--- /srv/rebuilderd/tmp/rebuilderdap1W5T/inputs/r-bioc-geneplotter_1.90.0+dfsg-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdap1W5T/out/r-bioc-geneplotter_1.90.0+dfsg-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-04 13:56:00.000000 debian-binary │ --rw-r--r-- 0 0 0 1700 2026-08-04 13:56:00.000000 control.tar.xz │ --rw-r--r-- 0 0 0 1508672 2026-08-04 13:56:00.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 1680 2026-08-04 13:56:00.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 1508780 2026-08-04 13:56:00.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 13:56:00.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 842 2026-08-04 13:56:00.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 801 2026-08-04 13:56:00.000000 ./control │ │ │ -rw-r--r-- 0 root (0) root (0) 2910 2026-08-04 13:56:00.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,13 @@ │ │ │ Package: r-bioc-geneplotter │ │ │ Version: 1.90.0+dfsg-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ Installed-Size: 1558 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-bioc-biobase, r-bioc-biocgenerics, r-cran-lattice, r-bioc-annotate, r-bioc-annotationdbi, r-cran-rcolorbrewer, r-pkg-team-core-architecture │ │ │ -Suggests: r-bioc-biocstyle, r-cran-knitr │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/geneplotter/ │ │ │ Description: R package of functions for plotting genomic data │ │ │ Geneplotter contains plotting functions for microarrays. │ │ │ . │ │ │ The functions cPlot and cColor allow the user to │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -15,37 +15,37 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 958 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1250 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/Meta/package.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 335 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1683 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 537 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/NEWS.Rd │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/R/geneplotter │ │ │ --rw-r--r-- 0 root (0) root (0) 90754 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/R/geneplotter.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 1209 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/R/geneplotter.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 90766 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/R/geneplotter.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 1211 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/R/geneplotter.rdx │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/data/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1969 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/data/IMCAEntrezLink.R │ │ │ -rw-r--r-- 0 root (0) root (0) 990912 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/data/expressionSet133a.rda │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1239 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/doc/byChroms.R │ │ │ -rw-r--r-- 0 root (0) root (0) 3075 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/doc/byChroms.Rmd │ │ │ -rw-r--r-- 0 root (0) root (0) 1831 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/doc/index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 1722 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/doc/visualize.R │ │ │ -rw-r--r-- 0 root (0) root (0) 4938 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/doc/visualize.Rnw │ │ │ -rw-r--r-- 0 root (0) root (0) 360467 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/doc/visualize.pdf │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1602 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/help/AnIndex │ │ │ -rw-r--r-- 0 root (0) root (0) 690 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 60676 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/help/geneplotter.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 577 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/help/geneplotter.rdx │ │ │ --rw-r--r-- 0 root (0) root (0) 311 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 61137 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/help/geneplotter.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 585 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/help/geneplotter.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 327 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 9860 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-04 13:56:00.000000 ./usr/lib/R/site-library/geneplotter/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 13:56:00.000000 ./usr/share/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 13:56:00.000000 ./usr/share/doc/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 13:56:00.000000 ./usr/share/doc/r-bioc-geneplotter/ │ │ │ -rw-r--r-- 0 root (0) root (0) 895 2026-08-04 13:56:00.000000 ./usr/share/doc/r-bioc-geneplotter/changelog.Debian.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2784 2026-08-04 13:54:58.000000 ./usr/share/doc/r-bioc-geneplotter/copyright │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 13:56:00.000000 ./usr/share/doc/r-bioc-geneplotter/examples/ │ │ │ -drwxr-xr-x 0 root (0) root (0) 0 2026-08-04 13:54:58.000000 ./usr/share/doc/r-bioc-geneplotter/examples/vignettes/ │ │ │ --rw-r--r-- 0 root (0) root (0) 3075 2026-08-04 13:54:58.000000 ./usr/share/doc/r-bioc-geneplotter/examples/vignettes/byChroms.Rmd │ │ │ --rw-r--r-- 0 root (0) root (0) 4938 2026-08-04 13:54:58.000000 ./usr/share/doc/r-bioc-geneplotter/examples/vignettes/visualize.Rnw │ │ │ +drwxr-xr-x 0 root (0) root (0) 0 2026-04-28 22:13:36.000000 ./usr/share/doc/r-bioc-geneplotter/examples/vignettes/ │ │ │ +-rw-r--r-- 0 root (0) root (0) 3075 2026-04-28 16:04:36.000000 ./usr/share/doc/r-bioc-geneplotter/examples/vignettes/byChroms.Rmd │ │ │ +-rw-r--r-- 0 root (0) root (0) 4938 2026-04-28 16:04:36.000000 ./usr/share/doc/r-bioc-geneplotter/examples/vignettes/visualize.Rnw │ │ ├── ./usr/lib/R/site-library/geneplotter/R/geneplotter.