--- /srv/rebuilderd/tmp/rebuilderdkIdswC/inputs/r-bioc-netsam_1.52.0+ds-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdkIdswC/out/r-bioc-netsam_1.52.0+ds-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-10 20:06:18.000000 debian-binary │ --rw-r--r-- 0 0 0 2268 2026-08-10 20:06:18.000000 control.tar.xz │ --rw-r--r-- 0 0 0 1127376 2026-08-10 20:06:18.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 2248 2026-08-10 20:06:18.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 1127396 2026-08-10 20:06:18.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 20:06:18.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 1727 2026-08-10 20:06:18.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 1675 2026-08-10 20:06:18.000000 ./control │ │ │ -rw-r--r-- 0 root (0) root (0) 3138 2026-08-10 20:06:18.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,14 @@ │ │ │ Package: r-bioc-netsam │ │ │ Version: 1.52.0+ds-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ Installed-Size: 3089 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-cran-seriation (>= 1.0-6), r-cran-igraph (>= 2.0.0), r-cran-wgcna (>= 1.34.0), r-bioc-biomart (>= 2.18.0), r-bioc-annotationdbi (>= 1.28.0), r-cran-doparallel (>= 1.0.10), r-cran-foreach (>= 1.4.0), r-cran-survival (>= 2.37-7), r-bioc-go.db (>= 2.10.0), r-cran-r2html (>= 2.2.0), r-cran-dbi (>= 0.5-1), r-pkg-team-core-architecture │ │ │ -Suggests: r-cran-runit, r-bioc-biocgenerics, r-bioc-org.hs.eg.db, r-cran-rmarkdown, r-cran-knitr, r-cran-markdown │ │ │ +Suggests: r-bioc-biocgenerics, r-cran-rmarkdown, r-cran-knitr │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/NetSAM/ │ │ │ Description: Network Seriation And Modularization │ │ │ Current high-throughput analyses for gene expression data │ │ │ commonly yield a genome-wide overview on genes affected │ │ │ by a disturbance (genetic mutation, drug, ...) to a tissue │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -14,16 +14,16 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 293 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/Meta/links.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 608 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1717 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/Meta/package.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 210 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 762 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/NAMESPACE │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/R/NetSAM │ │ │ --rw-r--r-- 0 root (0) root (0) 175892 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/R/NetSAM.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 1186 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/R/NetSAM.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 175902 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/R/NetSAM.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 1187 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/R/NetSAM.rdx │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/data/ │ │ │ -rw-r--r-- 0 root (0) root (0) 157650 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/data/NetSAMOutput_Example.rda │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 6628 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/doc/NetSAM.R │ │ │ -rw-r--r-- 0 root (0) root (0) 34450 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/doc/NetSAM.Rmd │ │ │ -rw-r--r-- 0 root (0) root (0) 243335 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/doc/NetSAM.pdf │ │ │ -rw-r--r-- 0 root (0) root (0) 1356 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/doc/index.html │ │ │ @@ -35,18 +35,18 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 8784 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/extdata/exampleNetwork.txt │ │ │ -rw-r--r-- 0 root (0) root (0) 10387 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/extdata/exampleNetwork_nonsymbol.net │ │ │ -rw-r--r-- 0 root (0) root (0) 1409 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/extdata/exampleSBT.sbt │ │ │ -rw-r--r-- 0 root (0) root (0) 1994 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/extdata/exampleSCT.sct │ │ │ -rw-r--r-- 0 root (0) root (0) 58755 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/extdata/sampleAnnotation.tsi │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 300 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/help/AnIndex │ │ │ --rw-r--r-- 0 root (0) root (0) 42662 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/help/NetSAM.