--- /srv/rebuilderd/tmp/rebuilderdS664Xg/inputs/r-bioc-goseq_1.64.0-1_all.deb
+++ /srv/rebuilderd/tmp/rebuilderdS664Xg/out/r-bioc-goseq_1.64.0-1_all.deb
├── file list
│ @@ -1,3 +1,3 @@
│  -rw-r--r--   0        0        0        4 2026-08-13 11:48:32.000000 debian-binary
│ --rw-r--r--   0        0        0     1608 2026-08-13 11:48:32.000000 control.tar.xz
│ --rw-r--r--   0        0        0   465468 2026-08-13 11:48:32.000000 data.tar.xz
│ +-rw-r--r--   0        0        0     1588 2026-08-13 11:48:32.000000 control.tar.xz
│ +-rw-r--r--   0        0        0   465204 2026-08-13 11:48:32.000000 data.tar.xz
├── control.tar.xz
│ ├── control.tar
│ │ ├── file list
│ │ │ @@ -1,3 +1,3 @@
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-13 11:48:32.000000 ./
│ │ │ --rw-r--r--   0 root         (0) root         (0)      771 2026-08-13 11:48:32.000000 ./control
│ │ │ +-rw-r--r--   0 root         (0) root         (0)      727 2026-08-13 11:48:32.000000 ./control
│ │ │  -rw-r--r--   0 root         (0) root         (0)     2374 2026-08-13 11:48:32.000000 ./md5sums
│ │ ├── ./control
│ │ │ @@ -1,14 +1,13 @@
│ │ │  Package: r-bioc-goseq
│ │ │  Version: 1.64.0-1
│ │ │  Architecture: all
│ │ │  Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
│ │ │  Installed-Size: 1776
│ │ │  Depends: r-api-4.0, r-api-bioc-3.23, r-cran-biasedurn, r-bioc-genelendatabase (>= 1.9.2), r-cran-mgcv, r-bioc-annotationdbi, r-bioc-go.db, r-bioc-biocgenerics, r-bioc-rtracklayer, r-bioc-genomicfeatures, r-bioc-seqinfo, r-pkg-team-core-architecture
│ │ │ -Suggests: r-bioc-edger, r-bioc-org.hs.eg.db
│ │ │  Section: gnu-r
│ │ │  Priority: optional
│ │ │  Homepage: https://bioconductor.org/packages/goseq/
│ │ │  Description: GNU R gene ontology analyser for RNA-seq and other length biased data
│ │ │   This GNU R package provides functions to detect Gene Ontology and/or
│ │ │   other user defined categories which are over/under represented in
│ │ │   RNA-seq data.
│ │ ├── ./md5sums
│ │ │ ├── ./md5sums
│ │ │ │┄ Files differ
├── data.tar.xz
│ ├── data.tar
│ │ ├── file list
│ │ │ @@ -16,31 +16,31 @@
│ │ │  -rw-r--r--   0 root         (0) root         (0)      615 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/Meta/nsInfo.rds
│ │ │  -rw-r--r--   0 root         (0) root         (0)     1485 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/Meta/package.rds
│ │ │  -rw-r--r--   0 root         (0) root         (0)      204 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/Meta/vignette.rds
│ │ │  -rw-r--r--   0 root         (0) root         (0)     1101 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/NAMESPACE
│ │ │  -rw-r--r--   0 root         (0) root         (0)      245 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/NEWS.md
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/R/
│ │ │  -rw-r--r--   0 root         (0) root         (0)     1058 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/R/goseq
│ │ │ --rw-r--r--   0 root         (0) root         (0)    35509 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/R/goseq.rdb
│ │ │ +-rw-r--r--   0 root         (0) root         (0)    35517 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/R/goseq.rdb
│ │ │  -rw-r--r--   0 root         (0) root         (0)      488 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/R/goseq.rdx
│ │ │  -rw-r--r--   0 root         (0) root         (0)      845 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/README.md
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/data/
│ │ │  -rw-r--r--   0 root         (0) root         (0)    85797 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/data/genes.RData
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/doc/
│ │ │  -rw-r--r--   0 root         (0) root         (0)     8225 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/doc/goseq.R