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -36,15 +36,15 @@ │ │ │ │ "imports" = " annotation = "annotation", ".__T__contents:Biobase" = ".__T__contents:Biobase", " │ │ │ │ "imports" = " contents = "contents", ".__T__esApply:Biobase" = ".__T__esApply:Biobase", " │ │ │ │ "imports" = " esApply = "esApply", ".__T__exprs:Biobase" = ".__T__exprs:Biobase", " │ │ │ │ "imports" = " exprs = "exprs", ".__T__featureNames:Biobase" = ".__T__featureNames:Biobase", " │ │ │ │ "imports" = " featureNames = "featureNames"), BiocGenerics = c(".__T__plotMA:BiocGenerics" = ".__T__plotMA:BiocGenerics", " │ │ │ │ "imports" = " plotMA = "plotMA"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-geneplotter/debian/r-bioc-geneplotter/usr/lib/R/site-library/geneplotter"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/debian/r-bioc-geneplotter/usr/lib/R/site-library/geneplotter"" │ │ │ │ "spec" = "c(name = "geneplotter", version = "1.90.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/geneplotter/R/geneplotter.rdx │ │ │ ├── geneplotter.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,232 +1,232 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 1373 52 │ │ │ │ │ +[1] 1385 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 1556 52 │ │ │ │ │ +[1] 1568 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__Makesense:geneplotter` │ │ │ │ │ -[1] 7292 52 │ │ │ │ │ +[1] 7304 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__imageMap:geneplotter` │ │ │ │ │ -[1] 11489 52 │ │ │ │ │ +[1] 11501 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__plotMA:BiocGenerics` │ │ │ │ │ -[1] 16790 53 │ │ │ │ │ +[1] 16802 53 │ │ │ │ │ │ │ │ │ │ $variables$.onAttach │ │ │ │ │ -[1] 16843 483 │ │ │ │ │ +[1] 16855 483 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 17326 56 │ │ │ │ │ +[1] 17338 56 │ │ │ │ │ │ │ │ │ │ $variables$.plotData │ │ │ │ │ -[1] 17382 1493 │ │ │ │ │ +[1] 17394 1493 │ │ │ │ │ │ │ │ │ │ $variables$GetColor │ │ │ │ │ -[1] 18875 1445 │ │ │ │ │ +[1] 18887 1445 │ │ │ │ │ │ │ │ │ │ $variables$Makesense │ │ │ │ │ -[1] 20320 435 │ │ │ │ │ +[1] 20332 435 │ │ │ │ │ │ │ │ │ │ $variables$alongChrom │ │ │ │ │ -[1] 20755 2738 │ │ │ │ │ +[1] 20767 2738 │ │ │ │ │ │ │ │ │ │ $variables$amplicon.plot │ │ │ │ │ -[1] 23493 3514 │ │ │ │ │ +[1] 23505 3514 │ │ │ │ │ │ │ │ │ │ $variables$buildACMainLabel │ │ │ │ │ -[1] 27007 673 │ │ │ │ │ +[1] 27019 673 │ │ │ │ │ │ │ │ │ │ $variables$cColor │ │ │ │ │ -[1] 27680 2268 │ │ │ │ │ +[1] 27692 2268 │ │ │ │ │ │ │ │ │ │ $variables$cPlot │ │ │ │ │ -[1] 29948 1708 │ │ │ │ │ +[1] 29960 1708 │ │ │ │ │ │ │ │ │ │ $variables$cScale │ │ │ │ │ -[1] 31656 551 │ │ │ │ │ +[1] 31668 551 │ │ │ │ │ │ │ │ │ │ $variables$closeHtmlPage │ │ │ │ │ -[1] 32207 292 │ │ │ │ │ +[1] 32219 292 │ │ │ │ │ │ │ │ │ │ $variables$cullACXPoints │ │ │ │ │ -[1] 32499 791 │ │ │ │ │ +[1] 32511 791 │ │ │ │ │ │ │ │ │ │ $variables$dChip.colors │ │ │ │ │ -[1] 33290 325 │ │ │ │ │ +[1] 33302 325 │ │ │ │ │ │ │ │ │ │ $variables$defMapFun │ │ │ │ │ -[1] 33615 713 │ │ │ │ │ +[1] 33627 713 │ │ │ │ │ │ │ │ │ │ $variables$dispACXaxis │ │ │ │ │ -[1] 34328 1456 │ │ │ │ │ +[1] 34340 1456 │ │ │ │ │ │ │ │ │ │ $variables$doACCumPlot │ │ │ │ │ -[1] 35784 3909 │ │ │ │ │ +[1] 35796 3909 │ │ │ │ │ │ │ │ │ │ $variables$doACImagePlot │ │ │ │ │ -[1] 39693 2870 │ │ │ │ │ +[1] 39705 2870 │ │ │ │ │ │ │ │ │ │ $variables$doACLocalPlot │ │ │ │ │ -[1] 42563 2805 │ │ │ │ │ +[1] 42575 2805 │ │ │ │ │ │ │ │ │ │ $variables$doACMatPlot │ │ │ │ │ -[1] 45368 753 │ │ │ │ │ +[1] 45380 753 │ │ │ │ │ │ │ │ │ │ $variables$emptyACPlot │ │ │ │ │ -[1] 46121 664 │ │ │ │ │ +[1] 46133 664 │ │ │ │ │ │ │ │ │ │ $variables$fixACPhysPoints │ │ │ │ │ -[1] 46785 1320 │ │ │ │ │ +[1] 46797 1320 │ │ │ │ │ │ │ │ │ │ $variables$getACClosestPos │ │ │ │ │ -[1] 48105 452 │ │ │ │ │ +[1] 48117 452 │ │ │ │ │ │ │ │ │ │ $variables$getACDataEnv │ │ │ │ │ -[1] 48557 561 │ │ │ │ │ +[1] 48569 561 │ │ │ │ │ │ │ │ │ │ $variables$getACExprs │ │ │ │ │ -[1] 49118 785 │ │ │ │ │ +[1] 49130 785 │ │ │ │ │ │ │ │ │ │ $variables$getACGeneSyms │ │ │ │ │ -[1] 49903 580 │ │ │ │ │ +[1] 49915 580 │ │ │ │ │ │ │ │ │ │ $variables$getACPlotLabs │ │ │ │ │ -[1] 50483 798 │ │ │ │ │ +[1] 50495 798 │ │ │ │ │ │ │ │ │ │ $variables$getACStrandVals │ │ │ │ │ -[1] 51281 2001 │ │ │ │ │ +[1] 51293 2001 │ │ │ │ │ │ │ │ │ │ $variables$getPlotExpressionColors │ │ │ │ │ -[1] 53282 494 │ │ │ │ │ +[1] 53294 494 │ │ │ │ │ │ │ │ │ │ $variables$greenred.colors │ │ │ │ │ -[1] 53776 347 │ │ │ │ │ +[1] 53788 347 │ │ │ │ │ │ │ │ │ │ $variables$groupedHeatmap │ │ │ │ │ -[1] 54123 4310 │ │ │ │ │ +[1] 54135 4310 │ │ │ │ │ │ │ │ │ │ $variables$highlightACDups │ │ │ │ │ -[1] 58433 1108 │ │ │ │ │ +[1] 58445 1108 │ │ │ │ │ │ │ │ │ │ $variables$histStack │ │ │ │ │ -[1] 59541 1468 │ │ │ │ │ +[1] 59553 1468 │ │ │ │ │ │ │ │ │ │ $variables$imageMap │ │ │ │ │ -[1] 61009 470 │ │ │ │ │ +[1] 61021 470 │ │ │ │ │ │ │ │ │ │ $variables$limitACXRange │ │ │ │ │ -[1] 61479 1763 │ │ │ │ │ +[1] 61491 1763 │ │ │ │ │ │ │ │ │ │ $variables$make.chromOrd │ │ │ │ │ -[1] 63242 2070 │ │ │ │ │ +[1] 63254 2070 │ │ │ │ │ │ │ │ │ │ $variables$multidensity │ │ │ │ │ -[1] 65312 188 │ │ │ │ │ +[1] 65324 188 │ │ │ │ │ │ │ │ │ │ $variables$multidensity.data.frame │ │ │ │ │ -[1] 65500 392 │ │ │ │ │ +[1] 65512 392 │ │ │ │ │ │ │ │ │ │ $variables$multidensity.formula │ │ │ │ │ -[1] 65892 1507 │ │ │ │ │ +[1] 65904 1507 │ │ │ │ │ │ │ │ │ │ $variables$multidensity.list │ │ │ │ │ -[1] 67399 3216 │ │ │ │ │ +[1] 67411 3216 │ │ │ │ │ │ │ │ │ │ $variables$multidensity.matrix │ │ │ │ │ -[1] 70615 739 │ │ │ │ │ +[1] 70627 739 │ │ │ │ │ │ │ │ │ │ $variables$multiecdf │ │ │ │ │ -[1] 71354 186 │ │ │ │ │ +[1] 71366 186 │ │ │ │ │ │ │ │ │ │ $variables$multiecdf.data.frame │ │ │ │ │ -[1] 71540 390 │ │ │ │ │ +[1] 71552 390 │ │ │ │ │ │ │ │ │ │ $variables$multiecdf.formula │ │ │ │ │ -[1] 71930 1503 │ │ │ │ │ +[1] 71942 1503 │ │ │ │ │ │ │ │ │ │ $variables$multiecdf.list │ │ │ │ │ -[1] 73433 2734 │ │ │ │ │ +[1] 73445 2734 │ │ │ │ │ │ │ │ │ │ $variables$multiecdf.matrix │ │ │ │ │ -[1] 76167 737 │ │ │ │ │ +[1] 76179 737 │ │ │ │ │ │ │ │ │ │ $variables$openHtmlPage │ │ │ │ │ -[1] 76904 666 │ │ │ │ │ +[1] 76916 666 │ │ │ │ │ │ │ │ │ │ $variables$plotChr │ │ │ │ │ -[1] 77570 7365 │ │ │ │ │ +[1] 77582 7365 │ │ │ │ │ │ │ │ │ │ $variables$plotExpressionGraph │ │ │ │ │ -[1] 84935 1519 │ │ │ │ │ +[1] 84947 1519 │ │ │ │ │ │ │ │ │ │ $variables$saveeps │ │ │ │ │ -[1] 86454 704 │ │ │ │ │ +[1] 86466 704 │ │ │ │ │ │ │ │ │ │ $variables$savepdf │ │ │ │ │ -[1] 87158 632 │ │ │ │ │ +[1] 87170 632 │ │ │ │ │ │ │ │ │ │ $variables$savepng │ │ │ │ │ -[1] 87790 639 │ │ │ │ │ +[1] 87802 639 │ │ │ │ │ │ │ │ │ │ $variables$savetiff │ │ │ │ │ -[1] 88429 789 │ │ │ │ │ +[1] 88441 789 │ │ │ │ │ │ │ │ │ │ $variables$scaleACData │ │ │ │ │ -[1] 89218 1536 │ │ │ │ │ +[1] 89230 1536 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 292 1081 │ │ │ │ │ +[1] 292 1093 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 9926 272 │ │ │ │ │ +[1] 9938 272 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 7344 1291 │ │ │ │ │ +[1] 7356 1291 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 8635 1291 │ │ │ │ │ +[1] 8647 1291 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 15410 1380 │ │ │ │ │ +[1] 15422 1380 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 15153 257 │ │ │ │ │ +[1] 15165 257 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 11541 1806 │ │ │ │ │ +[1] 11553 1806 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 13347 1806 │ │ │ │ │ +[1] 13359 1806 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 0 131 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ [1] 131 161 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 1425 131 │ │ │ │ │ +[1] 1437 131 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 5484 1808 │ │ │ │ │ +[1] 5496 1808 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 5224 260 │ │ │ │ │ +[1] 5236 260 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 1608 1808 │ │ │ │ │ +[1] 1620 1808 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 3416 1808 │ │ │ │ │ +[1] 3428 1808 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 10198 1291 │ │ │ │ │ +[1] 10210 1291 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/geneplotter/help/geneplotter.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -40,15 +40,15 @@ │ │ │ │ structure(list(structure("greenred.colors", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" does the same for the\n", Rd_tag = "TEXT"), │ │ │ │ structure(" green-black-red gradient. \n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A vector of RGB colors suitable for plotting in R.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("R. Gentleman, based on an original by C. Li. ", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" set.seed(10)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" x <- rnorm(10)\n", Rd_tag = "RCODE"), structure(" GetColor(x)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" dChip.colors(10)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/GetColor.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" dChip.colors(10)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/GetColor.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ Makesense (list) = structure(list(structure(list(structure("Produce Smoothed Sense/Anti-sense For All Chromosomes", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("Makesense", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("Makesense", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Makesense,matrix,character-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Makesense,ExpressionSet,missing-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -148,15 +148,15 @@ │ │ │ │ structure(list(structure("Robert Gentleman and Xiaochun Li", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure(" ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("plotChr", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" if (require(\"hgu133a.db\")) {\n", Rd_tag = "RCODE"), │ │ │ │ structure(" data(expressionSet133a)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" esetobj <- Makesense(exprs(expressionSet133a), \"hgu133a\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" esetobj2 <- Makesense(expressionSet133a[1:200, ])\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" }\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/Makesense.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" }\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/Makesense.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ alongChrom (list) = structure(list(structure(list(structure("A function for plotting expression data from an ExpressionSet for a\n", Rd_tag = "TEXT"), │ │ │ │ structure(" given chromosome.