--- /srv/rebuilderd/tmp/rebuilderd3BeVWT/inputs/r-bioc-megadepth_1.22.0+ds-1_all.deb
+++ /srv/rebuilderd/tmp/rebuilderd3BeVWT/out/r-bioc-megadepth_1.22.0+ds-1_all.deb
├── file list
│ @@ -1,3 +1,3 @@
│  -rw-r--r--   0        0        0        4 2026-08-04 11:29:09.000000 debian-binary
│ --rw-r--r--   0        0        0     2088 2026-08-04 11:29:09.000000 control.tar.xz
│ --rw-r--r--   0        0        0    88652 2026-08-04 11:29:09.000000 data.tar.xz
│ +-rw-r--r--   0        0        0     2040 2026-08-04 11:29:09.000000 control.tar.xz
│ +-rw-r--r--   0        0        0    88740 2026-08-04 11:29:09.000000 data.tar.xz
├── control.tar.xz
│ ├── control.tar
│ │ ├── file list
│ │ │ @@ -1,3 +1,3 @@
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-04 11:29:09.000000 ./
│ │ │ --rw-r--r--   0 root         (0) root         (0)     1113 2026-08-04 11:29:09.000000 ./control
│ │ │ +-rw-r--r--   0 root         (0) root         (0)      989 2026-08-04 11:29:09.000000 ./control
│ │ │  -rw-r--r--   0 root         (0) root         (0)     3954 2026-08-04 11:29:09.000000 ./md5sums
│ │ ├── ./control
│ │ │ @@ -1,14 +1,14 @@
│ │ │  Package: r-bioc-megadepth
│ │ │  Version: 1.22.0+ds-1
│ │ │  Architecture: all
│ │ │  Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
│ │ │  Installed-Size: 189
│ │ │  Depends: r-api-4.0, r-api-bioc-3.23, r-cran-xfun, r-cran-fs, r-bioc-genomicranges, r-cran-readr, r-cran-cmdfun, r-cran-dplyr, r-cran-magrittr, megadepth, r-pkg-team-core-architecture
│ │ │ -Suggests: r-cran-covr, r-cran-knitr, r-bioc-biocstyle, r-cran-sessioninfo, r-cran-rmarkdown, r-bioc-rtracklayer, r-bioc-genomeinfodb, r-cran-testthat
│ │ │ +Suggests: r-cran-testthat
│ │ │  Section: gnu-r
│ │ │  Priority: optional
│ │ │  Homepage: https://bioconductor.org/packages/megadepth/
│ │ │  Description: BioCOnductor BigWig and BAM related utilities
│ │ │   This package provides an R interface to Megadepth by Christopher
│ │ │   Wilks available at https://github.com/ChristopherWilks/megadepth. It is
│ │ │   particularly useful for computing the coverage of a set of genomic regions
│ │ ├── ./md5sums
│ │ │ ├── ./md5sums
│ │ │ │┄ Files differ
├── data.tar.xz
│ ├── data.tar
│ │ ├── file list
│ │ │ @@ -15,27 +15,27 @@
│ │ │  -rw-r--r--   0 root         (0) root         (0)      507 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/Meta/nsInfo.rds
│ │ │  -rw-r--r--   0 root         (0) root         (0)     1619 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/Meta/package.rds
│ │ │  -rw-r--r--   0 root         (0) root         (0)      214 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/Meta/vignette.rds
│ │ │  -rw-r--r--   0 root         (0) root         (0)      811 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/NAMESPACE
│ │ │  -rw-r--r--   0 root         (0) root         (0)      730 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/NEWS.md
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/R/
│ │ │  -rw-r--r--   0 root         (0) root         (0)     1058 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/R/megadepth
│ │ │ --rw-r--r--   0 root         (0) root         (0)    17750 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/R/megadepth.rdb
│ │ │ --rw-r--r--   0 root         (0) root         (0)      560 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/R/megadepth.rdx
│ │ │ +-rw-r--r--   0 root         (0) root         (0)    17758 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/R/megadepth.rdb
│ │ │ +-rw-r--r--   0 root         (0) root         (0)      561 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/R/megadepth.rdx
│ │ │  -rw-r--r--   0 root         (0) root         (0)    21621 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/README.md
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/doc/