│ │ │  -rw-r--r--   0 root         (0) root         (0)    29609 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/doc/goseq.Rnw
│ │ │  -rw-r--r--   0 root         (0) root         (0)     1566 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/doc/index.html
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/extdata/
│ │ │  -rw-r--r--   0 root         (0) root         (0)  1572957 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/extdata/Li_sum.txt
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/help/
│ │ │  -rw-r--r--   0 root         (0) root         (0)      194 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/help/AnIndex
│ │ │  -rw-r--r--   0 root         (0) root         (0)      169 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/help/aliases.rds
│ │ │ --rw-r--r--   0 root         (0) root         (0)    30971 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/help/goseq.rdb
│ │ │ --rw-r--r--   0 root         (0) root         (0)      373 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/help/goseq.rdx
│ │ │ --rw-r--r--   0 root         (0) root         (0)      205 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/help/paths.rds
│ │ │ +-rw-r--r--   0 root         (0) root         (0)    31176 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/help/goseq.rdb
│ │ │ +-rw-r--r--   0 root         (0) root         (0)      377 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/help/goseq.rdx
│ │ │ +-rw-r--r--   0 root         (0) root         (0)      218 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/help/paths.rds
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/html/
│ │ │  -rw-r--r--   0 root         (0) root         (0)     2222 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/html/00Index.html
│ │ │  -rw-r--r--   0 root         (0) root         (0)     2133 2026-08-13 11:48:32.000000 ./usr/lib/R/site-library/goseq/html/R.css
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-13 11:48:32.000000 ./usr/share/
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-13 11:48:32.000000 ./usr/share/doc/
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-13 11:48:32.000000 ./usr/share/doc/r-bioc-goseq/
│ │ │  -rw-r--r--   0 root         (0) root         (0)      974 2026-08-13 11:48:32.000000 ./usr/share/doc/r-bioc-goseq/changelog.Debian.gz
│ │ ├── ./usr/lib/R/site-library/goseq/R/goseq.rdb
│ │ │ ├── Rscript --vanilla - {}
│ │ │ │ @@ -35,15 +35,15 @@
│ │ │ │      "imports" = "    rtracklayer = c(getTable = "getTable"), rtracklayer = c(ucscGenomes = "ucscGenomes"), "
│ │ │ │      "imports" = "    rtracklayer = c(ucscTableQuery = "ucscTableQuery"), stats = c(approx = "approx"), "
│ │ │ │      "imports" = "    stats = c(binomial = "binomial"), stats = c(dhyper = "dhyper"), "
│ │ │ │      "imports" = "    stats = c(median = "median"), stats = c(phyper = "phyper"), "
│ │ │ │      "imports" = "    stats = c(runif = "runif"), utils = c(data = "data"), utils = c(installed.packages = "installed.packages"), "
│ │ │ │      "imports" = "    utils = c(tail = "tail"))"
│ │ │ │      "lazydata" = "<environment>"
│ │ │ │ -    "path" = ""/home/moeller/Salsa/r-bioc-goseq/debian/r-bioc-goseq/usr/lib/R/site-library/goseq""
│ │ │ │ +    "path" = ""/build/reproducible-path/r-bioc-goseq-1.64.0/debian/r-bioc-goseq/usr/lib/R/site-library/goseq""
│ │ │ │      "spec" = "c(name = "goseq", version = "1.64.0")"
│ │ │ │  }
│ │ │ │  
│ │ │ │  .__S3MethodsTable__. (environment) = 
│ │ │ │  {
│ │ │ │  }
│ │ ├── ./usr/lib/R/site-library/goseq/R/goseq.rdx
│ │ │ ├── goseq.rdx-content
│ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}
│ │ │ │ │ @@ -8,63 +8,63 @@
│ │ │ │ │  $variables$.ORG_PACKAGES
│ │ │ │ │  [1] 279 290
│ │ │ │ │  
│ │ │ │ │  $variables$.TXDB_ORGS
│ │ │ │ │  [1] 569  96
│ │ │ │ │  
│ │ │ │ │  $variables$.__NAMESPACE__.
│ │ │ │ │ -[1] 1777   52
│ │ │ │ │ +[1] 1785   52
│ │ │ │ │  
│ │ │ │ │  $variables$.__S3MethodsTable__.
