--- /srv/rebuilderd/tmp/rebuilderdRykhUm/inputs/r-bioc-gypsum_1.8.0+ds-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdRykhUm/out/r-bioc-gypsum_1.8.0+ds-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-06 23:44:33.000000 debian-binary │ --rw-r--r-- 0 0 0 1552 2026-08-06 23:44:33.000000 control.tar.xz │ --rw-r--r-- 0 0 0 210928 2026-08-06 23:44:33.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 1496 2026-08-06 23:44:33.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 212324 2026-08-06 23:44:33.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:44:33.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 887 2026-08-06 23:44:33.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 750 2026-08-06 23:44:33.000000 ./control │ │ │ -rw-r--r-- 0 root (0) root (0) 2103 2026-08-06 23:44:33.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,13 @@ │ │ │ Package: r-bioc-gypsum │ │ │ Version: 1.8.0+ds-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ -Installed-Size: 261 │ │ │ +Installed-Size: 262 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-cran-httr2, r-cran-jsonlite, r-cran-filelock, r-cran-rappdirs, r-pkg-team-core-architecture │ │ │ -Suggests: r-cran-knitr, r-cran-rmarkdown, r-cran-testthat, r-bioc-biocstyle, r-cran-digest, r-cran-dbi, r-cran-rsqlite, r-bioc-s4vectors │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/gypsum/ │ │ │ Description: Interface to the gypsum REST API │ │ │ Client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based │ │ │ file store in the ArtifactDB ecosystem. │ │ │ . │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -14,27 +14,27 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 714 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1222 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/Meta/package.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 217 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1445 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 1759 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/NEWS.Rd │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/R/gypsum │ │ │ --rw-r--r-- 0 root (0) root (0) 90324 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/R/gypsum.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 1611 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/R/gypsum.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 90334 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/R/gypsum.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 1606 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/R/gypsum.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 863 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/README.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1379 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/doc/index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2580 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/doc/userguide.R │ │ │ -rw-r--r-- 0 root (0) root (0) 8487 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/doc/userguide.Rmd │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1419 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/help/AnIndex │ │ │ -rw-r--r-- 0 root (0) root (0) 523 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 102059 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/help/gypsum.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 1098 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/help/gypsum.rdx │ │ │ --rw-r--r-- 0 root (0) root (0) 518 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 102917 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/help/gypsum.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 1095 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/help/gypsum.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 530 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 7125 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-06 23:44:33.000000 ./usr/lib/R/site-library/gypsum/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:44:33.000000 ./usr/share/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:44:33.000000 ./usr/share/doc/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:44:33.000000 ./usr/share/doc/r-bioc-gypsum/ │ │ │ -rw-r--r-- 0 root (0) root (0) 783 2026-08-06 23:44:33.000000 ./usr/share/doc/r-bioc-gypsum/changelog.Debian.gz │ │ ├── ./usr/lib/R/site-library/gypsum/R/gypsum.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -78,15 +78,15 @@ │ │ │ │ "imports" = "resps_successes = "resps_successes"), filelock = c(lock = "lock"), " │ │ │ │ "imports" = " filelock = c(unlock = "unlock"), jsonlite = c(fromJSON = "fromJSON"), " │ │ │ │ "imports" = " jsonlite = c(toJSON = "toJSON"), parallel = c(makeCluster = "makeCluster"), " │ │ │ │ "imports" = " parallel = c(parLapply = "parLapply"), parallel = c(stopCluster = "stopCluster"), " │ │ │ │ "imports" = " rappdirs = c(user_cache_dir = "user_cache_dir"), utils = c(URLencode = "URLencode"), " │ │ │ │ "imports" = " utils = c(tail = "tail"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-gypsum/debian/r-bioc-gypsum/usr/lib/R/site-library/gypsum"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/debian/r-bioc-gypsum/usr/lib/R/site-library/gypsum"" │ │ │ │ "spec" = "c(name = "gypsum", version = "1.8.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/gypsum/R/gypsum.rdx │ │ │ ├── gypsum.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,301 +1,301 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 1955 52 │ │ │ │ │ +[1] 1965 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 2138 52 │ │ │ │ │ +[1] 2148 52 │ │ │ │ │ │ │ │ │ │ $variables$.cast_datetime │ │ │ │ │ -[1] 2190 1073 │ │ │ │ │ +[1] 2200 1073 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 3263 51 │ │ │ │ │ +[1] 3273 51 │ │ │ │ │ │ │ │ │ │ $variables$.translateAddOperation │ │ │ │ │ -[1] 3314 819 │ │ │ │ │ +[1] 3324 819 │ │ │ │ │ │ │ │ │ │ $variables$.translateTextClause │ │ │ │ │ -[1] 4133 2966 │ │ │ │ │ +[1] 4143 2966 │ │ │ │ │ │ │ │ │ │ $variables$.translateTextQuery │ │ │ │ │ -[1] 7099 4819 │ │ │ │ │ +[1] 7109 4819 │ │ │ │ │ │ │ │ │ │ $variables$.upload_file │ │ │ │ │ -[1] 11918 1357 │ │ │ │ │ +[1] 11928 1357 │ │ │ │ │ │ │ │ │ │ $variables$BUCKET_CACHE_NAME │ │ │ │ │ -[1] 13275 51 │ │ │ │ │ +[1] 13285 51 │ │ │ │ │ │ │ │ │ │ $variables$Ops.gypsum.search.clause │ │ │ │ │ -[1] 13326 803 │ │ │ │ │ +[1] 13336 803 │ │ │ │ │ │ │ │ │ │ $variables$abortUpload │ │ │ │ │ -[1] 14129 694 │ │ │ │ │ +[1] 14139 694 │ │ │ │ │ │ │ │ │ │ $variables$accessToken │ │ │ │ │ -[1] 14823 1981 │ │ │ │ │ +[1] 14833 1981 │ │ │ │ │ │ │ │ │ │ $variables$acquire_lock │ │ │ │ │ -[1] 16804 885 │ │ │ │ │ +[1] 16814 885 │ │ │ │ │ │ │ │ │ │ $variables$add_query_parameter │ │ │ │ │ -[1] 17689 498 │ │ │ │ │ +[1] 17699 498 │ │ │ │ │ │ │ │ │ │ $variables$add_token_search_clause │ │ │ │ │ -[1] 18187 499 │ │ │ │ │ +[1] 18197 499 │ │ │ │ │ │ │ │ │ │ $variables$approveProbation │ │ │ │ │ -[1] 18686 782 │ │ │ │ │ +[1] 18696 782 │ │ │ │ │ │ │ │ │ │ $variables$build_query │ │ │ │ │ -[1] 19468 3587 │ │ │ │ │ +[1] 19478 3587 │ │ │ │ │ │ │ │ │ │ $variables$cacheDirectory │ │ │ │ │ -[1] 23215 749 │ │ │ │ │ +[1] 23225 749 │ │ │ │ │ │ │ │ │ │ $variables$chomp_url │ │ │ │ │ -[1] 23964 225 │ │ │ │ │ +[1] 23974 225 │ │ │ │ │ │ │ │ │ │ $variables$cloneVersion │ │ │ │ │ -[1] 24189 1791 │ │ │ │ │ +[1] 24199 1791 │ │ │ │ │ │ │ │ │ │ $variables$completeUpload │ │ │ │ │ -[1] 25980 695 │ │ │ │ │ +[1] 25990 695 │ │ │ │ │ │ │ │ │ │ $variables$config_cache_path │ │ │ │ │ -[1] 26675 261 │ │ │ │ │ +[1] 26685 261 │ │ │ │ │ │ │ │ │ │ $variables$createProject │ │ │ │ │ -[1] 26936 1507 │ │ │ │ │ +[1] 26946 1507 │ │ │ │ │ │ │ │ │ │ $variables$creds.env │ │ │ │ │ -[1] 28609 52 │ │ │ │ │ +[1] 28619 52 │ │ │ │ │ │ │ │ │ │ $variables$defineTextQuery │ │ │ │ │ -[1] 28661 278 │ │ │ │ │ +[1] 28671 278 │ │ │ │ │ │ │ │ │ │ $variables$download_and_rename_file │ │ │ │ │ -[1] 28939 543 │ │ │ │ │ +[1] 28949 543 │ │ │ │ │ │ │ │ │ │ $variables$fetchLatest │ │ │ │ │ -[1] 29482 436 │ │ │ │ │ +[1] 29492 436 │ │ │ │ │ │ │ │ │ │ $variables$fetchManifest │ │ │ │ │ -[1] 29918 403 │ │ │ │ │ +[1] 29928 403 │ │ │ │ │ │ │ │ │ │ $variables$fetchMetadataDatabase │ │ │ │ │ -[1] 30321 2049 │ │ │ │ │ +[1] 30331 2049 │ │ │ │ │ │ │ │ │ │ $variables$fetchMetadataSchema │ │ │ │ │ -[1] 32370 1298 │ │ │ │ │ +[1] 32380 1298 │ │ │ │ │ │ │ │ │ │ $variables$fetchPermissions │ │ │ │ │ -[1] 33668 935 │ │ │ │ │ +[1] 33678 935 │ │ │ │ │ │ │ │ │ │ $variables$fetchQuota │ │ │ │ │ -[1] 34603 350 │ │ │ │ │ +[1] 34613 350 │ │ │ │ │ │ │ │ │ │ $variables$fetchSummary │ │ │ │ │ -[1] 34953 976 │ │ │ │ │ +[1] 34963 976 │ │ │ │ │ │ │ │ │ │ $variables$fetchUsage │ │ │ │ │ -[1] 35929 416 │ │ │ │ │ +[1] 35939 416 │ │ │ │ │ │ │ │ │ │ $variables$formatObjectMetadata │ │ │ │ │ -[1] 36345 1493 │ │ │ │ │ +[1] 36355 1493 │ │ │ │ │ │ │ │ │ │ $variables$get_cacheable_json │ │ │ │ │ -[1] 37838 874 │ │ │ │ │ +[1] 37848 874 │ │ │ │ │ │ │ │ │ │ $variables$get_current_unix_time │ │ │ │ │ -[1] 38712 249 │ │ │ │ │ +[1] 38722 249 │ │ │ │ │ │ │ │ │ │ $variables$get_json │ │ │ │ │ -[1] 38961 515 │ │ │ │ │ +[1] 38971 515 │ │ │ │ │ │ │ │ │ │ $variables$get_last_modified_date │ │ │ │ │ -[1] 39476 1285 │ │ │ │ │ +[1] 39486 1285 │ │ │ │ │ │ │ │ │ │ $variables$gsc │ │ │ │ │ -[1] 40761 1997 │ │ │ │ │ +[1] 40771 1997 │ │ │ │ │ │ │ │ │ │ $variables$is.locked │ │ │ │ │ -[1] 42914 52 │ │ │ │ │ +[1] 42924 52 │ │ │ │ │ │ │ │ │ │ $variables$last_check │ │ │ │ │ -[1] 43132 52 │ │ │ │ │ +[1] 43142 52 │ │ │ │ │ │ │ │ │ │ $variables$listAssets │ │ │ │ │ -[1] 43184 333 │ │ │ │ │ +[1] 43194 333 │ │ │ │ │ │ │ │ │ │ $variables$listFiles │ │ │ │ │ -[1] 