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("alongChrom", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("alongChrom", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("buildACMainLabel", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -298,15 +298,15 @@ │ │ │ │ structure(" for (bs in c(TRUE,FALSE))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" alongChrom(sample.ExpressionSet, \"1\",z, xlim=xlim, plotFormat=\"image\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" scale=\"zscale\", byStrand=bs)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" ## A boxplot\n", Rd_tag = "RCODE"), │ │ │ │ structure(" for (st in c(TRUE,FALSE))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" alongChrom(sample.ExpressionSet, \"1\", z, plotFormat=\"local\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colors=cols, byStrand=st)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" } else print(\"Example can not be run without the hgu95av2 data package\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/alongChrom.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" } else print(\"Example can not be run without the hgu95av2 data package\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/alongChrom.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ amplicon.plot (list) = structure(list(structure(list(structure("Create an amplicon plot ", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("amplicon.plot", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("amplicon.plot", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure(" hplot ", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Given a two-sample test statistic and an ExpressionSet this function plots\n", Rd_tag = "TEXT"), │ │ │ │ @@ -335,15 +335,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" These plot should help in the search for such regions.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" No value is returned. This function is executed purely for side\n", Rd_tag = "TEXT"), │ │ │ │ structure(" effect.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Robert Gentleman ", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure(list(structure(list(structure("esApply", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("Biobase", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("make.chromOrd", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code")), Rd_tag = "\\seealso"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure(" ##none yet; takes too long\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/amplicon.plot.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure(" ##none yet; takes too long\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/amplicon.plot.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ cColor (list) = structure(list(structure(list(structure("A function for marking specific probes on a cPlot.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("cColor", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("cColor", 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 set of probes, will highlight them in the color desired on\n", Rd_tag = "TEXT"), │ │ │ │ @@ -402,15 +402,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" if (require(\"hgu95av2.db\")) {\n", Rd_tag = "RCODE"), │ │ │ │ structure(" z <- buildChromLocation(\"hgu95av2\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" cPlot(z)\n", Rd_tag = "RCODE"), structure(" probes <- c(\"266_s_at\", \"31411_at\", \"610_at\", \"failExample\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" cColor(probes, \"red\", z)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" probes2 <- c(\"960_g_at\", \"41807_at\", \"931_at\", \"39032_at\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" cColor(probes2, \"blue\", z)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" } else\n", Rd_tag = "RCODE"), structure(" print(\"Need hgu95av2.db data package for the example\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/cColor.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" ", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/cColor.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ cPlot (list) = structure(list(structure(list(structure("A plotting function for chromosomes.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("cPlot", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("cPlot", 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 chromLocation object, will plot all the gene locations from\n", Rd_tag = "TEXT"), │ │ │ │ @@ -478,15 +478,15 @@ │ │ │ │ structure(" z <- buildChromLocation(\"hgu95av2\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" if (interactive()) {\n", Rd_tag = "RCODE"), │ │ │ │ structure(" curPar <- par(ask=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" on.exit(par(curPar), add=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" }\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure(" for (sc in c(\"max\",\"relative\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" cPlot(z,c(\"1\",\"5\",\"10\",\"X\",\"Y\"),sc)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" } else print(\"This example can not be run without hgu95av2 data package\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/cPlot.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" } else print(\"This example can not be run without hgu95av2 data package\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/cPlot.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ cScale (list) = structure(list(structure(list(structure("A function for mapping chromosome length to a number of points.