--- /srv/rebuilderd/tmp/rebuilderdmjKEZk/inputs/r-bioc-biovizbase_1.60.0+ds-1_amd64.deb +++ /srv/rebuilderd/tmp/rebuilderdmjKEZk/out/r-bioc-biovizbase_1.60.0+ds-1_amd64.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-12 16:01:29.000000 debian-binary │ --rw-r--r-- 0 0 0 2284 2026-08-12 16:01:29.000000 control.tar.xz │ --rw-r--r-- 0 0 0 2848908 2026-08-12 16:01:29.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 2280 2026-08-12 16:01:29.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 2849740 2026-08-12 16:01:29.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:01:29.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 1293 2026-08-12 16:01:29.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 1279 2026-08-12 16:01:29.000000 ./control │ │ │ -rw-r--r-- 0 root (0) root (0) 4193 2026-08-12 16:01:29.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,14 @@ │ │ │ Package: r-bioc-biovizbase │ │ │ Version: 1.60.0+ds-1 │ │ │ Architecture: amd64 │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ -Installed-Size: 3233 │ │ │ +Installed-Size: 3234 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-cran-scales, r-cran-hmisc, r-cran-rcolorbrewer, r-cran-dichromat, r-bioc-biocgenerics, r-bioc-s4vectors (>= 0.23.19), r-bioc-iranges (>= 1.99.28), r-bioc-seqinfo, r-bioc-genomeinfodb (>= 1.45.5), r-bioc-genomicranges (>= 1.61.1), r-bioc-summarizedexperiment (>= 1.39.1), r-bioc-biostrings (>= 2.77.2), r-bioc-rsamtools (>= 2.25.1), r-bioc-genomicalignments (>= 1.45.1), r-bioc-genomicfeatures (>= 1.61.4), r-bioc-annotationdbi, r-bioc-variantannotation (>= 1.55.1), r-bioc-ensembldb (>= 2.33.1), r-bioc-annotationfilter (>= 0.99.8), r-cran-rlang, libc6 (>= 2.2.5), r-pkg-team-core-architecture │ │ │ -Suggests: r-bioc-bsgenome, r-bioc-rtracklayer, r-cran-runit │ │ │ +Suggests: r-bioc-bsgenome, r-bioc-rtracklayer │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/biovizBase/ │ │ │ Description: GNU R basic graphic utilities for visualization of genomic data │ │ │ The biovizBase package is designed to provide a set of utilities, color │ │ │ schemes and conventions for genomic data. It serves as the base for │ │ │ various high-level packages for biological data visualization. This │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -15,16 +15,16 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 1431 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1953 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/Meta/package.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 241 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 3691 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 606 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/NEWS │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/R/biovizBase │ │ │ --rw-r--r-- 0 root (0) root (0) 197748 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/R/biovizBase.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 2321 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/R/biovizBase.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 197757 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/R/biovizBase.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 2328 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/R/biovizBase.rdx │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/data/ │ │ │ -rw-r--r-- 0 root (0) root (0) 575174 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/data/Rdata.rdb │ │ │ -rw-r--r-- 0 root (0) root (0) 201 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/data/Rdata.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 309 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/data/Rdata.rdx │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1371 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/doc/index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 7617 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/doc/intro.R │ │ │ @@ -43,27 +43,27 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 5538 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/extdata/crc1-missense.csv │ │ │ -rw-r--r-- 0 root (0) root (0) 124509 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/extdata/plink.assoc.sub.txt │ │ │ -rw-r--r-- 0 root (0) root (0) 1261753 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/extdata/wg-brca1.sorted.bam │ │ │ -rw-r--r-- 0 root (0) root (0) 20832 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/extdata/wg-brca1.sorted.bam.bai │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 3253 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/help/AnIndex │ │ │ -rw-r--r-- 0 root (0) root (0) 1090 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 80065 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/help/biovizBase.