43517 1390 │ │ │ │ │ +[1] 43527 1390 │ │ │ │ │ │ │ │ │ │ $variables$listProjects │ │ │ │ │ -[1] 44907 260 │ │ │ │ │ +[1] 44917 260 │ │ │ │ │ │ │ │ │ │ $variables$listVersions │ │ │ │ │ -[1] 45167 350 │ │ │ │ │ +[1] 45177 350 │ │ │ │ │ │ │ │ │ │ $variables$list_for_prefix │ │ │ │ │ -[1] 45517 1283 │ │ │ │ │ +[1] 45527 1283 │ │ │ │ │ │ │ │ │ │ $variables$match_path_to_cache │ │ │ │ │ -[1] 46800 1194 │ │ │ │ │ +[1] 46810 1194 │ │ │ │ │ │ │ │ │ │ $variables$normalize_and_sanitize_path │ │ │ │ │ -[1] 47994 472 │ │ │ │ │ +[1] 48004 472 │ │ │ │ │ │ │ │ │ │ $variables$prepareDirectoryUpload │ │ │ │ │ -[1] 48466 2349 │ │ │ │ │ +[1] 48476 2349 │ │ │ │ │ │ │ │ │ │ $variables$process_error │ │ │ │ │ -[1] 50815 814 │ │ │ │ │ +[1] 50825 814 │ │ │ │ │ │ │ │ │ │ $variables$publicS3Config │ │ │ │ │ -[1] 51629 2118 │ │ │ │ │ +[1] 51639 2118 │ │ │ │ │ │ │ │ │ │ $variables$refreshLatest │ │ │ │ │ -[1] 53747 786 │ │ │ │ │ +[1] 53757 786 │ │ │ │ │ │ │ │ │ │ $variables$refreshUsage │ │ │ │ │ -[1] 54533 738 │ │ │ │ │ +[1] 54543 738 │ │ │ │ │ │ │ │ │ │ $variables$rejectProbation │ │ │ │ │ -[1] 55271 782 │ │ │ │ │ +[1] 55281 782 │ │ │ │ │ │ │ │ │ │ $variables$release_lock │ │ │ │ │ -[1] 56053 699 │ │ │ │ │ +[1] 56063 699 │ │ │ │ │ │ │ │ │ │ $variables$removeAsset │ │ │ │ │ -[1] 56752 433 │ │ │ │ │ +[1] 56762 433 │ │ │ │ │ │ │ │ │ │ $variables$removeProject │ │ │ │ │ -[1] 57185 351 │ │ │ │ │ +[1] 57195 351 │ │ │ │ │ │ │ │ │ │ $variables$removeVersion │ │ │ │ │ -[1] 57536 464 │ │ │ │ │ +[1] 57546 464 │ │ │ │ │ │ │ │ │ │ $variables$rename_file │ │ │ │ │ -[1] 58000 495 │ │ │ │ │ +[1] 58010 495 │ │ │ │ │ │ │ │ │ │ $variables$request_removal │ │ │ │ │ -[1] 58495 649 │ │ │ │ │ +[1] 58505 649 │ │ │ │ │ │ │ │ │ │ $variables$resolveLinks │ │ │ │ │ -[1] 59144 2141 │ │ │ │ │ +[1] 59154 2141 │ │ │ │ │ │ │ │ │ │ $variables$resolve_single_link │ │ │ │ │ -[1] 61285 1675 │ │ │ │ │ +[1] 61295 1675 │ │ │ │ │ │ │ │ │ │ $variables$restUrl │ │ │ │ │ -[1] 63144 479 │ │ │ │ │ +[1] 63154 479 │ │ │ │ │ │ │ │ │ │ $variables$sanitize_path │ │ │ │ │ -[1] 63623 422 │ │ │ │ │ +[1] 63633 422 │ │ │ │ │ │ │ │ │ │ $variables$sanitize_query │ │ │ │ │ -[1] 64045 3371 │ │ │ │ │ +[1] 64055 3371 │ │ │ │ │ │ │ │ │ │ $variables$sanitize_uploaders │ │ │ │ │ -[1] 67416 774 │ │ │ │ │ +[1] 67426 774 │ │ │ │ │ │ │ │ │ │ $variables$saveFile │ │ │ │ │ -[1] 68190 1361 │ │ │ │ │ +[1] 68200 1361 │ │ │ │ │ │ │ │ │ │ $variables$saveVersion │ │ │ │ │ -[1] 69551 1842 │ │ │ │ │ +[1] 69561 1842 │ │ │ │ │ │ │ │ │ │ $variables$save_file │ │ │ │ │ -[1] 71393 1330 │ │ │ │ │ +[1] 71403 1330 │ │ │ │ │ │ │ │ │ │ $variables$searchMetadata │ │ │ │ │ -[1] 72723 2142 │ │ │ │ │ +[1] 72733 2142 │ │ │ │ │ │ │ │ │ │ $variables$searchMetadataFilter │ │ │ │ │ -[1] 74865 879 │ │ │ │ │ +[1] 74875 879 │ │ │ │ │ │ │ │ │ │ $variables$searchMetadataText │ │ │ │ │ -[1] 75744 201 │ │ │ │ │ +[1] 75754 201 │ │ │ │ │ │ │ │ │ │ $variables$searchMetadataTextFilter │ │ │ │ │ -[1] 75945 206 │ │ │ │ │ +[1] 75955 206 │ │ │ │ │ │ │ │ │ │ $variables$setAccessToken │ │ │ │ │ -[1] 76151 3215 │ │ │ │ │ +[1] 76161 3215 │ │ │ │ │ │ │ │ │ │ $variables$setPermissions │ │ │ │ │ -[1] 79366 1706 │ │ │ │ │ +[1] 79376 1706 │ │ │ │ │ │ │ │ │ │ $variables$setQuota │ │ │ │ │ -[1] 81072 1199 │ │ │ │ │ +[1] 81082 1199 │ │ │ │ │ │ │ │ │ │ $variables$setup_token_search_subquery_basic │ │ │ │ │ -[1] 82271 360 │ │ │ │ │ +[1] 82281 360 │ │ │ │ │ │ │ │ │ │ $variables$setup_token_search_subquery_with_field │ │ │ │ │ -[1] 82631 375 │ │ │ │ │ +[1] 82641 375 │ │ │ │ │ │ │ │ │ │ $variables$startUpload │ │ │ │ │ -[1] 83006 3248 │ │ │ │ │ +[1] 83016 3248 │ │ │ │ │ │ │ │ │ │ $variables$token.cache │ │ │ │ │ -[1] 86415 53 │ │ │ │ │ +[1] 86425 53 │ │ │ │ │ │ │ │ │ │ $variables$token_cache_path │ │ │ │ │ -[1] 86468 262 │ │ │ │ │ +[1] 86478 262 │ │ │ │ │ │ │ │ │ │ $variables$translateTextQuery │ │ │ │ │ -[1] 86730 360 │ │ │ │ │ +[1] 86740 360 │ │ │ │ │ │ │ │ │ │ $variables$uenc │ │ │ │ │ -[1] 87090 237 │ │ │ │ │ +[1] 87100 237 │ │ │ │ │ │ │ │ │ │ $variables$unlockProject │ │ │ │ │ -[1] 87327 667 │ │ │ │ │ +[1] 87337 667 │ │ │ │ │ │ │ │ │ │ $variables$uploadDirectory │ │ │ │ │ -[1] 87994 1034 │ │ │ │ │ +[1] 88004 1034 │ │ │ │ │ │ │ │ │ │ $variables$uploadFiles │ │ │ │ │ -[1] 89028 799 │ │ │ │ │ +[1] 89038 799 │ │ │ │ │ │ │ │ │ │ $variables$validateMetadata │ │ │ │ │ -[1] 89827 497 │ │ │ │ │ +[1] 89837 497 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 289 1666 │ │ │ │ │ +[1] 289 1676 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 86254 161 │ │ │ │ │ +[1] 86264 161 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 0 131 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ [1] 131 158 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 2007 131 │ │ │ │ │ +[1] 2017 131 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 23055 160 │ │ │ │ │ +[1] 23065 160 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 28443 166 │ │ │ │ │ +[1] 28453 166 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 42758 156 │ │ │ │ │ +[1] 42768 156 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 42966 166 │ │ │ │ │ +[1] 42976 166 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 62960 184 │ │ │ │ │ +[1] 62970 184 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/gypsum/help/gypsum.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -35,15 +35,15 @@ │ │ │ │ structure(" version=\"v1\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" files=list.files(tmp, recursive=TRUE),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" probation=TRUE,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" directory=tmp\n", Rd_tag = "RCODE"), │ │ │ │ structure(" )\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure(" # Aborting the upload.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" abortUpload(init) \n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/abortUpload.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/abortUpload.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ accessToken (list) = structure(list(structure(list(structure("Get and set GitHub access tokens", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("accessToken", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("accessToken", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("setAccessToken", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Get and set GitHub access tokens for authentication to the gypsum API's endpoints.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -130,15 +130,15 @@ │ │ │ │ structure(" will return a string containing a token (or ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("NULL", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(", if no token is available and ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("request=FALSE", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(").\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("if (interactive()) {\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" accessToken()\n", Rd_tag = "RCODE"), structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/accessToken.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" accessToken()\n", Rd_tag = "RCODE"), structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/accessToken.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ approveProbation (list) = structure(list(structure(list(structure("Approve a probational upload", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("approveProbation", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("approveProbation", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Pretty much as it says: approve a probational upload of a version of a project's asset.\n", Rd_tag = "TEXT"), │ │ │ │ structure("This removes the ", Rd_tag = "TEXT"), structure(list( │ │ │ │ @@ -186,15 +186,15 @@ │ │ │ │ structure(" files=character(0),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" probation=TRUE\n", Rd_tag = "RCODE"), │ │ │ │ structure(" )\n", Rd_tag = "RCODE"), structure(" completeUpload(init) \n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" # Approving the probation:\n", Rd_tag = "RCODE"), │ │ │ │ structure(" approveProbation(\"test-R\", \"probation-approve\", \"v1\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" # Just cleaning up after we're done.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" removeProjectAsset(\"test-R\", \"probation-approve\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/approveProbation.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/approveProbation.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ cacheDirectory (list) = structure(list(structure(list(structure("Cache directory", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("cacheDirectory", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("cacheDirectory", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Specify the cache directory in the local filesystem for gypsum-related data.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("cacheDirectory(dir)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -218,15 +218,15 @@ │ │ │ │ structure("and the ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("previous", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(" setting is invisibly returned.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("cacheDirectory()\n", Rd_tag = "RCODE"), │ │ │ │ structure("old <- cacheDirectory(tempfile())\n", Rd_tag = "RCODE"), │ │ │ │ structure("cacheDirectory()\n", Rd_tag = "RCODE"), structure("cacheDirectory(old) # setting it back.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/cacheDirectory.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/cacheDirectory.