--- /srv/rebuilderd/tmp/rebuilderdqyRvFj/inputs/r-bioc-biocviews_1.80.0+ds-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdqyRvFj/out/r-bioc-biocviews_1.80.0+ds-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-07 00:06:39.000000 debian-binary │ --rw-r--r-- 0 0 0 2064 2026-08-07 00:06:39.000000 control.tar.xz │ --rw-r--r-- 0 0 0 671512 2026-08-07 00:06:39.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 2016 2026-08-07 00:06:39.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 672260 2026-08-07 00:06:39.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 00:06:39.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 857 2026-08-07 00:06:39.000000 ./control │ │ │ --rw-r--r-- 0 root (0) root (0) 3843 2026-08-07 00:06:39.000000 ./md5sums │ │ │ +-rw-r--r-- 0 root (0) root (0) 806 2026-08-07 00:06:39.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 3758 2026-08-07 00:06:39.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,14 @@ │ │ │ Package: r-bioc-biocviews │ │ │ Version: 1.80.0+ds-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ Installed-Size: 1948 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-bioc-biobase, r-bioc-graph (>= 1.9.26), r-bioc-rbgl (>= 1.13.5), r-cran-xml, r-cran-rcurl, r-cran-runit, r-cran-biocmanager, r-pkg-team-core-architecture │ │ │ -Suggests: r-bioc-biocgenerics, r-cran-knitr, r-cran-commonmark, r-bioc-biocstyle │ │ │ +Suggests: r-bioc-biocgenerics │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/biocViews/ │ │ │ Description: Categorized views of R package repositories │ │ │ Infrastructure to support 'views' used to classify │ │ │ Bioconductor packages. 'biocViews' are directed acyclic │ │ │ graphs of terms from a controlled vocabulary. There are three │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ │ │ │ ├── line order │ │ │ │ @@ -3,15 +3,14 @@ │ │ │ │ usr/lib/R/site-library/biocViews/Meta/Rd.rds │ │ │ │ usr/lib/R/site-library/biocViews/Meta/data.rds │ │ │ │ usr/lib/R/site-library/biocViews/Meta/features.rds │ │ │ │ usr/lib/R/site-library/biocViews/Meta/hsearch.rds │ │ │ │ usr/lib/R/site-library/biocViews/Meta/links.rds │ │ │ │ usr/lib/R/site-library/biocViews/Meta/nsInfo.rds │ │ │ │ usr/lib/R/site-library/biocViews/Meta/package.rds │ │ │ │ -usr/lib/R/site-library/biocViews/Meta/vignette.rds │ │ │ │ usr/lib/R/site-library/biocViews/NAMESPACE │ │ │ │ usr/lib/R/site-library/biocViews/NEWS │ │ │ │ usr/lib/R/site-library/biocViews/R/biocViews │ │ │ │ usr/lib/R/site-library/biocViews/R/biocViews.rdb │ │ │ │ usr/lib/R/site-library/biocViews/R/biocViews.rdx │ │ │ │ usr/lib/R/site-library/biocViews/README.md │ │ │ │ usr/lib/R/site-library/biocViews/css/package-detail.css.in ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -10,46 +10,45 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 2048 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/Meta/Rd.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 126 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/Meta/data.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 123 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/Meta/features.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1971 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/Meta/hsearch.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1073 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/Meta/links.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 991 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1527 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/Meta/package.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 258 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1849 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 2774 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/NEWS │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/R/biocViews │ │ │ --rw-r--r-- 0 root (0) root (0) 426700 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/R/biocViews.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 2381 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/R/biocViews.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 426709 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/R/biocViews.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 2378 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/R/biocViews.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 463 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/README.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/css/ │ │ │ -rw-r--r-- 0 root (0) root (0) 653 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/css/package-detail.css.in │ │ │ -rw-r--r-- 0 root (0) root (0) 426 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/css/repository-detail.css.in │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/data/ │ │ │ -rw-r--r-- 0 root (0) root (0) 5570 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/data/biocViewsVocab.rda │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 955 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/doc/HOWTO-BCV.R │ │ │ -rw-r--r-- 0 root (0) root (0) 5258 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/doc/HOWTO-BCV.Rmd │ │ │ -rw-r--r-- 0 root (0) root (0) 641007 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/doc/HOWTO-BCV.html │ │ │ -rw-r--r-- 0 root (0) root (0) 7597 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/doc/VIEWS │ │ │ -rw-r--r-- 0 root (0) root (0) 1967 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/doc/createReposHtml.R │ │ │ -rw-r--r-- 0 root (0) root (0) 6101 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/doc/createReposHtml.Rmd │ │ │ -rw-r--r-- 0 root (0) root (0) 638328 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/doc/createReposHtml.html │ │ │ --rw-r--r-- 0 root (0) root (0) 2110 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/doc/index.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 1748 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/doc/index.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/dot/ │ │ │ -rw-r--r-- 0 root (0) root (0) 18019 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/dot/biocViewsVocab.dot │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/extdata/ │ │ │ -rw-r--r-- 0 root (0) root (0) 28672 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/extdata/biocViewsVocab.sqlite │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 3126 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/help/AnIndex │ │ │ -rw-r--r-- 0 root (0) root (0) 873 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 83756 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/help/biocViews.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 1022 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/help/biocViews.rdx │ │ │ --rw-r--r-- 0 root (0) root (0) 519 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 84643 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/help/biocViews.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 1028 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/help/biocViews.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 528 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 11509 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/htmlfrags/ │ │ │ -rw-r--r-- 0 root (0) root (0) 291 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/htmlfrags/topfrag.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/script/ │ │ │ -rw-r--r-- 0 root (0) root (0) 5483 2026-08-07 00:06:39.000000 ./usr/lib/R/site-library/biocViews/script/recommend_biocViews_rpacks.R │ │ ├── ./usr/lib/R/site-library/biocViews/R/biocViews.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -1931,15 +1931,15 @@ │ │ │ │ "imports" = " ".__T__adj:graph" = ".__T__adj:graph", adj = "adj", ".__T__edges:graph" = ".__T__edges:graph", " │ │ │ │ "imports" = " edges = "edges", ".__T__inEdges:graph" = ".__T__inEdges:graph", " │ │ │ │ "imports" = " inEdges = "inEdges", ".__T__nodes:graph" = ".__T__nodes:graph", " │ │ │ │ "imports" = " nodes = "nodes", ".__T__subGraph:graph" = ".__T__subGraph:graph", " │ │ │ │ "imports" = " subGraph = "subGraph"), XML = c(".__T__saveXML:XML" = ".__T__saveXML:XML", " │ │ │ │ "imports" = " saveXML = "saveXML"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-biocviews/debian/r-bioc-biocviews/usr/lib/R/site-library/biocViews"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/debian/r-bioc-biocviews/usr/lib/R/site-library/biocViews"" │ │ │ │ "spec" = "c(name = "biocViews", version = "1.80.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/biocViews/R/biocViews.rdx │ │ │ ├── biocViews.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -41,450 +41,450 @@ │ │ │ │ │ $variables$.__C__pdVigsAndDownloads │ │ │ │ │ [1] 30117 2019 │ │ │ │ │ │ │ │ │ │ $variables$.