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("cScale", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("cScale", 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 number of points (generally representing the number of points\n", Rd_tag = "TEXT"), │ │ │ │ @@ -525,29 +525,29 @@ │ │ │ │ structure(" ## but need to fiddle w/ the warn level to not fail the example anyways.\n", Rd_tag = "RCODE"), │ │ │ │ structure(" curWarn <- options(warn=0)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" on.exit(options(warn), add=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" if (require(\"hgu95av2.db\")) {\n", Rd_tag = "RCODE"), │ │ │ │ structure(" z <- buildChromLocation(\"hgu95av2\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" for (sc in c(\"max\",\"relative\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" scale <- cScale(1000, chromLengths(z),sc,\"Y\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" } else print(\"This example needs the hgu95av2 data package\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/cScale.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" } else print(\"This example needs the hgu95av2 data package\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/cScale.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ eset133a (list) = structure(list(structure(list(structure("A small dataset for testing", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("expressionSet133a", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("expressionSet133a", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\tAn artificial Affymetrix hgu133a dataset, with one \n", Rd_tag = "TEXT"), │ │ │ │ structure("covariate 'cov1'.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("data(expressionSet133a)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" The data are artifical. There are 6 cases labeled 1 to\n", Rd_tag = "TEXT"), │ │ │ │ structure(" 6 and and 22283 genes as in an Affymetrix U133a chips. \n", Rd_tag = "TEXT"), │ │ │ │ structure(" There is one covariate (factor) whose values are \"type 1\"\n", Rd_tag = "TEXT"), │ │ │ │ structure(" for the first 3 samples and \"type 2\" for the last 3 samples.\n", Rd_tag = "TEXT")), Rd_tag = "\\format"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(expressionSet133a)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/eset133a.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(expressionSet133a)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/eset133a.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ groupedHeatmap (list) = structure(list(structure(list(structure("Heatmap of a matrix with grouped rows and columns", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("groupedHeatmap", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("groupedHeatmap", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("The function uses ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("grid.rect", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("grid", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ @@ -610,15 +610,15 @@ │ │ │ │ structure(list(structure(list(structure(list(structure("grid.text", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("grid", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("grid.rect", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("grid", Rd_tag = "TEXT"))), Rd_tag = "\\code")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(\"mtcars\")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("groupedHeatmap(\n", Rd_tag = "RCODE"), structure(" scale(mtcars),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" frow = factor(sapply(strsplit(rownames(mtcars), \" \"), \"[\", 1)),\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" fcol = factor(round(seq_len(ncol(mtcars))/3)))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/groupedHeatmap.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" fcol = factor(round(seq_len(ncol(mtcars))/3)))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/groupedHeatmap.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ histStack (list) = structure(list(structure(list(structure("Stacked histogram", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("histStack", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("histStack", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -665,15 +665,15 @@ │ │ │ │ structure(list(structure("Wolfgang Huber ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("http://www.ebi.ac.uk/huber", Rd_tag = "VERB")), Rd_tag = "\\url")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" x <- list(rnorm(42), rnorm(42)+2)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" br <- seq(-3, 5, length=13)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" cols <- c(\"#1D267B\", \"#ceffc0\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" histStack(x, breaks=br, col=cols)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" histStack(x, breaks=br, col=cols,\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" breaksFun=function(z) paste(signif(z, 3)))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/histStack.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" breaksFun=function(z) paste(signif(z, 3)))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/histStack.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ imageMap (list) = structure(list(structure(list(structure("Write an HTML IMG tag together with a MAP image map.