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ cloneVersion (list) = structure(list(structure(list(structure("Clone a version's directory structure", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("cloneVersion", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("cloneVersion", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Clone the directory structure for a versioned asset into a separate location.\n", Rd_tag = "TEXT"), │ │ │ │ structure("This is typically used to prepare a new version for a lightweight upload.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -331,15 +331,15 @@ │ │ │ │ structure("list.files(tmp, recursive=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("Sys.readlink(file.path(tmp, \"foo\", \"bar.txt\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Files should be replaced rather than modified via the symlink:\n", Rd_tag = "RCODE"), │ │ │ │ structure("existing <- file.path(tmp, \"foo\", \"bar.txt\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("unlink(existing) # Deleting the symlink...\n", Rd_tag = "RCODE"), │ │ │ │ structure("write(file=existing, \"YAY\") # ... and writing a replacement file.\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Symlinks are converted to upload links:\n", Rd_tag = "RCODE"), │ │ │ │ - structure("prepareDirectoryUpload(tmp)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/cloneVersion.Rd", class = "Rd", meta = list( │ │ │ │ + structure("prepareDirectoryUpload(tmp)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/cloneVersion.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ completeUpload (list) = structure(list(structure(list(structure("Complete an upload", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("completeUpload", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("completeUpload", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Complete an upload session after all files have been uploaded.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("completeUpload(init, url = restUrl())\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -375,15 +375,15 @@ │ │ │ │ structure(" version=\"v1\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" files=list.files(tmp, recursive=TRUE),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" probation=TRUE,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" directory=tmp\n", Rd_tag = "RCODE"), │ │ │ │ structure(" )\n", Rd_tag = "RCODE"), structure(" uploadFiles(init, directory=tmp)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" # Finishing the upload.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" completeUpload(init) \n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/completeUpload.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/completeUpload.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ createProject (list) = structure(list(structure(list(structure("Create a new project", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("createProject", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("createProject", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Create a new project with the associated permissions.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("createProject(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -441,15 +441,15 @@ │ │ │ │ structure(list(structure("removeProject", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to remove a project.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("if (interactive()) {\n", Rd_tag = "RCODE"), │ │ │ │ structure(" createProject(\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \"test-R-create\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" owners=\"LTLA\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" uploaders=list(list(id=\"ArtifactDB-bot\"))\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" )\n", Rd_tag = "RCODE"), structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/createProject.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" )\n", Rd_tag = "RCODE"), structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/createProject.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fetchLatest (list) = structure(list(structure(list(structure("Fetch the latest version", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fetchLatest", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fetchLatest", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Fetch the latest version of a project's asset.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchLatest(project, asset, url = restUrl(), config = NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -467,15 +467,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("String containing the latest version of the project.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("refreshLatest", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to refresh the latest version.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchLatest(\"test-R\", \"basic\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/fetchLatest.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchLatest.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fetchManifest (list) = structure(list(structure(list(structure("Fetch version manifest", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fetchManifest", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fetchManifest", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Fetch the manifest for a version of an asset of a project.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchManifest(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -532,15 +532,15 @@ │ │ │ │ structure("path", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT"), structure("If the link destination is itself a link, an ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("ancestor", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" list will be present that specifies the final location of the file after resolving all intermediate links.\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchManifest(\"test-R\", \"basic\", \"v1\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/fetchManifest.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchManifest.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fetchMetadataDatabase (list) = structure(list(structure(list(structure("Fetch a metadata database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fetchMetadataDatabase", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fetchMetadataDatabase", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Fetch a SQLite database containing metadata from the gypsum backend\n", Rd_tag = "TEXT"), │ │ │ │ structure("(see ", Rd_tag = "TEXT"), structure(list(structure("https://github.com/ArtifactDB/bioconductor-metadata-index", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ @@ -572,15 +572,15 @@ │ │ │ │ structure("New checks are performed when one hour or more has elapsed since the last check.\n", Rd_tag = "TEXT"), │ │ │ │ structure("If the check fails, a warning is raised and the function returns the currently cached file.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("String containing a path to the downloaded database.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fetchMetadataSchema", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to get the JSON schema used to define the database tables.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchMetadataDatabase()\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/fetchMetadataDatabase.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchMetadataDatabase()\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchMetadataDatabase.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fetchMetadataSchema (list) = structure(list(structure(list(structure("Fetch a metadata schema", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fetchMetadataSchema", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fetchMetadataSchema", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Fetch a JSON schema file for metadata to be inserted into a SQLite database\n", Rd_tag = "TEXT"), │ │ │ │ structure("(see ", Rd_tag = "TEXT"), structure(list(structure("https://github.com/ArtifactDB/bioconductor-metadata-index", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ @@ -612,15 +612,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("validateMetadata", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to validate metadata against a chosen schema.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("fetchMetadataDatabase", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to obtain the SQLite database of metadata.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchMetadataSchema()\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/fetchMetadataSchema.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchMetadataSchema()\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchMetadataSchema.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fetchPermissions (list) = structure(list(structure(list(structure("Fetch project permissions", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fetchPermissions", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fetchPermissions", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Fetch the permissions for a project.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchPermissions(project, url = restUrl(), config = NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -669,15 +669,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("setPermissions", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to set the permissions.