__C__rdPackageTable │ │ │ │ │ [1] 32136 1612 │ │ │ │ │ │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 37504 52 │ │ │ │ │ +[1] 37513 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 37687 52 │ │ │ │ │ +[1] 37696 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__coerce:methods` │ │ │ │ │ -[1] 86367 52 │ │ │ │ │ +[1] 86376 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__htmlDoc:biocViews` │ │ │ │ │ -[1] 90216 53 │ │ │ │ │ +[1] 90225 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__htmlFilename:biocViews` │ │ │ │ │ -[1] 92723 53 │ │ │ │ │ +[1] 92732 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__htmlValue:biocViews` │ │ │ │ │ -[1] 138871 53 │ │ │ │ │ +[1] 138880 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__show:methods` │ │ │ │ │ -[1] 304519 53 │ │ │ │ │ +[1] 304528 53 │ │ │ │ │ │ │ │ │ │ $variables$.cleanupDependency │ │ │ │ │ -[1] 304572 699 │ │ │ │ │ +[1] 304581 699 │ │ │ │ │ │ │ │ │ │ $variables$.extract_citation │ │ │ │ │ -[1] 305271 1804 │ │ │ │ │ +[1] 305280 1804 │ │ │ │ │ │ │ │ │ │ $variables$.findBranchReadDot │ │ │ │ │ -[1] 307075 2365 │ │ │ │ │ +[1] 307084 2365 │ │ │ │ │ │ │ │ │ │ $variables$.getBioCDevelUrl │ │ │ │ │ -[1] 309440 1047 │ │ │ │ │ +[1] 309449 1047 │ │ │ │ │ │ │ │ │ │ $variables$.getChildEdgeFromDot │ │ │ │ │ -[1] 310487 503 │ │ │ │ │ +[1] 310496 503 │ │ │ │ │ │ │ │ │ │ $variables$.getChildren │ │ │ │ │ -[1] 310990 648 │ │ │ │ │ +[1] 310999 648 │ │ │ │ │ │ │ │ │ │ $variables$.msg │ │ │ │ │ -[1] 311638 347 │ │ │ │ │ +[1] 311647 347 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 311985 54 │ │ │ │ │ +[1] 311994 54 │ │ │ │ │ │ │ │ │ │ $variables$.parseDot │ │ │ │ │ -[1] 312039 487 │ │ │ │ │ +[1] 312048 487 │ │ │ │ │ │ │ │ │ │ $variables$.printf │ │ │ │ │ -[1] 312526 242 │ │ │ │ │ +[1] 312535 242 │ │ │ │ │ │ │ │ │ │ $variables$.wordsfromDESCRIPTION │ │ │ │ │ -[1] 312768 1638 │ │ │ │ │ +[1] 312777 1638 │ │ │ │ │ │ │ │ │ │ $variables$.wordsfromMANVIN │ │ │ │ │ -[1] 314406 1239 │ │ │ │ │ +[1] 314415 1239 │ │ │ │ │ │ │ │ │ │ $variables$.write_citation_as_HTML │ │ │ │ │ -[1] 315645 2006 │ │ │ │ │ +[1] 315654 2006 │ │ │ │ │ │ │ │ │ │ $variables$.write_repository_db │ │ │ │ │ -[1] 317651 1257 │ │ │ │ │ +[1] 317660 1257 │ │ │ │ │ │ │ │ │ │ $variables$StangleHTMLVignettes │ │ │ │ │ -[1] 318908 1709 │ │ │ │ │ +[1] 318917 1709 │ │ │ │ │ │ │ │ │ │ $variables$build_db_from_source │ │ │ │ │ -[1] 320617 1650 │ │ │ │ │ +[1] 320626 1650 │ │ │ │ │ │ │ │ │ │ $variables$build_meta_aliases_db │ │ │ │ │ -[1] 322267 1277 │ │ │ │ │ +[1] 322276 1277 │ │ │ │ │ │ │ │ │ │ $variables$build_meta_rdxrefs_db │ │ │ │ │ -[1] 323544 1278 │ │ │ │ │ +[1] 323553 1278 │ │ │ │ │ │ │ │ │ │ $variables$cleanText │ │ │ │ │ -[1] 324822 550 │ │ │ │ │ +[1] 324831 550 │ │ │ │ │ │ │ │ │ │ $variables$cleanUnpackDir │ │ │ │ │ -[1] 325372 598 │ │ │ │ │ +[1] 325381 598 │ │ │ │ │ │ │ │ │ │ $variables$createPackageDetailList │ │ │ │ │ -[1] 325970 1223 │ │ │ │ │ +[1] 325979 1223 │ │ │ │ │ │ │ │ │ │ $variables$dump_concept │ │ │ │ │ -[1] 327193 773 │ │ │ │ │ +[1] 327202 773 │ │ │ │ │ │ │ │ │ │ $variables$extractCitations │ │ │ │ │ -[1] 327966 1053 │ │ │ │ │ +[1] 327975 1053 │ │ │ │ │ │ │ │ │ │ $variables$extractHTMLDocuments │ │ │ │ │ -[1] 329019 1656 │ │ │ │ │ +[1] 329028 1656 │ │ │ │ │ │ │ │ │ │ $variables$extractINSTALLfiles │ │ │ │ │ -[1] 330675 309 │ │ │ │ │ +[1] 330684 309 │ │ │ │ │ │ │ │ │ │ $variables$extractManuals │ │ │ │ │ -[1] 330984 2824 │ │ │ │ │ +[1] 330993 2824 │ │ │ │ │ │ │ │ │ │ $variables$extractNEWS │ │ │ │ │ -[1] 333808 2162 │ │ │ │ │ +[1] 333817 2162 │ │ │ │ │ │ │ │ │ │ $variables$extractReadmes │ │ │ │ │ -[1] 335970 309 │ │ │ │ │ +[1] 335979 309 │ │ │ │ │ │ │ │ │ │ $variables$extractTopLevelFiles │ │ │ │ │ -[1] 336279 1256 │ │ │ │ │ +[1] 336288 1256 │ │ │ │ │ │ │ │ │ │ $variables$extractVignettes │ │ │ │ │ -[1] 337535 1489 │ │ │ │ │ +[1] 337544 1489 │ │ │ │ │ │ │ │ │ │ $variables$genReposControlFiles │ │ │ │ │ -[1] 339024 1568 │ │ │ │ │ +[1] 339033 1568 │ │ │ │ │ │ │ │ │ │ $variables$getBiocSubViews │ │ │ │ │ -[1] 340592 618 │ │ │ │ │ +[1] 340601 618 │ │ │ │ │ │ │ │ │ │ $variables$getBiocViews │ │ │ │ │ -[1] 341210 779 │ │ │ │ │ +[1] 341219 779 │ │ │ │ │ │ │ │ │ │ $variables$getCurrentbiocViews │ │ │ │ │ -[1] 341989 1346 │ │ │ │ │ +[1] 341998 1346 │ │ │ │ │ │ │ │ │ │ $variables$getDcfValues │ │ │ │ │ -[1] 343335 850 │ │ │ │ │ +[1] 343344 850 │ │ │ │ │ │ │ │ │ │ $variables$getDocumentTitles │ │ │ │ │ -[1] 344185 1997 │ │ │ │ │ +[1] 344194 1997 │ │ │ │ │ │ │ │ │ │ $variables$getFileExistsAttr │ │ │ │ │ -[1] 346182 789 │ │ │ │ │ +[1] 346191 789 │ │ │ │ │ │ │ │ │ │ $variables$getFileLinks │ │ │ │ │ -[1] 346971 1231 │ │ │ │ │ +[1] 346980 1231 │ │ │ │ │ │ │ │ │ │ $variables$getHtmlTitle │ │ │ │ │ -[1] 348202 611 │ │ │ │ │ +[1] 348211 611 │ │ │ │ │ │ │ │ │ │ $variables$getNEWSFromFile │ │ │ │ │ -[1] 348813 3114 │ │ │ │ │ +[1] 348822 3114 │ │ │ │ │ │ │ │ │ │ $variables$getPackageDescriptions │ │ │ │ │ -[1] 351927 1679 │ │ │ │ │ +[1] 351936 1679 │ │ │ │ │ │ │ │ │ │ $variables$getPackageNEWS │ │ │ │ │ -[1] 353606 3931 │ │ │ │ │ +[1] 353615 3931 │ │ │ │ │ │ │ │ │ │ $variables$getPackageTitles │ │ │ │ │ -[1] 357537 1304 │ │ │ │ │ +[1] 357546 1304 │ │ │ │ │ │ │ │ │ │ $variables$getPacksAndViews │ │ │ │ │ -[1] 358841 1958 │ │ │ │ │ +[1] 358850 1958 │ │ │ │ │ │ │ │ │ │ $variables$getPdfTitle │ │ │ │ │ -[1] 360799 240 │ │ │ │ │ +[1] 360808 240 │ │ │ │ │ │ │ │ │ │ $variables$getRefmanLinks │ │ │ │ │ -[1] 361039 896 │ │ │ │ │ +[1] 361048 896 │ │ │ │ │ │ │ │ │ │ $variables$getReverseDepends │ │ │ │ │ -[1] 361935 1563 │ │ │ │ │ +[1] 361944 1563 │ │ │ │ │ │ │ │ │ │ $variables$getRootNode │ │ │ │ │ -[1] 363498 437 │ │ │ │ │ +[1] 363507 437 │ │ │ │ │ │ │ │ │ │ $variables$getSubTerms │ │ │ │ │ -[1] 363935 343 │ │ │ │ │ +[1] 363944 343 │ │ │ │ │ │ │ │ │ │ $variables$getVignetteIndexEntry │ │ │ │ │ -[1] 364278 562 │ │ │ │ │ +[1] 364287 562 │ │ │ │ │ │ │ │ │ │ $variables$guessPackageType │ │ │ │ │ -[1] 364840 1127 │ │ │ │ │ +[1] 364849 1127 │ │ │ │ │ │ │ │ │ │ $variables$htmlDoc │ │ │ │ │ -[1] 365967 415 │ │ │ │ │ +[1] 365976 415 │ │ │ │ │ │ │ │ │ │ $variables$htmlFilename │ │ │ │ │ -[1] 366382 422 │ │ │ │ │ +[1] 366391 422 │ │ │ │ │ │ │ │ │ │ $variables$htmlValue │ │ │ │ │ -[1] 366804 402 │ │ │ │ │ +[1] 366813 402 │ │ │ │ │ │ │ │ │ │ $variables$is_file │ │ │ │ │ -[1] 367206 329 │ │ │ │ │ +[1] 367215 329 │ │ │ │ │ │ │ │ │ │ $variables$loadPackageDetails │ │ │ │ │ -[1] 367535 517 │ │ │ │ │ +[1] 367544 517 │ │ │ │ │ │ │ │ │ │ $variables$loadViews │ │ │ │ │ -[1] 368052 1577 │ │ │ │ │ +[1] 368061 1577 │ │ │ │ │ │ │ │ │ │ $variables$makeHtmlHeader │ │ │ │ │ -[1] 369629 754 │ │ │ │ │ +[1] 369638 754 │ │ │ │ │ │ │ │ │ │ $variables$mangleEmail │ │ │ │ │ -[1] 370383 1911 │ │ │ │ │ +[1] 370392 1911 │ │ │ │ │ │ │ │ │ │ $variables$myStangle │ │ │ │ │ -[1] 372294 1329 │ │ │ │ │ +[1] 372303 1329 │ │ │ │ │ │ │ │ │ │ $variables$normalizeTags │ │ │ │ │ -[1] 373623 1088 │ │ │ │ │ +[1] 373632 1088 │ │ │ │ │ │ │ │ │ │ $variables$permulist │ │ │ │ │ -[1] 374711 722 │ │ │ │ │ +[1] 374720 722 │ │ │ │ │ │ │ │ │ │ $variables$pkgName │ │ │ │ │ -[1] 375433 365 │ │ │ │ │ +[1] 375442 365 │ │ │ │ │ │ │ │ │ │ $variables$printNEWS │ │ │ │ │ -[1] 375798 2554 │ │ │ │ │ +[1] 375807 2554 │ │ │ │ │ │ │ │ │ │ $variables$printNewPackageTitles │ │ │ │ │ -[1] 378352 941 │ │ │ │ │ +[1] 378361 941 │ │ │ │ │ │ │ │ │ │ $variables$processTagsField │ │ │ │ │ -[1] 379293 991 │ │ │ │ │ +[1] 379302 991 │ │ │ │ │ │ │ │ │ │ $variables$pump │ │ │ │ │ -[1] 380284 775 │ │ │ │ │ +[1] 380293 775 │ │ │ │ │ │ │ │ │ │ $variables$readPackageInfo │ │ │ │ │ -[1] 381059 2692 │ │ │ │ │ +[1] 381068 2692 │ │ │ │ │ │ │ │ │ │ $variables$read_REPOSITORY │ │ │ │ │ -[1] 383751 1263 │ │ │ │ │ +[1] 383760 1263 │ │ │ │ │ │ │ │ │ │ $variables$recommendBiocViews │ │ │ │ │ -[1] 385014 6145 │ │ │ │ │ +[1] 385023 6145 │ │ │ │ │ │ │ │ │ │ $variables$recommendPackages │ │ │ │ │ -[1] 391159 2746 │ │ │ │ │ +[1] 391168 2746 │ │ │ │ │ │ │ │ │ │ $variables$removeEmail │ │ │ │ │ -[1] 393905 403 │ │ │ │ │ +[1] 393914 403 │ │ │ │ │ │ │ │ │ │ $variables$setDependsOnMeImportsMeSuggestsMe │ │ │ │ │ -[1] 394308 1862 │ │ │ │ │ +[1] 394317 1862 │ │ │ │ │ │ │ │ │ │ $variables$showVoc │ │ │ │ │ -[1] 396170 1249 │ │ │ │ │ +[1] 396179 1249 │ │ │ │ │ │ │ │ │ │ $variables$tableHelper │ │ │ │ │ -[1] 397419 901 │ │ │ │ │ +[1] 397428 901 │ │ │ │ │ │ │ │ │ │ $variables$tellSubTop │ │ │ │ │ -[1] 398320 849 │ │ │ │ │ +[1] 398329 849 │ │ │ │ │ │ │ │ │ │ $variables$tellSuperTop │ │ │ │ │ -[1] 399169 910 │ │ │ │ │ +[1] 399178 910 │ │ │ │ │ │ │ │ │ │ $variables$unpack │ │ │ │ │ -[1] 400079 404 │ │ │ │ │ +[1] 400088 404 │ │ │ │ │ │ │ │ │ │ $variables$validate_bioc_views │ │ │ │ │ -[1] 400483 1039 │ │ │ │ │ +[1] 400492 1039 │ │ │ │ │ │ │ │ │ │ $variables$viewRowToPackageDetail │ │ │ │ │ -[1] 401522 2766 │ │ │ │ │ +[1] 401531 2766 │ │ │ │ │ │ │ │ │ │ $variables$viewsHelper │ │ │ │ │ -[1] 404288 664 │ │ │ │ │ +[1] 404297 664 │ │ │ │ │ │ │ │ │ │ $variables$writeBiocViews │ │ │ │ │ -[1] 404952 1005 │ │ │ │ │ +[1] 404961 1005 │ │ │ │ │ │ │ │ │ │ $variables$writeHtmlDoc │ │ │ │ │ -[1] 405957 609 │ │ │ │ │ +[1] 405966 609 │ │ │ │ │ │ │ │ │ │ $variables$writePackageDetailHtml │ │ │ │ │ -[1] 406566 1180 │ │ │ │ │ +[1] 406575 1180 │ │ │ │ │ │ │ │ │ │ $variables$writeRFilesFromVignettes │ │ │ │ │ -[1] 407746 434 │ │ │ │ │ +[1] 407755 434 │ │ │ │ │ │ │ │ │ │ $variables$writeRepositoryHtml │ │ │ │ │ -[1] 408180 1122 │ │ │ │ │ +[1] 408189 1122 │ │ │ │ │ │ │ │ │ │ $variables$writeRepositoryIndexHtml │ │ │ │ │ -[1] 409302 688 │ │ │ │ │ +[1] 409311 688 │ │ │ │ │ │ │ │ │ │ $variables$writeTopLevelView │ │ │ │ │ -[1] 409990 648 │ │ │ │ │ +[1] 409999 648 │ │ │ │ │ │ │ │ │ │ $variables$write_REPOSITORY │ │ │ │ │ -[1] 410638 731 │ │ │ │ │ +[1] 410647 731 │ │ │ │ │ │ │ │ │ │ $variables$write_SYMBOLS │ │ │ │ │ -[1] 411369 2418 │ │ │ │ │ +[1] 411378 2418 │ │ │ │ │ │ │ │ │ │ $variables$write_VIEWS │ │ │ │ │ -[1] 413787 12913 │ │ │ │ │ +[1] 413796 12913 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 34038 3466 │ │ │ │ │ +[1] 34038 3475 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 84983 622 │ │ │ │ │ +[1] 84992 622 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 89037 1179 │ │ │ │ │ +[1] 89046 1179 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 88777 260 │ │ │ │ │ +[1] 88786 260 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 86419 1179 │ │ │ │ │ +[1] 86428 1179 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 87598 1179 │ │ │ │ │ +[1] 87607 1179 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 91992 731 │ │ │ │ │ +[1] 92001 731 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 91731 261 │ │ │ │ │ +[1] 91740 261 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 90269 731 │ │ │ │ │ +[1] 90278 731 