]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 77%] Linking CXX static library libtwopaco.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -P CMakeFiles/twopaco.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -E cmake_link_script CMakeFiles/twopaco.dir/link.txt --verbose=1 /usr/bin/ar qc libtwopaco.a CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o CMakeFiles/twopaco.dir/constructor.cpp.o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o CMakeFiles/twopaco.dir/compressedstring.cpp.o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o CMakeFiles/twopaco.dir/test.cpp.o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o CMakeFiles/twopaco.dir/common.cpp.o /usr/bin/ranlib libtwopaco.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 77%] Built target twopaco /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/unitTests.dir/link.d CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -o unitTests -L/build/reproducible-path/salmon-1.10.2+ds1/lib -L/build/reproducible-path/salmon-1.10.2+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex libsalmon_core.a libalevin_core.a -lgff libUnitTestsMain.a /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_timer.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libstaden-read.so /usr/lib/x86_64-linux-gnu/libhtscodecs.so /usr/lib/x86_64-linux-gnu/libcurl.so -lz -lm -llzma -lbz2 -ltbb -ltbbmalloc -lgomp -lrt -ldl /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 Copying unitTests cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E copy /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src/unitTests /build/reproducible-path/salmon-1.10.2+ds1/tests/unitTests make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 77%] Built target unitTests [ 78%] Linking CXX static library libpuffer.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/puffer.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/puffer.dir/link.txt --verbose=1 /usr/bin/ar qc libpuffer.a CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o CMakeFiles/puffer.dir/edlib.cpp.o CMakeFiles/puffer.dir/Util.cpp.o CMakeFiles/puffer.dir/rank9sel.cpp.o CMakeFiles/puffer.dir/rank9b.cpp.o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o CMakeFiles/puffer.dir/PufferfishStats.cpp.o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o CMakeFiles/puffer.dir/FastxParser.cpp.o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o CMakeFiles/puffer.dir/PufferFS.cpp.o CMakeFiles/puffer.dir/xxhash.c.o CMakeFiles/puffer.dir/FixFasta.cpp.o CMakeFiles/puffer.dir/MemCollector.cpp.o CMakeFiles/puffer.dir/MemChainer.cpp.o CMakeFiles/puffer.dir/PuffAligner.cpp.o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o /usr/bin/ranlib libpuffer.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 78%] Built target puffer make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 80%] Building CXX object src/CMakeFiles/salmon.dir/EMUtils.cpp.o [ 80%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/EMUtils.cpp.o -MF CMakeFiles/salmon.dir/EMUtils.cpp.o.d -o CMakeFiles/salmon.dir/EMUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/EMUtils.cpp cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o -MF CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o.d -o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedEMOptimizer.cpp [ 82%] Building CXX object src/CMakeFiles/salmon.dir/Salmon.cpp.o [ 82%] Building CXX object src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o [ 82%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o -MF CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o.d -o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/BuildSalmonIndex.cpp cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/Salmon.cpp.o -MF CMakeFiles/salmon.dir/Salmon.cpp.o.d -o CMakeFiles/salmon.dir/Salmon.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/Salmon.cpp cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o -MF CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o.d -o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp [ 83%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o -MF CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o.d -o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedGibbsSampler.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/pcg_random.hpp:104, from /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedGibbsSampler.cpp:22: /build/reproducible-path/salmon-1.10.2+ds1/include/pcg_extras.hpp:563:51: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 563 | fnv(IntType(2166136261U ^ sizeof(IntType)), __DATE__ __TIME__ __FILE__); | ^~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/pcg_extras.hpp:563:60: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 563 | fnv(IntType(2166136261U ^ sizeof(IntType)), __DATE__ __TIME__ __FILE__); | ^~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12, from /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedEMOptimizer.cpp:22: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonIndex.hpp:11, from /build/reproducible-path/salmon-1.10.2+ds1/src/Salmon.cpp:49: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, from /build/reproducible-path/salmon-1.10.2+ds1/include/Transcript.hpp:8, from /build/reproducible-path/salmon-1.10.2+ds1/include/EMUtils.hpp:6, from /build/reproducible-path/salmon-1.10.2+ds1/src/EMUtils.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonIndex.hpp:11, from /build/reproducible-path/salmon-1.10.2+ds1/src/BuildSalmonIndex.cpp:34: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, from /build/reproducible-path/salmon-1.10.2+ds1/include/Transcript.hpp:8, from /build/reproducible-path/salmon-1.10.2+ds1/include/ClusterForest.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadExperiment.hpp:5, from /build/reproducible-path/salmon-1.10.2+ds1/include/CollapsedCellOptimizer.hpp:11, from /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:5: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12, from /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedGibbsSampler.cpp:30: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 84%] Building CXX object src/CMakeFiles/salmon.dir/Graph.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/Graph.cpp.o -MF CMakeFiles/salmon.dir/Graph.cpp.o.d -o CMakeFiles/salmon.dir/Graph.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/Graph.cpp [ 85%] Building CXX object src/CMakeFiles/salmon.dir/DedupUMI.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/DedupUMI.cpp.o -MF CMakeFiles/salmon.dir/DedupUMI.cpp.o.d -o CMakeFiles/salmon.dir/DedupUMI.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadExperiment.hpp:7: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = const short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const short unsigned int&; Key = short unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:747:45: required from here 747 | arboFragCounts[gid][it.first] += it.second; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = const short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const short unsigned int&; Key = short unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:747:45: required from here 747 | arboFragCounts[gid][it.first] += it.second; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1087:29: required from ‘bool CollapsedCellOptimizer::optimize(EqMapT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, AlevinOpts&, GZipWriter&, std::vector >&, std::vector&, CFreqMapT&, size_t) [with ProtocolT = alevin::protocols::DropSeq; EqMapT = libcuckoo::cuckoohash_map, std::allocator >, 4>; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 1087 | mRnaGenes.insert(geneIdxMap[ gene ]); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1426:68: required from here 1426 | size_t numLowConfidentBarcode); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1087:29: required from ‘bool CollapsedCellOptimizer::optimize(EqMapT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, AlevinOpts&, GZipWriter&, std::vector >&, std::vector&, CFreqMapT&, size_t) [with ProtocolT = alevin::protocols::DropSeq; EqMapT = libcuckoo::cuckoohash_map, std::allocator >, 4>; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 1087 | mRnaGenes.insert(geneIdxMap[ gene ]); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1426:68: required from here 1426 | size_t numLowConfidentBarcode); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 86%] Building CXX object src/CMakeFiles/salmon.dir/Alevin.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/Alevin.cpp.o -MF CMakeFiles/salmon.dir/Alevin.cpp.o.d -o CMakeFiles/salmon.dir/Alevin.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:27, from /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:8, from /build/reproducible-path/salmon-1.10.2+ds1/src/Graph.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:27, from /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:8, from /build/reproducible-path/salmon-1.10.2+ds1/include/DedupUMI.hpp:4, from /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 87%] Building CXX object src/CMakeFiles/salmon.dir/AlevinHash.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/AlevinHash.cpp.o -MF CMakeFiles/salmon.dir/AlevinHash.cpp.o.d -o CMakeFiles/salmon.dir/AlevinHash.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:48: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::pair&; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::pair&; Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Graph.cpp:10:29: required from here 10 | index = vertMap[node]; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::pair; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:65: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h: In instantiation of ‘T* spp::libc_allocator::reallocate(pointer, size_t) [with T = std::pair, unsigned int>; pointer = std::pair, unsigned int>*; size_t = long unsigned int]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1383:38: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1383 | _group = alloc.reallocate(_group, num_alloc); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::pair&; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::pair&; Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Graph.cpp:10:29: required from here 10 | index = vertMap[node]; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h:425:51: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair, unsigned int>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 425 | pointer res = static_cast(realloc(p, new_size * sizeof(T))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/streambuf:43, from /usr/include/c++/14/bits/streambuf_iterator.h:35, from /usr/include/c++/14/iterator:66, from /usr/include/boost/graph/graph_traits.hpp:14, from /usr/include/boost/graph/depth_first_search.hpp:17, from /usr/include/boost/graph/connected_components.hpp:15, from /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:4: /usr/include/c++/14/bits/stl_pair.h:284:12: note: ‘struct std::pair, unsigned int>’ declared here 284 | struct pair | ^~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::pair&; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::pair&; Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Graph.cpp:10:29: required from here 10 | index = vertMap[node]; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::pair; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -MF CMakeFiles/salmon.dir/SalmonAlevin.cpp.o.d -o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinHash.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 88%] Building CXX object src/CMakeFiles/salmon.dir/WhiteList.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/WhiteList.cpp.o -MF CMakeFiles/salmon.dir/WhiteList.cpp.o.d -o CMakeFiles/salmon.dir/WhiteList.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/WhiteList.cpp [ 89%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantify.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantify.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinOpts.hpp:5, from /build/reproducible-path/salmon-1.10.2+ds1/include/SingleCellProtocols.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/WhiteList.hpp:14, from /build/reproducible-path/salmon-1.10.2+ds1/src/WhiteList.