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchPermissions(\"test-R\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/fetchPermissions.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchPermissions.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fetchQuota (list) = structure(list(structure(list(structure("Fetch project quota details", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fetchQuota", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fetchQuota", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Fetch the quota details for a project.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchQuota(project, url = restUrl(), config = NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -698,15 +698,15 @@ │ │ │ │ structure("and ", Rd_tag = "TEXT"), structure(list(structure("year", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(", the creation year (i.e., time zero) for this project.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("setQuota", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to set the quota details.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchQuota(\"test-R\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/fetchQuota.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchQuota.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fetchSummary (list) = structure(list(structure(list(structure("Fetch version summary", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fetchSummary", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fetchSummary", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Fetch the summary for a version of an asset of a project.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchSummary(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -760,15 +760,15 @@ │ │ │ │ structure(" (optional), a logical scalar indicating whether the upload is probational.\n", Rd_tag = "TEXT"), │ │ │ │ structure("If missing, this can be assumed to be ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("FALSE", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchSummary(\"test-R\", \"basic\", \"v1\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/fetchSummary.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchSummary.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fetchUsage (list) = structure(list(structure(list(structure("Fetch project usage details", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fetchUsage", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fetchUsage", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Fetch the quota usage for a project.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchUsage(project, url = restUrl(), config = NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -783,15 +783,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Numeric scalar specifying the quota usage for the project, in bytes.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("refreshUsage", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to recompute the used quota.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("fetchUsage(\"test-R\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/fetchUsage.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchUsage.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ formatObjectMetadata (list) = structure(list(structure(list(structure("Format object-related metadata", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("formatObjectMetadata", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("formatObjectMetadata", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Create object-related metadata to validate against the default schema from ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("fetchMetadataSchema", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ @@ -804,15 +804,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("List containing the object-related metadata, typically stored in the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("applications.takane", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" field of the metadata.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("df <- S4Vectors::DataFrame(alpha=LETTERS, numeric=runif(26))\n", Rd_tag = "RCODE"), │ │ │ │ structure("formatObjectMetadata(df)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/formatObjectMetadata.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/formatObjectMetadata.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ listAssets (list) = structure(list(structure(list(structure("List assets", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("listAssets", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("listAssets", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -826,15 +826,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("config", Rd_tag = "TEXT")), │ │ │ │ list(structure("Deprecated and ignored.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Character vector of asset names.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("listAssets(\"test-R\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/listAssets.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/listAssets.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ listFiles (list) = structure(list(structure(list(structure("List files for a version", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("listFiles", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("listFiles", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("List files belonging to a version of a project asset.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("listFiles(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -870,15 +870,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("config", Rd_tag = "TEXT")), │ │ │ │ list(structure("Deprecated and ignored.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Character vector of relative paths of files associated with the versioned asset.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("listFiles(\"test-R\", \"basic\", \"v1\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/listFiles.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/listFiles.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ listProjects (list) = structure(list(structure(list(structure("List all projects", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("listProjects", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("listProjects", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("List all projects in the gypsum backent.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("listProjects(url = restUrl(), config = NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -888,15 +888,15 @@ │ │ │ │ structure(list(list(structure("config", Rd_tag = "TEXT")), │ │ │ │ list(structure("Deprecated and ignored.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Character vector of project names.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("if (interactive()) {\n", Rd_tag = "RCODE"), │ │ │ │ structure(" listProjects()\n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/listProjects.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/listProjects.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ listVersions (list) = structure(list(structure(list(structure("List asset versions", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("listVersions", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("listVersions", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("List all versions of a project asset.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("listVersions(project, asset, url = restUrl(), config = NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -911,15 +911,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("config", Rd_tag = "TEXT")), │ │ │ │ list(structure("Deprecated and ignored.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Character vector of versions.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("listVersions(\"test-R\", \"basic\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/listVersions.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/listVersions.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ prepareDirectoryUpload (list) = structure(list(structure(list(structure("Prepare to upload a directory", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("prepareDirectoryUpload", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("prepareDirectoryUpload", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Prepare to upload a directory's contents via ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("startUpload", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ @@ -1004,15 +1004,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("cloneVersion", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to prepare the symlinks.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("tmp <- tempfile()\n", Rd_tag = "RCODE"), │ │ │ │ structure("out <- cloneVersion(\"test-R\", \"basic\", \"v1\", destination=tmp)\n", Rd_tag = "RCODE"), │ │ │ │ structure("write(file=file.path(tmp, \"heanna\"), \"sumire\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("prepareDirectoryUpload(tmp)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/prepareDirectoryUpload.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/prepareDirectoryUpload.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ publicS3Config (list) = structure(list(structure(list(structure("Public S3 configuration", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("publicS3Config", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("publicS3Config", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Fetch S3 credentials and other configuration details for read-only access to the underlying gypsum bucket.