│ │ │  -rw-r--r--   0 root         (0) root         (0)     1390 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/doc/index.html
│ │ │  -rw-r--r--   0 root         (0) root         (0)     7521 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/doc/megadepth.R
│ │ │  -rw-r--r--   0 root         (0) root         (0)    19484 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/doc/megadepth.Rmd
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/help/
│ │ │  -rw-r--r--   0 root         (0) root         (0)      330 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/help/AnIndex
│ │ │  -rw-r--r--   0 root         (0) root         (0)      193 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/help/aliases.rds
│ │ │ --rw-r--r--   0 root         (0) root         (0)    23829 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/help/megadepth.rdb
│ │ │ --rw-r--r--   0 root         (0) root         (0)      361 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/help/megadepth.rdx
│ │ │ --rw-r--r--   0 root         (0) root         (0)      217 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/help/paths.rds
│ │ │ +-rw-r--r--   0 root         (0) root         (0)    24040 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/help/megadepth.rdb
│ │ │ +-rw-r--r--   0 root         (0) root         (0)      357 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/help/megadepth.rdx
│ │ │ +-rw-r--r--   0 root         (0) root         (0)      234 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/help/paths.rds
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/html/
│ │ │  -rw-r--r--   0 root         (0) root         (0)     2547 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/html/00Index.html
│ │ │  -rw-r--r--   0 root         (0) root         (0)     2133 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/html/R.css
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/tests/
│ │ │  -rw-r--r--   0 root         (0) root         (0)    11787 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/tests/long_reads.bam
│ │ │  -rw-r--r--   0 root         (0) root         (0)     3132 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/tests/test.bam
│ │ │  -rw-r--r--   0 root         (0) root         (0)      968 2026-08-04 11:29:09.000000 ./usr/lib/R/site-library/megadepth/tests/test.bam.all.bw
│ │ ├── ./usr/lib/R/site-library/megadepth/R/megadepth.rdb
│ │ │ ├── Rscript --vanilla - {}
│ │ │ │ @@ -9,15 +9,15 @@
│ │ │ │      "imports" = "    dplyr = c(mutate = "mutate"), dplyr = c(select = "select"), "
│ │ │ │      "imports" = "    dplyr = c(summarise = "summarise"), fs = c(dir_exists = "dir_exists"), "
│ │ │ │      "imports" = "    magrittr = c("%>%" = "%>%"), readr = c(cols = "cols"), readr = c(read_delim = "read_delim"), "
│ │ │ │      "imports" = "    utils = c(download.file = "download.file"), utils = c(file_test = "file_test"), "
│ │ │ │      "imports" = "    xfun = c(is_macos = "is_macos"), xfun = c(is_windows = "is_windows"), "
│ │ │ │      "imports" = "    xfun = c(same_path = "same_path"))"
│ │ │ │      "lazydata" = "<environment>"
│ │ │ │ -    "path" = ""/home/moeller/Salsa/r-bioc-megadepth/debian/r-bioc-megadepth/usr/lib/R/site-library/megadepth""
│ │ │ │ +    "path" = ""/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/debian/r-bioc-megadepth/usr/lib/R/site-library/megadepth""
│ │ │ │      "spec" = "c(name = "megadepth", version = "1.22.0")"
│ │ │ │  }
│ │ │ │  
│ │ │ │  .__S3MethodsTable__. (environment) = 
│ │ │ │  {
│ │ │ │  }
│ │ ├── ./usr/lib/R/site-library/megadepth/R/megadepth.rdx
│ │ │ ├── megadepth.rdx-content
│ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}
│ │ │ │ │ @@ -1,91 +1,91 @@
│ │ │ │ │  $variables
│ │ │ │ │  $variables$.__NAMESPACE__.
│ │ │ │ │ -[1] 884  52
│ │ │ │ │ +[1] 892  52
│ │ │ │ │  
│ │ │ │ │  $variables$.__S3MethodsTable__.