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 456 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/help/NetSAM.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 42888 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/help/NetSAM.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 459 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/help/NetSAM.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 206 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 259 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 274 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 2717 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/unitTests/ │ │ │ -rw-r--r-- 0 root (0) root (0) 330 2026-08-10 20:06:18.000000 ./usr/lib/R/site-library/NetSAM/unitTests/test_NetSAM.R │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 20:06:18.000000 ./usr/share/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 20:06:18.000000 ./usr/share/doc/ │ │ ├── ./usr/lib/R/site-library/NetSAM/R/NetSAM.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -1409,15 +1409,15 @@ │ │ │ │ "imports" = " dist = "dist", hclust = "hclust", kruskal.test = "kruskal.test", " │ │ │ │ "imports" = " lm = "lm", median = "median", order.dendrogram = "order.dendrogram", " │ │ │ │ "imports" = " p.adjust = "p.adjust", phyper = "phyper", pnorm = "pnorm", " │ │ │ │ "imports" = " pt = "pt", sd = "sd", t.test = "t.test", wilcox.test = "wilcox.test"" │ │ │ │ "imports" = " ), utils = c(read.csv = "read.csv", read.table = "read.table", " │ │ │ │ "imports" = " write.table = "write.table"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-netsam/debian/r-bioc-netsam/usr/lib/R/site-library/NetSAM"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-netsam-1.52.0+ds/debian/r-bioc-netsam/usr/lib/R/site-library/NetSAM"" │ │ │ │ "spec" = "c(name = "NetSAM", version = "1.52.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/NetSAM/R/NetSAM.rdx │ │ │ ├── NetSAM.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -29,171 +29,171 @@ │ │ │ │ │ $variables$.SURTest │ │ │ │ │ [1] 17480 1641 │ │ │ │ │ │ │ │ │ │ $variables$.SURTest_single │ │ │ │ │ [1] 19121 687 │ │ │ │ │ │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 36134 52 │ │ │ │ │ +[1] 36144 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 36317 52 │ │ │ │ │ +[1] 36327 52 │ │ │ │ │ │ │ │ │ │ $variables$.autoSearchIdType │ │ │ │ │ -[1] 36369 3634 │ │ │ │ │ +[1] 36379 3634 │ │ │ │ │ │ │ │ │ │ $variables$.calculateConsensusNetwork │ │ │ │ │ -[1] 40003 1811 │ │ │ │ │ +[1] 40013 1811 │ │ │ │ │ │ │ │ │ │ $variables$.calculateNANum │ │ │ │ │ -[1] 41814 282 │ │ │ │ │ +[1] 41824 282 │ │ │ │ │ │ │ │ │ │ $variables$.calculateRandomWalkerAdjectMatrix │ │ │ │ │ -[1] 42096 2642 │ │ │ │ │ +[1] 42106 2642 │ │ │ │ │ │ │ │ │ │ $variables$.calculateSigCorr │ │ │ │ │ -[1] 44738 1468 │ │ │ │ │ +[1] 44748 1468 │ │ │ │ │ │ │ │ │ │ $variables$.createGMTFile │ │ │ │ │ -[1] 46206 2667 │ │ │ │ │ +[1] 46216 2667 │ │ │ │ │ │ │ │ │ │ $variables$.createHMIFile │ │ │ │ │ -[1] 48873 2522 │ │ │ │ │ +[1] 48883 2522 │ │ │ │ │ │ │ │ │ │ $variables$.createHTML_GO │ │ │ │ │ -[1] 51395 2621 │ │ │ │ │ +[1] 51405 2621 │ │ │ │ │ │ │ │ │ │ $variables$.createHTML_feature │ │ │ │ │ -[1] 54016 3141 │ │ │ │ │ +[1] 54026 3141 │ │ │ │ │ │ │ │ │ │ $variables$.enrichmentFunction │ │ │ │ │ -[1] 57157 2689 │ │ │ │ │ +[1] 57167 2689 │ │ │ │ │ │ │ │ │ │ $variables$.evaluateWalktrapStep │ │ │ │ │ -[1] 59846 4148 │ │ │ │ │ +[1] 59856 4148 │ │ │ │ │ │ │ │ │ │ $variables$.extractSubNetwork │ │ │ │ │ -[1] 63994 1206 │ │ │ │ │ +[1] 64004 1206 │ │ │ │ │ │ │ │ │ │ $variables$.fdrFilter │ │ │ │ │ -[1] 65200 748 │ │ │ │ │ +[1] 65210 748 │ │ │ │ │ │ │ │ │ │ $variables$.findBestNeighbor │ │ │ │ │ -[1] 65948 684 │ │ │ │ │ +[1] 65958 684 │ │ │ │ │ │ │ │ │ │ $variables$.fit_power_law │ │ │ │ │ -[1] 66632 1853 │ │ │ │ │ +[1] 66642 1853 │ │ │ │ │ │ │ │ │ │ $variables$.getClass │ │ │ │ │ -[1] 68485 292 │ │ │ │ │ +[1] 68495 292 │ │ │ │ │ │ │ │ │ │ $variables$.identifyHierOr │ │ │ │ │ -[1] 68777 3615 │ │ │ │ │ +[1] 68787 3615 │ │ │ │ │ │ │ │ │ │ $variables$.identifyModule │ │ │ │ │ -[1] 72392 3236 │ │ │ │ │ +[1] 72402 3236 │ │ │ │ │ │ │ │ │ │ $variables$.identifySig │ │ │ │ │ -[1] 75628 633 │ │ │ │ │ +[1] 75638 633 │ │ │ │ │ │ │ │ │ │ $variables$.identifySig_Unweighted │ │ │ │ │ -[1] 76261 3091 │ │ │ │ │ +[1] 76271 3091 │ │ │ │ │ │ │ │ │ │ $variables$.identifySig_Weighted │ │ │ │ │ -[1] 79352 3109 │ │ │ │ │ +[1] 79362 3109 │ │ │ │ │ │ │ │ │ │ $variables$.normalizeNetwork │ │ │ │ │ -[1] 82461 655 │ │ │ │ │ +[1] 82471 655 │ │ │ │ │ │ │ │ │ │ $variables$.onAttach │ │ │ │ │ -[1] 83116 284 │ │ │ │ │ +[1] 83126 284 │ │ │ │ │ │ │ │ │ │ $variables$.orderDiffLevel │ │ │ │ │ -[1] 83400 1678 │ │ │ │ │ +[1] 83410 1678 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 85078 51 │ │ │ │ │ +[1] 85088 51 │ │ │ │ │ │ │ │ │ │ $variables$.paste_dataframe │ │ │ │ │ -[1] 85129 477 │ │ │ │ │ +[1] 85139 477 │ │ │ │ │ │ │ │ │ │ $variables$.prcomp_WGCNA │ │ │ │ │ -[1] 85606 857 │ │ │ │ │ +[1] 85616 857 │ │ │ │ │ │ │ │ │ │ $variables$.rankBasedCoexp │ │ │ │ │ -[1] 86463 1793 │ │ │ │ │ +[1] 86473 1793 │ │ │ │ │ │ │ │ │ │ $variables$.returnMaxPos │ │ │ │ │ -[1] 88256 225 │ │ │ │ │ +[1] 88266 225 │ │ │ │ │ │ │ │ │ │ $variables$.sbtToSymbol │ │ │ │ │ -[1] 88481 2863 │ │ │ │ │ +[1] 88491 2863 │ │ │ │ │ │ │ │ │ │ $variables$.sctToSymbol │ │ │ │ │ -[1] 91344 2152 │ │ │ │ │ +[1] 91354 2152 │ │ │ │ │ │ │ │ │ │ $variables$.testCCTFormat │ │ │ │ │ -[1] 93496 2607 │ │ │ │ │ +[1] 93506 2607 │ │ │ │ │ │ │ │ │ │ $variables$.testTSIFormat │ │ │ │ │ -[1] 96103 7197 │ │ │ │ │ +[1] 96113 7197 │ │ │ │ │ │ │ │ │ │ $variables$.transformFromWalktrapToHclust │ │ │ │ │ -[1] 103300 1618 │ │ │ │ │ +[1] 103310 1618 │ │ │ │ │ │ │ │ │ │ $variables$.valueBasedCoexp │ │ │ │ │ -[1] 104918 856 │ │ │ │ │ +[1] 104928 856 │ │ │ │ │ │ │ │ │ │ $variables$.walktrapcommunity │ │ │ │ │ -[1] 105774 561 │ │ │ │ │ +[1] 105784 561 │ │ │ │ │ │ │ │ │ │ $variables$GOAssociation │ │ │ │ │ -[1] 106335 8074 │ │ │ │ │ +[1] 106345 8074 │ │ │ │ │ │ │ │ │ │ $variables$MatNet │ │ │ │ │ -[1] 114409 7727 │ │ │ │ │ +[1] 114419 7727 │ │ │ │ │ │ │ │ │ │ $variables$MatSAM │ │ │ │ │ -[1] 122136 15713 │ │ │ │ │ +[1] 122146 15713 │ │ │ │ │ │ │ │ │ │ $variables$NetAnalyzer │ │ │ │ │ -[1] 137849 6259 │ │ │ │ │ +[1] 137859 6259 │ │ │ │ │ │ │ │ │ │ $variables$NetSAM │ │ │ │ │ -[1] 144108 13004 │ │ │ │ │ +[1] 144118 13004 │ │ │ │ │ │ │ │ │ │ $variables$consensusNet │ │ │ │ │ -[1] 157112 1825 │ │ │ │ │ +[1] 157122 1825 │ │ │ │ │ │ │ │ │ │ $variables$featureAssociation │ │ │ │ │ -[1] 158937 6185 │ │ │ │ │ +[1] 158947 6185 │ │ │ │ │ │ │ │ │ │ $variables$mapToSymbol │ │ │ │ │ -[1] 165122 5466 │ │ │ │ │ +[1] 165132 5466 │ │ │ │ │ │ │ │ │ │ $variables$mergeDuplicate │ │ │ │ │ -[1] 170588 3141 │ │ │ │ │ +[1] 170598 3141 │ │ │ │ │ │ │ │ │ │ $variables$read_graph_ncol │ │ │ │ │ -[1] 173729 861 │ │ │ │ │ +[1] 173739 861 │ │ │ │ │ │ │ │ │ │ $variables$testFileFormat │ │ │ │ │ -[1] 174590 1302 │ │ │ │ │ +[1] 174600 1302 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 20098 16036 │ │ │ │ │ +[1] 20098 16046 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 19808 131 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ [1] 19939 159 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 36186 131 │ │ │ │ │ +[1] 36196 131 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/NetSAM/help/NetSAM.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -39,15 +39,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\t", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("MatSAM", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\t", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("NetSAM", 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("\tdata(NetSAMOutput_Example)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\toutputHtmlFile <- paste(getwd(),\"/GOAsso_HTML\",sep=\"\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\tGOAsso <- GOAssociation(NetSAMOutput=netsam_output, outputHtmlFile=outputHtmlFile, organism=\"hsapiens\", fdrmethod=\"BH\", fdrth=0.05, topNum=5)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-netsam/man/GOAssociation.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\tGOAsso <- GOAssociation(NetSAMOutput=netsam_output, outputHtmlFile=outputHtmlFile, organism=\"hsapiens\", fdrmethod=\"BH\", fdrth=0.05, topNum=5)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/GOAssociation.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ MatNet (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("\tConstruction of correlation network from a matrix\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("MatNet", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("MatNet", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure(" methods ", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -134,15 +134,15 @@ │ │ │ │ structure(list(list(structure("nThreads", Rd_tag = "TEXT")), │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure("\tMatNet function supports parallel computing based on multiple cores. The default is 3.