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("publicS3Config(refresh = FALSE, url = restUrl(), cache = cacheDirectory())\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1045,15 +1045,15 @@ │ │ │ │ structure(", a string containing the name of the bucket.\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(), Rd_tag = "\\item"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("endpoint", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(", a string containing the URL for the S3 API.\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("publicS3Config()\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/publicS3Config.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/publicS3Config.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ refreshLatest (list) = structure(list(structure(list(structure("Refresh the latest version", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("refreshLatest", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("refreshLatest", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Recompute the latest version of a project's asset.\n", Rd_tag = "TEXT"), │ │ │ │ structure("This is useful on rare occasions where multiple simultaneous uploads cause the latest version to be slightly out of sync.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1076,15 +1076,15 @@ │ │ │ │ structure(" if there are no non-probational versions.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fetchLatest", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to get the latest version without recomputing it.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("if (interactive()) {\n", Rd_tag = "RCODE"), │ │ │ │ structure(" refreshLatest(\"test-R\", \"basic\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/refreshLatest.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/refreshLatest.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ refreshUsage (list) = structure(list(structure(list(structure("Refresh the quota usage", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("refreshUsage", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("refreshUsage", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Recompute the quota usage of a project.\n", Rd_tag = "TEXT"), │ │ │ │ structure("This is useful on rare occasions where multiple simultaneous uploads cause the usage calculations to be out of sync.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1102,15 +1102,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Numeric scalar specifying the total quota usage of this project, in bytes.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fetchUsage", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to get the usage without recomputing it.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("if (interactive()) {\n", Rd_tag = "RCODE"), │ │ │ │ structure(" refreshUsage(\"test-R\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/refreshUsage.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/refreshUsage.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ rejectProbation (list) = structure(list(structure(list(structure("Reject a probational upload", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("rejectProbation", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("rejectProbation", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Pretty much as it says: reject a probational upload of a version of a project's asset.\n", Rd_tag = "TEXT"), │ │ │ │ structure("This removes all files associated with that version.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1154,15 +1154,15 @@ │ │ │ │ structure(" asset=\"probation-reject\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" version=\"v1\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" files=character(0),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" probation=TRUE\n", Rd_tag = "RCODE"), │ │ │ │ structure(" )\n", Rd_tag = "RCODE"), structure(" completeUpload(init) \n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" # Rejecting the probation:\n", Rd_tag = "RCODE"), │ │ │ │ structure(" rejectProbation(\"test-R\", \"probation-reject\", \"v1\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/rejectProbation.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/rejectProbation.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ removeAsset (list) = structure(list(structure(list(structure("Remove an asset", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("removeAsset", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("removeAsset", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Remove an asset of a project from the gypsum backend.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("removeAsset(project, asset, url = restUrl(), token = accessToken())\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1195,15 +1195,15 @@ │ │ │ │ structure(" project=\"test-R\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" asset=\"removal\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" version=\"v1\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" files=character(0),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" probation=TRUE\n", Rd_tag = "RCODE"), │ │ │ │ structure(" )\n", Rd_tag = "RCODE"), structure(" completeUpload(init) \n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" removeAsset(\"test-R\", asset=\"removal\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/removeAsset.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/removeAsset.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ removeProject (list) = structure(list(structure(list(structure("Remove a project", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("removeProject", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("removeProject", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Remove a project from the gypsum backend.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("removeProject(project, url = restUrl(), token = accessToken())\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1228,15 +1228,15 @@ │ │ │ │ structure("removeAsset", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" and ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("removeVersion", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to remove an asset or version.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("if (interactive()) {\n", Rd_tag = "RCODE"), │ │ │ │ structure(" createProject(\"test-R-remove\", owners=\"LTLA\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" removeProject(\"test-R-remove\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/removeProject.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/removeProject.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ removeVersion (list) = structure(list(structure(list(structure("Remove a version of an asset", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("removeVersion", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("removeVersion", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Remove a version of an asset from the gypsum backend.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("removeVersion(project, asset, version, url = restUrl(), token = accessToken())\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1271,15 +1271,15 @@ │ │ │ │ structure(" project=\"test-R\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" asset=\"removal\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" version=\"v1\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" files=character(0),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" probation=TRUE\n", Rd_tag = "RCODE"), │ │ │ │ structure(" )\n", Rd_tag = "RCODE"), structure(" completeUpload(init) \n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" removeVersion(\"test-R\", asset=\"removal\", version=\"v1\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/removeVersion.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/removeVersion.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ resolveLinks (list) = structure(list(structure(list(structure("Resolve links in the cache directory", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("resolveLinks", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("resolveLinks", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Create hard links (or copies, if filesystem links are not supported) for linked-from files to their link destinations.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("resolveLinks(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -1314,15 +1314,15 @@ │ │ │ │ structure(" is returned on successful completion.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("cache <- tempfile()\n", Rd_tag = "RCODE"), │ │ │ │ structure("saveVersion(\"test-R\", \"basic\", \"v3\", relink=FALSE, cache=cache)\n", Rd_tag = "RCODE"), │ │ │ │ structure("list.files(cache, recursive=TRUE, all.files=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("resolveLinks(\"test-R\", \"basic\", \"v3\", cache=cache)\n", Rd_tag = "RCODE"), │ │ │ │ structure("list.files(cache, recursive=TRUE, all.files=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/resolveLinks.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/resolveLinks.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ restUrl (list) = structure(list(structure(list(structure("URL for the REST API", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("restUrl", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("restUrl", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Get or set the URL for the gypsum REST API.