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 1159 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/help/biovizBase.rdx │ │ │ --rw-r--r-- 0 root (0) root (0) 576 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 81048 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/help/biovizBase.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 1162 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/help/biovizBase.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 587 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 11213 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/libs/ │ │ │ -rw-r--r-- 0 root (0) root (0) 14408 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/libs/biovizBase.so │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/unitTests/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1087 2026-08-12 16:01:29.000000 ./usr/lib/R/site-library/biovizBase/unitTests/test_ensdb.R │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:01:29.000000 ./usr/share/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:01:29.000000 ./usr/share/doc/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:01:29.000000 ./usr/share/doc/r-bioc-biovizbase/ │ │ │ -rw-r--r-- 0 root (0) root (0) 894 2026-08-12 16:01:29.000000 ./usr/share/doc/r-bioc-biovizbase/changelog.Debian.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 5360 2026-08-12 15:57:10.000000 ./usr/share/doc/r-bioc-biovizbase/copyright │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:01:29.000000 ./usr/share/doc/r-bioc-biovizbase/examples/ │ │ │ -drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 15:56:17.000000 ./usr/share/doc/r-bioc-biovizbase/examples/vignettes/ │ │ │ --rw-r--r-- 0 root (0) root (0) 5344 2026-08-12 15:56:17.000000 ./usr/share/doc/r-bioc-biovizbase/examples/vignettes/intro-shrink-single.pdf │ │ │ --rw-r--r-- 0 root (0) root (0) 5690 2026-08-12 15:56:17.000000 ./usr/share/doc/r-bioc-biovizbase/examples/vignettes/intro-shrinkageFun.pdf │ │ │ --rw-r--r-- 0 root (0) root (0) 35822 2026-08-12 15:56:17.000000 ./usr/share/doc/r-bioc-biovizbase/examples/vignettes/intro.Rnw │ │ │ +drwxr-xr-x 0 root (0) root (0) 0 2026-04-28 20:56:20.000000 ./usr/share/doc/r-bioc-biovizbase/examples/vignettes/ │ │ │ +-rw-r--r-- 0 root (0) root (0) 5344 2026-04-28 16:09:07.000000 ./usr/share/doc/r-bioc-biovizbase/examples/vignettes/intro-shrink-single.pdf │ │ │ +-rw-r--r-- 0 root (0) root (0) 5690 2026-04-28 16:09:07.000000 ./usr/share/doc/r-bioc-biovizbase/examples/vignettes/intro-shrinkageFun.pdf │ │ │ +-rw-r--r-- 0 root (0) root (0) 35822 2026-04-28 16:09:07.000000 ./usr/share/doc/r-bioc-biovizbase/examples/vignettes/intro.Rnw │ │ ├── ./usr/lib/R/site-library/biovizBase/R/biovizBase.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -1010,15 +1010,15 @@ │ │ │ │ "imports" = " isActiveSeq = "isActiveSeq", ".__T__isActiveSeq<-:GenomicFeatures" = ".__T__isActiveSeq<-:GenomicFeatures", " │ │ │ │ "imports" = " "isActiveSeq<-" = "isActiveSeq<-", ".__T__transcripts:GenomicFeatures" = ".__T__transcripts:GenomicFeatures", " │ │ │ │ "imports" = " transcripts = "transcripts", ".__T__transcriptsByOverlaps:GenomicFeatures" = ".__T__transcriptsByOverlaps:GenomicFeatures", " │ │ │ │ "imports" = " transcriptsByOverlaps = "transcriptsByOverlaps"), ensembldb = c(".__T__exons:GenomicFeatures" = ".__T__exons:GenomicFeatures", " │ │ │ │ "imports" = " exons = "exons", ".__T__listColumns:ensembldb" = ".__T__listColumns:ensembldb", " │ │ │ │ "imports" = " listColumns = "listColumns", transcripts = "transcripts"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-biovizbase/debian/r-bioc-biovizbase/usr/lib/R/site-library/biovizBase"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/debian/r-bioc-biovizbase/usr/lib/R/site-library/biovizBase"" │ │ │ │ "spec" = "c(name = "biovizBase", version = "1.60.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/biovizBase/R/biovizBase.rdx │ │ │ ├── biovizBase.