│ │ │ │ │ -[1] 1960   52
│ │ │ │ │ +[1] 1968   52
│ │ │ │ │  
│ │ │ │ │  $variables$.onAttach
│ │ │ │ │ -[1] 2012  542
│ │ │ │ │ +[1] 2020  542
│ │ │ │ │  
│ │ │ │ │  $variables$.packageName
│ │ │ │ │ -[1] 2554   49
│ │ │ │ │ +[1] 2562   49
│ │ │ │ │  
│ │ │ │ │  $variables$getgo
│ │ │ │ │ -[1] 2603 4065
│ │ │ │ │ +[1] 2611 4065
│ │ │ │ │  
│ │ │ │ │  $variables$getlength
│ │ │ │ │ -[1] 6668 7440
│ │ │ │ │ +[1] 6676 7440
│ │ │ │ │  
│ │ │ │ │  $variables$goseq
│ │ │ │ │ -[1] 14108 10163
│ │ │ │ │ +[1] 14116 10163
│ │ │ │ │  
│ │ │ │ │  $variables$makespline
│ │ │ │ │ -[1] 24271  3461
│ │ │ │ │ +[1] 24279  3461
│ │ │ │ │  
│ │ │ │ │  $variables$nullp
│ │ │ │ │ -[1] 27732  1309
│ │ │ │ │ +[1] 27740  1309
│ │ │ │ │  
│ │ │ │ │  $variables$plotPWF
│ │ │ │ │ -[1] 29041  3060
│ │ │ │ │ +[1] 29049  3060
│ │ │ │ │  
│ │ │ │ │  $variables$pp
│ │ │ │ │ -[1] 32101   569
│ │ │ │ │ +[1] 32109   569
│ │ │ │ │  
│ │ │ │ │  $variables$reversemapping
│ │ │ │ │ -[1] 32670   568
│ │ │ │ │ +[1] 32678   568
│ │ │ │ │  
│ │ │ │ │  $variables$supportedOrganisms
│ │ │ │ │ -[1] 33238  2271
│ │ │ │ │ +[1] 33246  2271
│ │ │ │ │  
│ │ │ │ │  
│ │ │ │ │  $references
│ │ │ │ │  $references$`env::1`
│ │ │ │ │ -[1] 953 824
│ │ │ │ │ +[1] 953 832
│ │ │ │ │  
│ │ │ │ │  $references$`env::2`
│ │ │ │ │  [1] 665 131
│ │ │ │ │  
│ │ │ │ │  $references$`env::3`
│ │ │ │ │  [1] 796 157
│ │ │ │ │  
│ │ │ │ │  $references$`env::4`
│ │ │ │ │ -[1] 1829  131
│ │ │ │ │ +[1] 1837  131
│ │ │ │ │  
│ │ │ │ │  
│ │ │ │ │  $compressed
│ │ │ │ │  [1] TRUE
│ │ ├── ./usr/lib/R/site-library/goseq/help/goseq.rdb
│ │ │ ├── Rscript --vanilla - {}
│ │ │ │ @@ -21,15 +21,15 @@
│ │ │ │              structure("Determination of tag density required for digital\n", Rd_tag = "TEXT"), 
│ │ │ │              structure("transcriptome analysis: application to an androgen-sensitive prostate cancer\n", Rd_tag = "TEXT"), 
│ │ │ │              structure("model", Rd_tag = "TEXT")), Rd_tag = "\\emph"), 
│ │ │ │          structure(" Proceedings of the National Academy of Sciences of the United States\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("of America Date: Dec 23 Vol: 105 Issue: 51 Pages: 20179-84\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("data(genes)\n", Rd_tag = "RCODE"), structure("head(genes)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-goseq/man/genes.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-goseq-1.64.0/man/genes.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  getgo (list) = structure(list(structure(list(structure("Fetch GO categories", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("getgo", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("getgo", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Obtains all gene ontology (GO) categories associated with a set of genes\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("using the relevant organism package.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -100,15 +100,15 @@
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("genes <- c(\"ENSG00000124208\", \n", Rd_tag = "RCODE"), 
│ │ │ │          structure("           \"ENSG00000182463\", \n", Rd_tag = "RCODE"), 
│ │ │ │          structure("           \"ENSG00000124201\", \n", Rd_tag = "RCODE"), 
│ │ │ │          structure("           \"ENSG00000124205\", \n", Rd_tag = "RCODE"), 
│ │ │ │          structure("           \"ENSG00000124207\")\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("getgo(genes,'hg19','ensGene')\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-goseq/man/getgo.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-goseq-1.64.0/man/getgo.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  getlength (list) = structure(list(structure(list(structure("Retrieves Gene length data", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("getlength", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("getlength", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Gets the length of each gene in a vector.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("getlength(genes, genome, id)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │ @@ -170,15 +170,15 @@
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("genes <- c(\"ENSG00000124208\", \n", Rd_tag = "RCODE"), 
│ │ │ │          structure("           \"ENSG00000182463\", \n", Rd_tag = "RCODE"), 