│ │ │ │ │ -[1] 1067   52
│ │ │ │ │ +[1] 1075   52
│ │ │ │ │  
│ │ │ │ │  $variables$.__global__
│ │ │ │ │ -[1] 1119  140
│ │ │ │ │ +[1] 1127  140
│ │ │ │ │  
│ │ │ │ │  $variables$.packageName
│ │ │ │ │ -[1] 1259   54
│ │ │ │ │ +[1] 1267   54
│ │ │ │ │  
│ │ │ │ │  $variables$bam_to_bigwig
│ │ │ │ │ -[1] 1313 1184
│ │ │ │ │ +[1] 1321 1184
│ │ │ │ │  
│ │ │ │ │  $variables$bam_to_junctions
│ │ │ │ │ -[1] 2497  878
│ │ │ │ │ +[1] 2505  878
│ │ │ │ │  
│ │ │ │ │  $variables$bin_paths
│ │ │ │ │ -[1] 3375 1191
│ │ │ │ │ +[1] 3383 1191
│ │ │ │ │  
│ │ │ │ │  $variables$find_exec
│ │ │ │ │ -[1] 4566 1355
│ │ │ │ │ +[1] 4574 1355
│ │ │ │ │  
│ │ │ │ │  $variables$find_megadepth
│ │ │ │ │ -[1] 6080  371
│ │ │ │ │ +[1] 6088  371
│ │ │ │ │  
│ │ │ │ │  $variables$get_coverage
│ │ │ │ │ -[1] 6451  572
│ │ │ │ │ +[1] 6459  572
│ │ │ │ │  
│ │ │ │ │  $variables$install_megadepth
│ │ │ │ │ -[1] 7023 1747
│ │ │ │ │ +[1] 7031 1747
│ │ │ │ │  
│ │ │ │ │  $variables$install_megadepth_bin
│ │ │ │ │ -[1] 8770 1303
│ │ │ │ │ +[1] 8778 1303
│ │ │ │ │  
│ │ │ │ │  $variables$megadepth_cmd
│ │ │ │ │ -[1] 10073   245
│ │ │ │ │ +[1] 10081   245
│ │ │ │ │  
│ │ │ │ │  $variables$megadepth_latest
│ │ │ │ │ -[1] 10318   593
│ │ │ │ │ +[1] 10326   593
│ │ │ │ │  
│ │ │ │ │  $variables$megadepth_shell
│ │ │ │ │ -[1] 10911   455
│ │ │ │ │ +[1] 10919   455
│ │ │ │ │  
│ │ │ │ │  $variables$megadepth_shell2
│ │ │ │ │ -[1] 11366   448
│ │ │ │ │ +[1] 11374   448
│ │ │ │ │  
│ │ │ │ │  $variables$pkg_file
│ │ │ │ │ -[1] 11814   291
│ │ │ │ │ +[1] 11822   291
│ │ │ │ │  
│ │ │ │ │  $variables$prefix_exists
│ │ │ │ │ -[1] 12105   677
│ │ │ │ │ +[1] 12113   677
│ │ │ │ │  
│ │ │ │ │  $variables$prefix_files
│ │ │ │ │ -[1] 12782   747
│ │ │ │ │ +[1] 12790   747
│ │ │ │ │  
│ │ │ │ │  $variables$process_junction_table
│ │ │ │ │ -[1] 13529  1603
│ │ │ │ │ +[1] 13537  1603
│ │ │ │ │  
│ │ │ │ │  $variables$read_coverage
│ │ │ │ │ -[1] 15132   534
│ │ │ │ │ +[1] 15140   534
│ │ │ │ │  
│ │ │ │ │  $variables$read_coverage_table
│ │ │ │ │ -[1] 15666   585
│ │ │ │ │ +[1] 15674   585
│ │ │ │ │  
│ │ │ │ │  $variables$read_junction_table
│ │ │ │ │ -[1] 16251  1499
│ │ │ │ │ +[1] 16259  1499
│ │ │ │ │  
│ │ │ │ │  
│ │ │ │ │  $references
│ │ │ │ │  $references$`env::1`
│ │ │ │ │ -[1] 290 594
│ │ │ │ │ +[1] 290 602
│ │ │ │ │  
│ │ │ │ │  $references$`env::2`
│ │ │ │ │  [1]   0 131
│ │ │ │ │  
│ │ │ │ │  $references$`env::3`
│ │ │ │ │  [1] 131 159
│ │ │ │ │  
│ │ │ │ │  $references$`env::4`
│ │ │ │ │ -[1] 936 131
│ │ │ │ │ +[1] 944 131
│ │ │ │ │  
│ │ │ │ │  $references$`env::5`
│ │ │ │ │ -[1] 5921  159
│ │ │ │ │ +[1] 5929  159
│ │ │ │ │  
│ │ │ │ │  
│ │ │ │ │  $compressed
│ │ │ │ │  [1] TRUE
│ │ ├── ./usr/lib/R/site-library/megadepth/help/megadepth.rdb
│ │ │ ├── Rscript --vanilla - {}
│ │ │ │ @@ -76,15 +76,15 @@
│ │ │ │          structure("    )\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("    ## Compute the coverage\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("    bw_cov <- get_coverage(\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("        example_bw[\"all.bw\"],\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("        op = \"mean\",\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("        annotation = annotation_file\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("    )\n", Rd_tag = "RCODE"), structure("    bw_cov\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-megadepth/man/bam_to_bigwig.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/bam_to_bigwig.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  bam_to_junctions (list) = structure(list(structure(list(structure("Extract junctions from a BAM file", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("bam_to_junctions", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("bam_to_junctions", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Given a BAM file, extract junction information including co-ordinates,\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("strand, anchor length for each junction read. For details on the format of\n", Rd_tag = "TEXT"), 
│ │ │ │ @@ -166,15 +166,15 @@
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("## Find the example BAM file\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("example_bam <- system.file(\"tests\", \"test.bam\",\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("    package = \"megadepth\", mustWork = TRUE\n", Rd_tag = "RCODE"), 