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("imageMap-methods", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("imageMap", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("imageMap-methods", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("imageMap,matrix-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -800,15 +800,15 @@ │ │ │ │ structure(" title =sample(as.character(packageDescription(\"geneplotter\")),nrow(coord),replace=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" con = file(f2, open=\"w\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" imageMap(coord, con,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" list(HREF=paste(\"http://\", href, sep=\"\"),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" TITLE=title, TARGET=rep(\"main\", nrow(coord))), fpng)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" close(con)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure(" cat(\"Now have a look at file \", f1, \" with your browser.\\n\", sep=\"\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/imageMap.Rd", class = "Rd", meta = list( │ │ │ │ + structure("}\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/imageMap.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ make.chromOrd (list) = structure(list(structure(list(structure("Make a chromOrd object ", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("make.chromOrd", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("make.chromOrd", 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 makes a chromOrd object.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -827,15 +827,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A list of chromOrd type. One element for each chromosome. Suitable for\n", Rd_tag = "TEXT"), │ │ │ │ structure(" reordering other values according to the chromosomal location.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure(" Robert Gentleman ", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure(" ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("amplicon.plot", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" data(sample.ExpressionSet)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" make.chromOrd(\"hgu95A\", featureNames(sample.ExpressionSet))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/make.chromOrd.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" make.chromOrd(\"hgu95A\", featureNames(sample.ExpressionSet))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/make.chromOrd.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ multiecdf (list) = structure(list(structure(list(structure("Multiple empirical cumulative distribution functions (ecdf) and densities", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("multiecdf", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("multiecdf", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("multiecdf.list", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("multiecdf.formula", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1048,15 +1048,15 @@ │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("density", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("stats", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" words = strsplit(packageDescription(\"geneplotter\")$Description, \" \")[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ structure(" factr = factor(sample(words, 2000, replace = TRUE))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" x = rnorm(length(factr), mean=as.integer(factr))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \n", Rd_tag = "RCODE"), structure(" multiecdf(x ~ factr)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" multidensity(x ~ factr)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/multiecdf.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" multidensity(x ~ factr)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/multiecdf.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ openHtmlPage (list) = structure(list(structure(list(structure("Open and close an HTML file for writing.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("openHtmlPage", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("openHtmlPage", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("closeHtmlPage", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("IO", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -1085,15 +1085,15 @@ │ │ │ │ structure(". ", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Wolfgang Huber ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("http://www.dkfz.de/abt0840/whuber", Rd_tag = "VERB")), Rd_tag = "\\url")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" fn <- tempfile()\n", Rd_tag = "RCODE"), │ │ │ │ structure(" con <- openHtmlPage(fn, \"My page\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" writeLines(\"Hello world\", con)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" closeHtmlPage(con)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" readLines(paste(fn, \".html\", sep=\"\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/openHtmlPage.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" readLines(paste(fn, \".html\", sep=\"\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/openHtmlPage.