\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("For data with missing values, the function will take longer time to calculate correlation between each pair of ids than data without missing value.\n", Rd_tag = "TEXT")), Rd_tag = "\\note"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\tJing Wang\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\tinputMatDir <- system.file(\"extdata\",\"exampleExpressionData.cct\",package=\"NetSAM\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\tmatNetwork <- MatNet(inputMat=inputMatDir, collapse_mode=\"maxSD\", naPer=0.7, meanPer=0.8, varPer=0.8, corrType=\"spearman\", matNetMethod=\"rank\", valueThr=0.6, rankBest=0.003, networkType=\"signed\", netFDRMethod=\"BH\", netFDRThr=0.05, idNumThr=(-1),nThreads=3)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-netsam/man/MatNet.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\tmatNetwork <- MatNet(inputMat=inputMatDir, collapse_mode=\"maxSD\", naPer=0.7, meanPer=0.8, varPer=0.8, corrType=\"spearman\", matNetMethod=\"rank\", valueThr=0.6, rankBest=0.003, networkType=\"signed\", netFDRMethod=\"BH\", netFDRThr=0.05, idNumThr=(-1),nThreads=3)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/MatNet.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ MatSAM (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("\tCorrelation network construction, seriation and modularization from a matrix\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("MatSAM", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("MatSAM", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure(" methods ", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -316,15 +316,15 @@ │ │ │ │ structure(list(structure(list(structure("NetSAM", 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("\tinputMatDir <- system.file(\"extdata\",\"exampleExpressionData.cct\",package=\"NetSAM\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\tcat(inputMatDir)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\tsampleAnnDir <- system.file(\"extdata\",\"sampleAnnotation.tsi\",package=\"NetSAM\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\tcat(sampleAnnDir)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\toutputFileName <- paste(getwd(),\"/MatSAM\",sep=\"\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\tmatModule <- MatSAM(inputMat=inputMatDir, sampleAnn=sampleAnnDir, outputFileName=outputFileName, outputFormat=\"msm\", organism=\"hsapiens\", map_to_symbol=FALSE, idType=\"auto\", collapse_mode=\"maxSD\", naPer=0.7, meanPer=0.8, varPer=0.8, corrType=\"spearman\", matNetMethod=\"rank\", valueThr=0.6, rankBest=0.003, networkType=\"signed\", netFDRMethod=\"BH\", netFDRThr=0.05, minModule=0.003, stepIte=FALSE, maxStep=4, moduleSigMethod=\"cutoff\", modularityThr=0.2, ZRanNum=10, PerRanNum=100, ranSig=0.05, idNumThr=(-1), nThreads=3)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-netsam/man/MatSAM.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\tmatModule <- MatSAM(inputMat=inputMatDir, sampleAnn=sampleAnnDir, outputFileName=outputFileName, outputFormat=\"msm\", organism=\"hsapiens\", map_to_symbol=FALSE, idType=\"auto\", collapse_mode=\"maxSD\", naPer=0.7, meanPer=0.8, varPer=0.8, corrType=\"spearman\", matNetMethod=\"rank\", valueThr=0.6, rankBest=0.003, networkType=\"signed\", netFDRMethod=\"BH\", netFDRThr=0.05, minModule=0.003, stepIte=FALSE, maxStep=4, moduleSigMethod=\"cutoff\", modularityThr=0.2, ZRanNum=10, PerRanNum=100, ranSig=0.05, idNumThr=(-1), nThreads=3)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/MatSAM.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ NetAnalyzer (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("\tNetwork analyzer\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("NetAnalyzer", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("NetAnalyzer", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure(" methods ", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -351,15 +351,15 @@ │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure("\tThe name of the output file.\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("\tThe function will output two \"txt\" files and five \"pdf\" files. Two \"txt\" files contain degree, clustering coefficient, betweeness and closeness centrality for each node and the shortest path distance for each pair of nodes. Five \"pdf\" files are the distributions of these measurements.