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 91000 731 │ │ │ │ │ +[1] 91009 731 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 123592 15279 │ │ │ │ │ +[1] 123601 15279 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 33748 131 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 123334 258 │ │ │ │ │ +[1] 123343 258 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 92776 15279 │ │ │ │ │ +[1] 92785 15279 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 108055 15279 │ │ │ │ │ +[1] 108064 15279 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 303710 809 │ │ │ │ │ +[1] 303719 809 │ │ │ │ │ │ │ │ │ │ $references$`env::24` │ │ │ │ │ -[1] 303251 459 │ │ │ │ │ +[1] 303260 459 │ │ │ │ │ │ │ │ │ │ $references$`env::25` │ │ │ │ │ -[1] 264129 19561 │ │ │ │ │ +[1] 264138 19561 │ │ │ │ │ │ │ │ │ │ $references$`env::26` │ │ │ │ │ -[1] 138924 170 │ │ │ │ │ +[1] 138933 170 │ │ │ │ │ │ │ │ │ │ $references$`env::27` │ │ │ │ │ -[1] 139094 1516 │ │ │ │ │ +[1] 139103 1516 │ │ │ │ │ │ │ │ │ │ $references$`env::28` │ │ │ │ │ -[1] 261655 2474 │ │ │ │ │ +[1] 261664 2474 │ │ │ │ │ │ │ │ │ │ $references$`env::29` │ │ │ │ │ -[1] 247212 143 │ │ │ │ │ +[1] 247221 143 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ [1] 33879 159 │ │ │ │ │ │ │ │ │ │ $references$`env::30` │ │ │ │ │ -[1] 242082 5130 │ │ │ │ │ +[1] 242091 5130 │ │ │ │ │ │ │ │ │ │ $references$`env::31` │ │ │ │ │ -[1] 241361 721 │ │ │ │ │ +[1] 241370 721 │ │ │ │ │ │ │ │ │ │ $references$`env::32` │ │ │ │ │ -[1] 149347 143 │ │ │ │ │ +[1] 149356 143 │ │ │ │ │ │ │ │ │ │ $references$`env::33` │ │ │ │ │ -[1] 140610 8737 │ │ │ │ │ +[1] 140619 8737 │ │ │ │ │ │ │ │ │ │ $references$`env::34` │ │ │ │ │ -[1] 236603 4758 │ │ │ │ │ +[1] 236612 4758 │ │ │ │ │ │ │ │ │ │ $references$`env::35` │ │ │ │ │ -[1] 160498 48999 │ │ │ │ │ +[1] 160507 48999 │ │ │ │ │ │ │ │ │ │ $references$`env::36` │ │ │ │ │ -[1] 157586 336 │ │ │ │ │ +[1] 157595 336 │ │ │ │ │ │ │ │ │ │ $references$`env::37` │ │ │ │ │ -[1] 150581 7005 │ │ │ │ │ +[1] 150590 7005 │ │ │ │ │ │ │ │ │ │ $references$`env::38` │ │ │ │ │ -[1] 149490 1091 │ │ │ │ │ +[1] 149499 1091 │ │ │ │ │ │ │ │ │ │ $references$`env::39` │ │ │ │ │ -[1] 157922 2268 │ │ │ │ │ +[1] 157931 2268 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 37556 131 │ │ │ │ │ +[1] 37565 131 │ │ │ │ │ │ │ │ │ │ $references$`env::40` │ │ │ │ │ -[1] 160190 308 │ │ │ │ │ +[1] 160199 308 │ │ │ │ │ │ │ │ │ │ $references$`env::41` │ │ │ │ │ -[1] 209497 27106 │ │ │ │ │ +[1] 209506 27106 │ │ │ │ │ │ │ │ │ │ $references$`env::42` │ │ │ │ │ -[1] 253147 2511 │ │ │ │ │ +[1] 253156 2511 │ │ │ │ │ │ │ │ │ │ $references$`env::43` │ │ │ │ │ -[1] 252989 158 │ │ │ │ │ +[1] 252998 158 │ │ │ │ │ │ │ │ │ │ $references$`env::44` │ │ │ │ │ -[1] 247355 5634 │ │ │ │ │ +[1] 247364 5634 │ │ │ │ │ │ │ │ │ │ $references$`env::45` │ │ │ │ │ -[1] 261512 143 │ │ │ │ │ +[1] 261521 143 │ │ │ │ │ │ │ │ │ │ $references$`env::46` │ │ │ │ │ -[1] 256381 5131 │ │ │ │ │ +[1] 256390 5131 │ │ │ │ │ │ │ │ │ │ $references$`env::47` │ │ │ │ │ -[1] 255658 723 │ │ │ │ │ +[1] 255667 723 │ │ │ │ │ │ │ │ │ │ $references$`env::48` │ │ │ │ │ -[1] 283690 19561 │ │ │ │ │ +[1] 283699 19561 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 85853 514 │ │ │ │ │ +[1] 85862 514 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 85605 248 │ │ │ │ │ +[1] 85614 248 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 39511 22736 │ │ │ │ │ +[1] 39520 22736 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 37739 1772 │ │ │ │ │ +[1] 37748 1772 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 62247 22736 │ │ │ │ │ +[1] 62256 22736 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/biocViews/doc/index.html │ │ │ @@ -10,33 +10,22 @@ │ │ │ │ │ │
│ │ │
│ │ │ [Up] │ │ │ [Top] │ │ │
│ │ │

Vignettes from package 'biocViews'

│ │ │ - │ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
biocViews::HOWTO-BCVbiocViews-HOWTOHTMLsourceR code
biocViews::createReposHtmlbiocViews-CreateRepositoryHTMLHTMLsourceR code
│ │ │ +The package contains no vignette meta-information. │ │ │

Other files in the doc directory

│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │ + │ │ │ + │ │ │ │ │ │ + │ │ │ + │ │ │ + │ │ │
HOWTO-BCV.R
HOWTO-BCV.Rmd
HOWTO-BCV.html
VIEWS
createReposHtml.R
createReposHtml.Rmd
createReposHtml.html
│ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,8 +1,13 @@ │ │ │ │ ************ VViiggnneetttteess aanndd ootthheerr ddooccuummeennttaattiioonn[[[[RR llooggoo]]]] ************ │ │ │ │ =============================================================================== │ │ │ │ _[_[_U_p_]_]_[_[_T_o_p_]_] │ │ │ │ ********** VViiggnneetttteess ffrroomm ppaacckkaaggee ''bbiiooccVViieewwss'' ********** │ │ │ │ - _b_i_o_c_V_i_e_w_s_:_:_H_O_W_T_O_-_B_C_V biocViews-HOWTO _H_T_M_L _s_o_u_r_c_e _R_ _c_o_d_e │ │ │ │ -_b_i_o_c_V_i_e_w_s_:_:_c_r_e_a_t_e_R_e_p_o_s_H_t_m_l biocViews-CreateRepositoryHTML _H_T_M_L _s_o_u_r_c_e _R_ _c_o_d_e │ │ │ │ +The package contains no vignette meta-information. │ │ │ │ ********** OOtthheerr ffiilleess iinn tthhee ddoocc ddiirreeccttoorryy ********** │ │ │ │ + _H_O_W_T_O_-_B_C_V_._R │ │ │ │ + _H_O_W_T_O_-_B_C_V_._R_m_d │ │ │ │ + _H_O_W_T_O_-_B_C_V_._h_t_m_l │ │ │ │ _V_I_E_W_S │ │ │ │ + _c_r_e_a_t_e_R_e_p_o_s_H_t_m_l_._R │ │ │ │ + _c_r_e_a_t_e_R_e_p_o_s_H_t_m_l_._R_m_d │ │ │ │ + _c_r_e_a_t_e_R_e_p_o_s_H_t_m_l_._h_t_m_l │ │ ├── ./usr/lib/R/site-library/biocViews/help/biocViews.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -94,15 +94,15 @@ │ │ │ │ structure(": ... ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("show", Rd_tag = "TEXT")), │ │ │ │ list(structure(list(structure("signature(object = \"BiocView\")", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(": ... ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\t ", Rd_tag = "TEXT")), Rd_tag = "\\describe"), │ │ │ │ structure("\n", Rd_tag = "TEXT"))), Rd_tag = "\\section"), │ │ │ │ - structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/BiocView-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/BiocView-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ Htmlized-class (list) = structure(list(structure(list(structure("Class \"Htmlized\"", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("Htmlized-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("Htmlized-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("htmlDoc,Htmlized-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("classes", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -117,15 +117,15 @@ │ │ │ │ list(structure(list(structure("signature(object = \"Htmlized\")", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(": Return the\n", Rd_tag = "TEXT"), │ │ │ │ structure(" html-ized representation of ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("object", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" as a complete HTML document.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\t ", Rd_tag = "TEXT")), Rd_tag = "\\describe"), │ │ │ │ structure("\n", Rd_tag = "TEXT"))), Rd_tag = "\\section"), │ │ │ │ - structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/Htmlized-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/Htmlized-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ PackageDetail-class (list) = structure(list(structure(list(structure("Class \"PackageDetail\"", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("PackageDetail-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("PackageDetail-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("pdAuthorMaintainerInfo-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("pdVignetteInfo-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -384,15 +384,15 @@ │ │ │ │ structure(" win.binary.ver=\"bin/windows/contrib/4.0/MyFancyPackage_1.2.2.zip\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" mac.binary.ver=\"bin/macosx/contrib/4.0/MyFancyPackage_1.2.3.tgz\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" dependsOnMe=c(\"PackageThatExposesMe\"),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" importsMe=c(\"AnEvenFancierPackage\",\"AMuchFancierPackage\"),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" suggestsMe=\"PackageThatUsesMeInVignette\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" reposRoot=\"http://foo.bar.org\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("html <- htmlValue(pd)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("pd\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/PackageDetail-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure("pd\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/PackageDetail-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ RepositoryDetail-class (list) = structure(list(structure(list(structure("Class \"RepositoryDetail\"", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("RepositoryDetail-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("RepositoryDetail-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("rdPackageTable-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("htmlDoc,RepositoryDetail-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -457,15 +457,15 @@ │ │ │ │ structure(": ... ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("htmlValue", Rd_tag = "TEXT")), │ │ │ │ list(structure(list(structure("signature(object = \"RepositoryDetail\")", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(": ... ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\t ", Rd_tag = "TEXT")), Rd_tag = "\\describe"), │ │ │ │ structure("\n", Rd_tag = "TEXT"))), Rd_tag = "\\section"), │ │ │ │ - structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/RepositoryDetail-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/RepositoryDetail-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ biocViews-package (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("Categorized views of R package repositories\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("biocViews-package", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("biocViews-package", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("biocViews", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -552,15 +552,15 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(), Rd_tag = "\\tab"), │ │ │ │ structure(" Further information for repository admins", Rd_tag = "TEXT"), │ │ │ │ structure(list(), Rd_tag = "\\cr"), structure("\n", Rd_tag = "TEXT"))), Rd_tag = "\\tabular"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("VJ Carey , BJ Harshfield , S Falcon \n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("Maintainer: Biocore Team c/o BioC user list \n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(biocViewsVocab)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("getSubTerms(biocViewsVocab, \"Technology\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/biocViews-package.Rd", class = "Rd", meta = list( │ │ │ │ + structure("getSubTerms(biocViewsVocab, \"Technology\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/biocViews-package.Rd", class = "Rd", meta = list( │ │ │ │ docType = "package", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ biocViewsVocab (list) = structure(list(structure(list(structure("Bioconductor Task Views Vocabulary Data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("biocViewsVocab", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("biocViewsVocab", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A ", Rd_tag = "TEXT"), │ │ │ │ @@ -577,15 +577,15 @@ │ │ │ │ structure("graph", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" package is used to\n", Rd_tag = "TEXT"), │ │ │ │ structure(" convert to ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("graphNEL-class", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(biocViewsVocab)\n", Rd_tag = "RCODE"), │ │ │ │ structure("biocViewsVocab\n", Rd_tag = "RCODE"), structure("## If you have Rgraphviz available, you can\n", Rd_tag = "RCODE"), │ │ │ │ - structure("## plot the vocabulary with plot(biocViewsVocab)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/biocViewsVocab.Rd", class = "Rd", meta = list( │ │ │ │ + structure("## plot the vocabulary with plot(biocViewsVocab)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/biocViewsVocab.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ build-dbs (list) = structure(list(structure(list(structure("Helper functions to generate HTML pages for reference manuals", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("build-dbs", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("build-dbs", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("build_db_from_source", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("build_meta_aliases_db", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -659,15 +659,15 @@ │ │ │ │ structure(" reposRoot <- \"~/minibioc/packages/3.20/bioc/\"\n", Rd_tag = "RCODE"), │ │ │ │ structure(" web_dir <- file.path(reposRoot, \"web\", \"packages\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" meta_folder <- file.path(contrib.url(reposRoot), \"Meta\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" if (!dir.exists(meta_folder)) dir.create(meta_folder, recursive = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" rdxrefs_db_file <- file.path(meta_folder, \"rdxrefs.rds\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" meta_rdxrefs_db <- build_meta_rdxrefs_db(web_dir, rdxrefs_db_file)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" saveRDS(meta_rdxrefs_db, rdxrefs_db_file, version = 2)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/build-dbs.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/build-dbs.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ dump_concept (list) = structure(list(structure(list(structure("produce character stream for use with Protege entities/class hierarchy ingestion \n", Rd_tag = "TEXT"), │ │ │ │ structure("based on biocViews subgraphs", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("dump_concept", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("dump_concept", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("produce character stream for use with Protege entities/class hierarchy ingestion \n", Rd_tag = "TEXT"), │ │ │ │ @@ -676,15 +676,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("x", Rd_tag = "TEXT")), list(structure("character(1) name of a node in the biocViewsVocab graph", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("edob", Rd_tag = "TEXT")), │ │ │ │ list(structure("a list as produced by graph::edges", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("a character atom with x abutting left and edge targets tab-indented\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("cat(substring(dump_concept(\"ResearchField\"), 1, 152), \"\\n\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/dump_concept.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("cat(substring(dump_concept(\"ResearchField\"), 1, 152), \"\\n\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/dump_concept.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractManuals (list) = structure(list(structure(list(structure("Extract Rd man pages and build pdf reference manuals from local package\n", Rd_tag = "TEXT"), │ │ │ │ structure(" repository", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractManuals", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractManuals", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("extractCitations", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -725,15 +725,15 @@ │ │ │ │ structure(list(list(structure("destDir", Rd_tag = "TEXT")), │ │ │ │ list(structure("character vector specifying the directory in which the\n", Rd_tag = "TEXT"), │ │ │ │ structure(" extracted files will be written. If missing, files will be written\n", Rd_tag = "TEXT"), │ │ │ │ structure(" to ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("/manuals", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("Patrick Aboyoun", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/extractManuals.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Patrick Aboyoun", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/extractManuals.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ extractNEWS (list) = structure(list(structure(list(structure("Extract NEWS files from source package tarballs", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractNEWS", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractNEWS", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Extracts NEWS files from source tarballs of packages.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -743,15 +743,15 @@ │ │ │ │ list(structure("Top level path for CRAN-style repos", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("srcContrib", Rd_tag = "TEXT")), │ │ │ │ list(structure("Location of source packages", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("destDir", Rd_tag = "TEXT")), │ │ │ │ list(structure("where to extract", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/extractNEWS.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/extractNEWS.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ extractTopLevelFiles (list) = structure(list(structure(list(structure("Extract files from the top level of source package tarballs", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractTopLevelFiles", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractTopLevelFiles", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Extracts files from source tarballs of packages.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -764,15 +764,15 @@ │ │ │ │ list(structure("Location of source packages", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("destDir", Rd_tag = "TEXT")), │ │ │ │ list(structure("where to extract", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("fileName", Rd_tag = "TEXT")), │ │ │ │ list(structure("name of file to extract", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/extractTopLevelFiles.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/extractTopLevelFiles.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ extractVignettes (list) = structure(list(structure(list(structure("Extract pdf vignettes from local package repository", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractVignettes", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractVignettes", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("extractHTMLDocuments", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -819,15 +819,15 @@ │ │ │ │ structure(list(list(structure("destDir", Rd_tag = "TEXT")), │ │ │ │ list(structure("character vector specifying the directory in which the\n", Rd_tag = "TEXT"), │ │ │ │ structure(" extracted files will be written. If missing, files will be written\n", Rd_tag = "TEXT"), │ │ │ │ structure(" to ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("/vignettes", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/extractVignettes.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/extractVignettes.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ genReposControlFiles (list) = structure(list(structure(list(structure("Generate CRAN-style repository control files", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("genReposControlFiles", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("genReposControlFiles", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" This function generates control files for CRAN-style repositories.