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:60: /build/reproducible-path/salmon-1.10.2+ds1/include/BarcodeModel.hpp: In function ‘void alevin::model::coinTossBarcodeModel(std::string, const std::vector >&, MapT&)’: /build/reproducible-path/salmon-1.10.2+ds1/include/BarcodeModel.hpp:168:31: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::string’ {aka ‘const std::__cxx11::basic_string’} [-Wrange-loop-construct] 168 | for(const std::string trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/BarcodeModel.hpp:168:31: note: use reference type to prevent copying 168 | for(const std::string trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = std::vector; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = std::vector]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:32:17: required from here 32 | tidMap[txp].emplace_back(eqId); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = std::vector; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = std::vector]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; value_type = std::pair, std::pair > >; reference = std::pair, std::pair > >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; pointer = std::pair, std::pair > >*; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, std::pair > >; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::pair >, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; value_type = std::pair, std::pair > >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = std::pair >; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; mapped_type = std::pair >]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:285:29: required from here 285 | eqclassHash[genesVec].first += 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, std::pair > >, spp::libc_allocator, std::pair > > > >::value_type’ {aka ‘std::pair, std::pair > >’} to ‘spp::sparsegroup, std::pair > >, spp::libc_allocator, std::pair > > > >::mutable_reference’ {aka ‘std::pair, std::pair > >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = std::pair >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = std::pair >]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = short unsigned int&; Key = short unsigned int; T = short unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = short unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:286:47: required from here 286 | eqclassHash[genesVec].second[readspmol] += 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = short unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = short unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:413:29: required from here 413 | eqclassHash[genesVec] += 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:477:29: required from here 477 | vertexIndices[gene] = gid; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = std::vector; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = std::vector]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:32:17: required from here 32 | tidMap[txp].emplace_back(eqId); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = std::vector; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = std::vector]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; mutable_value_type = std::pair, std::pair > >; reference = std::pair, std::pair > >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; pointer = std::pair, std::pair > >*; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, std::pair > >; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::pair >, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; value_type = std::pair, std::pair > >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = std::pair >; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; mapped_type = std::pair >]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:285:29: required from here 285 | eqclassHash[genesVec].first += 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, std::pair > >, spp::libc_allocator, std::pair > > > >::value_type’ {aka ‘std::pair, std::pair > >’} to ‘spp::sparsegroup, std::pair > >, spp::libc_allocator, std::pair > > > >::mutable_reference’ {aka ‘std::pair, std::pair > >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = std::pair >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = std::pair >]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = short unsigned int&; Key = short unsigned int; T = short unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = short unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:286:47: required from here 286 | eqclassHash[genesVec].second[readspmol] += 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = short unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = short unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:413:29: required from here 413 | eqclassHash[genesVec] += 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:477:29: required from here 477 | vertexIndices[gene] = gid; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from ‘void spp::sparsetable::move(size_type, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int; reference = std::pair, unsigned int>&]’ 2251 | which_group(i).set(_alloc, pos_in_group(i), val); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from ‘void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2830 | table.move(bucknum, *it); // moves the value to here | ~~~~~~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2948 | _move_from(mover, ht, min_buckets_wanted); | ^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2680:30: required from ‘bool spp::sparse_hashtable::_maybe_shrink() [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >]’ 2680 | sparse_hashtable tmp(MoveDontCopy, *this, sz); | ^~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from ‘void spp::sparse_hashtable::resize(size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2846 | _maybe_shrink(); | ^~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3799:51: required from ‘void spp::sparse_hash_map::resize(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 3799 | void resize(size_type cnt) { rep.resize(cnt); } | ~~~~~~~~~~^~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3801:41: required from ‘void spp::sparse_hash_map::reserve(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 3801 | void reserve(size_type cnt) { resize(cnt); } // c++11 | ^~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:39:25: required from here 39 | vertexIndexMap.reserve(numClasses); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::pair; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:65: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h: In instantiation of ‘T* spp::libc_allocator::reallocate(pointer, size_t) [with T = std::pair, unsigned int>; pointer = std::pair, unsigned int>*; size_t = long unsigned int]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1383:38: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1383 | _group = alloc.reallocate(_group, num_alloc); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from ‘void spp::sparsetable::move(size_type, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int; reference = std::pair, unsigned int>&]’ 2251 | which_group(i).set(_alloc, pos_in_group(i), val); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from ‘void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2830 | table.move(bucknum, *it); // moves the value to here | ~~~~~~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2948 | _move_from(mover, ht, min_buckets_wanted); | ^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2680:30: required from ‘bool spp::sparse_hashtable::_maybe_shrink() [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >]’ 2680 | sparse_hashtable tmp(MoveDontCopy, *this, sz); | ^~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from ‘void spp::sparse_hashtable::resize(size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2846 | _maybe_shrink(); | ^~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3799:51: required from ‘void spp::sparse_hash_map::resize(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 3799 | void resize(size_type cnt) { rep.resize(cnt); } | ~~~~~~~~~~^~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3801:41: required from ‘void spp::sparse_hash_map::reserve(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 3801 | void reserve(size_type cnt) { resize(cnt); } // c++11 | ^~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:39:25: required from here 39 | vertexIndexMap.reserve(numClasses); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h:425:51: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair, unsigned int>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 425 | pointer res = static_cast(realloc(p, new_size * sizeof(T))); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/streambuf:43, from /usr/include/c++/14/bits/streambuf_iterator.h:35, from /usr/include/c++/14/iterator:66, from /usr/include/boost/graph/graph_traits.hpp:14, from /usr/include/boost/graph/depth_first_search.hpp:17, from /usr/include/boost/graph/connected_components.hpp:15, from /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:4: /usr/include/c++/14/bits/stl_pair.h:284:12: note: ‘struct std::pair, unsigned int>’ declared here 284 | struct pair | ^~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from ‘void spp::sparsetable::move(size_type, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int; reference = std::pair, unsigned int>&]’ 2251 | which_group(i).set(_alloc, pos_in_group(i), val); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from ‘void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2830 | table.move(bucknum, *it); // moves the value to here | ~~~~~~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from ‘spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2948 | _move_from(mover, ht, min_buckets_wanted); | ^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2680:30: required from ‘bool spp::sparse_hashtable::_maybe_shrink() [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >]’ 2680 | sparse_hashtable tmp(MoveDontCopy, *this, sz); | ^~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from ‘void spp::sparse_hashtable::resize(size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 2846 | _maybe_shrink(); | ^~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3799:51: required from ‘void spp::sparse_hash_map::resize(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 3799 | void resize(size_type cnt) { rep.resize(cnt); } | ~~~~~~~~~~^~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3801:41: required from ‘void spp::sparse_hash_map::reserve(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]’ 3801 | void reserve(size_type cnt) { resize(cnt); } // c++11 | ^~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:39:25: required from here 39 | vertexIndexMap.reserve(numClasses); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::pair; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:76: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of ‘void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::DropSeq; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from ‘void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from ‘void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]’ 938 | processBarcodes(barcodeFiles, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 939 | readFiles, | ~~~~~~~~~~ 940 | aopt, | ~~~~~ 941 | barcodeSoftMap, | ~~~~~~~~~~~~~~~ 942 | trueBarcodes, | ~~~~~~~~~~~~~ 943 | freqCounter, | ~~~~~~~~~~~~ 944 | numLowConfidentBarcode); | ~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1084:23: required from here 1084 | initiatePipeline(aopt, sopt, orderedOptions, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1085 | vm, commentString, noTgMap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1086 | barcodeFiles, readFiles, salmonIndex); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::__cxx11::basic_string’ [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of ‘void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::InDropV2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from ‘void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::InDropV2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from ‘void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::InDropV2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]’ 938 | processBarcodes(barcodeFiles, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 939 | readFiles, | ~~~~~~~~~~ 940 | aopt, | ~~~~~ 941 | barcodeSoftMap, | ~~~~~~~~~~~~~~~ 942 | trueBarcodes, | ~~~~~~~~~~~~~ 943 | freqCounter, | ~~~~~~~~~~~~ 944 | numLowConfidentBarcode); | ~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1094:25: required from here 1094 | initiatePipeline(aopt, sopt, orderedOptions, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1095 | vm, commentString, noTgMap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1096 | barcodeFiles, readFiles, salmonIndex); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::__cxx11::basic_string’ [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of ‘void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CITESeq; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from ‘void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CITESeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from ‘void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CITESeq; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]’ 938 | processBarcodes(barcodeFiles, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 939 | readFiles, | ~~~~~~~~~~ 940 | aopt, | ~~~~~ 941 | barcodeSoftMap, | ~~~~~~~~~~~~~~~ 942 | trueBarcodes, | ~~~~~~~~~~~~~ 943 | freqCounter, | ~~~~~~~~~~~~ 944 | numLowConfidentBarcode); | ~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1110:25: required from here 1110 | initiatePipeline(aopt, sopt, orderedOptions, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1111 | vm, commentString, noTgMap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1112 | barcodeFiles, readFiles, salmonIndex); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::__cxx11::basic_string’ [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of ‘void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::ChromiumV3; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from ‘void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::ChromiumV3; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from ‘void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::ChromiumV3; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]’ 938 | processBarcodes(barcodeFiles, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 939 | readFiles, | ~~~~~~~~~~ 940 | aopt, | ~~~~~ 941 | barcodeSoftMap, | ~~~~~~~~~~~~~~~ 942 | trueBarcodes, | ~~~~~~~~~~~~~ 943 | freqCounter, | ~~~~~~~~~~~~ 944 | numLowConfidentBarcode); | ~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1122:23: required from here 1122 | initiatePipeline(aopt, sopt, orderedOptions, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1123 | vm, commentString, noTgMap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1124 | barcodeFiles, readFiles, salmonIndex); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::__cxx11::basic_string’ [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of ‘void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Chromium; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from ‘void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Chromium; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from ‘void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::Chromium; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]’ 938 | processBarcodes(barcodeFiles, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 939 | readFiles, | ~~~~~~~~~~ 940 | aopt, | ~~~~~ 941 | barcodeSoftMap, | ~~~~~~~~~~~~~~~ 942 | trueBarcodes, | ~~~~~~~~~~~~~ 943 | freqCounter, | ~~~~~~~~~~~~ 944 | numLowConfidentBarcode); | ~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1129:23: required from here 1129 | initiatePipeline(aopt, sopt, orderedOptions, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1130 | vm, commentString, noTgMap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1131 | barcodeFiles, readFiles, salmonIndex); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::__cxx11::basic_string’ [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of ‘void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Gemcode; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from ‘void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Gemcode; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from ‘void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::Gemcode; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]’ 938 | processBarcodes(barcodeFiles, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 939 | readFiles, | ~~~~~~~~~~ 940 | aopt, | ~~~~~ 941 | barcodeSoftMap, | ~~~~~~~~~~~~~~~ 942 | trueBarcodes, | ~~~~~~~~~~~~~ 943 | freqCounter, | ~~~~~~~~~~~~ 944 | numLowConfidentBarcode); | ~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1136:23: required from here 1136 | initiatePipeline(aopt, sopt, orderedOptions, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1137 | vm, commentString, noTgMap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1138 | unmateFiles, readFiles, salmonIndex); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::__cxx11::basic_string’ [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of ‘void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CELSeq; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from ‘void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CELSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from ‘void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]’ 938 | processBarcodes(barcodeFiles, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 939 | readFiles, | ~~~~~~~~~~ 940 | aopt, | ~~~~~ 941 | barcodeSoftMap, | ~~~~~~~~~~~~~~~ 942 | trueBarcodes, | ~~~~~~~~~~~~~ 943 | freqCounter, | ~~~~~~~~~~~~ 944 | numLowConfidentBarcode); | ~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1143:23: required from here 1143 | initiatePipeline(aopt, sopt, orderedOptions, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1144 | vm, commentString, noTgMap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1145 | barcodeFiles, readFiles, salmonIndex); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::__cxx11::basic_string’ [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of ‘void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CELSeq2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from ‘void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CELSeq2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from ‘void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]’ 938 | processBarcodes(barcodeFiles, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 939 | readFiles, | ~~~~~~~~~~ 940 | aopt, | ~~~~~ 941 | barcodeSoftMap, | ~~~~~~~~~~~~~~~ 942 | trueBarcodes, | ~~~~~~~~~~~~~ 943 | freqCounter, | ~~~~~~~~~~~~ 944 | numLowConfidentBarcode); | ~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1150:23: required from here 1150 | initiatePipeline(aopt, sopt, orderedOptions, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1151 | vm, commentString, noTgMap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1152 | barcodeFiles, readFiles, salmonIndex); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::__cxx11::basic_string’ [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of ‘void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SplitSeqV1; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from ‘void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SplitSeqV1; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from ‘void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV1; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]’ 938 | processBarcodes(barcodeFiles, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 939 | readFiles, | ~~~~~~~~~~ 940 | aopt, | ~~~~~ 941 | barcodeSoftMap, | ~~~~~~~~~~~~~~~ 942 | trueBarcodes, | ~~~~~~~~~~~~~ 943 | freqCounter, | ~~~~~~~~~~~~ 944 | numLowConfidentBarcode); | ~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1157:23: required from here 1157 | initiatePipeline(aopt, sopt, orderedOptions, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1158 | vm, commentString, noTgMap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1159 | barcodeFiles, readFiles, salmonIndex); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::__cxx11::basic_string’ [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of ‘void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SplitSeqV2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from ‘void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SplitSeqV2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from ‘void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]’ 938 | processBarcodes(barcodeFiles, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 939 | readFiles, | ~~~~~~~~~~ 940 | aopt, | ~~~~~ 941 | barcodeSoftMap, | ~~~~~~~~~~~~~~~ 942 | trueBarcodes, | ~~~~~~~~~~~~~ 943 | freqCounter, | ~~~~~~~~~~~~ 944 | numLowConfidentBarcode); | ~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1164:23: required from here 1164 | initiatePipeline(aopt, sopt, orderedOptions, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1165 | vm, commentString, noTgMap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1166 | barcodeFiles, readFiles, salmonIndex); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::__cxx11::basic_string’ [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of ‘void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::QuartzSeq2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from ‘void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::QuartzSeq2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from ‘void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::QuartzSeq2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]’ 938 | processBarcodes(barcodeFiles, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 939 | readFiles, | ~~~~~~~~~~ 940 | aopt, | ~~~~~ 941 | barcodeSoftMap, | ~~~~~~~~~~~~~~~ 942 | trueBarcodes, | ~~~~~~~~~~~~~ 943 | freqCounter, | ~~~~~~~~~~~~ 944 | numLowConfidentBarcode); | ~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1171:23: required from here 1171 | initiatePipeline(aopt, sopt, orderedOptions, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1172 | vm, commentString, noTgMap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1173 | barcodeFiles, readFiles, salmonIndex); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::__cxx11::basic_string’ [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of ‘void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SciSeq3; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from ‘void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SciSeq3; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from ‘void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::SciSeq3; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]’ 938 | processBarcodes(barcodeFiles, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 939 | readFiles, | ~~~~~~~~~~ 940 | aopt, | ~~~~~ 941 | barcodeSoftMap, | ~~~~~~~~~~~~~~~ 942 | trueBarcodes, | ~~~~~~~~~~~~~ 943 | freqCounter, | ~~~~~~~~~~~~ 944 | numLowConfidentBarcode); | ~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1177:23: required from here 1177 | initiatePipeline(aopt, sopt, orderedOptions, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1178 | vm, commentString, noTgMap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1179 | barcodeFiles, readFiles, salmonIndex); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::__cxx11::basic_string’ [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of ‘void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Custom; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from ‘void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Custom; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from ‘void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::Custom; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]’ 938 | processBarcodes(barcodeFiles, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 939 | readFiles, | ~~~~~~~~~~ 940 | aopt, | ~~~~~ 941 | barcodeSoftMap, | ~~~~~~~~~~~~~~~ 942 | trueBarcodes, | ~~~~~~~~~~~~~ 943 | freqCounter, | ~~~~~~~~~~~~ 944 | numLowConfidentBarcode); | ~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1183:23: required from here 1183 | initiatePipeline(aopt, sopt, orderedOptions, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1184 | vm, commentString, noTgMap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1185 | barcodeFiles, readFiles, salmonIndex); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::__cxx11::basic_string’ [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of ‘void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CustomGeometry; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]’: /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from ‘void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CustomGeometry; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from ‘void initiatePipeline(AlevinOpts&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CustomGeometry; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]’ 938 | processBarcodes(barcodeFiles, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 939 | readFiles, | ~~~~~~~~~~ 940 | aopt, | ~~~~~ 941 | barcodeSoftMap, | ~~~~~~~~~~~~~~~ 942 | trueBarcodes, | ~~~~~~~~~~~~~ 943 | freqCounter, | ~~~~~~~~~~~~ 944 | numLowConfidentBarcode); | ~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1189:23: required from here 1189 | initiatePipeline(aopt, sopt, orderedOptions, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1190 | vm, commentString, noTgMap, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1191 | barcodeFiles, readFiles, salmonIndex); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable ‘trueBarcode’ creates a copy from type ‘const std::__cxx11::basic_string’ [-Wrange-loop-construct] 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & [ 90%] Building CXX object src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinHash.hpp:10, from /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:58: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantify.cpp:75: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinHash.hpp:10: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:12:31: required from here 12 | txpIdxMap[ transcripts[i] ] = i; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:35:23: required from here 35 | txpToGeneMap[tid] = gid; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = long unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = long unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:98:21: required from here 98 | barcodeMap[i] = i; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = long unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; value_type = std::pair, long unsigned int>; reference = std::pair, long unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; pointer = std::pair, long unsigned int>*; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, long unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, long unsigned int>; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, long unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, long unsigned int>::DefaultValue; KT = const std::__cxx11::basic_string&; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; value_type = std::pair, long unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = long unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; mapped_type = long unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:105:26: required from here 105 | trueBarcodeMap[bc] = idx; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::value_type’ {aka ‘std::pair, long unsigned int>’} to ‘spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::mutable_reference’ {aka ‘std::pair, long unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = long unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:12:31: required from here 12 | txpIdxMap[ transcripts[i] ] = i; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:35:23: required from here 35 | txpToGeneMap[tid] = gid; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = long unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = long unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:98:21: required from here 98 | barcodeMap[i] = i; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = long unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; mutable_value_type = std::pair, long unsigned int>; reference = std::pair, long unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; pointer = std::pair, long unsigned int>*; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, long unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, long unsigned int>; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, long unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, long unsigned int>::DefaultValue; KT = const std::__cxx11::basic_string&; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; value_type = std::pair, long unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = long unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; mapped_type = long unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:105:26: required from here 105 | trueBarcodeMap[bc] = idx; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::value_type’ {aka ‘std::pair, long unsigned int>’} to ‘spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::mutable_reference’ {aka ‘std::pair, long unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = long unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 91%] Building CXX object src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -MF CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o.d -o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentStartPositionDistribution.cpp /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::DropSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2777:62: required from here 2777 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::DropSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2777:62: required from here 2777 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CITESeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CITESeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2791:62: required from here 2791 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CITESeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CITESeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2791:62: required from here 2791 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::InDropV2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDropV2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDropV2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::InDropV2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2804:58: required from here 2804 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::InDropV2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDropV2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDropV2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::InDropV2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2804:58: required from here 2804 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::ChromiumV3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::ChromiumV3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2817:58: required from here 2817 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::ChromiumV3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::ChromiumV3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2817:58: required from here 2817 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Chromium; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::Chromium; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2830:58: required from here 2830 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Chromium; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::Chromium; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2830:58: required from here 2830 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Gemcode; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::Gemcode; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2843:58: required from here 2843 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Gemcode; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::Gemcode; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2843:58: required from here 2843 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CELSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2856:58: required from here 2856 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CELSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2856:58: required from here 2856 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CELSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2869:58: required from here 2869 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CELSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2869:58: required from here 2869 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, from /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp:12: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SplitSeqV1; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV1; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV1; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV1; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2882:58: required from here 2882 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::SplitSeqV1; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV1; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV1; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV1; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2882:58: required from here 2882 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SplitSeqV2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2895:58: required from here 2895 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::SplitSeqV2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2895:58: required from here 2895 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::QuartzSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::QuartzSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2908:58: required from here 2908 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::QuartzSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::QuartzSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2908:58: required from here 2908 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SciSeq3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SciSeq3; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SciSeq3; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::SciSeq3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2923:62: required from here 2923 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::SciSeq3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SciSeq3; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SciSeq3; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::SciSeq3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2923:62: required from here 2923 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Custom; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::Custom; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2940:58: required from here 2940 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Custom; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::Custom; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2940:58: required from here 2940 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CustomGeometry; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CustomGeometry; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2954:58: required from here 2954 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of ‘void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CustomGeometry; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]’: /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from ‘sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]’ 1730 | process_reads_sc_sketch( | ~~~~~~~~~~~~~~~~~~~~~~~^ 1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1735 | ); | ~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from ‘void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; size_t = long unsigned int]’ 1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from ‘bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]’ 2094 | sc_align_read_library(experiment, rl, sidx, transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2095 | numObservedFragments, numAssignedFragments, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2096 | smallSeqs, nSeqs, burnedIn, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2097 | fragLengthDist, salmonOpts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2098 | num_chunks, | ~~~~~~~~~~~ 2099 | rad_file, | ~~~~~~~~~ 2100 | unmapped_bc_file, | ~~~~~~~~~~~~~~~~~ 2101 | fileMutex, | ~~~~~~~~~~ 2102 | unmapped_bc_mutex, | ~~~~~~~~~~~~~~~~~~ 2103 | ioMutex, numQuantThreads, groupVec, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2104 | alevinOpts, mstats); | ~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from ‘int alevin_sc_align(AlevinOpts&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CustomGeometry; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]’ 2521 | bool mapping_ok = do_sc_align(experiment, sopt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2522 | mstats, sopt.numThreads, aopt); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2954:58: required from here 2954 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable ‘expectedLibraryFormat’ set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter ‘transcripts’ [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ [ 92%] Building CXX object src/CMakeFiles/salmon.dir/GZipWriter.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/GZipWriter.cpp.o -MF CMakeFiles/salmon.dir/GZipWriter.cpp.o.d -o CMakeFiles/salmon.dir/GZipWriter.