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\tJing Wang\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\tinputNetworkDir <- system.file(\"extdata\",\"exampleNetwork.net\",package=\"NetSAM\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\toutputFileName <- paste(getwd(),\"/NetSAM\",sep=\"\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\tNetAnalyzer(inputNetworkDir,outputFileName,\"unweighted\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-netsam/man/NetAnalyzer.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\tNetAnalyzer(inputNetworkDir,outputFileName,\"unweighted\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/NetAnalyzer.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ NetSAM (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("\tNetwork Seriation and Modularization\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("NetSAM", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("NetSAM", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure(" methods ", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -473,15 +473,15 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\tIf output format is \"nsm\", the function will output not only a \"nsm\" file but also a list object containing module information, gene order information and network information. If output format is \"gmt\", the function will output the \"gmt\" file and a matrix object containing the module and annotation information.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\tBecause the seriation step requires pair-wise distance between all nodes, NetSAM is memory consuming. We recommend to use the 64 bit version of R to run the NetSAM. For networks with less than 10,000 nodes, we recommend to use a computer with 8GB memory. For networks with more than 10,000 nodes, a computer with at least 16GB memory is recommended.\n", Rd_tag = "TEXT")), Rd_tag = "\\note"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\tJing Wang\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\tinputNetworkDir <- system.file(\"extdata\",\"exampleNetwork.net\",package=\"NetSAM\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\toutputFileName <- paste(getwd(),\"/NetSAM\",sep=\"\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\tresult <- NetSAM(inputNetwork=inputNetworkDir, outputFileName=outputFileName, outputFormat=\"nsm\", edgeType=\"unweighted\", map_to_genesymbol=FALSE, organism=\"hsapiens\", idType=\"auto\",minModule=0.003, stepIte=FALSE, maxStep=4, moduleSigMethod=\"cutoff\", modularityThr=0.2, ZRanNum=10, PerRanNum=100, ranSig=0.05, edgeThr=(-1), nodeThr=(-1), nThreads=3)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-netsam/man/NetSAM.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\tresult <- NetSAM(inputNetwork=inputNetworkDir, outputFileName=outputFileName, outputFormat=\"nsm\", edgeType=\"unweighted\", map_to_genesymbol=FALSE, organism=\"hsapiens\", idType=\"auto\",minModule=0.003, stepIte=FALSE, maxStep=4, moduleSigMethod=\"cutoff\", modularityThr=0.2, ZRanNum=10, PerRanNum=100, ranSig=0.05, edgeThr=(-1), nodeThr=(-1), nThreads=3)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/NetSAM.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ NetSAM-package (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("\tNetwork Seriation and Modularization\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("NetSAM-package", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("NetSAM-package", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure(" package ", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -509,15 +509,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\tJing Wang\n", Rd_tag = "TEXT"), │ │ │ │ structure("\tMaintainer: Zhiao Shi \n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\tNetGestalt: integrating multidimensional omics data over biological networks. Nature Methods 10, 597-598 (2013).\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\t", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("NetSAM", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\t", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("MatSAM", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-netsam/man/NetSAM-package.