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -890,15 +890,15 @@ │ │ │ │ structure(list(structure(list(structure("write_PACKAGES", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("tools:write_PACKAGES", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractVignettes", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("write_REPOSITORY", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("write_VIEWS", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/genReposControlFiles.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/genReposControlFiles.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ getBiocSubViews (list) = structure(list(structure(list(structure("Build a list of BiocView objects from a package repository", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getBiocSubViews", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getBiocSubViews", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" This function returns a list of ", Rd_tag = "TEXT"), │ │ │ │ @@ -969,15 +969,15 @@ │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("writeBiocViews", 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(biocViewsVocab)\n", Rd_tag = "RCODE"), │ │ │ │ structure("reposPath <- system.file(\"doc\", package=\"biocViews\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("reposUrl <- paste(\"file://\", reposPath, sep=\"\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("biocViews <- getBiocSubViews(reposUrl, biocViewsVocab, \"Software\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("print(biocViews[1:2])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/getBiocSubViews.Rd", class = "Rd", meta = list( │ │ │ │ + structure("print(biocViews[1:2])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/getBiocSubViews.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ getBiocViews (list) = structure(list(structure(list(structure("Build a list of BiocView objects from a package repository", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getBiocViews", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getBiocViews", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Given the URL to a CRAN-style package repository containing a\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1037,15 +1037,15 @@ │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("writeBiocViews", 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(biocViewsVocab)\n", Rd_tag = "RCODE"), │ │ │ │ structure("reposPath <- system.file(\"doc\", package=\"biocViews\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("reposUrl <- paste(\"file://\", reposPath, sep=\"\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("biocViews <- getBiocViews(reposUrl, biocViewsVocab, \"NoViewProvided\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("print(biocViews[1:2])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/getBiocViews.Rd", class = "Rd", meta = list( │ │ │ │ + structure("print(biocViews[1:2])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/getBiocViews.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ getCurrentbiocViews (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("Get a list of biocViews for each branch\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getCurrentbiocViews", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getCurrentbiocViews", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function looks returns a list containing all the biocViews that are present\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1061,15 +1061,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("AnnotationData", Rd_tag = "TEXT")), │ │ │ │ list(structure("biocViews from the AnnotationData branch", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sonali Arora\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("ans <- getCurrentbiocViews()\n", Rd_tag = "RCODE"), │ │ │ │ structure("## only the first 6 from each branch are shown here. \n", Rd_tag = "RCODE"), │ │ │ │ - structure("lapply(ans, head)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/getCurrentbiocViews.Rd", class = "Rd", meta = list( │ │ │ │ + structure("lapply(ans, head)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/getCurrentbiocViews.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ getPackageNEWS (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(" Retrieve and print package NEWS\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getPackageNEWS", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getPackageNEWS", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("printNEWS", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1155,15 +1155,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A list of ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("news_db", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" files, as returned by ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("utils::news", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" for each package for which relevant NEWS is available.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Martin Morgan ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("mtmorgan@fhcrc.org", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ - structure(" and Lori Shepherd\n", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/getPackageNEWS.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" and Lori Shepherd\n", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/getPackageNEWS.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ getPackageTitles (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(" Retrieve list of package titles and print package Description\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getPackageTitles", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getPackageTitles", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("getPackageTitles", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1236,15 +1236,15 @@ │ │ │ │ structure("rmSoft = getPackageTitles(currBranch=\"RELEASE_3_7\", status=\"removed\")\n", Rd_tag = "VERB"), │ │ │ │ structure("# get depreacted package for 3.7\n", Rd_tag = "VERB"), │ │ │ │ structure("deprecatedSoft = setdiff(getPackageTitles(status=\"removed\"), rmSoft)\n", Rd_tag = "VERB"), │ │ │ │ structure("\n", Rd_tag = "VERB"), structure("# repeated above for data-experiment packages\n", Rd_tag = "VERB"), │ │ │ │ structure("newData = getPackageTitles(manifest=\"data-experiment.txt\")\n", Rd_tag = "VERB"), │ │ │ │ structure("rmData = getPackageTitles(currBranch=\"RELEASE_3_7\", manifest=\"data-experiment.txt\", status=\"removed\")\n", Rd_tag = "VERB"), │ │ │ │ structure("deprecatedData = setdiff(getPackageTitles(manifest=\"data-experiment.txt\", status=\"removed\"), rmData)\n", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/getPackageTitles.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/getPackageTitles.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ getPacksAndViews (list) = structure(list(structure(list(structure("Parse VIEWS file for views and packages", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getPacksAndViews", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getPacksAndViews", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("permulist", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("makeVocInfo", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1286,15 +1286,15 @@ │ │ │ │ structure(list(structure("views", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(": Vector of view memberships. Names are package names.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("pkgList", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(": A list of ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("PackageDetail-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" objects.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/getPacksAndViews.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/getPacksAndViews.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ getSubTerms (list) = structure(list(structure(list(structure("Retrieve a term and its children from a vocab DAG", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getSubTerms", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getSubTerms", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Given a Directed Acyclic Graph (DAG) represented as a ", Rd_tag = "TEXT"), │ │ │ │ @@ -1316,15 +1316,15 @@ │ │ │ │ list(structure("A string giving a term in the vocabulary (a node in ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("dag", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(")", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A character vector of term names.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("S. Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(biocViewsVocab)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("getSubTerms(biocViewsVocab, \"Software\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/getSubTerms.Rd", class = "Rd", meta = list( │ │ │ │ + structure("getSubTerms(biocViewsVocab, \"Software\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/getSubTerms.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ guessPackageType (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(" Guess Package Type (Software, ExperimentData, AnnotationData) using existing biocViews.\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("guessPackageType", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("guessPackageType", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" biocViews are \"keywords\" which are used to describe a given package. They\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1339,15 +1339,15 @@ │ │ │ │ structure(list(list(structure("biocViews", Rd_tag = "TEXT")), │ │ │ │ list(structure(" A character vector containing a list of biocViews.