│ │ │ │          structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("## Run bam_to_junctions()\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("example_jxs <- bam_to_junctions(example_bam, overwrite = TRUE)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("## Path to the output file generated by bam_to_junctions()\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("example_jxs\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-megadepth/man/bam_to_junctions.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("example_jxs\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/bam_to_junctions.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  get_coverage (list) = structure(list(structure(list(structure("Compute coverage summarizations across a set of regions", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("get_coverage", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("get_coverage", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("Coverage functions", Rd_tag = "TEXT")), Rd_tag = "\\concept"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Given an input set of annotation regions, compute coverage summarizations\n", Rd_tag = "TEXT"), 
│ │ │ │ @@ -258,15 +258,15 @@
│ │ │ │          structure("        round(sapply(regionCov[c(1, 3:4, 2)], function(x) mean(x$value)), 2),\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("        bw_cov$score,\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("    )\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("    ## If we compute the sum, there's no need to round\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("    testthat::expect_equivalent(\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("        sapply(regionCov[c(1, 3:4, 2)], function(x) sum(x$value)),\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("        get_coverage(example_bw, op = \"sum\", annotation = annotation_file)$score,\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("    )\n", Rd_tag = "RCODE"), structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-megadepth/man/get_coverage.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("    )\n", Rd_tag = "RCODE"), structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/get_coverage.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  hideOutput (NULL) = NULL
│ │ │ │  
│ │ │ │  install_megadepth (list) = structure(list(structure(list(structure("Install Megadepth", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("install_megadepth", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("install_megadepth", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │ @@ -340,15 +340,15 @@
│ │ │ │          structure(list(structure("NULL", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(". The main use is to install Megadepth.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function is based on blogdown::install_hugo() which is available from\n", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(structure("https://github.com/rstudio/blogdown/blob/master/R/install.R", Rd_tag = "VERB")), Rd_tag = "\\url"), 
│ │ │ │          structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("## Install megadepth\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("install_megadepth()\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-megadepth/man/install_megadepth.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("install_megadepth()\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/install_megadepth.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  megadepth_cmd (list) = structure(list(structure(list(structure("Run Megadepth commands", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("megadepth_cmd", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("megadepth_cmd", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("megadepth_shell", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Wrapper functions to run Megadepth commands via\n", Rd_tag = "TEXT"), 
│ │ │ │ @@ -408,15 +408,15 @@