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/NetSAM-package.Rd", class = "Rd", meta = list( │ │ │ │ docType = "package", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ consensusNet (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("\tConstruction of a consensus coexpression network\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("consensusNet", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("consensusNet", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure(" methods ", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -587,15 +587,15 @@ │ │ │ │ structure(list(list(structure("nThreads", Rd_tag = "TEXT")), │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure("\t consensusNet function supports parallel computing based on multiple cores. The default is 4.\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("\tJing Wang\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" inputMatDir <- system.file(\"extdata\",\"exampleExpressionData.cct\",package=\"NetSAM\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" data <- read.table(inputMatDir, header=TRUE, row.names=1, stringsAsFactors=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" net <- consensusNet(data, organism=\"hsapiens\",bootstrapNum=10, naPer=0.5, meanPer=0.8,varPer=0.8,method=\"rank_unsig\",value=3/1000,pth=1e-6, nMatNet=2, nThreads=4)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-netsam/man/consensusNet.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" net <- consensusNet(data, organism=\"hsapiens\",bootstrapNum=10, naPer=0.5, meanPer=0.8,varPer=0.8,method=\"rank_unsig\",value=3/1000,pth=1e-6, nMatNet=2, nThreads=4)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/consensusNet.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ featureAssociation (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("\tCalculate the associations between modules and sample features\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("featureAssociation", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("featureAssociation", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure(" methods ", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -652,15 +652,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\t", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("NetSAM", 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("\tinputMatDir <- system.file(\"extdata\",\"exampleExpressionData.cct\",package=\"NetSAM\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\tsampleAnnDir <- system.file(\"extdata\",\"sampleAnnotation.tsi\",package=\"NetSAM\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\tdata(NetSAMOutput_Example)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\toutputHtmlFile <- paste(getwd(),\"/featureAsso_HTML\",sep=\"\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\tfeatureAsso <- featureAssociation(inputMat= inputMatDir, sampleAnn=sampleAnnDir, NetSAMOutput=netsam_output, outputHtmlFile=outputHtmlFile, CONMethod=\"spearman\", CATMethod=\"kruskal\", BINMethod=\"ranktest\", fdrmethod=\"BH\",pth=0.05,collapse_mode=\"maxSD\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-netsam/man/featureAssociation.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\tfeatureAsso <- featureAssociation(inputMat= inputMatDir, sampleAnn=sampleAnnDir, NetSAMOutput=netsam_output, outputHtmlFile=outputHtmlFile, CONMethod=\"spearman\", CATMethod=\"kruskal\", BINMethod=\"ranktest\", fdrmethod=\"BH\",pth=0.05,collapse_mode=\"maxSD\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/featureAssociation.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ mapToSymbol (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("\tMap other ids to gene symbols\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mapToSymbol", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ @@ -748,15 +748,15 @@ │ │ │ │ structure("\tmatrix_symbol <- mapToSymbol(inputData=inputMatDir,organism=\"hsapiens\",inputType=\"matrix\",idType=\"affy_hg_u133_plus_2\",collapse_mode=\"maxSD\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\t\n", Rd_tag = "RCODE"), structure("\t###transform ids in the sbt file to gene symbols###\n", Rd_tag = "RCODE"), │ │ │ │ structure("\tinputSBTDir <- system.file(\"extdata\",\"exampleSBT.sbt\",package=\"NetSAM\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\tsbt_symbol <- mapToSymbol(inputData= inputSBTDir,organism=\"hsapiens\",inputType=\"sbt\",idType=\"affy_hg_u133_plus_2\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\t\n", Rd_tag = "RCODE"), structure("\t###transform ids in the sct file to gene symbols###\n", Rd_tag = "RCODE"), │ │ │ │ structure("\tinputSCTDir <- system.file(\"extdata\",\"exampleSCT.sct\",package=\"NetSAM\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\tsct_symbol <- mapToSymbol(inputData= inputSCTDir,organism=\"hsapiens\",inputType=\"sct\",idType=\"affy_hg_u133_plus_2\",collapse_mode=\"min\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-netsam/man/mapToSymbol.