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure(" \n", Rd_tag = "TEXT"), structure(" A character(1) of package type: either \"Software\",\n", Rd_tag = "TEXT"), │ │ │ │ structure(" \"ExperperimentData\", or \"AnnotationData\". \n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Lori Shepherd\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" guessPackageType(c(\"clustering\", \"classification\"))\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" guessPackageType(c(\"Organism\", \"Homo Sapien\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/guessPackageType.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" guessPackageType(c(\"Organism\", \"Homo Sapien\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/guessPackageType.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ htmlDoc (list) = structure(list(structure(list(structure("Create a complete HTML document representation of an object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("htmlDoc", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("htmlDoc", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1367,15 +1367,15 @@ │ │ │ │ structure(list(structure("XMLNode", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" from the ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("XML", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" package.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure(list(structure(list(structure("htmlValue", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ - structure("htmlFilename", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/htmlDoc.Rd", class = "Rd", meta = list( │ │ │ │ + structure("htmlFilename", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/htmlDoc.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ htmlFilename (list) = structure(list(structure(list(structure("Return a filename for an object's HTML representation", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("htmlFilename", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("htmlFilename", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("htmlFilename,character-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -1390,15 +1390,15 @@ │ │ │ │ list(structure("Not currently used", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A character vector of length one containing the filename.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure(list(structure(list(structure("htmlValue", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("htmlDoc", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/htmlFilename.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/htmlFilename.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ htmlValue (list) = structure(list(structure(list(structure("HTML Representation of an Object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("htmlValue", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("htmlValue", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" This generic function should return an ", Rd_tag = "TEXT"), │ │ │ │ @@ -1413,15 +1413,15 @@ │ │ │ │ structure(list(structure("XMLNode", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" from the ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("XML", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" package.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure(list(structure(list(structure("htmlDoc", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ - structure("htmlFilename", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/htmlValue.Rd", class = "Rd", meta = list( │ │ │ │ + structure("htmlFilename", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/htmlValue.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ recommendBiocViews (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(" Recommend biocViews for an existing Package.\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("recommendBiocViews", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("recommendBiocViews", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Packages being added to the Bioconductor Project require biocViews in their \n", Rd_tag = "TEXT"), │ │ │ │ @@ -1474,15 +1474,15 @@ │ │ │ │ structure(" expected to go through this list and find which biocViews best describe \n", Rd_tag = "TEXT"), │ │ │ │ structure(" their package.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(), Rd_tag = "\\item"), │ │ │ │ structure(" \"remove\" are those biocViews which are inconsistent with the \n", Rd_tag = "TEXT"), │ │ │ │ structure(" Bioconductor biocViews. (Hint - check for spelling, cases and plural) \n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sonali Arora. \n", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/recommendBiocViews.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sonali Arora. \n", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/recommendBiocViews.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ recommendPackages (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(" Recommend Packages using existing biocViews.\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("recommendPackages", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("recommendPackages", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" biocViews are \"keywords\" which are used to describe a given package. They\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1508,15 +1508,15 @@ │ │ │ │ structure(" or more of the biocViews.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure(" \n", Rd_tag = "TEXT"), structure(" A character vector containing a list of packages. If multiple biocViews\n", Rd_tag = "TEXT"), │ │ │ │ structure(" are given as input, the result returns packages tagged with all or atleast \n", Rd_tag = "TEXT"), │ │ │ │ structure(" one of the input biocViews. \n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Sonali Arora. \n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure(" recommendPackages(c(\"clustering\", \"classification\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/recommendPackages.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure(" recommendPackages(c(\"clustering\", \"classification\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/recommendPackages.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ │ │ @@ -1543,15 +1543,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("invisible(NULL)", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" if tests pass.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Dan Tenenbaum ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("dtenenba@fhcrc.org", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("validate_bioc_views(\"biocViews\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/validation_tests.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("validate_bioc_views(\"biocViews\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/validation_tests.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ writeBiocViews (list) = structure(list(structure(list(structure("Write a list of BiocView objects to HTML", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("writeBiocViews", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("writeBiocViews", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" This function serializes a list of ", Rd_tag = "TEXT"), │ │ │ │ @@ -1575,15 +1575,15 @@ │ │ │ │ structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("getBiocViews", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("genReposControlFiles", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("write_VIEWS", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/writeBiocViews.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/writeBiocViews.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ writeHtmlDoc (list) = structure(list(structure(list(structure("Write an XML DOM containing HTML to a file", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("writeHtmlDoc", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("writeHtmlDoc", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure(" utilities ", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Given a DOM tree from the XML package and a filename, write the DOM to\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1592,15 +1592,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("html", Rd_tag = "TEXT")), │ │ │ │ list(structure("A DOM object from the XML package", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("file", Rd_tag = "TEXT")), │ │ │ │ list(structure("A string giving the filename", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("S. Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/writeHtmlDoc.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("S. Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/writeHtmlDoc.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ writePackageDetailHtml (list) = structure(list(structure(list(structure("Write HTML files for packages in a CRAN-style repository", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("writePackageDetailHtml", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("writePackageDetailHtml", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" This function creates package \"homepages\" that describe the package\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1616,15 +1616,15 @@ │ │ │ │ list(structure("The files will be written to this directory.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("backgroundColor", Rd_tag = "TEXT")), │ │ │ │ list(structure("A character vector giving the background color\n", Rd_tag = "TEXT"), │ │ │ │ structure(" for the body in the CSS file.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ - structure(list(structure(list(structure(list(structure("writeRepositoryHtml", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/writePackageDetailHtml.