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/GZipWriter.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47, from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:95: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 93%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantMerge.cpp /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2647:50: required from ‘int alevinQuant(AlevinOpts&, SalmonOpts&, SoftMapT&, TrueBcsT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, boost::program_options::parsed_options&, CFreqMapT&, size_t, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; boost::program_options::parsed_options = boost::program_options::basic_parsed_options; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 2647 | trueBarcodesIndexMap[ trueBarcodesVec[i] ] = i; /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2786:54: required from here 2786 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2647:50: required from ‘int alevinQuant(AlevinOpts&, SalmonOpts&, SoftMapT&, TrueBcsT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, boost::program_options::parsed_options&, CFreqMapT&, size_t, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; boost::program_options::parsed_options = boost::program_options::basic_parsed_options; CFreqMapT = tsl::array_map; size_t = long unsigned int]’ 2647 | trueBarcodesIndexMap[ trueBarcodesVec[i] ] = i; /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2786:54: required from here 2786 | std::unique_ptr& salmonIndex); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type’ {aka ‘std::pair, unsigned int>’} to ‘spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference’ {aka ‘std::pair, unsigned int>&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadExperiment.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonMappingUtils.hpp:44, from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantify.cpp:93: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 94%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -MF CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o.d -o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/ProgramOptionsGenerator.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12, from /build/reproducible-path/salmon-1.10.2+ds1/src/GZipWriter.cpp:9: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 94%] Building CXX object src/CMakeFiles/salmon.dir/FASTAParser.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/FASTAParser.cpp.o -MF CMakeFiles/salmon.dir/FASTAParser.cpp.o.d -o CMakeFiles/salmon.dir/FASTAParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FASTAParser.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantMerge.cpp:29: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/ProgramOptionsGenerator.hpp:5, from /build/reproducible-path/salmon-1.10.2+ds1/src/ProgramOptionsGenerator.cpp:4: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/src/FASTAParser.cpp:11: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 95%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o -MF CMakeFiles/salmon.dir/AlignmentModel.cpp.o.d -o CMakeFiles/salmon.dir/AlignmentModel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentCommon.hpp:10, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentModel.hpp:6, from /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:8: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 96%] Building CXX object src/CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o -MF CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o.d -o CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp [ 97%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -MF CMakeFiles/salmon.dir/AlignmentCommon.cpp.o.d -o CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentCommon.cpp [ 98%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantifyAlignments.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentCommon.hpp:10, from /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentCommon.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp: In member function ‘AlignmentModel::AlnModelProb AlignmentModel::logLikelihood(bam_seq_t*, bam_seq_t*, Transcript&, std::vector >&)’: /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:96:33: warning: unused parameter ‘primary’ [-Wunused-parameter] 96 | bam_seq_t* read, bam_seq_t* primary, Transcript& ref, | ~~~~~~~~~~~^~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp: In member function ‘double AlignmentModel::logLikelihood(const ReadPair&, const ReadPair&, Transcript&)’: /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:230:75: warning: unused parameter ‘primary’ [-Wunused-parameter] 230 | double AlignmentModel::logLikelihood(const ReadPair& hit, const ReadPair& primary, Transcript& ref) { | ~~~~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp: In member function ‘void AlignmentModel::update(const ReadPair&, const ReadPair&, Transcript&, double, double)’: /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:429:66: warning: unused parameter ‘primary’ [-Wunused-parameter] 429 | void AlignmentModel::update(const ReadPair& hit, const ReadPair& primary, | ~~~~~~~~~~~~~~~~^~~~~~~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/ONTAlignmentModel.hpp:9, from /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:11: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ [ 99%] Building CXX object src/CMakeFiles/salmon.dir/BAMUtils.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/BAMUtils.cpp.o -MF CMakeFiles/salmon.dir/BAMUtils.cpp.o.d -o CMakeFiles/salmon.dir/BAMUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/BAMUtils.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12, from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantifyAlignments.cpp:33: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the ‘< >’ /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In constructor ‘ONTAlignmentModel::ONTAlignmentModel(double, uint32_t)’: /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:17:45: warning: unused parameter ‘alpha’ [-Wunused-parameter] 17 | ONTAlignmentModel::ONTAlignmentModel(double alpha, uint32_t readBins) | ~~~~~~~^~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function ‘double ONTAlignmentModel::logLikelihood(const UnpairedRead&, const UnpairedRead&, Transcript&)’: /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:53:22: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘const uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 53 | if(counts.sclips() >= cigarRLen) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function ‘void ONTAlignmentModel::update(const UnpairedRead&, const UnpairedRead&, Transcript&, double, double)’: /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:137:56: warning: unused parameter ‘p’ [-Wunused-parameter] 137 | Transcript& ref, double p, double mass) { | ~~~~~~~^ /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function ‘void ONTAlignmentModel::printModel(std::ostream&)’: /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:194:50: warning: unused parameter ‘os’ [-Wunused-parameter] 194 | void ONTAlignmentModel::printModel(std::ostream& os) { | ~~~~~~~~~~~~~~^~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]’ 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup, spp::libc_allocator > >::value_type’ {aka ‘std::pair’} to ‘spp::sparsegroup, spp::libc_allocator > >::mutable_reference’ {aka ‘std::pair&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of ‘void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]’: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from ‘void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]’ 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from ‘void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from ‘spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]’ 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from ‘spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]’ 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from ‘spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]’ 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from ‘spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]’ 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting ‘spp::sparsegroup >, spp::libc_allocator > > >::value_type’ {aka ‘std::pair >’} to ‘spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference’ {aka ‘std::pair >&’} does not use ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]’ [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable salmon cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/salmon.dir/link.d CMakeFiles/salmon.dir/EMUtils.cpp.o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o CMakeFiles/salmon.dir/Salmon.cpp.o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o CMakeFiles/salmon.dir/Graph.cpp.o CMakeFiles/salmon.dir/DedupUMI.cpp.o CMakeFiles/salmon.dir/Alevin.cpp.o CMakeFiles/salmon.dir/AlevinHash.cpp.o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o CMakeFiles/salmon.dir/WhiteList.cpp.o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o CMakeFiles/salmon.dir/GZipWriter.cpp.o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o CMakeFiles/salmon.dir/FASTAParser.cpp.o CMakeFiles/salmon.dir/AlignmentModel.cpp.o CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o CMakeFiles/salmon.dir/AlignmentCommon.cpp.o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o CMakeFiles/salmon.dir/BAMUtils.cpp.o -o salmon -L/build/reproducible-path/salmon-1.10.2+ds1/lib -L/build/reproducible-path/salmon-1.10.2+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" ../external/pufferfish/src/libpuffer.a libsalmon_core.a ../external/pufferfish/external/twopaco/graphconstructor/libtwopaco.a ../external/pufferfish/external/twopaco/graphdump/libgraphdump.a ../external/pufferfish/external/ntcard/libntcard.a -lgff -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex /usr/lib/x86_64-linux-gnu/libcurl.so -lz -lm /usr/lib/x86_64-linux-gnu/libstaden-read.so /usr/lib/x86_64-linux-gnu/libhtscodecs.so -llzma -lbz2 -lgomp ../external/pufferfish/src/libksw2pp.a libalevin_core.a -ltbb -ltbbmalloc -ljemalloc -lrt -ldl make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [100%] Built target salmon make[3]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' mv doc/source/license.rst doc/ # unused PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml doc/source doc/build/html Running Sphinx v8.1.3 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 6 source files that are out of date updating environment: [new config] 6 added, 0 changed, 0 removed reading sources... [ 17%] alevin reading sources... [ 33%] building reading sources... [ 50%] file_formats reading sources... [ 67%] index reading sources... [ 83%] library_type reading sources... [100%] salmon /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:36: WARNING: Title underline too short. Providing multiple read files to Alevin ------------ [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:36: WARNING: Title underline too short. Providing multiple read files to Alevin ------------ [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:56: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:79: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:83: WARNING: Title overline too short. """""""""""" ``--whitelist`` """""""""""" [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:83: WARNING: Title overline too short. """""""""""" ``--whitelist`` """""""""""" [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:93: WARNING: Title overline too short. """""""""""" ``--noQuant`` """""""""""" [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:93: WARNING: Title overline too short. """""""""""" ``--noQuant`` """""""""""" [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:99: WARNING: Title overline too short. """""""""""" ``--noDedup`` """""""""""" [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:99: WARNING: Title overline too short. """""""""""" ``--noDedup`` """""""""""" [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:127: WARNING: Title overline too short. """""""""""" ``--dumpBfh`` """""""""""" [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:127: WARNING: Title overline too short. """""""""""" ``--dumpBfh`` """""""""""" [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:133: WARNING: Title overline too short. """""""""""" ``--dumpFeatures`` """""""""""" [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:133: WARNING: Title overline too short. """""""""""" ``--dumpFeatures`` """""""""""" [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:139: WARNING: Title overline too