│ │ │ │          structure("megadepth_shell(version = TRUE)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("## megadepth_cmd() requires using directly the command line syntax for\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("## Megadepth\n", Rd_tag = "RCODE"), structure("megadepth_cmd(\"--version\", stdout = TRUE)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("## Compare the help files:\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("# megadepth_shell() captures the standard output and returns a character()\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("# megadepth_cmd() shows the standard output on the console\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("megadepth_shell(\"--help\")\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("megadepth_cmd(\"--help\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-megadepth/man/megadepth_cmd.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("megadepth_cmd(\"--help\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/megadepth_cmd.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  process_junction_table (list) = structure(list(structure(list(structure("Process junctions into a STAR compatible format", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("process_junction_table", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("process_junction_table", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Parses the junctions outputted from ", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(structure("process_junction_table()", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │ @@ -449,15 +449,15 @@
│ │ │ │          structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("## Run bam_to_junctions()\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("example_jxs <- bam_to_junctions(example_bam, overwrite = TRUE)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("## Read the junctions in as a tibble\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("all_jxs <- read_junction_table(example_jxs[[\"all_jxs.tsv\"]])\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("## Process junctions into a STAR-compatible format\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("processed_jxs <- process_junction_table(all_jxs)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE"), structure("processed_jxs\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-megadepth/man/process_junction_table.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE"), structure("processed_jxs\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/process_junction_table.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  read_coverage (list) = structure(list(structure(list(structure("Read a coverage TSV file created by Megadepth", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("read_coverage", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("read_coverage", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("read_coverage_table", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("Coverage functions", Rd_tag = "TEXT")), Rd_tag = "\\concept"), 
│ │ │ │ @@ -523,15 +523,15 @@
│ │ │ │          structure("bw_cov_manual <- read_coverage(tsv_file)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("stopifnot(identical(bw_cov, bw_cov_manual))\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("## To get an RleList object, just like the one you would get\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("## from using rtracklayer::import.bw(as = \"RleList\") directly on the\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("## BigWig file, use:\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("GenomicRanges::coverage(bw_cov_manual)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("## The coverage data can also be read as a `tibble::tibble()`\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("read_coverage_table(tsv_file)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-megadepth/man/read_coverage.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("read_coverage_table(tsv_file)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/read_coverage.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  read_junction_table (list) = structure(list(structure(list(structure("Read a junction TSV file created by Megadepth as a table", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("read_junction_table", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("read_junction_table", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Read an ", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(structure("*all_jxs.tsv", Rd_tag = "VERB")), Rd_tag = "\\verb"), 
│ │ │ │ @@ -568,15 +568,15 @@
│ │ │ │          structure("example_bam <- system.file(\"tests\", \"test.bam\",\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("    package = \"megadepth\", mustWork = TRUE\n", Rd_tag = "RCODE"), 