│ │ │ │          structure("           \"ENSG00000124201\", \n", Rd_tag = "RCODE"), 
│ │ │ │          structure("           \"ENSG00000124205\", \n", Rd_tag = "RCODE"), 
│ │ │ │          structure("           \"ENSG00000124207\")\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("getlength(genes,'hg19','ensGene')\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-goseq/man/getlength.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-goseq-1.64.0/man/getlength.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  goseq (list) = structure(list(structure(list(structure("goseq Gene Ontology analyser", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("goseq", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("goseq", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Does selection-unbiased testing for category enrichment amongst\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("differentially expressed (DE) genes for RNA-seq data.  By default, tests\n", Rd_tag = "TEXT"), 
│ │ │ │ @@ -356,15 +356,15 @@
│ │ │ │              structure("getgo", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure(", ", Rd_tag = "TEXT"), structure(list(structure(list(
│ │ │ │              structure("getlength", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("data(genes)\n", Rd_tag = "RCODE"), structure("pwf <- nullp(genes,'hg19','ensGene')\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("pvals <- goseq(pwf,'hg19','ensGene')\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("head(pvals)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-goseq/man/goseq.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("head(pvals)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-goseq-1.64.0/man/goseq.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  goseq-pkg (list) = structure(list(structure(list(structure("goseq", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("goseq-pkg", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("goseq-package", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("goseq-pkg", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), 
│ │ │ │ @@ -391,15 +391,15 @@
│ │ │ │          structure(list(structure("\n", Rd_tag = "TEXT"), structure("  ", Rd_tag = "TEXT"), 
│ │ │ │              structure(list(), Rd_tag = "\\item"), structure(" ", Rd_tag = "TEXT"), 
│ │ │ │              structure(list(structure("https://github.com/federicomarini/goseq", Rd_tag = "VERB")), Rd_tag = "\\url"), 
│ │ │ │              structure("\n", Rd_tag = "TEXT"), structure("  ", Rd_tag = "TEXT"), 
│ │ │ │              structure(list(), Rd_tag = "\\item"), structure(" Report bugs at ", Rd_tag = "TEXT"), 
│ │ │ │              structure(list(structure("https://github.com/federicomarini/goseq/issues", Rd_tag = "VERB")), Rd_tag = "\\url"), 
│ │ │ │              structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), 
│ │ │ │ -        structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-goseq/man/goseq-pkg.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-goseq-1.64.0/man/goseq-pkg.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "package", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  hideOutput (NULL) = NULL
│ │ │ │  
│ │ │ │  makespline (list) = structure(list(structure(list(structure("Monotonic Spline", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("makespline", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("makespline", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │ @@ -455,15 +455,15 @@
│ │ │ │          structure(".  In particular this function is a\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("modification of an example given in the man page for ", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(structure("pcls", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("y <- c( rbinom(50,p=0.4,size=1), rbinom(50,p=0.6,size=1) )\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("x <- 1:100\n", Rd_tag = "RCODE"), structure("plot(x,y)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("p <- makespline(x,y)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("lines(x,p)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-goseq/man/makespline.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("lines(x,p)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-goseq-1.64.0/man/makespline.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  nullp (list) = structure(list(structure(list(structure("Probability Weighting Function", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("nullp", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("nullp", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculates a Probability Weighting Function for a set of genes based on a\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("given set of biased data (usually gene length) and each genes status as\n", Rd_tag = "TEXT"), 