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ plotChr (list) = structure(list(structure(list(structure("Plot Smoothed Sense/Anti-sense of Specified Chromosomes", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotChr", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotChr", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("hplot", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("For a given chromosome, plot the smooths of the sense and the \n", Rd_tag = "TEXT"), │ │ │ │ @@ -1155,15 +1155,15 @@ │ │ │ │ structure("plotChr(\"21\", esetobj, cols, log=TRUE, geneSymbols=FALSE, lines.at=gs)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# add vertical lines at genes of interest\n", Rd_tag = "RCODE"), │ │ │ │ structure("# with specified colors:\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("gs <- c(\"220372_at\", \"35776_at\", \"200943_at\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("cc <- c(\"blue\", \"cyan\",\"magenta\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotChr(\"21\", esetobj, cols, log=TRUE, geneSymbols=FALSE, lines.at=gs,\n", Rd_tag = "RCODE"), │ │ │ │ structure("lines.col=cc)\n", Rd_tag = "RCODE"), structure("if (interactive())\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" par(op)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/plotChr.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" par(op)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/plotChr.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ plotExpressionGraph (list) = structure(list(structure(list(structure("A function to plot a graph colored by expression data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotExpressionGraph", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotExpressionGraph", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("getPlotExpressionColors", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("IMCAEntrezLink", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1301,15 +1301,15 @@ │ │ │ │ structure("\t data(IMCAEntrezLink)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" data(fibroEset)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" attrs <- getDefaultAttrs()\n", Rd_tag = "RCODE"), │ │ │ │ structure(" attrs$graph$rankdir <- \"LR\"\n", Rd_tag = "RCODE"), │ │ │ │ structure(" plotExpressionGraph(IMCAGraph, IMCAEntrezLink,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" exprs(fibroEset)[,1],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" hgu95av2ENTREZID, attrs = attrs)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" }\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/plotExpressionGraph.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" }\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/plotExpressionGraph.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ plotMA (list) = structure(list(structure(list(structure("Generate an MA plot", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotMA-methods", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotMA", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("plotMA-methods", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("plotMA,data.frame-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1372,15 +1372,15 @@ │ │ │ │ structure(list(structure(list(structure("plot", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(".\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 = "RCODE"), structure(" plotMA(\n", Rd_tag = "RCODE"), │ │ │ │ structure(" data.frame(\n", Rd_tag = "RCODE"), structure(" `M` = exp(rexp(1000)),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" `A` = rnorm(1000) -> tmp,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" `isde` = abs(tmp)>2) \n", Rd_tag = "RCODE"), │ │ │ │ - structure(" )\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/plotMA.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" )\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/plotMA.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ │ │ @@ -1487,10 +1487,10 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" x = seq(0, 20*pi, len=1000)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" plot(x*sin(x), x*cos(x), type=\"l\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" try({ ## on some machines, some of the devices may not be available\n", Rd_tag = "RCODE"), │ │ │ │ structure(" c(\n", Rd_tag = "RCODE"), structure(" savepdf(\"spiral\", dir=tempdir()),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" savepng(\"spiral\", dir=tempdir()),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" saveeps(\"spiral\", dir=tempdir()),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" savetiff(\"spiral\", dir=tempdir())\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" )\n", Rd_tag = "RCODE"), structure(" }) \n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geneplotter/man/savepng.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" )\n", Rd_tag = "RCODE"), structure(" }) \n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/savepng.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/geneplotter/help/geneplotter.rdx │ │ │ ├── geneplotter.