│ │ │ │          structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("## Run bam_to_junctions()\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("example_jxs <- bam_to_junctions(example_bam, overwrite = TRUE)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("## Read the junctions in as a tibble\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("all_jxs <- read_junction_table(example_jxs[[\"all_jxs.tsv\"]])\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE"), structure("all_jxs\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-megadepth/man/read_junction_table.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE"), structure("all_jxs\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/read_junction_table.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) {
│ │ ├── ./usr/lib/R/site-library/megadepth/help/megadepth.rdx
│ │ │ ├── megadepth.rdx-content
│ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}
│ │ │ │ │ @@ -1,55 +1,55 @@
│ │ │ │ │  $variables
│ │ │ │ │  $variables$bam_to_bigwig
│ │ │ │ │ -[1]  285 2972
│ │ │ │ │ +[1]  298 2984
│ │ │ │ │  
│ │ │ │ │  $variables$bam_to_junctions
│ │ │ │ │ -[1] 3544 2892
│ │ │ │ │ +[1] 3582 2904
│ │ │ │ │  
│ │ │ │ │  $variables$get_coverage
│ │ │ │ │ -[1] 6719 3320
│ │ │ │ │ +[1] 6783 3334
│ │ │ │ │  
│ │ │ │ │  $variables$install_megadepth
│ │ │ │ │ -[1] 10322  3199
│ │ │ │ │ +[1] 10413  3213
│ │ │ │ │  
│ │ │ │ │  $variables$megadepth_cmd
│ │ │ │ │ -[1] 13800  2535
│ │ │ │ │ +[1] 13919  2550
│ │ │ │ │  
│ │ │ │ │  $variables$process_junction_table
│ │ │ │ │ -[1] 16626  1879
│ │ │ │ │ +[1] 16774  1890
│ │ │ │ │  
│ │ │ │ │  $variables$read_coverage
│ │ │ │ │ -[1] 18789  2824
│ │ │ │ │ +[1] 18962  2836
│ │ │ │ │  
│ │ │ │ │  $variables$read_junction_table
│ │ │ │ │ -[1] 21902  1927
│ │ │ │ │ +[1] 22101  1939
│ │ │ │ │  
│ │ │ │ │  
│ │ │ │ │  $references
│ │ │ │ │  $references$`env::1`
│ │ │ │ │ -[1]   0 285
│ │ │ │ │ +[1]   0 298
│ │ │ │ │  
│ │ │ │ │  $references$`env::2`
│ │ │ │ │ -[1] 3257  287
│ │ │ │ │ +[1] 3282  300
│ │ │ │ │  
│ │ │ │ │  $references$`env::3`
│ │ │ │ │ -[1] 6436  283
│ │ │ │ │ +[1] 6486  297
│ │ │ │ │  
│ │ │ │ │  $references$`env::4`
│ │ │ │ │ -[1] 10039   283
│ │ │ │ │ +[1] 10117   296
│ │ │ │ │  
│ │ │ │ │  $references$`env::5`
│ │ │ │ │ -[1] 13521   279
│ │ │ │ │ +[1] 13626   293
│ │ │ │ │  
│ │ │ │ │  $references$`env::6`
│ │ │ │ │ -[1] 16335   291
│ │ │ │ │ +[1] 16469   305
│ │ │ │ │  
│ │ │ │ │  $references$`env::7`
│ │ │ │ │ -[1] 18505   284
│ │ │ │ │ +[1] 18664   298
│ │ │ │ │  
│ │ │ │ │  $references$`env::8`
│ │ │ │ │ -[1] 21613   289
│ │ │ │ │ +[1] 21798   303
│ │ │ │ │  
│ │ │ │ │  
│ │ │ │ │  $compressed
│ │ │ │ │  [1] TRUE
│ │ ├── ./usr/lib/R/site-library/megadepth/help/paths.rds
│ │ │ ├── paths.rds-content
│ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}
│ │ │ │ │ @@ -1,10 +1,10 @@
│ │ │ │ │ -[1] "/home/moeller/Salsa/r-bioc-megadepth/man/bam_to_bigwig.Rd"         
│ │ │ │ │ -[2] "/home/moeller/Salsa/r-bioc-megadepth/man/bam_to_junctions.Rd"      
│ │ │ │ │ -[3] "/home/moeller/Salsa/r-bioc-megadepth/man/get_coverage.Rd"          
│ │ │ │ │ -[4] "/home/moeller/Salsa/r-bioc-megadepth/man/install_megadepth.Rd"     
│ │ │ │ │ -[5] "/home/moeller/Salsa/r-bioc-megadepth/man/megadepth_cmd.Rd"         
│ │ │ │ │ -[6] "/home/moeller/Salsa/r-bioc-megadepth/man/process_junction_table.Rd"
│ │ │ │ │ -[7] "/home/moeller/Salsa/r-bioc-megadepth/man/read_coverage.Rd"         
│ │ │ │ │ -[8] "/home/moeller/Salsa/r-bioc-megadepth/man/read_junction_table.Rd"   
│ │ │ │ │ +[1] "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/bam_to_bigwig.Rd"         
│ │ │ │ │ +[2] "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/bam_to_junctions.Rd"      
│ │ │ │ │ +[3] "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/get_coverage.Rd"          
│ │ │ │ │ +[4] "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/install_megadepth.Rd"     
│ │ │ │ │ +[5] "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/megadepth_cmd.Rd"         
│ │ │ │ │ +[6] "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/process_junction_table.Rd"
│ │ │ │ │ +[7] "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/read_coverage.Rd"         
│ │ │ │ │ +[8] "/build/reproducible-path/r-bioc-megadepth-1.22.0+ds/man/read_junction_table.Rd"   
│ │ │ │ │  attr(,"first")
│ │ │ │ │ -[1] 42
│ │ │ │ │ +[1] 57