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/mapToSymbol.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ mergeDuplicate (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("\tMerge the duplicate Ids in the matrix data\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mergeDuplicate", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mergeDuplicate", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure(" methods ", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -778,25 +778,25 @@ │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure("\tThe method to collapse duplicate ids. \"mean\", \"median\", \"maxSD\", \"maxIQR\", \"max\" and \"min\" represent the mean, median, max standard deviation, max interquartile range, maximum and minimum of values for ids in each sample. The default is \"maxSD\".\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\tThe function will return the data matrix with unique Ids.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\tJing Wang\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\tinputMatDir <- system.file(\"extdata\",\"exampleExpressionData_nonsymbol.cct\",package=\"NetSAM\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\tinputMat <- read.table(inputMatDir,header=TRUE,sep=\"\\t\",stringsAsFactors=FALSE,check.names=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\tmergedData <- mergeDuplicate(id=inputMat[,1],data=inputMat[,2:ncol(inputMat)],collapse_mode=\"maxSD\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-netsam/man/mergeDuplicate.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\tmergedData <- mergeDuplicate(id=inputMat[,1],data=inputMat[,2:ncol(inputMat)],collapse_mode=\"maxSD\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/mergeDuplicate.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ netsam_output (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(" An example of the list object returned by NetSAM function\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("netsam_output", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("netsam_output", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" The list object contains at least three parts: gene order information, module information and network information. This object can be used as an input of the function featureAssociation or GOAssociation.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("data(NetSAMOutput_Example)", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ - structure(list(structure("list", Rd_tag = "TEXT")), Rd_tag = "\\format")), Rdfile = "/home/moeller/Salsa/r-bioc-netsam/man/netsam_output.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("list", Rd_tag = "TEXT")), Rd_tag = "\\format")), Rdfile = "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/netsam_output.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ │ │ @@ -830,10 +830,10 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\t If there is no format error, the function will return the standardized data matrix and sample annotation data. Otherwise, the function will output the detailed position of the errors.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\tIf the users set inputMat as \"\", the testFileFormat function only test format of sample annotation data. If the users set sampleAnn as \"\", the testFileFormat function only test format of data matrix. \n", Rd_tag = "TEXT")), Rd_tag = "\\note"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("\tJing Wang\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\tinputMatDir <- system.file(\"extdata\",\"exampleExpressionData.cct\",package=\"NetSAM\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\tsampleAnnDir <- system.file(\"extdata\",\"sampleAnnotation.tsi\",package=\"NetSAM\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\t\n", Rd_tag = "RCODE"), structure("\tformatedData <- testFileFormat(inputMat=inputMatDir,sampleAnn=sampleAnnDir,collapse_mode=\"maxSD\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-netsam/man/testFileFormat.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\t\n", Rd_tag = "RCODE"), structure("\tformatedData <- testFileFormat(inputMat=inputMatDir,sampleAnn=sampleAnnDir,collapse_mode=\"maxSD\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/testFileFormat.