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,115 +1,115 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$GetColor │ │ │ │ │ -[1] 279 2043 │ │ │ │ │ +[1] 290 2055 │ │ │ │ │ │ │ │ │ │ $variables$Makesense │ │ │ │ │ -[1] 2602 3775 │ │ │ │ │ +[1] 2636 3791 │ │ │ │ │ │ │ │ │ │ $variables$alongChrom │ │ │ │ │ -[1] 6658 5244 │ │ │ │ │ +[1] 6719 5259 │ │ │ │ │ │ │ │ │ │ $variables$amplicon.plot │ │ │ │ │ -[1] 12184 1870 │ │ │ │ │ +[1] 12270 1887 │ │ │ │ │ │ │ │ │ │ $variables$cColor │ │ │ │ │ -[1] 14331 2681 │ │ │ │ │ +[1] 14445 2693 │ │ │ │ │ │ │ │ │ │ $variables$cPlot │ │ │ │ │ -[1] 17288 3052 │ │ │ │ │ +[1] 17425 3065 │ │ │ │ │ │ │ │ │ │ $variables$cScale │ │ │ │ │ -[1] 20616 2116 │ │ │ │ │ +[1] 20778 2129 │ │ │ │ │ │ │ │ │ │ $variables$eset133a │ │ │ │ │ -[1] 23013 869 │ │ │ │ │ +[1] 23197 886 │ │ │ │ │ │ │ │ │ │ $variables$groupedHeatmap │ │ │ │ │ -[1] 24165 2633 │ │ │ │ │ +[1] 24377 2648 │ │ │ │ │ │ │ │ │ │ $variables$histStack │ │ │ │ │ -[1] 27078 2112 │ │ │ │ │ +[1] 27315 2125 │ │ │ │ │ │ │ │ │ │ $variables$imageMap │ │ │ │ │ -[1] 29470 5294 │ │ │ │ │ +[1] 29730 5310 │ │ │ │ │ │ │ │ │ │ $variables$make.chromOrd │ │ │ │ │ -[1] 35048 1356 │ │ │ │ │ +[1] 35335 1373 │ │ │ │ │ │ │ │ │ │ $variables$multiecdf │ │ │ │ │ -[1] 36684 6897 │ │ │ │ │ +[1] 36998 6912 │ │ │ │ │ │ │ │ │ │ $variables$openHtmlPage │ │ │ │ │ -[1] 43863 1515 │ │ │ │ │ +[1] 44203 1531 │ │ │ │ │ │ │ │ │ │ $variables$plotChr │ │ │ │ │ -[1] 45655 2790 │ │ │ │ │ +[1] 46022 2806 │ │ │ │ │ │ │ │ │ │ $variables$plotExpressionGraph │ │ │ │ │ -[1] 48731 5005 │ │ │ │ │ +[1] 49125 5021 │ │ │ │ │ │ │ │ │ │ $variables$plotMA │ │ │ │ │ -[1] 54012 2521 │ │ │ │ │ +[1] 54434 2536 │ │ │ │ │ │ │ │ │ │ $variables$savepng │ │ │ │ │ -[1] 56810 3866 │ │ │ │ │ +[1] 57258 3879 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 279 │ │ │ │ │ +[1] 0 290 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 26798 280 │ │ │ │ │ +[1] 27025 290 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 29190 280 │ │ │ │ │ +[1] 29440 290 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 34764 284 │ │ │ │ │ +[1] 35040 295 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 36404 280 │ │ │ │ │ +[1] 36708 290 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 43581 282 │ │ │ │ │ +[1] 43910 293 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 45378 277 │ │ │ │ │ +[1] 45734 288 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 48445 286 │ │ │ │ │ +[1] 48828 297 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 53736 276 │ │ │ │ │ +[1] 54146 288 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 56533 277 │ │ │ │ │ +[1] 56970 288 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 2322 280 │ │ │ │ │ +[1] 2345 291 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 6377 281 │ │ │ │ │ +[1] 6427 292 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 11902 282 │ │ │ │ │ +[1] 11978 292 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 14054 277 │ │ │ │ │ +[1] 14157 288 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 17012 276 │ │ │ │ │ +[1] 17138 287 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 20340 276 │ │ │ │ │ +[1] 20490 288 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 22732 281 │ │ │ │ │ +[1] 22907 290 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 23882 283 │ │ │ │ │ +[1] 24083 294 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/geneplotter/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,20 +1,20 @@ │ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-geneplotter/man/GetColor.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-geneplotter/man/Makesense.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-geneplotter/man/alongChrom.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-geneplotter/man/amplicon.plot.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-geneplotter/man/cColor.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-geneplotter/man/cPlot.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-geneplotter/man/cScale.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-geneplotter/man/eset133a.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-geneplotter/man/groupedHeatmap.Rd" │ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-geneplotter/man/histStack.Rd" │ │ │ │ │ -[11] "/home/moeller/Salsa/r-bioc-geneplotter/man/imageMap.Rd" │ │ │ │ │ -[12] "/home/moeller/Salsa/r-bioc-geneplotter/man/make.chromOrd.Rd" │ │ │ │ │ -[13] "/home/moeller/Salsa/r-bioc-geneplotter/man/multiecdf.Rd" │ │ │ │ │ -[14] "/home/moeller/Salsa/r-bioc-geneplotter/man/openHtmlPage.Rd" │ │ │ │ │ -[15] "/home/moeller/Salsa/r-bioc-geneplotter/man/plotChr.Rd" │ │ │ │ │ -[16] "/home/moeller/Salsa/r-bioc-geneplotter/man/plotExpressionGraph.Rd" │ │ │ │ │ -[17] "/home/moeller/Salsa/r-bioc-geneplotter/man/plotMA.Rd" │ │ │ │ │ -[18] "/home/moeller/Salsa/r-bioc-geneplotter/man/savepng.Rd" │ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/GetColor.Rd" │ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/Makesense.Rd" │ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/alongChrom.Rd" │ │ │ │ │ + [4] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/amplicon.plot.Rd" │ │ │ │ │ + [5] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/cColor.Rd" │ │ │ │ │ + [6] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/cPlot.Rd" │ │ │ │ │ + [7] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/cScale.Rd" │ │ │ │ │ + [8] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/eset133a.Rd" │ │ │ │ │ + [9] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/groupedHeatmap.Rd" │ │ │ │ │ +[10] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/histStack.Rd" │ │ │ │ │ +[11] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/imageMap.Rd" │ │ │ │ │ +[12] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/make.chromOrd.Rd" │ │ │ │ │ +[13] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/multiecdf.Rd" │ │ │ │ │ +[14] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/openHtmlPage.Rd" │ │ │ │ │ +[15] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/plotChr.Rd" │ │ │ │ │ +[16] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/plotExpressionGraph.Rd" │ │ │ │ │ +[17] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/plotMA.Rd" │ │ │ │ │ +[18] "/build/reproducible-path/r-bioc-geneplotter-1.90.0+dfsg/man/savepng.Rd" │ │ │ │ │ attr(,"first") │ │ │ │ │ -[1] 44 │ │ │ │ │ +[1] 61