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure(list(structure(list(structure("writeRepositoryHtml", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/writePackageDetailHtml.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ writeRFilesFromVignettes (list) = structure(list(structure(list(structure("Write R files from vignettes", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("writeRFilesFromVignettes", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("writeRFilesFromVignettes", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Ensures that .R files from vignette code chunks are written out.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1645,15 +1645,15 @@ │ │ │ │ list(structure("Full URL of VIEWS file", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("downloadStatsUrl", Rd_tag = "TEXT")), │ │ │ │ list(structure("URL to download stats page", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("devHistoryUrl", Rd_tag = "TEXT")), │ │ │ │ list(structure("Dev history URL", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/writeRFilesFromVignettes.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/writeRFilesFromVignettes.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ writeRepositoryHtml (list) = structure(list(structure(list(structure("Write package descriptions and a repository index as HTML", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("writeRepositoryHtml", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("writeRepositoryHtml", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" This function generates an HTML file for each package in a repository\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1714,15 +1714,15 @@ │ │ │ │ structure("FALSE", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("backgroundColor", Rd_tag = "TEXT")), │ │ │ │ list(structure("A character vector giving the background color\n", Rd_tag = "TEXT"), │ │ │ │ structure(" for the body in the CSS file.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/writeRepositoryHtml.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Seth Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/writeRepositoryHtml.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ writeTopLevelView (list) = structure(list(structure(list(structure("Write the view for the root of a vocabulary to disk", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("writeTopLevelView", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("writeTopLevelView", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities ", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Given a directory and a vocabulary represented as a ", Rd_tag = "TEXT"), │ │ │ │ @@ -1737,15 +1737,15 @@ │ │ │ │ structure(list(list(structure("vocab", Rd_tag = "TEXT")), │ │ │ │ list(structure("A ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("graphNEL", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" instance giving the DAG of terms. It\n", Rd_tag = "TEXT"), │ │ │ │ structure(" should have a root node. That is, there should be exactly one node\n", Rd_tag = "TEXT"), │ │ │ │ structure(" with no incoming edges.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("S. Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/writeTopLevelView.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("S. Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/writeTopLevelView.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ write_REPOSITORY (list) = structure(list(structure(list(structure("Write a REPOSITORY control file for a CRAN-style package repository", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("write_REPOSITORY", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("write_REPOSITORY", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" This function writes a ", Rd_tag = "TEXT"), │ │ │ │ @@ -1790,15 +1790,15 @@ │ │ │ │ structure(list(structure(list(structure("write_PACKAGES", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("tools:write_PACKAGES", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractVignettes", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("genReposControlFiles", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("write_VIEWS", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/write_REPOSITORY.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/write_REPOSITORY.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ write_SYMBOLS (list) = structure(list(structure(list(structure("Write a SYMBOLS file", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("write_SYMBOLS", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("write_SYMBOLS", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Writes a DCF formatted file, SYMBOLS, containing the symbols\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1846,15 +1846,15 @@ │ │ │ │ structure("dir", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("S. Falcon", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("write_PACKAGES", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("tools:write_PACKAGES", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("write_VIEWS", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/write_SYMBOLS.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/write_SYMBOLS.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ write_VIEWS (list) = structure(list(structure(list(structure("Write a VIEWS control file for a CRAN-style package repository", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("write_VIEWS", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("write_VIEWS", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" This function writes a ", Rd_tag = "TEXT"), │ │ │ │ @@ -1920,10 +1920,10 @@ │ │ │ │ structure(list(structure(list(structure("write_PACKAGES", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("tools:write_PACKAGES", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("extractVignettes", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("genReposControlFiles", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("write_REPOSITORY", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-biocviews/man/write_VIEWS.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/write_VIEWS.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/biocViews/help/biocViews.rdx │ │ │ ├── biocViews.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,223 +1,223 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$`BiocView-class` │ │ │ │ │ -[1] 284 3181 │ │ │ │ │ +[1] 296 3195 │ │ │ │ │ │ │ │ │ │ $variables$`Htmlized-class` │ │ │ │ │ -[1] 3751 1047 │ │ │ │ │ +[1] 3787 1058 │ │ │ │ │ │ │ │ │ │ $variables$`PackageDetail-class` │ │ │ │ │ -[1] 5087 7855 │ │ │ │ │ +[1] 5146 7869 │ │ │ │ │ │ │ │ │ │ $variables$`RepositoryDetail-class` │ │ │ │ │ -[1] 13233 2341 │ │ │ │ │ +[1] 13318 2358 │ │ │ │ │ │ │ │ │ │ $variables$`biocViews-package` │ │ │ │ │ -[1] 15860 3312 │ │ │ │ │ +[1] 15972 3323 │ │ │ │ │ │ │ │ │ │ $variables$biocViewsVocab │ │ │ │ │ -[1] 19455 1283 │ │ │ │ │ +[1] 19588 1296 │ │ │ │ │ │ │ │ │ │ $variables$`build-dbs` │ │ │ │ │ -[1] 21018 3055 │ │ │ │ │ +[1] 21175 3067 │ │ │ │ │ │ │ │ │ │ $variables$dump_concept │ │ │ │ │ -[1] 24356 1022 │ │ │ │ │ +[1] 24538 1034 │ │ │ │ │ │ │ │ │ │ $variables$extractManuals │ │ │ │ │ -[1] 25665 1922 │ │ │ │ │ +[1] 25869 1933 │ │ │ │ │ │ │ │ │ │ $variables$extractNEWS │ │ │ │ │ -[1] 27872 876 │ │ │ │ │ +[1] 28098 889 │ │ │ │ │ │ │ │ │ │ $variables$extractTopLevelFiles │ │ │ │ │ -[1] 29040 968 │ │ │ │ │ +[1] 29290 982 │ │ │ │ │ │ │ │ │ │ $variables$extractVignettes │ │ │ │ │ -[1] 30295 2048 │ │ │ │ │ +[1] 30571 2061 │ │ │ │ │ │ │ │ │ │ $variables$genReposControlFiles │ │ │ │ │ -[1] 32630 2832 │ │ │ │ │ +[1] 32933 2842 │ │ │ │ │ │ │ │ │ │ $variables$getBiocSubViews │ │ │ │ │ -[1] 35749 3169 │ │ │ │ │ +[1] 36072 3182 │ │ │ │ │ │ │ │ │ │ $variables$getBiocViews │ │ │ │ │ -[1] 39202 2641 │ │ │ │ │ +[1] 39549 2654 │ │ │ │ │ │ │ │ │ │ $variables$getCurrentbiocViews │ │ │ │ │ -[1] 42131 1176 │ │ │ │ │ +[1] 42502 1191 │ │ │ │ │ │ │ │ │ │ $variables$getPackageNEWS │ │ │ │ │ -[1] 43595 3118 │ │ │ │ │ +[1] 43992 3131 │ │ │ │ │ │ │ │ │ │ $variables$getPackageTitles │ │ │ │ │ -[1] 47000 2832 │ │ │ │ │ +[1] 47422 2846 │ │ │ │ │ │ │ │ │ │ $variables$getPacksAndViews │ │ │ │ │ -[1] 50119 2013 │ │ │ │ │ +[1] 50567 2027 │ │ │ │ │ │ │ │ │ │ $variables$getSubTerms │ │ │ │ │ -[1] 52417 1380 │ │ │ │ │ +[1] 52889 1393 │ │ │ │ │ │ │ │ │ │ $variables$guessPackageType │ │ │ │ │ -[1] 54087 1295 │ │ │ │ │ +[1] 54582 1307 │ │ │ │ │ │ │ │ │ │ $variables$htmlDoc │ │ │ │ │ -[1] 55664 1218 │ │ │ │ │ +[1] 56180 1232 │ │ │ │ │ │ │ │ │ │ $variables$htmlFilename │ │ │ │ │ -[1] 57162 1146 │ │ │ │ │ +[1] 57705 1161 │ │ │ │ │ │ │ │ │ │ $variables$htmlValue │ │ │ │ │ -[1] 58591 1113 │ │ │ │ │ +[1] 59159 1127 │ │ │ │ │ │ │ │ │ │ $variables$recommendBiocViews │ │ │ │ │ -[1] 59992 2496 │ │ │ │ │ +[1] 60585 2507 │ │ │ │ │ │ │ │ │ │ $variables$recommendPackages │ │ │ │ │ -[1] 62776 1562 │ │ │ │ │ +[1] 63392 1575 │ │ │ │ │ │ │ │ │ │ $variables$validation_tests │ │ │ │ │ -[1] 64626 1181 │ │ │ │ │ +[1] 65266 1194 │ │ │ │ │ │ │ │ │ │ $variables$writeBiocViews │ │ │ │ │ -[1] 66092 1400 │ │ │ │ │ +[1] 66756 1416 │ │ │ │ │ │ │ │ │ │ $variables$writeHtmlDoc │ │ │ │ │ -[1] 67777 886 │ │ │ │ │ +[1] 68467 899 │ │ │ │ │ │ │ │ │ │ $variables$writePackageDetailHtml │ │ │ │ │ -[1] 68954 1233 │ │ │ │ │ +[1] 69670 1248 │ │ │ │ │ │ │ │ │ │ $variables$writeRFilesFromVignettes │ │ │ │ │ -[1] 70479 1186 │ │ │ │ │ +[1] 71222 1202 │ │ │ │ │ │ │ │ │ │ $variables$writeRepositoryHtml │ │ │ │ │ -[1] 71956 2355 │ │ │ │ │ +[1] 72725 2370 │ │ │ │ │ │ │ │ │ │ $variables$writeTopLevelView │ │ │ │ │ -[1] 74601 1191 │ │ │ │ │ +[1] 