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("restUrl(url)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1337,15 +1337,15 @@ │ │ │ │ structure(" is provided, it is used to replace the current setting of the URL,\n", Rd_tag = "TEXT"), │ │ │ │ structure("and the ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("previous", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(" setting of the URL is invisibly returned.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("restUrl()\n", Rd_tag = "RCODE"), │ │ │ │ structure("old <- restUrl(\"https://some-other.rest-api.io\") # replace it.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("restUrl()\n", Rd_tag = "RCODE"), structure("restUrl(old) # setting it back.\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/restUrl.Rd", class = "Rd", meta = list( │ │ │ │ + structure("restUrl()\n", Rd_tag = "RCODE"), structure("restUrl(old) # setting it back.\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/restUrl.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ │ │ @@ -1416,15 +1416,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("saveVersion", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to save all files with the same prefix.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("cacheDirectory", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", for file caching.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("out <- saveFile(\"test-R\", \"basic\", \"v1\", \"blah.txt\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("readLines(out)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/saveFile.Rd", class = "Rd", meta = list( │ │ │ │ + structure("readLines(out)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/saveFile.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ saveVersion (list) = structure(list(structure(list(structure("Save all files for a version of a project asset", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("saveVersion", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("saveVersion", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Download all files associated with a version of an asset of a project from the gypsum bucket.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("saveVersion(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -1474,15 +1474,15 @@ │ │ │ │ structure(list(structure("saveFile", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to save a single file.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("cacheDirectory", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", for file caching.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("out <- saveVersion(\"test-R\", \"basic\", \"v1\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("list.files(out, recursive=TRUE, all.files=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/saveVersion.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/saveVersion.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ searchMetadata (list) = structure(list(structure(list(structure("Search the metadata database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("searchMetadata", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("searchMetadata", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("gypsum.search.clause", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Ops.gypsum.search.clause", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1733,15 +1733,15 @@ │ │ │ │ structure("searchMetadata(path, query, include.metadata=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Throwing in some wildcards.\n", Rd_tag = "RCODE"), │ │ │ │ structure("has.neuro <- gsc(\"Neuro%\", partial=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("searchMetadata(path, has.neuro, include.metadata=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# We can also query other properties.\n", Rd_tag = "RCODE"), │ │ │ │ structure("datasets <- gsc(project=\"scRNAseq\") & gsc(asset=\"l%\", partial=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("searchMetadata(path, datasets, include.metadata=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/searchMetadata.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/searchMetadata.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ setPermissions (list) = structure(list(structure(list(structure("Set project permissions", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("setPermissions", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("setPermissions", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Set the owner and uploader permissions for a project.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("setPermissions(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -1804,15 +1804,15 @@ │ │ │ │ structure(" # Creating a project for demonstration purposes.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" createProject(\"test-R-perms\", owners=\"LTLA\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" # Setting extra permissions on this project.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" setPermissions(\"test-R-perms\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" owners=\"jkanche\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" uploaders=list(list(id=\"lawremi\", until=Sys.time() + 1000))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" )\n", Rd_tag = "RCODE"), structure("}\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/setPermissions.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/setPermissions.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ setQuota (list) = structure(list(structure(list(structure("Set project quota", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("setQuota", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("setQuota", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Set the storage quota for a project.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("setQuota(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -1857,15 +1857,15 @@ │ │ │ │ structure(list(structure("fetchQuota", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to fetch the quota.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("if (interactive()) {\n", Rd_tag = "RCODE"), │ │ │ │ structure(" # Creating a project for demonstration purposes.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" createProject(\"test-R-quota\", owners=\"LTLA\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" # Setting a baseline of 10 GB with 5 GB in growth per year.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" setQuota(\"test-R-quota\", baseline=10^10, growth=5^9, year=2019)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/setQuota.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/setQuota.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ startUpload (list) = structure(list(structure(list(structure("Start an upload", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("startUpload", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("startUpload", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Start an upload of a new version of an asset, or a new asset of a project.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("startUpload(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -2017,15 +2017,15 @@ │ │ │ │ structure(" project=\"test-R\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" asset=\"upload-start-check\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" version=\"v1\", \n", Rd_tag = "RCODE"), │ │ │ │ structure(" files=list.files(tmp, recursive=TRUE),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" directory=tmp\n", Rd_tag = "RCODE"), │ │ │ │ structure(" )\n", Rd_tag = "RCODE"), structure(" print(blob)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" abortUpload(blob) # just cleaning up after we're done.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/startUpload.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/startUpload.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ translateTextQuery (list) = structure(list(structure(list(structure("Translate a plain-text query to a gypsum.search.clause", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("translateTextQuery", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("translateTextQuery", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Translate a plain-text query in user-friendly format to a ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("gypsum.search.clause", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ @@ -2085,15 +2085,15 @@ │ │ │ │ structure("query", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("str(translateTextQuery(\"foo AND bar\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("str(translateTextQuery(\"foo AND bar%\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("str(translateTextQuery(\"(foo AND NOT bar) OR whee\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("str(translateTextQuery(\"blah:foo whee AND stuff: bar blob\"))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/translateTextQuery.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/translateTextQuery.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ unlockProject (list) = structure(list(structure(list(structure("Unlock a project", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("unlockProject", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("unlockProject", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Unlock a project on the gypsum backend.