short. """""""""""" ``--dumpMtx`` """""""""""" [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:139: WARNING: Title overline too short. """""""""""" ``--dumpMtx`` """""""""""" [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:155: WARNING: Title overline too short. """""""""""""""""""""" ``--numCellBootstraps`` """""""""""""""""""""" [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:155: WARNING: Title overline too short. """""""""""""""""""""" ``--numCellBootstraps`` """""""""""""""""""""" [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:214: WARNING: Title underline too short. Output Quality Check ------------- [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:214: WARNING: Title underline too short. Output Quality Check ------------- [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:263: WARNING: Title underline too short. BibTex ---- [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:263: WARNING: Title underline too short. BibTex ---- [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:297: WARNING: Duplicate explicit target name: "swish". [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:299: WARNING: Footnote [#] is not referenced. [ref.footnote] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:301: WARNING: Footnote [#] is not referenced. [ref.footnote] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:303: WARNING: Footnote [#] is not referenced. [ref.footnote] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:305: WARNING: Footnote [#] is not referenced. [ref.footnote] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:307: WARNING: Footnote [#] is not referenced. [ref.footnote] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:309: WARNING: Footnote [#] is not referenced. [ref.footnote] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:311: WARNING: Footnote [#] is not referenced. [ref.footnote] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/salmon.rst:2: WARNING: Duplicate explicit target name: "here". [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/salmon.rst:2: WARNING: Duplicate explicit target name: "here". [docutils] looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/basic.css Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/sidebar.js Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/classic.css Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/sidebar.js copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 17%] alevin writing output... [ 33%] building writing output... [ 50%] file_formats writing output... [ 67%] index writing output... [ 83%] library_type writing output... [100%] salmon generating indices... genindex done writing additional pages... search done copying images... [100%] ReadLibraryIllustration.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 33 warnings. The HTML pages are in doc/build/html. mv doc/license.rst doc/source/ cd obj*/src && \ help2man --no-discard-stderr --no-info --name="highly-accurate, transcript-level quantification estimates from RNA-seq data"\ ./salmon > ../../debian/salmon.1 && \ for option in index quant swim; do help2man --no-discard-stderr \ --version-string="1.10.2+ds1" --no-info "./salmon --no-version-check ${option}" \ --include=../../debian/salmon-${option}-man-include \ > ../../debian/salmon-${option}.1; done make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1' dh_auto_test --no-parallel cd obj-x86_64-linux-gnu && make -j1 test ARGS\+=--verbose ARGS\+=-j1 make[2]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j1 UpdateCTestConfiguration from :/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: unit_tests 1: Test command: /usr/bin/cmake "-DTOPLEVEL_DIR=/build/reproducible-path/salmon-1.10.2+ds1" "-P" "/build/reproducible-path/salmon-1.10.2+ds1/cmake/UnitTests.cmake" 1: Working Directory: /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src 1: Test timeout computed to be: 10000000 1: -- For unit tests, will set working directory to /build/reproducible-path/salmon-1.10.2+ds1/tests 1: =============================================================================== 1: All tests passed (2001943 assertions in 4 test cases) 1: 1/2 Test #1: unit_tests ....................... Passed 0.24 sec test 2 Start 2: salmon_read_test_quasi 2: Test command: /usr/bin/cmake "-DTOPLEVEL_DIR=/build/reproducible-path/salmon-1.10.2+ds1" "-P" "/build/reproducible-path/salmon-1.10.2+ds1/cmake/TestSalmonQuasi.cmake" 2: Working Directory: /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src 2: Test timeout computed to be: 10000000 2: sample_data/ 2: sample_data/reads_2.fastq 2: sample_data/sample_alignments.bam 2: sample_data/transcripts.fasta 2: sample_data/reads_1.fastq 2: index ["sample_salmon_quasi_index"] did not previously exist . . . creating it 2: [2025-06-23 03:30:13.438] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode. 2: [2025-06-23 03:30:13.438] [jLog] [info] building index 2: out : sample_salmon_quasi_index 2: [2025-06-23 03:30:13.438] [puff::index::jointLog] [info] Running fixFasta 2: 2: [Step 1 of 4] : counting k-mers 2: 2: [2025-06-23 03:30:13.441] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides 2: [2025-06-23 03:30:13.441] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts 2: wrote 15 cleaned references 2: [2025-06-23 03:30:13.442] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers 2: [2025-06-23 03:30:13.442] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20 2: Threads = 2 2: Vertex length = 31 2: Hash functions = 5 2: Filter size = 1048576 2: Capacity = 2 2: Files: 2: sample_salmon_quasi_index/ref_k31_fixed.fa 2: -------------------------------------------------------------------------------- 2: Round 0, 0:1048576 2: Pass Filling Filtering 2: 1 0 0 2: 2 0 0 2: True junctions count = 14 2: False junctions count = 18 2: Hash table size = 32 2: Candidate marks count = 56 2: -------------------------------------------------------------------------------- 2: Reallocating bifurcations time: 0 2: True marks count: 51 2: Edges construction time: 0 2: -------------------------------------------------------------------------------- 2: Distinct junctions = 14 2: 2: TwoPaCo::buildGraphMain:: allocated with scalable_malloc; freeing. 2: TwoPaCo::buildGraphMain:: Calling scalable_allocation_command(TBBMALLOC_CLEAN_ALL_BUFFERS, 0); 2: allowedIn: 12 2: Max Junction ID: 70 2: seen.size():569 kmerInfo.size():71 2: approximateContigTotalLength: 17465 2: counters for complex kmers: 2: (prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0 2: contig count: 24 element count: 19592 complex nodes: 0 2: # of ones in rank vector: 23 2: [2025-06-23 03:30:13.465] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file. 2: [2025-06-23 03:30:13.465] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory sample_salmon_quasi_index 2: size = 19592 2: ----------------------------------------- 2: | Loading contigs | Time = 62.482 us 2: ----------------------------------------- 2: size = 19592 2: ----------------------------------------- 2: | Loading contig boundaries | Time = 49.36 us 2: ----------------------------------------- 2: Number of ones: 23 2: Number of ones per inventory item: 512 2: Inventory entries filled: 1 2: 23 2: [2025-06-23 03:30:13.465] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure. 2: [2025-06-23 03:30:13.465] [puff::index::jointLog] [info] contig count for validation: 23 2: [2025-06-23 03:30:13.465] [puff::index::jointLog] [info] Total # of Contigs : 23 2: [2025-06-23 03:30:13.465] [puff::index::jointLog] [info] Total # of numerical Contigs : 23 2: [2025-06-23 03:30:13.465] [puff::index::jointLog] [info] Total # of contig vec entries: 36 2: [2025-06-23 03:30:13.465] [puff::index::jointLog] [info] bits per offset entry 6 2: [2025-06-23 03:30:13.465] [puff::index::jointLog] [info] Done constructing the contig vector. 24 2: [2025-06-23 03:30:13.465] [puff::index::jointLog] [info] # segments = 23 2: [2025-06-23 03:30:13.465] [puff::index::jointLog] [info] total length = 19592 2: [2025-06-23 03:30:13.465] [puff::index::jointLog] [info] Reading the reference files ... 2: [2025-06-23 03:30:13.466] [puff::index::jointLog] [info] positional integer width = 15 2: [2025-06-23 03:30:13.466] [puff::index::jointLog] [info] seqSize = 19592 2: [2025-06-23 03:30:13.466] [puff::index::jointLog] [info] rankSize = 19592 2: [2025-06-23 03:30:13.466] [puff::index::jointLog] [info] edgeVecSize = 0 2: [2025-06-23 03:30:13.466] [puff::index::jointLog] [info] num 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remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec 2: [2025-06-23 03:30:13.475] [puff::index::jointLog] [info] mphf size = 0.0125198 MB 2: [2025-06-23 03:30:13.475] [puff::index::jointLog] [info] chunk size = 9796 2: [2025-06-23 03:30:13.475] [puff::index::jointLog] [info] chunk 0 = [0, 9796) 2: [2025-06-23 03:30:13.475] [puff::index::jointLog] [info] chunk 1 = [9796, 19562) 2: [2025-06-23 03:30:13.476] [puff::index::jointLog] [info] finished populating pos vector 2: [2025-06-23 03:30:13.476] [puff::index::jointLog] [info] writing index components 2: [2025-06-23 03:30:13.476] [puff::index::jointLog] [info] finished writing dense pufferfish index 2: [2025-06-23 03:30:13.476] [jLog] [info] done building index 2: for info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 2: Bitarray 105024 bits (100.00 %) (array + ranks ) 2: final hash 0 bits (0.00 %) (nb in final hash 0) 2: ### salmon (selective-alignment-based) v1.10.2 2: ### [ program ] => salmon 2: ### [ command ] => quant 2: ### [ index ] => { sample_salmon_quasi_index } 2: ### [ libType ] => { IU } 2: ### [ mates1 ] => { reads_1.fastq } 2: ### [ mates2 ] => { reads_2.fastq } 2: ### [ output ] => { sample_salmon_quasi_quant } 2: Logs will be written to sample_salmon_quasi_quant/logs 2: [2025-06-23 03:30:13.528] [jointLog] [info] setting maxHashResizeThreads to 24 2: ----------------------------------------- 2: | Loading contig table | Time = 29.369 us 2: ----------------------------------------- 2: size = 24 2: ----------------------------------------- 2: | Loading contig offsets | Time = 70.748 us 2: ----------------------------------------- 2: ----------------------------------------- 2: | Loading reference lengths | Time = 6.269 us 2: ----------------------------------------- 2: ----------------------------------------- 2: | Loading mphf table | Time = 49.293 us 2: ----------------------------------------- 2: size = 19592 2: Number of ones: 23 2: Number of ones per inventory item: 512 2: Inventory entries filled: 1 2: ----------------------------------------- 2: | Loading contig boundaries | Time = 93.538 us 2: ----------------------------------------- 2: size = 19592 2: ----------------------------------------- 2: | Loading sequence | Time = 57.426 us 2: ----------------------------------------- 2: size = 18902 2: ----------------------------------------- 2: | Loading positions | Time = 73.692 us 2: ----------------------------------------- 2: size = 28562 2: ----------------------------------------- 2: | Loading reference sequence | Time = 46.552 us 2: ----------------------------------------- 2: ----------------------------------------- 2: | Loading reference accumulative lengths | Time = 6.282 us 2: ----------------------------------------- 2: [2025-06-23 03:30:13.528] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. 2: [2025-06-23 03:30:13.528] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 2: [2025-06-23 03:30:13.528] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35. 2: [2025-06-23 03:30:13.528] [jointLog] [info] parsing read library format 2: [2025-06-23 03:30:13.528] [jointLog] [info] There is 1 library. 2: [2025-06-23 03:30:13.528] [jointLog] [info] Loading pufferfish index 2: [2025-06-23 03:30:13.528] [jointLog] [info] Loading dense pufferfish index. 2: [2025-06-23 03:30:13.529] [jointLog] [info] done 2: [2025-06-23 03:30:13.592] [jointLog] [info] Index contained 15 targets 2: [2025-06-23 03:30:13.592] [jointLog] [info] Number of decoys : 0 2: 2: 2: 2: 2: 2: 2: 2: 2: [2025-06-23 03:30:13.784] [jointLog] [info] Computed 28 rich equivalence classes for further processing 2: [2025-06-23 03:30:13.784] [jointLog] [info] Counted 10000 total reads in the equivalence classes 2: 2: 2: 2: 2: [2025-06-23 03:30:13.793] [jointLog] [info] Number of mappings discarded because of alignment score : 67 2: [2025-06-23 03:30:13.793] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0 2: [2025-06-23 03:30:13.793] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 2: [2025-06-23 03:30:13.793] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0 2: [2025-06-23 03:30:13.793] [jointLog] [warning] Only 10000 fragments were mapped, but the number of burn-in fragments was set to 5000000. 