75395 1206 │ │ │ │ │ │ │ │ │ │ $variables$write_REPOSITORY │ │ │ │ │ -[1] 76079 2070 │ │ │ │ │ +[1] 76901 2082 │ │ │ │ │ │ │ │ │ │ $variables$write_SYMBOLS │ │ │ │ │ -[1] 78436 2070 │ │ │ │ │ +[1] 79282 2086 │ │ │ │ │ │ │ │ │ │ $variables$write_VIEWS │ │ │ │ │ -[1] 80789 2967 │ │ │ │ │ +[1] 81664 2979 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 284 │ │ │ │ │ +[1] 0 296 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 27587 285 │ │ │ │ │ +[1] 27802 296 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 28748 292 │ │ │ │ │ +[1] 28987 303 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 30008 287 │ │ │ │ │ +[1] 30272 299 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 32343 287 │ │ │ │ │ +[1] 32632 301 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 35462 287 │ │ │ │ │ +[1] 35775 297 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 38918 284 │ │ │ │ │ +[1] 39254 295 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 41843 288 │ │ │ │ │ +[1] 42203 299 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 43307 288 │ │ │ │ │ +[1] 43693 299 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 46713 287 │ │ │ │ │ +[1] 47123 299 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 49832 287 │ │ │ │ │ +[1] 50268 299 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 3465 286 │ │ │ │ │ +[1] 3491 296 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 52132 285 │ │ │ │ │ +[1] 52594 295 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 53797 290 │ │ │ │ │ +[1] 54282 300 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 55382 282 │ │ │ │ │ +[1] 55889 291 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 56882 280 │ │ │ │ │ +[1] 57412 293 │ │ │ │ │ │ │ │ │ │ $references$`env::24` │ │ │ │ │ -[1] 58308 283 │ │ │ │ │ +[1] 58866 293 │ │ │ │ │ │ │ │ │ │ $references$`env::25` │ │ │ │ │ -[1] 59704 288 │ │ │ │ │ +[1] 60286 299 │ │ │ │ │ │ │ │ │ │ $references$`env::26` │ │ │ │ │ -[1] 62488 288 │ │ │ │ │ +[1] 63092 300 │ │ │ │ │ │ │ │ │ │ $references$`env::27` │ │ │ │ │ -[1] 64338 288 │ │ │ │ │ +[1] 64967 299 │ │ │ │ │ │ │ │ │ │ $references$`env::28` │ │ │ │ │ -[1] 65807 285 │ │ │ │ │ +[1] 66460 296 │ │ │ │ │ │ │ │ │ │ $references$`env::29` │ │ │ │ │ -[1] 67492 285 │ │ │ │ │ +[1] 68172 295 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 4798 289 │ │ │ │ │ +[1] 4845 301 │ │ │ │ │ │ │ │ │ │ $references$`env::30` │ │ │ │ │ -[1] 68663 291 │ │ │ │ │ +[1] 69366 304 │ │ │ │ │ │ │ │ │ │ $references$`env::31` │ │ │ │ │ -[1] 70187 292 │ │ │ │ │ +[1] 70918 304 │ │ │ │ │ │ │ │ │ │ $references$`env::32` │ │ │ │ │ -[1] 71665 291 │ │ │ │ │ +[1] 72424 301 │ │ │ │ │ │ │ │ │ │ $references$`env::33` │ │ │ │ │ -[1] 74311 290 │ │ │ │ │ +[1] 75095 300 │ │ │ │ │ │ │ │ │ │ $references$`env::34` │ │ │ │ │ -[1] 75792 287 │ │ │ │ │ +[1] 76601 300 │ │ │ │ │ │ │ │ │ │ $references$`env::35` │ │ │ │ │ -[1] 78149 287 │ │ │ │ │ +[1] 78983 299 │ │ │ │ │ │ │ │ │ │ $references$`env::36` │ │ │ │ │ -[1] 80506 283 │ │ │ │ │ +[1] 81368 296 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 12942 291 │ │ │ │ │ +[1] 13015 303 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 15574 286 │ │ │ │ │ +[1] 15676 296 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 19172 283 │ │ │ │ │ +[1] 19295 293 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 20738 280 │ │ │ │ │ +[1] 20884 291 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 24073 283 │ │ │ │ │ +[1] 24242 296 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 25378 287 │ │ │ │ │ +[1] 25572 297 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/biocViews/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,38 +1,38 @@ │ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-biocviews/man/BiocView-class.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-biocviews/man/Htmlized-class.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-biocviews/man/PackageDetail-class.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-biocviews/man/RepositoryDetail-class.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-biocviews/man/biocViews-package.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-biocviews/man/biocViewsVocab.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-biocviews/man/build-dbs.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-biocviews/man/dump_concept.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-biocviews/man/extractManuals.Rd" │ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-biocviews/man/extractNEWS.Rd" │ │ │ │ │ -[11] "/home/moeller/Salsa/r-bioc-biocviews/man/extractTopLevelFiles.Rd" │ │ │ │ │ -[12] "/home/moeller/Salsa/r-bioc-biocviews/man/extractVignettes.Rd" │ │ │ │ │ -[13] "/home/moeller/Salsa/r-bioc-biocviews/man/genReposControlFiles.Rd" │ │ │ │ │ -[14] "/home/moeller/Salsa/r-bioc-biocviews/man/getBiocSubViews.Rd" │ │ │ │ │ -[15] "/home/moeller/Salsa/r-bioc-biocviews/man/getBiocViews.Rd" │ │ │ │ │ -[16] "/home/moeller/Salsa/r-bioc-biocviews/man/getCurrentbiocViews.Rd" │ │ │ │ │ -[17] "/home/moeller/Salsa/r-bioc-biocviews/man/getPackageNEWS.Rd" │ │ │ │ │ -[18] "/home/moeller/Salsa/r-bioc-biocviews/man/getPackageTitles.Rd" │ │ │ │ │ -[19] "/home/moeller/Salsa/r-bioc-biocviews/man/getPacksAndViews.Rd" │ │ │ │ │ -[20] "/home/moeller/Salsa/r-bioc-biocviews/man/getSubTerms.Rd" │ │ │ │ │ -[21] "/home/moeller/Salsa/r-bioc-biocviews/man/guessPackageType.Rd" │ │ │ │ │ -[22] "/home/moeller/Salsa/r-bioc-biocviews/man/htmlDoc.Rd" │ │ │ │ │ -[23] "/home/moeller/Salsa/r-bioc-biocviews/man/htmlFilename.Rd" │ │ │ │ │ -[24] "/home/moeller/Salsa/r-bioc-biocviews/man/htmlValue.Rd" │ │ │ │ │ -[25] "/home/moeller/Salsa/r-bioc-biocviews/man/recommendBiocViews.Rd" │ │ │ │ │ -[26] "/home/moeller/Salsa/r-bioc-biocviews/man/recommendPackages.Rd" │ │ │ │ │ -[27] "/home/moeller/Salsa/r-bioc-biocviews/man/validation_tests.Rd" │ │ │ │ │ -[28] "/home/moeller/Salsa/r-bioc-biocviews/man/writeBiocViews.Rd" │ │ │ │ │ -[29] "/home/moeller/Salsa/r-bioc-biocviews/man/writeHtmlDoc.Rd" │ │ │ │ │ -[30] "/home/moeller/Salsa/r-bioc-biocviews/man/writePackageDetailHtml.Rd" │ │ │ │ │ -[31] "/home/moeller/Salsa/r-bioc-biocviews/man/writeRFilesFromVignettes.Rd" │ │ │ │ │ -[32] "/home/moeller/Salsa/r-bioc-biocviews/man/writeRepositoryHtml.Rd" │ │ │ │ │ -[33] "/home/moeller/Salsa/r-bioc-biocviews/man/writeTopLevelView.Rd" │ │ │ │ │ -[34] "/home/moeller/Salsa/r-bioc-biocviews/man/write_REPOSITORY.Rd" │ │ │ │ │ -[35] "/home/moeller/Salsa/r-bioc-biocviews/man/write_SYMBOLS.Rd" │ │ │ │ │ -[36] "/home/moeller/Salsa/r-bioc-biocviews/man/write_VIEWS.Rd" │ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/BiocView-class.Rd" │ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/Htmlized-class.Rd" │ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/PackageDetail-class.Rd" │ │ │ │ │ + [4] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/RepositoryDetail-class.Rd" │ │ │ │ │ + [5] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/biocViews-package.Rd" │ │ │ │ │ + [6] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/biocViewsVocab.Rd" │ │ │ │ │ + [7] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/build-dbs.Rd" │ │ │ │ │ + [8] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/dump_concept.Rd" │ │ │ │ │ + [9] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/extractManuals.Rd" │ │ │ │ │ +[10] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/extractNEWS.Rd" │ │ │ │ │ +[11] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/extractTopLevelFiles.Rd" │ │ │ │ │ +[12] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/extractVignettes.Rd" │ │ │ │ │ +[13] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/genReposControlFiles.Rd" │ │ │ │ │ +[14] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/getBiocSubViews.Rd" │ │ │ │ │ +[15] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/getBiocViews.Rd" │ │ │ │ │ +[16] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/getCurrentbiocViews.Rd" │ │ │ │ │ +[17] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/getPackageNEWS.Rd" │ │ │ │ │ +[18] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/getPackageTitles.Rd" │ │ │ │ │ +[19] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/getPacksAndViews.Rd" │ │ │ │ │ +[20] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/getSubTerms.Rd" │ │ │ │ │ +[21] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/guessPackageType.Rd" │ │ │ │ │ +[22] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/htmlDoc.Rd" │ │ │ │ │ +[23] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/htmlFilename.Rd" │ │ │ │ │ +[24] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/htmlValue.Rd" │ │ │ │ │ +[25] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/recommendBiocViews.Rd" │ │ │ │ │ +[26] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/recommendPackages.Rd" │ │ │ │ │ +[27] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/validation_tests.Rd" │ │ │ │ │ +[28] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/writeBiocViews.Rd" │ │ │ │ │ +[29] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/writeHtmlDoc.Rd" │ │ │ │ │ +[30] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/writePackageDetailHtml.Rd" │ │ │ │ │ +[31] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/writeRFilesFromVignettes.Rd" │ │ │ │ │ +[32] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/writeRepositoryHtml.Rd" │ │ │ │ │ +[33] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/writeTopLevelView.Rd" │ │ │ │ │ +[34] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/write_REPOSITORY.Rd" │ │ │ │ │ +[35] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/write_SYMBOLS.Rd" │ │ │ │ │ +[36] "/build/reproducible-path/r-bioc-biocviews-1.80.0+ds/man/write_VIEWS.Rd" │ │ │ │ │ attr(,"first") │ │ │ │ │ -[1] 42 │ │ │ │ │ +[1] 57