│ │ │ │ @@ -560,15 +560,15 @@
│ │ │ │          structure(",\n", Rd_tag = "TEXT"), structure(list(structure(list(
│ │ │ │              structure("goseq", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure(", ", Rd_tag = "TEXT"), structure(list(structure(list(
│ │ │ │              structure("getlength", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(genes)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("pwf <- nullp(genes, 'hg19', 'ensGene')\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-goseq/man/nullp.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-goseq-1.64.0/man/nullp.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  plotPWF (list) = structure(list(structure(list(structure("Plot the Probability Weighting Function", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("plotPWF", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("plotPWF", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plots the Probability Weighting Function created by ", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(structure(list(structure("nullp", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │ @@ -633,15 +633,15 @@
│ │ │ │          structure("\n", Rd_tag = "TEXT"), structure("Genome Biology Date: Feb 2010 Vol: 11 Issue: 2 Pages: R14\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure(list(
│ │ │ │          structure(list(structure("nullp", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(genes)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("pwf <- nullp(genes, 'hg19', 'ensGene',plot.fit=FALSE)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("plotPWF(pwf,binsize=200)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-goseq/man/plotPWF.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-goseq-1.64.0/man/plotPWF.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  pp (list) = structure(list(structure(list(structure("Prints progress through a loop", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("pp", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("pp", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Prints progress through a loop\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("pp(total, count, i = i)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │ @@ -650,15 +650,15 @@
│ │ │ │          structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(list(structure("count", Rd_tag = "TEXT")), 
│ │ │ │              list(structure("current iteration", Rd_tag = "TEXT"))), Rd_tag = "\\item"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(list(structure("i", Rd_tag = "TEXT")), 
│ │ │ │              list(structure("index of the loop", Rd_tag = "TEXT"))), Rd_tag = "\\item"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), 
│ │ │ │ -    structure(list(structure("\n", Rd_tag = "TEXT"), structure("message indicating the progress\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-goseq/man/pp.Rd", class = "Rd", meta = list(
│ │ │ │ +    structure(list(structure("\n", Rd_tag = "TEXT"), structure("message indicating the progress\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-goseq-1.64.0/man/pp.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) {
│ │ │ │ @@ -694,10 +694,10 @@
│ │ │ │          structure(") existing for the\n", Rd_tag = "TEXT"), structure("organism. In general, if either the lengths or GO terms are not supported,\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("the user must enter this information manually.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("A data.frame containing supported genomes and gene ids\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Nadia Davidson ", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(structure("nadia.davidson@mcri.edu.au", Rd_tag = "TEXT")), Rd_tag = "\\email"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("supportedOrganisms()\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-goseq/man/supportedOrganisms.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-goseq-1.64.0/man/supportedOrganisms.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ ├── ./usr/lib/R/site-library/goseq/help/goseq.rdx