2: The effective lengths have been computed using the observed mappings. 2: 2: [2025-06-23 03:30:13.793] [jointLog] [info] Mapping rate = 100% 2: 2: [2025-06-23 03:30:13.793] [jointLog] [info] finished quantifyLibrary() 2: [2025-06-23 03:30:13.793] [jointLog] [info] Starting optimizer 2: [2025-06-23 03:30:13.794] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate 2: [2025-06-23 03:30:13.794] [jointLog] [info] iteration = 0 | max rel diff. = 14.87 2: [2025-06-23 03:30:13.795] [jointLog] [info] iteration = 100 | max rel diff. = 2.94625e-05 2: [2025-06-23 03:30:13.795] [jointLog] [info] Finished optimizer 2: [2025-06-23 03:30:13.795] [jointLog] [info] writing output 2: 2: Salmon (read) ran successfully 2/2 Test #2: salmon_read_test_quasi ........... Passed 1.14 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 1.38 sec make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1' dh_auto_install cd obj-x86_64-linux-gnu && make -j6 install DESTDIR=/build/reproducible-path/salmon-1.10.2\+ds1/debian/salmon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/salmon-1.10.2+ds1 -B/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libntcard.a -- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets.cmake -- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets-release.cmake -- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libgraphdump.a -- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets.cmake -- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets-release.cmake -- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libtwopaco.a -- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake -- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake -- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/bin/salmon -- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libsalmon_core.a Installation complete. Please ensure the following paths are set properly. ========================================================================== Please add /usr/bin to your PATH Please add /usr/lib to your LD_LIBRARY_PATH ========================================================================== make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' rm -Rvf /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets-release.cmake' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets.cmake' removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake' removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libtwopaco.a' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets-release.cmake' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets.cmake' removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libsalmon_core.a' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libntcard.a' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libgraphdump.a' removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib' make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1' dh_install -a dh_installdocs -a dh_sphinxdoc -a dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/themetoggle.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/copybutton.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/menu.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/search-focus.js dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'salmon' in '../salmon_1.10.2+ds1-1+b5_amd64.deb'. dpkg-deb: building package 'salmon-dbgsym' in '../salmon-dbgsym_1.10.2+ds1-1+b5_amd64.deb'. dpkg-genbuildinfo --build=any -O../salmon_1.10.2+ds1-1+b5_amd64.buildinfo dpkg-genchanges --build=any -O../salmon_1.10.2+ds1-1+b5_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2025-06-23T03:30:43Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 23 Jun 2025 03:30:44 +0000 | +------------------------------------------------------------------------------+ salmon_1.10.2+ds1-1+b5_amd64.changes: ------------------------------------- Format: 1.8 Date: Thu, 03 Apr 2025 06:13:14 +0000 Source: salmon (1.10.2+ds1-1) Binary: salmon salmon-dbgsym Binary-Only: yes Architecture: amd64 Version: 1.10.2+ds1-1+b5 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team Changed-By: amd64 / i386 Build Daemon (x86-ubc-01) Description: salmon - wicked-fast transcript quantification from RNA-seq data Changes: salmon (1.10.2+ds1-1+b5) sid; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for outdated Built-Using (sphinx/7.4.7-3) Checksums-Sha1: e4c3940d378a4969bf549d87dfd99f1f8d36a6c0 43080672 salmon-dbgsym_1.10.2+ds1-1+b5_amd64.deb d808d1cd81c1b843df66c293a0bfd992117412c7 11877 salmon_1.10.2+ds1-1+b5_amd64.buildinfo b822b80f3607c241a55ef57fca306f9974e51538 3421076 salmon_1.10.2+ds1-1+b5_amd64.deb Checksums-Sha256: 8e2fc1b295273bef749f3087297236b8c04f3ea744ccfd51e26b3b9699c28a23 43080672 salmon-dbgsym_1.10.2+ds1-1+b5_amd64.deb d74f6ceefd2b6866d29be3274d7295bb9839d3d3bf6926522060fe8b492d2a50 11877 salmon_1.10.2+ds1-1+b5_amd64.buildinfo 593be3237a41f97b6f14e73382a6f80c5f111dfa886308fce19c438fa0a9a469 3421076 salmon_1.10.2+ds1-1+b5_amd64.deb Files: 6a3e292723fc40953b40793a10725891 43080672 debug optional salmon-dbgsym_1.10.2+ds1-1+b5_amd64.deb 64412590e1f559c61f47965a5acfaaae 11877 science optional salmon_1.10.2+ds1-1+b5_amd64.buildinfo ba610ec53f69b970d3edbb45705c136d 3421076 science optional salmon_1.10.2+ds1-1+b5_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Mon, 23 Jun 2025 03:30:45 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: salmon (1.10.2+ds1-1) Binary: salmon salmon-dbgsym Architecture: amd64 Version: 1.10.2+ds1-1+b5 Binary-Only-Changes: salmon (1.10.2+ds1-1+b5) sid; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for outdated Built-Using (sphinx/7.4.7-3) . -- amd64 / i386 Build Daemon (x86-ubc-01) Thu, 03 Apr 2025 06:13:14 +0000 Checksums-Md5: 6a3e292723fc40953b40793a10725891 43080672 salmon-dbgsym_1.10.2+ds1-1+b5_amd64.deb ba610ec53f69b970d3edbb45705c136d 3421076 salmon_1.10.2+ds1-1+b5_amd64.deb Checksums-Sha1: e4c3940d378a4969bf549d87dfd99f1f8d36a6c0 43080672 salmon-dbgsym_1.10.2+ds1-1+b5_amd64.deb b822b80f3607c241a55ef57fca306f9974e51538 3421076 salmon_1.10.2+ds1-1+b5_amd64.deb Checksums-Sha256: 8e2fc1b295273bef749f3087297236b8c04f3ea744ccfd51e26b3b9699c28a23 43080672 salmon-dbgsym_1.10.2+ds1-1+b5_amd64.deb 593be3237a41f97b6f14e73382a6f80c5f111dfa886308fce19c438fa0a9a469 3421076 salmon_1.10.2+ds1-1+b5_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 23 Jun 2025 03:30:42 +0000 Build-Path: /build/reproducible-path/salmon-1.10.2+ds1 Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.17-4), autopoint (= 0.23.1-1), autotools-dev (= 20240727.1), base-files (= 13.7), base-passwd (= 3.6.7), bash (= 5.2.37-1.1+b2), binutils (= 2.44-3), binutils-common (= 2.44-3), binutils-x86-64-linux-gnu (= 2.44-3), bsdextrautils (= 2.41-3), bsdutils (= 1:2.41-3), build-essential (= 12.12), bzip2 (= 1.0.8-6), ca-certificates (= 20241223), cmake (= 3.31.6-2), cmake-data (= 3.31.6-2), comerr-dev (= 2.1-1.47.2-1+b1), coreutils (= 9.5-1+b1), cpp (= 4:14.2.0-1), cpp-14 (= 14.2.0-19), cpp-14-x86-64-linux-gnu (= 14.2.0-19), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.24.2), debianutils (= 5.21), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-3), docutils-common (= 0.21.2+dfsg-2), docutils-doc (= 0.21.2+dfsg-2), dpkg (= 1.22.18), dpkg-dev (= 1.22.18), dwz (= 0.15-1+b1), file (= 1:5.46-4), findutils (= 4.10.0-3), fonts-font-awesome (= 5.0.10+really4.7.0~dfsg-4.1), fonts-lato (= 2.015-1), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-19), g++-14-x86-64-linux-gnu (= 14.2.0-19), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-14 (= 14.2.0-19), gcc-14-base (= 14.2.0-19), gcc-14-x86-64-linux-gnu (= 14.2.0-19), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-1), gettext-base (= 0.23.1-1), grep (= 3.11-4), groff-base (= 1.23.0-7), gzip (= 1.13-1), help2man (= 1.49.3), hostname (= 3.25), icu-devtools (= 76.1-3), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.21.3-5), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.7.4-1.1), libasan8 (= 14.2.0-19), libatomic1 (= 14.2.0-19), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2+b2), libbinutils (= 2.44-3), libblkid1 (= 2.41-3), libboost-atomic1.83-dev (= 1.83.0-4.2), libboost-atomic1.83.0 (= 1.83.0-4.2), libboost-chrono1.83-dev (= 1.83.0-4.2), libboost-chrono1.83.0t64 (= 1.83.0-4.2), libboost-date-time1.83-dev (= 1.83.0-4.2), libboost-date-time1.83.0 (= 1.83.0-4.2), libboost-filesystem-dev (= 1.83.0.2+b2), libboost-filesystem1.83-dev (= 1.83.0-4.2), libboost-filesystem1.83.0 (= 1.83.0-4.2), libboost-iostreams-dev (= 1.83.0.2+b2), libboost-iostreams1.83-dev (= 1.83.0-4.2), libboost-iostreams1.83.0 (= 1.83.0-4.2), libboost-program-options-dev (= 1.83.0.2+b2), libboost-program-options1.83-dev (= 1.83.0-4.2), libboost-program-options1.83.0 (= 1.83.0-4.2), libboost-regex1.83-dev (= 1.83.0-4.2), libboost-regex1.83.0 (= 1.83.0-4.2), libboost-serialization1.83-dev (= 1.83.0-4.2), libboost-serialization1.83.0 (= 1.83.0-4.2), libboost-system-dev (= 1.83.0.2+b2), libboost-system1.83-dev (= 1.83.0-4.2), libboost-system1.83.0 (= 1.83.0-4.2), libboost-thread-dev (= 1.83.0.2+b2), libboost-thread1.83-dev (= 1.83.0-4.2), libboost-thread1.83.0 (= 1.83.0-4.2), libboost-timer-dev (= 1.83.0.2+b2), libboost-timer1.83-dev (= 1.83.0-4.2), libboost-timer1.83.0 (= 1.83.0-4.2), libboost1.83-dev (= 1.83.0-4.2), libbrotli-dev (= 1.1.0-2+b7), libbrotli1 (= 1.1.0-2+b7), libbwa-dev (= 0.7.18-1), libbz2-1.0 (= 1.0.8-6), libbz2-dev (= 1.0.8-6), libc-bin (= 2.41-6), libc-dev-bin (= 2.41-6), libc6 (= 2.41-6), libc6-dev (= 2.41-6), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-4), libcares2 (= 1.34.4-2.1), libcc1-0 (= 14.2.0-19), libcereal-dev (= 1.3.2+dfsg-5), libcom-err2 (= 1.47.2-1+b1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.44-3), libctf0 (= 2.44-3), libcurl3t64-gnutls (= 8.13.0-1), libcurl4-gnutls-dev (= 8.13.0-1), libcurl4t64 (= 8.13.0-1), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.278), libdebhelper-perl (= 13.24.2), libdivsufsort-dev (= 2.0.1-6+b1), libdivsufsort3 (= 2.0.1-6+b1), libdpkg-perl (= 1.22.18), libeigen3-dev (= 3.4.0-4), libelf1t64 (= 0.192-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libexpat1 (= 2.7.1-1), libffi8 (= 3.4.7-1), libfile-stripnondeterminism-perl (= 1.14.1-2), libfmt-dev (= 10.1.1+ds1-4), libfmt10 (= 10.1.1+ds1-4), libgcc-14-dev (= 14.2.0-19), libgcc-s1 (= 14.2.0-19), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgff-dev (= 2.0.0-3), libgmp-dev (= 2:6.3.0+dfsg-3), libgmp10 (= 2:6.3.0+dfsg-3), libgmpxx4ldbl (= 2:6.3.0+dfsg-3), libgnutls-dane0t64 (= 3.8.9-2), libgnutls-openssl27t64 (= 3.8.9-2), libgnutls28-dev (= 3.8.9-2), libgnutls30t64 (= 3.8.9-2), libgomp1 (= 14.2.0-19), libgprofng0 (= 2.44-3), libgssapi-krb5-2 (= 1.21.3-5), libgssrpc4t64 (= 1.21.3-5), libhogweed6t64 (= 3.10.1-1), libhtscodecs-dev (= 1.6.1-2), libhtscodecs2 (= 1.6.1-2), libhwasan0 (= 14.2.0-19), libhwloc15 (= 2.12.0-1), libicu-dev (= 76.1-3), libicu76 (= 76.1-3), libidn2-0 (= 2.3.8-2), libidn2-dev (= 2.3.8-2), libisl23 (= 0.27-1), libitm1 (= 14.2.0-19), libjansson4 (= 2.14-2+b3), libjellyfish-2.0-2 (= 2.3.1-4+b1), libjellyfish-2.0-dev (= 2.3.1-4+b1), libjemalloc-dev (= 5.3.0-3), libjemalloc2 (= 5.3.0-3), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-sphinxdoc (= 8.1.3-5), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libjson-perl (= 4.10000-1), libjsoncpp26 (= 1.9.6-3), libk5crypto3 (= 1.21.3-5), libkadm5clnt-mit12 (= 1.21.3-5), libkadm5srv-mit12 (= 1.21.3-5), libkdb5-10t64 (= 1.21.3-5), libkeyutils1 (= 1.6.3-4), libkrb5-3 (= 1.21.3-5), libkrb5-dev (= 1.21.3-5), libkrb5support0 (= 1.21.3-5), liblastlog2-2 (= 2.41-3), libldap-dev (= 2.6.9+dfsg-2), libldap2 (= 2.6.9+dfsg-2), liblocale-gettext-perl (= 1.07-7+b1), liblsan0 (= 14.2.0-19), liblz4-1 (= 1.10.0-4), liblzma-dev (= 5.6.4-1), liblzma5 (= 5.6.4-1), libmagic-mgc (= 1:5.46-4), libmagic1t64 (= 1:5.46-4), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41-3), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libncursesw6 (= 6.5+20250216-2), libnettle8t64 (= 3.10.1-1), libnghttp2-14 (= 1.64.0-1), libnghttp2-dev (= 1.64.0-1), libnghttp3-9 (= 1.8.0-1), libnghttp3-dev (= 1.8.0-1), libngtcp2-16 (= 1.11.0-1), libngtcp2-crypto-gnutls-dev (= 1.11.0-1), libngtcp2-crypto-gnutls8 (= 1.11.0-1), libngtcp2-dev (= 1.11.0-1), libnode115 (= 20.19.0+dfsg-1), libp11-kit-dev (= 0.25.5-3), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.7.0-3), libpam-modules-bin (= 1.7.0-3), libpam-runtime (= 1.7.0-3), libpam0g (= 1.7.0-3), libpcre2-8-0 (= 10.45-1), libperl5.40 (= 5.40.1-2), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-4), libproc2-0 (= 2:4.0.4-7), libpsl-dev (= 0.21.2-1.1+b1), libpsl5t64 (= 0.21.2-1.1+b1), libpthread-stubs0-dev (= 