\n", Rd_tag = "TEXT"), │ │ │ │ structure("This is typically caused by a partial upload that was not properly aborted.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2113,15 +2113,15 @@ │ │ │ │ structure(" is invisibly returned if the project was successfully removed.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Aaron Lun\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("abortUpload", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", to correctly abort an upload upon failure.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("if (interactive()) {\n", Rd_tag = "RCODE"), │ │ │ │ structure(" unlockProject(\"test-R\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/unlockProject.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/unlockProject.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ uploadDirectory (list) = structure(list(structure(list(structure("Upload a directory to the gypsum backend", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("uploadDirectory", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("uploadDirectory", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Convenience method to upload a directory to the gypsum backend as a versioned asset of a project.\n", Rd_tag = "TEXT"), │ │ │ │ structure("This requires uploader permissions to the relevant project.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2212,15 +2212,15 @@ │ │ │ │ structure("dir.create(file.path(tmp, \"foo\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("write(file=file.path(tmp, \"foo\", \"bar.txt\"), 1:10)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("if (interactive()) {\n", Rd_tag = "RCODE"), │ │ │ │ structure(" # Uploading a probational version for test purposes.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" uploadDirectory(staging, \"test-R\", \"upload-dir-check\", version, probation=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" # Cleaning up after ourselves.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" gypsum::rejectProbation(\"test-R\", \"upload-dir-check\", version)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/uploadDirectory.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/uploadDirectory.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ uploadFiles (list) = structure(list(structure(list(structure("Upload files for a versioned asset", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("uploadFiles", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("uploadFiles", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Upload files in an initialized upload session for a version of an asset.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("uploadFiles(init, directory = NULL, url = restUrl(), concurrent = 1)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2274,15 +2274,15 @@ │ │ │ │ structure(" files=list.files(tmp, recursive=TRUE),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" directory=tmp\n", Rd_tag = "RCODE"), │ │ │ │ structure(" )\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure(" # Executing the upload for all files.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" uploadFiles(init, directory=tmp)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" # Cleaning up after we're done.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" abortUpload(init) \n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/uploadFiles.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/uploadFiles.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ validateMetadata (list) = structure(list(structure(list(structure("Validate metadata against a JSON schema", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("validateMetadata", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("validateMetadata", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Validate metadata against a JSON schema for a SQLite database.\n", Rd_tag = "TEXT"), │ │ │ │ structure("This ensures that it can be successfully inserted in the database in downstream indexing steps.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2319,10 +2319,10 @@ │ │ │ │ structure(" ),\n", Rd_tag = "RCODE"), structure(" taxonomy_id=list(\"9606\"),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" genome=list(\"GRCm38\"),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" maintainer_name=\"Darth Vader\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" maintainer_email=\"vader@empire.gov\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" bioconductor_version=\"3.10\"\n", Rd_tag = "RCODE"), │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("validateMetadata(metadata)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gypsum/man/validateMetadata.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/validateMetadata.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/gypsum/help/gypsum.rdx │ │ │ ├── gypsum.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,253 +1,253 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$abortUpload │ │ │ │ │ -[1] 276 1781 │ │ │ │ │ +[1] 286 1792 │ │ │ │ │ │ │ │ │ │ $variables$accessToken │ │ │ │ │ -[1] 2334 3499 │ │ │ │ │ +[1] 2364 3512 │ │ │ │ │ │ │ │ │ │ $variables$approveProbation │ │ │ │ │ -[1] 6115 2075 │ │ │ │ │ +[1] 6165 2087 │ │ │ │ │ │ │ │ │ │ $variables$cacheDirectory │ │ │ │ │ -[1] 8470 1492 │ │ │ │ │ +[1] 8541 1504 │ │ │ │ │ │ │ │ │ │ $variables$cloneVersion │ │ │ │ │ -[1] 10240 4436 │ │ │ │ │ +[1] 10332 4447 │ │ │ │ │ │ │ │ │ │ $variables$completeUpload │ │ │ │ │ -[1] 14955 1810 │ │ │ │ │ +[1] 15067 1820 │ │ │ │ │ │ │ │ │ │ $variables$createProject │ │ │ │ │ -[1] 17044 2364 │ │ │ │ │ +[1] 17175 2377 │ │ │ │ │ │ │ │ │ │ $variables$fetchLatest │ │ │ │ │ -[1] 19686 1218 │ │ │ │ │ +[1] 19840 1231 │ │ │ │ │ │ │ │ │ │ $variables$fetchManifest │ │ │ │ │ -[1] 21184 2397 │ │ │ │ │ +[1] 21360 2407 │ │ │ │ │ │ │ │ │ │ $variables$fetchMetadataDatabase │ │ │ │ │ -[1] 23868 1972 │ │ │ │ │ +[1] 24061 1984 │ │ │ │ │ │ │ │ │ │ $variables$fetchMetadataSchema │ │ │ │ │ -[1] 26126 1843 │ │ │ │ │ +[1] 26338 1855 │ │ │ │ │ │ │ │ │ │ $variables$fetchPermissions │ │ │ │ │ -[1] 28250 2133 │ │ │ │ │ +[1] 28484 2147 │ │ │ │ │ │ │ │ │ │ $variables$fetchQuota │ │ │ │ │ -[1] 30661 1379 │ │ │ │ │ +[1] 30918 1393 │ │ │ │ │ │ │ │ │ │ $variables$fetchSummary │ │ │ │ │ -[1] 32319 2215 │ │ │ │ │ +[1] 32599 2227 │ │ │ │ │ │ │ │ │ │ $variables$fetchUsage │ │ │ │ │ -[1] 34812 1185 │ │ │ │ │ +[1] 35112 1197 │ │ │ │ │ │ │ │ │ │ $variables$formatObjectMetadata │ │ │ │ │ -[1] 36283 1261 │ │ │ │ │ +[1] 36602 1275 │ │ │ │ │ │ │ │ │ │ $variables$listAssets │ │ │ │ │ -[1] 37821 1038 │ │ │ │ │ +[1] 38161 1050 │ │ │ │ │ │ │ │ │ │ $variables$listFiles │ │ │ │ │ -[1] 39135 1778 │ │ │ │ │ +[1] 39496 1790 │ │ │ │ │ │ │ │ │ │ $variables$listProjects │ │ │ │ │ -[1] 41191 1003 │ │ │ │ │ +[1] 41573 1018 │ │ │ │ │ │ │ │ │ │ $variables$listVersions │ │ │ │ │ -[1] 42472 1118 │ │ │ │ │ +[1] 42878 1131 │ │ │ │ │ │ │ │ │ │ $variables$prepareDirectoryUpload │ │ │ │ │ -[1] 43877 3476 │ │ │ │ │ +[1] 44304 3488 │ │ │ │ │ │ │ │ │ │ $variables$publicS3Config │ │ │ │ │ -[1] 47634 1870 │ │ │ │ │ +[1] 48082 1881 │ │ │ │ │ │ │ │ │ │ $variables$refreshLatest │ │ │ │ │ -[1] 49784 1535 │ │ │ │ │ +[1] 50252 1546 │ │ │ │ │ │ │ │ │ │ $variables$refreshUsage │ │ │ │ │ -[1] 51598 1397 │ │ │ │ │ +[1] 52086 1409 │ │ │ │ │ │ │ │ │ │ $variables$rejectProbation │ │ │ │ │ -[1] 53275 1962 │ │ │ │ │ +[1] 53784 1975 │ │ │ │ │ │ │ │ │ │ $variables$removeAsset │ │ │ │ │ -[1] 55514 1691 │ │ │ │ │ +[1] 56045 1703 │ │ │ │ │ │ │ │ │ │ $variables$removeProject │ │ │ │ │ -[1] 57484 1498 │ │ │ │ │ +[1] 58037 1511 │ │ │ │ │ │ │ │ │ │ $variables$removeVersion │ │ │ │ │ -[1] 59261 1771 │ │ │ │ │ +[1] 59836 1784 │ │ │ │ │ │ │ │ │ │ $variables$resolveLinks │ │ │ │ │ -[1] 61311 1716 │ │ │ │ │ +[1] 61909 1728 │ │ │ │ │ │ │ │ │ │ $variables$restUrl │ │ │ │ │ -[1] 63302 1145 │ │ │ │ │ +[1] 63921 1157 │ │ │ │ │ │ │ │ │ │ $variables$saveFile │ │ │ │ │ -[1] 64723 2648 │ │ │ │ │ +[1] 65362 2657 │ │ │ │ │ │ │ │ │ │ $variables$saveVersion │ │ │ │ │ -[1] 67648 2232 │ │ │ │ │ +[1] 68305 2244 │ │ │ │ │ │ │ │ │ │ $variables$searchMetadata │ │ │ │ │ -[1] 70160 7794 │ │ │ │ │ +[1] 70838 7806 │ │ │ │ │ │ │ │ │ │ $variables$setPermissions │ │ │ │ │ -[1] 78233 2548 │ │ │ │ │ +[1] 78932 2561 │ │ │ │ │ │ │ │ │ │ $variables$setQuota │ │ │ │ │ -[1] 81057 2070 │ │ │ │ │ +[1] 81777 2090 │ │ │ │ │ │ │ │ │ │ $variables$startUpload │ │ │ │ │ -[1] 83404 5047 │ │ │ │ │ +[1] 84153 5056 │ │ │ │ │ │ │ │ │ │ $variables$translateTextQuery │ │ │ │ │ -[1] 88736 2883 │ │ │ │ │ +[1] 89502 2895 │ │ │ │ │ │ │ │ │ │ $variables$unlockProject │ │ │ │ │ -[1] 91898 1396 │ │ │ │ │ +[1] 92684 1410 │ │ │ │ │ │ │ │ │ │ $variables$uploadDirectory │ │ │ │ │ -[1] 93575 3577 │ │ │ │ │ +[1] 94383 3588 │ │ │ │ │ │ │ │ │ │ $variables$uploadFiles │ │ │ │ │ -[1] 97429 2390 │ │ │ │ │ +[1] 98257 2400 │ │ │ │ │ │ │ │ │ │ $variables$validateMetadata │ │ │ │ │ -[1] 100101 1958 │ │ │ │ │ +[1] 100947 1970 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 276 │ │ │ │ │ +[1] 0 286 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 23581 287 │ │ │ │ │ +[1] 23767 294 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 25840 286 │ │ │ │ │ +[1] 26045 293 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 27969 281 │ │ │ │ │ +[1] 28193 291 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 30383 278 │ │ │ │ │ +[1] 30631 287 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 32040 279 │ │ │ │ │ +[1] 32311 288 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 34534 278 │ │ │ │ │ +[1] 34826 286 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 35997 286 │ │ │ │ │ +[1] 36309 293 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 37544 277 │ │ │ │ │ +[1] 37877 284 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 38859 276 │ │ │ │ │ +[1] 39211 285 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 40913 278 │ │ │ │ │ +[1] 41286 287 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 2057 277 │ │ │ │ │ +[1] 2078 286 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 42194 278 │ │ │ │ │ +[1] 42591 287 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 43590 287 │ │ │ │ │ +[1] 44009 295 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 47353 281 │ │ │ │ │ +[1] 47792 290 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 49504 280 │ │ │ │ │ +[1] 49963 289 │ │ │ │ │ │ │ │ │ │ $references$`env::24` │ │ │ │ │ -[1] 51319 279 │ │ │ │ │ +[1] 51798 288 │ │ │ │ │ │ │ │ │ │ $references$`env::25` │ │ │ │ │ -[1] 52995 280 │ │ │ │ │ +[1] 53495 289 │ │ │ │ │ │ │ │ │ │ $references$`env::26` │ │ │ │ │ -[1] 55237 277 │ │ │ │ │ +[1] 55759 286 │ │ │ │ │ │ │ │ │ │ $references$`env::27` │ │ │ │ │ -[1] 57205 279 │ │ │ │ │ +[1] 57748 289 │ │ │ │ │ │ │ │ │ │ $references$`env::28` │ │ │ │ │ -[1] 58982 279 │ │ │ │ │ +[1] 59548 288 │ │ │ │ │ │ │ │ │ │ $references$`env::29` │ │ │ │ │ -[1] 61032 279 │ │ │ │ │ +[1] 61620 289 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 5833 282 │ │ │ │ │ +[1] 5876 289 │ │ │ │ │ │ │ │ │ │ $references$`env::30` │ │ │ │ │ -[1] 63027 275 │ │ │ │ │ +[1] 63637 284 │ │ │ │ │ │ │ │ │ │ $references$`env::31` │ │ │ │ │ -[1] 64447 276 │ │ │ │ │ +[1] 65078 284 │ │ │ │ │ │ │ │ │ │ $references$`env::32` │ │ │ │ │ -[1] 67371 277 │ │ │ │ │ +[1] 68019 286 │ │ │ │ │ │ │ │ │ │ $references$`env::33` │ │ │ │ │ -[1] 69880 280 │ │ │ │ │ +[1] 70549 289 │ │ │ │ │ │ │ │ │ │ $references$`env::34` │ │ │ │ │ -[1] 77954 279 │ │ │ │ │ +[1] 78644 288 │ │ │ │ │ │ │ │ │ │ $references$`env::35` │ │ │ │ │ -[1] 80781 276 │ │ │ │ │ +[1] 81493 284 │ │ │ │ │ │ │ │ │ │ $references$`env::36` │ │ │ │ │ -[1] 83127 277 │ │ │ │ │ +[1] 83867 286 │ │ │ │ │ │ │ │ │ │ $references$`env::37` │ │ │ │ │ -[1] 88451 285 │ │ │ │ │ +[1] 89209 293 │ │ │ │ │ │ │ │ │ │ $references$`env::38` │ │ │ │ │ -[1] 91619 279 │ │ │ │ │ +[1] 92397 287 │ │ │ │ │ │ │ │ │ │ $references$`env::39` │ │ │ │ │ -[1] 93294 281 │ │ │ │ │ +[1] 94094 289 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 8190 280 │ │ │ │ │ +[1] 8252 289 │ │ │ │ │ │ │ │ │ │ $references$`env::40` │ │ │ │ │ -[1] 97152 277 │ │ │ │ │ +[1] 97971 286 │ │ │ │ │ │ │ │ │ │ $references$`env::41` │ │ │ │ │ -[1] 99819 282 │ │ │ │ │ +[1] 100657 290 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 9962 278 │ │ │ │ │ +[1] 10045 287 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 14676 279 │ │ │ │ │ +[1] 14779 288 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 16765 279 │ │ │ │ │ +[1] 16887 288 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 19408 278 │ │ │ │ │ +[1] 19552 288 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 20904 280 │ │ │ │ │ +[1] 21071 289 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/gypsum/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,43 +1,43 @@ │ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-gypsum/man/abortUpload.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-gypsum/man/accessToken.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-gypsum/man/approveProbation.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-gypsum/man/cacheDirectory.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-gypsum/man/cloneVersion.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-gypsum/man/completeUpload.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-gypsum/man/createProject.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-gypsum/man/fetchLatest.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-gypsum/man/fetchManifest.Rd" │ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-gypsum/man/fetchMetadataDatabase.Rd" │ │ │ │ │ -[11] "/home/moeller/Salsa/r-bioc-gypsum/man/fetchMetadataSchema.Rd" │ │ │ │ │ -[12] "/home/moeller/Salsa/r-bioc-gypsum/man/fetchPermissions.Rd" │ │ │ │ │ -[13] "/home/moeller/Salsa/r-bioc-gypsum/man/fetchQuota.Rd" │ │ │ │ │ -[14] "/home/moeller/Salsa/r-bioc-gypsum/man/fetchSummary.Rd" │ │ │ │ │ -[15] "/home/moeller/Salsa/r-bioc-gypsum/man/fetchUsage.Rd" │ │ │ │ │ -[16] "/home/moeller/Salsa/r-bioc-gypsum/man/formatObjectMetadata.Rd" │ │ │ │ │ -[17] "/home/moeller/Salsa/r-bioc-gypsum/man/listAssets.Rd" │ │ │ │ │ -[18] "/home/moeller/Salsa/r-bioc-gypsum/man/listFiles.Rd" │ │ │ │ │ -[19] "/home/moeller/Salsa/r-bioc-gypsum/man/listProjects.Rd" │ │ │ │ │ -[20] "/home/moeller/Salsa/r-bioc-gypsum/man/listVersions.Rd" │ │ │ │ │ -[21] "/home/moeller/Salsa/r-bioc-gypsum/man/prepareDirectoryUpload.Rd" │ │ │ │ │ -[22] "/home/moeller/Salsa/r-bioc-gypsum/man/publicS3Config.Rd" │ │ │ │ │ -[23] "/home/moeller/Salsa/r-bioc-gypsum/man/refreshLatest.Rd" │ │ │ │ │ -[24] "/home/moeller/Salsa/r-bioc-gypsum/man/refreshUsage.Rd" │ │ │ │ │ -[25] "/home/moeller/Salsa/r-bioc-gypsum/man/rejectProbation.Rd" │ │ │ │ │ -[26] "/home/moeller/Salsa/r-bioc-gypsum/man/removeAsset.Rd" │ │ │ │ │ -[27] "/home/moeller/Salsa/r-bioc-gypsum/man/removeProject.Rd" │ │ │ │ │ -[28] "/home/moeller/Salsa/r-bioc-gypsum/man/removeVersion.Rd" │ │ │ │ │ -[29] "/home/moeller/Salsa/r-bioc-gypsum/man/resolveLinks.Rd" │ │ │ │ │ -[30] "/home/moeller/Salsa/r-bioc-gypsum/man/restUrl.Rd" │ │ │ │ │ -[31] "/home/moeller/Salsa/r-bioc-gypsum/man/saveFile.Rd" │ │ │ │ │ -[32] "/home/moeller/Salsa/r-bioc-gypsum/man/saveVersion.Rd" │ │ │ │ │ -[33] "/home/moeller/Salsa/r-bioc-gypsum/man/searchMetadata.Rd" │ │ │ │ │ -[34] "/home/moeller/Salsa/r-bioc-gypsum/man/setPermissions.Rd" │ │ │ │ │ -[35] "/home/moeller/Salsa/r-bioc-gypsum/man/setQuota.Rd" │ │ │ │ │ -[36] "/home/moeller/Salsa/r-bioc-gypsum/man/startUpload.Rd" │ │ │ │ │ -[37] "/home/moeller/Salsa/r-bioc-gypsum/man/translateTextQuery.Rd" │ │ │ │ │ -[38] "/home/moeller/Salsa/r-bioc-gypsum/man/unlockProject.Rd" │ │ │ │ │ -[39] "/home/moeller/Salsa/r-bioc-gypsum/man/uploadDirectory.Rd" │ │ │ │ │ -[40] "/home/moeller/Salsa/r-bioc-gypsum/man/uploadFiles.Rd" │ │ │ │ │ -[41] "/home/moeller/Salsa/r-bioc-gypsum/man/validateMetadata.Rd" │ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/abortUpload.Rd" │ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/accessToken.Rd" │ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/approveProbation.Rd" │ │ │ │ │ + [4] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/cacheDirectory.Rd" │ │ │ │ │ + [5] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/cloneVersion.Rd" │ │ │ │ │ + [6] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/completeUpload.Rd" │ │ │ │ │ + [7] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/createProject.Rd" │ │ │ │ │ + [8] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchLatest.Rd" │ │ │ │ │ + [9] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchManifest.Rd" │ │ │ │ │ +[10] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchMetadataDatabase.Rd" │ │ │ │ │ +[11] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchMetadataSchema.Rd" │ │ │ │ │ +[12] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchPermissions.Rd" │ │ │ │ │ +[13] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchQuota.Rd" │ │ │ │ │ +[14] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchSummary.Rd" │ │ │ │ │ +[15] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/fetchUsage.Rd" │ │ │ │ │ +[16] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/formatObjectMetadata.Rd" │ │ │ │ │ +[17] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/listAssets.Rd" │ │ │ │ │ +[18] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/listFiles.Rd" │ │ │ │ │ +[19] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/listProjects.Rd" │ │ │ │ │ +[20] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/listVersions.Rd" │ │ │ │ │ +[21] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/prepareDirectoryUpload.Rd" │ │ │ │ │ +[22] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/publicS3Config.Rd" │ │ │ │ │ +[23] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/refreshLatest.Rd" │ │ │ │ │ +[24] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/refreshUsage.Rd" │ │ │ │ │ +[25] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/rejectProbation.Rd" │ │ │ │ │ +[26] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/removeAsset.Rd" │ │ │ │ │ +[27] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/removeProject.Rd" │ │ │ │ │ +[28] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/removeVersion.Rd" │ │ │ │ │ +[29] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/resolveLinks.Rd" │ │ │ │ │ +[30] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/restUrl.Rd" │ │ │ │ │ +[31] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/saveFile.Rd" │ │ │ │ │ +[32] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/saveVersion.Rd" │ │ │ │ │ +[33] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/searchMetadata.Rd" │ │ │ │ │ +[34] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/setPermissions.Rd" │ │ │ │ │ +[35] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/setQuota.Rd" │ │ │ │ │ +[36] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/startUpload.Rd" │ │ │ │ │ +[37] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/translateTextQuery.Rd" │ │ │ │ │ +[38] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/unlockProject.Rd" │ │ │ │ │ +[39] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/uploadDirectory.Rd" │ │ │ │ │ +[40] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/uploadFiles.Rd" │ │ │ │ │ +[41] "/build/reproducible-path/r-bioc-gypsum-1.8.0+ds/man/validateMetadata.Rd" │ │ │ │ │ attr(,"first") │ │ │ │ │ -[1] 39 │ │ │ │ │ +[1] 53