│ │ │ ├── goseq.rdx-content
│ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}
│ │ │ │ │ @@ -1,67 +1,67 @@
│ │ │ │ │  $variables
│ │ │ │ │  $variables$genes
│ │ │ │ │ -[1]  271 1591
│ │ │ │ │ +[1]  283 1601
│ │ │ │ │  
│ │ │ │ │  $variables$getgo
│ │ │ │ │ -[1] 2135 3040
│ │ │ │ │ +[1] 2168 3050
│ │ │ │ │  
│ │ │ │ │  $variables$getlength
│ │ │ │ │ -[1] 5453 2863
│ │ │ │ │ +[1] 5506 2873
│ │ │ │ │  
│ │ │ │ │  $variables$`goseq-pkg`
│ │ │ │ │ -[1] 8592 1485
│ │ │ │ │ +[1] 8665 1498
│ │ │ │ │  
│ │ │ │ │  $variables$goseq
│ │ │ │ │ -[1] 10348  6957
│ │ │ │ │ +[1] 10445  6966
│ │ │ │ │  
│ │ │ │ │  $variables$makespline
│ │ │ │ │ -[1] 17584  2470
│ │ │ │ │ +[1] 17699  2479
│ │ │ │ │  
│ │ │ │ │  $variables$nullp
│ │ │ │ │ -[1] 20328  4128
│ │ │ │ │ +[1] 20462  4139
│ │ │ │ │  
│ │ │ │ │  $variables$plotPWF
│ │ │ │ │ -[1] 24731  3070
│ │ │ │ │ +[1] 24888  3079
│ │ │ │ │  
│ │ │ │ │  $variables$pp
│ │ │ │ │ -[1] 28073   853
│ │ │ │ │ +[1] 28248   865
│ │ │ │ │  
│ │ │ │ │  $variables$supportedOrganisms
│ │ │ │ │ -[1] 29211  1760
│ │ │ │ │ +[1] 29406  1770
│ │ │ │ │  
│ │ │ │ │  
│ │ │ │ │  $references
│ │ │ │ │  $references$`env::1`
│ │ │ │ │ -[1]   0 271
│ │ │ │ │ +[1]   0 283
│ │ │ │ │  
│ │ │ │ │  $references$`env::10`
│ │ │ │ │ -[1] 28926   285
│ │ │ │ │ +[1] 29113   293
│ │ │ │ │  
│ │ │ │ │  $references$`env::2`
│ │ │ │ │ -[1] 1862  273
│ │ │ │ │ +[1] 1884  284
│ │ │ │ │  
│ │ │ │ │  $references$`env::3`
│ │ │ │ │ -[1] 5175  278
│ │ │ │ │ +[1] 5218  288
│ │ │ │ │  
│ │ │ │ │  $references$`env::4`
│ │ │ │ │ -[1] 8316  276
│ │ │ │ │ +[1] 8379  286
│ │ │ │ │  
│ │ │ │ │  $references$`env::5`
│ │ │ │ │ -[1] 10077   271
│ │ │ │ │ +[1] 10163   282
│ │ │ │ │  
│ │ │ │ │  $references$`env::6`
│ │ │ │ │ -[1] 17305   279
│ │ │ │ │ +[1] 17411   288
│ │ │ │ │  
│ │ │ │ │  $references$`env::7`
│ │ │ │ │ -[1] 20054   274
│ │ │ │ │ +[1] 20178   284
│ │ │ │ │  
│ │ │ │ │  $references$`env::8`
│ │ │ │ │ -[1] 24456   275
│ │ │ │ │ +[1] 24601   287
│ │ │ │ │  
│ │ │ │ │  $references$`env::9`
│ │ │ │ │ -[1] 27801   272
│ │ │ │ │ +[1] 27967   281
│ │ │ │ │  
│ │ │ │ │  
│ │ │ │ │  $compressed
│ │ │ │ │  [1] TRUE
│ │ ├── ./usr/lib/R/site-library/goseq/help/paths.rds
│ │ │ ├── paths.rds-content
│ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}
│ │ │ │ │ @@ -1,12 +1,12 @@
│ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-goseq/man/genes.Rd"             
│ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-goseq/man/getgo.Rd"             
│ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-goseq/man/getlength.Rd"         
│ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-goseq/man/goseq-pkg.Rd"         
│ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-goseq/man/goseq.Rd"             
│ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-goseq/man/makespline.Rd"        
│ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-goseq/man/nullp.Rd"             
│ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-goseq/man/plotPWF.Rd"           
│ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-goseq/man/pp.Rd"                
│ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-goseq/man/supportedOrganisms.Rd"
│ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-goseq-1.64.0/man/genes.Rd"             
│ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-goseq-1.64.0/man/getgo.Rd"             
│ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-goseq-1.64.0/man/getlength.Rd"         
│ │ │ │ │ + [4] "/build/reproducible-path/r-bioc-goseq-1.64.0/man/goseq-pkg.Rd"         
│ │ │ │ │ + [5] "/build/reproducible-path/r-bioc-goseq-1.64.0/man/goseq.Rd"             
│ │ │ │ │ + [6] "/build/reproducible-path/r-bioc-goseq-1.64.0/man/makespline.Rd"        
│ │ │ │ │ + [7] "/build/reproducible-path/r-bioc-goseq-1.64.0/man/nullp.Rd"             
│ │ │ │ │ + [8] "/build/reproducible-path/r-bioc-goseq-1.64.0/man/plotPWF.Rd"           
│ │ │ │ │ + [9] "/build/reproducible-path/r-bioc-goseq-1.64.0/man/pp.Rd"                
│ │ │ │ │ +[10] "/build/reproducible-path/r-bioc-goseq-1.64.0/man/supportedOrganisms.Rd"
│ │ │ │ │  attr(,"first")
│ │ │ │ │ -[1] 38
│ │ │ │ │ +[1] 50