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/NetSAM/help/NetSAM.rdx │ │ │ ├── NetSAM.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,79 +1,79 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$GOAssociation │ │ │ │ │ -[1] 279 2137 │ │ │ │ │ +[1] 285 2150 │ │ │ │ │ │ │ │ │ │ $variables$MatNet │ │ │ │ │ -[1] 2691 4384 │ │ │ │ │ +[1] 2717 4398 │ │ │ │ │ │ │ │ │ │ $variables$MatSAM │ │ │ │ │ -[1] 7350 8601 │ │ │ │ │ +[1] 7397 8614 │ │ │ │ │ │ │ │ │ │ $variables$NetAnalyzer │ │ │ │ │ -[1] 16230 1789 │ │ │ │ │ +[1] 16296 1801 │ │ │ │ │ │ │ │ │ │ $variables$`NetSAM-package` │ │ │ │ │ -[1] 18302 1676 │ │ │ │ │ +[1] 18385 1690 │ │ │ │ │ │ │ │ │ │ $variables$NetSAM │ │ │ │ │ -[1] 20253 5987 │ │ │ │ │ +[1] 20358 5999 │ │ │ │ │ │ │ │ │ │ $variables$consensusNet │ │ │ │ │ -[1] 26519 3317 │ │ │ │ │ +[1] 26641 3329 │ │ │ │ │ │ │ │ │ │ $variables$featureAssociation │ │ │ │ │ -[1] 30120 3049 │ │ │ │ │ +[1] 30258 3063 │ │ │ │ │ │ │ │ │ │ $variables$mapToSymbol │ │ │ │ │ -[1] 33448 4077 │ │ │ │ │ +[1] 33605 4088 │ │ │ │ │ │ │ │ │ │ $variables$mergeDuplicate │ │ │ │ │ -[1] 37805 1660 │ │ │ │ │ +[1] 37979 1673 │ │ │ │ │ │ │ │ │ │ $variables$netsam_output │ │ │ │ │ -[1] 39743 740 │ │ │ │ │ +[1] 39935 754 │ │ │ │ │ │ │ │ │ │ $variables$testFileFormat │ │ │ │ │ -[1] 40762 1900 │ │ │ │ │ +[1] 40974 1914 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 279 │ │ │ │ │ +[1] 0 285 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 37525 280 │ │ │ │ │ +[1] 37693 286 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 39465 278 │ │ │ │ │ +[1] 39652 283 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 40483 279 │ │ │ │ │ +[1] 40689 285 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 2416 275 │ │ │ │ │ +[1] 2435 282 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 7075 275 │ │ │ │ │ +[1] 7115 282 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 15951 279 │ │ │ │ │ +[1] 16011 285 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 18019 283 │ │ │ │ │ +[1] 18097 288 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 19978 275 │ │ │ │ │ +[1] 20075 283 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 26240 279 │ │ │ │ │ +[1] 26357 284 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 29836 284 │ │ │ │ │ +[1] 29970 288 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 33169 279 │ │ │ │ │ +[1] 33321 284 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/NetSAM/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,14 +1,14 @@ │ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-netsam/man/GOAssociation.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-netsam/man/MatNet.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-netsam/man/MatSAM.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-netsam/man/NetAnalyzer.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-netsam/man/NetSAM-package.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-netsam/man/NetSAM.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-netsam/man/consensusNet.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-netsam/man/featureAssociation.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-netsam/man/mapToSymbol.Rd" │ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-netsam/man/mergeDuplicate.Rd" │ │ │ │ │ -[11] "/home/moeller/Salsa/r-bioc-netsam/man/netsam_output.Rd" │ │ │ │ │ -[12] "/home/moeller/Salsa/r-bioc-netsam/man/testFileFormat.Rd" │ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/GOAssociation.Rd" │ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/MatNet.Rd" │ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/MatSAM.Rd" │ │ │ │ │ + [4] "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/NetAnalyzer.Rd" │ │ │ │ │ + [5] "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/NetSAM-package.Rd" │ │ │ │ │ + [6] "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/NetSAM.Rd" │ │ │ │ │ + [7] "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/consensusNet.Rd" │ │ │ │ │ + [8] "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/featureAssociation.Rd" │ │ │ │ │ + [9] "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/mapToSymbol.Rd" │ │ │ │ │ +[10] "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/mergeDuplicate.Rd" │ │ │ │ │ +[11] "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/netsam_output.Rd" │ │ │ │ │ +[12] "/build/reproducible-path/r-bioc-netsam-1.52.0+ds/man/testFileFormat.Rd" │ │ │ │ │ attr(,"first") │ │ │ │ │ -[1] 39 │ │ │ │ │ +[1] 54