0.5-1), libpython3-stdlib (= 3.13.2-2), libpython3.13-minimal (= 3.13.2-3), libpython3.13-stdlib (= 3.13.2-3), libquadmath0 (= 14.2.0-19), libreadline8t64 (= 8.2-6), librhash1 (= 1.4.5-1), librtmp-dev (= 2.4+20151223.gitfa8646d.1-2+b5), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5), libsasl2-2 (= 2.1.28+dfsg1-9), libsasl2-modules-db (= 2.1.28+dfsg1-9), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe1 (= 2.44-3), libsimde-dev (= 0.8.2-3), libsmartcols1 (= 2.41-3), libsparsehash-dev (= 2.0.3-2), libspdlog-dev (= 1:1.15.1+ds-1), libspdlog1.15 (= 1:1.15.1+ds-1), libsqlite3-0 (= 3.46.1-2), libssh2-1-dev (= 1.11.1-1), libssh2-1t64 (= 1.11.1-1), libssl-dev (= 3.4.1-1), libssl3t64 (= 3.4.1-1), libstaden-read-dev (= 1.15.0-1.1+b2), libstaden-read14t64 (= 1.15.0-1.1+b2), libstdc++-14-dev (= 14.2.0-19), libstdc++6 (= 14.2.0-19), libsystemd0 (= 257.4-9), libtasn1-6 (= 4.20.0-2), libtasn1-6-dev (= 4.20.0-2), libtbb-dev (= 2022.1.0-1), libtbb12 (= 2022.1.0-1), libtbbbind-2-5 (= 2022.1.0-1), libtbbmalloc2 (= 2022.1.0-1), libtclap-dev (= 1.2.5-1+b2), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 14.2.0-19), libubsan1 (= 14.2.0-19), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.4-9), libunbound8 (= 1.22.0-1+b1), libunistring5 (= 1.3-2), libuuid1 (= 2.41-3), libuv1t64 (= 1.50.0-2), libxml2 (= 2.12.7+dfsg+really2.9.14-0.4), libxxhash0 (= 0.8.3-2), libzstd-dev (= 1.5.7+dfsg-1), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.21-1), m4 (= 1.4.19-7), make (= 4.4.1-1), man-db (= 2.13.0-1), mawk (= 1.3.4.20250131-1), media-types (= 13.0.0), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), netbase (= 6.5), nettle-dev (= 3.10.1-1), node-acorn (= 8.8.1+ds+~cs25.17.7-2), node-balanced-match (= 2.0.0-1), node-brace-expansion (= 2.0.1+~1.1.0-1), node-cjs-module-lexer (= 1.2.3+dfsg-1), node-commander (= 9.4.1-1), node-corepack (= 0.24.0-4), node-mathjax-full (= 3.2.2+~cs4.2.1-4), node-minimatch (= 9.0.3-5), node-mj-context-menu (= 0.9.1+ds-2), node-speech-rule-engine (= 4.0.7+~0.1.31-2), node-undici (= 7.3.0+dfsg1+~cs24.12.11-1), node-xtend (= 4.0.2-3), nodejs (= 20.19.0+dfsg-1), openssl (= 3.4.1-1), openssl-provider-legacy (= 3.4.1-1), patch (= 2.7.6-7), perl (= 5.40.1-2), perl-base (= 5.40.1-2), perl-modules-5.40 (= 5.40.1-2), pkg-config (= 1.8.1-4), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-7), python-babel-localedata (= 2.17.0-1), python-requests-doc (= 2.32.3+dfsg-5), python3 (= 3.13.2-2), python3-alabaster (= 0.7.16-0.1), python3-babel (= 2.17.0-1), python3-certifi (= 2025.1.31+ds-1), python3-chardet (= 5.2.0+dfsg-2), python3-charset-normalizer (= 3.4.1-1+b1), python3-defusedxml (= 0.7.1-3), python3-doc (= 3.13.2-2), python3-docs-theme (= 2025.2-1), python3-docutils (= 0.21.2+dfsg-2), python3-idna (= 3.10-1), python3-imagesize (= 1.4.1-1), python3-jinja2 (= 3.1.6-1), python3-markupsafe (= 2.1.5-1+b3), python3-minimal (= 3.13.2-2), python3-packaging (= 24.2-1), python3-pygments (= 2.18.0+dfsg-2), python3-requests (= 2.32.3+dfsg-5), python3-roman (= 5.0-1), python3-snowballstemmer (= 2.2.0-4), python3-sphinx (= 8.1.3-5), python3-sphinx-rtd-theme (= 3.0.2+dfsg-2), python3-sphinxcontrib.jquery (= 4.1-5), python3-urllib3 (= 2.3.0-2), python3.13 (= 3.13.2-3), python3.13-doc (= 3.13.2-3), python3.13-minimal (= 3.13.2-3), rapidjson-dev (= 1.1.0+dfsg2-7.3), rapmap-dev (= 0.15.0+dfsg-4), readline-common (= 8.2-6), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sgml-base (= 1.31), sphinx-common (= 8.1.3-5), sphinx-doc (= 8.1.3-5), sphinx-rtd-theme-common (= 3.0.2+dfsg-2), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), tzdata (= 2025b-1), util-linux (= 2.41-3), xml-core (= 0.19), xz-utils (= 5.6.4-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=6" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1743660794" +------------------------------------------------------------------------------+ | Package contents Mon, 23 Jun 2025 03:30:45 +0000 | +------------------------------------------------------------------------------+ salmon-dbgsym_1.10.2+ds1-1+b5_amd64.deb --------------------------------------- new Debian package, version 2.0. size 43080672 bytes: control archive=544 bytes. 399 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: salmon-dbgsym Source: salmon (1.10.2+ds1-1) Version: 1.10.2+ds1-1+b5 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 45279 Depends: salmon (= 1.10.2+ds1-1+b5) Section: debug Priority: optional Description: debug symbols for salmon Build-Ids: 22e76fc68b7848cd4b1bf72f125b01ecf335ee31 drwxr-xr-x root/root 0 2025-04-03 06:13 ./ drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/ drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/lib/ drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/lib/debug/ drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/lib/debug/.build-id/22/ -rw-r--r-- root/root 46354960 2025-04-03 06:13 ./usr/lib/debug/.build-id/22/e76fc68b7848cd4b1bf72f125b01ecf335ee31.debug drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/ drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/doc/ lrwxrwxrwx root/root 0 2025-04-03 06:13 ./usr/share/doc/salmon-dbgsym -> salmon salmon_1.10.2+ds1-1+b5_amd64.deb -------------------------------- new Debian package, version 2.0. size 3421076 bytes: control archive=2512 bytes. 1573 bytes, 23 lines control 3901 bytes, 50 lines md5sums Package: salmon Source: salmon (1.10.2+ds1-1) Version: 1.10.2+ds1-1+b5 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 13103 Depends: libboost-filesystem1.83.0 (>= 1.83.0), libboost-iostreams1.83.0 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libc6 (>= 2.38), libgcc-s1 (>= 3.4), libjemalloc2 (>= 5.0.0), libstaden-read14t64 (>= 1.14.12), libstdc++6 (>= 14), libtbb12 (>= 2021.4.0), libtbbmalloc2 (>= 2017~U7), zlib1g (>= 1:1.1.4), libjs-sphinxdoc (>= 8.1) Built-Using: sphinx (= 8.1.3-5) Section: science Priority: optional Homepage: https://github.com/COMBINE-lab/salmon Description: wicked-fast transcript quantification from RNA-seq data Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves is accuracy and speed via a number of different innovations, including the use of lightweight alignments (accurate but fast-to-compute proxies for traditional read alignments) and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely into many different pipelines. For example, you can choose to make use of the lightweight alignments by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. computed with your favorite aligner), and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances for your experiment. drwxr-xr-x root/root 0 2025-04-03 06:13 ./ drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/ drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/bin/ -rwxr-xr-x root/root 9252320 2025-04-03 06:13 ./usr/bin/salmon drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/ drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/doc-base/ -rw-r--r-- root/root 1091 2019-11-14 13:50 ./usr/share/doc-base/salmon.salmon drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/doc/salmon/ -rw-r--r-- root/root 239 2025-04-03 06:13 ./usr/share/doc/salmon/changelog.Debian.amd64.gz -rw-r--r-- root/root 1346 2025-04-03 06:13 ./usr/share/doc/salmon/changelog.Debian.gz -rw-r--r-- root/root 7314 2020-11-26 18:10 ./usr/share/doc/salmon/copyright drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/doc/salmon/examples/ -rw-r--r-- root/root 1283063 2013-05-27 20:19 ./usr/share/doc/salmon/examples/reads_1.fastq -rw-r--r-- root/root 1283063 2013-05-27 20:19 ./usr/share/doc/salmon/examples/reads_2.fastq -rw-r--r-- root/root 770758 2020-04-22 04:25 ./usr/share/doc/salmon/examples/sample_alignments.bam -rw-r--r-- root/root 29213 2013-05-27 20:20 ./usr/share/doc/salmon/examples/transcripts.fasta drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/doc/salmon/html/ drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/doc/salmon/html/_images/ -rw-r--r-- root/root 169638 2023-06-26 20:51 ./usr/share/doc/salmon/html/_images/ReadLibraryIllustration.png drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/doc/salmon/html/_sources/ -rw-r--r-- root/root 22297 2023-06-26 20:51 ./usr/share/doc/salmon/html/_sources/alevin.rst.txt -rw-r--r-- root/root 4300 2023-06-26 20:51 ./usr/share/doc/salmon/html/_sources/building.rst.txt -rw-r--r-- root/root 11809 2023-06-26 20:51 ./usr/share/doc/salmon/html/_sources/file_formats.rst.txt -rw-r--r-- root/root 522 2023-06-26 20:51 ./usr/share/doc/salmon/html/_sources/index.rst.txt -rw-r--r-- root/root 4245 2023-06-26 20:51 ./usr/share/doc/salmon/html/_sources/library_type.rst.txt -rw-r--r-- root/root 45909 2023-06-26 20:51 ./usr/share/doc/salmon/html/_sources/salmon.rst.txt drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/doc/salmon/html/_static/ -rw-r--r-- root/root 14815 2025-04-03 06:13 ./usr/share/doc/salmon/html/_static/basic.css -rw-r--r-- root/root 4759 2025-04-03 06:13 ./usr/share/doc/salmon/html/_static/classic.css -rw-r--r-- root/root 3508 2025-02-19 11:17 ./usr/share/doc/salmon/html/_static/copybutton.js -rw-r--r-- root/root 28 2025-01-31 10:28 ./usr/share/doc/salmon/html/_static/default.css lrwxrwxrwx 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root/root 15467 2025-02-19 11:17 ./usr/share/doc/salmon/html/_static/pydoctheme.css -rw-r--r-- root/root 3252 2025-02-19 11:17 ./usr/share/doc/salmon/html/_static/pydoctheme_dark.css -rw-r--r-- root/root 4929 2025-04-03 06:13 ./usr/share/doc/salmon/html/_static/pygments.css -rw-r--r-- root/root 5055 2025-04-03 06:13 ./usr/share/doc/salmon/html/_static/pygments_dark.css -rw-r--r-- root/root 559 2025-02-19 11:17 ./usr/share/doc/salmon/html/_static/search-focus.js lrwxrwxrwx root/root 0 2025-04-03 06:13 ./usr/share/doc/salmon/html/_static/searchtools.js -> ../../../../javascript/sphinxdoc/1.0/searchtools.js -rw-r--r-- root/root 2617 2025-04-03 06:13 ./usr/share/doc/salmon/html/_static/sidebar.js lrwxrwxrwx root/root 0 2025-04-03 06:13 ./usr/share/doc/salmon/html/_static/sphinx_highlight.js -> ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js -rw-r--r-- root/root 779 2025-02-19 11:17 ./usr/share/doc/salmon/html/_static/themetoggle.js -rw-r--r-- root/root 53646 2025-04-03 06:13 ./usr/share/doc/salmon/html/alevin.html -rw-r--r-- root/root 17930 2025-04-03 06:13 ./usr/share/doc/salmon/html/building.html -rw-r--r-- root/root 29485 2025-04-03 06:13 ./usr/share/doc/salmon/html/file_formats.html -rw-r--r-- root/root 8785 2025-04-03 06:13 ./usr/share/doc/salmon/html/genindex.html -rw-r--r-- root/root 15188 2025-04-03 06:13 ./usr/share/doc/salmon/html/index.html -rw-r--r-- root/root 18859 2025-04-03 06:13 ./usr/share/doc/salmon/html/library_type.html -rw-r--r-- root/root 404 2025-04-03 06:13 ./usr/share/doc/salmon/html/objects.inv -rw-r--r-- root/root 98794 2025-04-03 06:13 ./usr/share/doc/salmon/html/salmon.html -rw-r--r-- root/root 7061 2025-04-03 06:13 ./usr/share/doc/salmon/html/search.html -rw-r--r-- root/root 29072 2025-04-03 06:13 ./usr/share/doc/salmon/html/searchindex.js drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/man/ drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/man/man1/ -rw-r--r-- root/root 1374 2025-04-03 06:13 ./usr/share/man/man1/salmon-index.1.gz -rw-r--r-- root/root 530 2025-04-03 06:13 ./usr/share/man/man1/salmon-quant.1.gz -rw-r--r-- root/root 325 2025-04-03 06:13 ./usr/share/man/man1/salmon-swim.1.gz -rw-r--r-- root/root 433 2025-04-03 06:13 ./usr/share/man/man1/salmon.1.gz drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/salmon/ drwxr-xr-x root/root 0 2025-04-03 06:13 ./usr/share/salmon/build-test-logs/ -rw-r--r-- root/root 90928 2025-04-03 06:13 ./usr/share/salmon/build-test-logs/LastTest.log +------------------------------------------------------------------------------+ | Post Build Mon, 23 Jun 2025 03:30:46 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 23 Jun 2025 03:30:46 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 23 Jun 2025 03:30:49 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 1162992 Build-Time: 391 Distribution: unstable Host Architecture: amd64 Install-Time: 5 Job: /srv/rebuilderd/tmp/rebuilderdJmxW9F/inputs/salmon_1.10.2+ds1-1.dsc Machine Architecture: amd64 Package: salmon Package-Time: 414 Source-Version: 1.10.2+ds1-1 Space: 1162992 Status: successful Version: 1.10.2+ds1-1+b5 -------------------------------------------------------------------------------- Finished at 2025-06-23T03:30:43Z Build needed 00:06:54, 1162992k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderdJmxW9F/out checking salmon-dbgsym_1.10.2+ds1-1+b5_amd64.deb: size... sha256... md5... sha1... all OK checking salmon_1.10.2+ds1-1+b5_amd64.deb: size differs for salmon_1.10.2+ds1-1+b5_amd64.deb