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -23,510 +23,510 @@ │ │ │ │ │ $variables$.RNABasesColor │ │ │ │ │ [1] 3073 248 │ │ │ │ │ │ │ │ │ │ $variables$.RNABasesNColor │ │ │ │ │ [1] 3321 261 │ │ │ │ │ │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 17225 52 │ │ │ │ │ +[1] 17234 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 17408 52 │ │ │ │ │ +[1] 17417 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__addStepping:biovizBase` │ │ │ │ │ -[1] 21224 52 │ │ │ │ │ +[1] 21233 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__crunch:biovizBase` │ │ │ │ │ -[1] 36680 52 │ │ │ │ │ +[1] 36689 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__estimateCoverage:biovizBase` │ │ │ │ │ -[1] 42554 53 │ │ │ │ │ +[1] 42563 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__getFragLength:biovizBase` │ │ │ │ │ -[1] 47779 53 │ │ │ │ │ +[1] 47788 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__getGaps:biovizBase` │ │ │ │ │ -[1] 52342 53 │ │ │ │ │ +[1] 52351 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__getXLab:biovizBase` │ │ │ │ │ -[1] 55375 53 │ │ │ │ │ +[1] 55384 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__getXScale:biovizBase` │ │ │ │ │ -[1] 58869 53 │ │ │ │ │ +[1] 58878 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__getYLab:biovizBase` │ │ │ │ │ -[1] 61303 53 │ │ │ │ │ +[1] 61312 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__maxGap:biovizBase` │ │ │ │ │ -[1] 63313 53 │ │ │ │ │ +[1] 63322 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__mold:biovizBase` │ │ │ │ │ -[1] 71557 53 │ │ │ │ │ +[1] 71566 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__shrinkageFun:biovizBase` │ │ │ │ │ -[1] 74754 53 │ │ │ │ │ +[1] 74763 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__spliceSummary:biovizBase` │ │ │ │ │ -[1] 81098 53 │ │ │ │ │ +[1] 81107 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__splitByFacets:biovizBase` │ │ │ │ │ -[1] 85224 53 │ │ │ │ │ +[1] 85233 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__transformToArch:biovizBase` │ │ │ │ │ -[1] 88749 53 │ │ │ │ │ +[1] 88758 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__transformToDf:biovizBase` │ │ │ │ │ -[1] 91905 53 │ │ │ │ │ +[1] 91914 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__transformToGenome:biovizBase` │ │ │ │ │ -[1] 97867 53 │ │ │ │ │ +[1] 97876 53 │ │ │ │ │ │ │ │ │ │ $variables$.all_aesthetics │ │ │ │ │ -[1] 97920 238 │ │ │ │ │ +[1] 97929 238 │ │ │ │ │ │ │ │ │ │ $variables$.checkFacetsRestrict │ │ │ │ │ -[1] 98158 1219 │ │ │ │ │ +[1] 98167 1219 │ │ │ │ │ │ │ │ │ │ $variables$.colorschemes.num │ │ │ │ │ -[1] 99377 934 │ │ │ │ │ +[1] 99386 934 │ │ │ │ │ │ │ │ │ │ $variables$.cytobandColor │ │ │ │ │ -[1] 100311 386 │ │ │ │ │ +[1] 100320 386 │ │ │ │ │ │ │ │ │ │ $variables$.getCytobandColor │ │ │ │ │ -[1] 100697 1152 │ │ │ │ │ +[1] 100706 1152 │ │ │ │ │ │ │ │ │ │ $variables$.onLoad │ │ │ │ │ -[1] 101849 792 │ │ │ │ │ +[1] 101858 792 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 102641 55 │ │ │ │ │ +[1] 102650 55 │ │ │ │ │ │ │ │ │ │ $variables$.strandColor │ │ │ │ │ -[1] 102696 236 │ │ │ │ │ +[1] 102705 236 │ │ │ │ │ │ │ │ │ │ $variables$.transformSeqinfo │ │ │ │ │ -[1] 102932 630 │ │ │ │ │ +[1] 102941 630 │ │ │ │ │ │ │ │ │ │ $variables$GCcontent │ │ │ │ │ -[1] 103562 877 │ │ │ │ │ +[1] 103571 877 │ │ │ │ │ │ │ │ │ │ $variables$addStepping │ │ │ │ │ -[1] 104439 418 │ │ │ │ │ +[1] 104448 418 │ │ │ │ │ │ │ │ │ │ $variables$blind.pal.info │ │ │ │ │ -[1] 104857 556 │ │ │ │ │ +[1] 104866 556 │ │ │ │ │ │ │ │ │ │ $variables$brewer.pal.blind.info │ │ │ │ │ -[1] 105413 281 │ │ │ │ │ +[1] 105422 281 │ │ │ │ │ │ │ │ │ │ $variables$centroidPos │ │ │ │ │ -[1] 105694 1251 │ │ │ │ │ +[1] 105703 1251 │ │ │ │ │ │ │ │ │ │ $variables$check.integer │ │ │ │ │ -[1] 106945 441 │ │ │ │ │ +[1] 106954 441 │ │ │ │ │ │ │ │ │ │ $variables$colorBlindSafePal │ │ │ │ │ -[1] 107386 2437 │ │ │ │ │ +[1] 107395 2437 │ │ │ │ │ │ │ │ │ │ $variables$containLetters │ │ │ │ │ -[1] 109823 642 │ │ │ │ │ +[1] 109832 642 │ │ │ │ │ │ │ │ │ │ $variables$crunch │ │ │ │ │ -[1] 110465 414 │ │ │ │ │ +[1] 110474 414 │ │ │ │ │ │ │ │ │ │ $variables$dichromat.pal.blind.info │ │ │ │ │ -[1] 110879 325 │ │ │ │ │ +[1] 110888 325 │ │ │ │ │ │ │ │ │ │ $variables$estimateCoverage │ │ │ │ │ -[1] 111204 420 │ │ │ │ │ +[1] 111213 420 │ │ │ │ │ │ │ │ │ │ $variables$fetch │ │ │ │ │ -[1] 111624 10310 │ │ │ │ │ +[1] 111633 10310 │ │ │ │ │ │ │ │ │ │ $variables$flatGrl │ │ │ │ │ -[1] 121934 634 │ │ │ │ │ +[1] 121943 634 │ │ │ │ │ │ │ │ │ │ $variables$genBlindPalInfo │ │ │ │ │ -[1] 122568 822 │ │ │ │ │ +[1] 122577 822 │ │ │ │ │ │ │ │ │ │ $variables$genBrewerBlindPalInfo │ │ │ │ │ -[1] 123390 1370 │ │ │ │ │ +[1] 123399 1370 │ │ │ │ │ │ │ │ │ │ $variables$genDichromatPalInfo │ │ │ │ │ -[1] 124760 1045 │ │ │ │ │ +[1] 124769 1045 │ │ │ │ │ │ │ │ │ │ $variables$genGenesymbolTable │ │ │ │ │ -[1] 125805 1652 │ │ │ │ │ +[1] 125814 1652 │ │ │ │ │ │ │ │ │ │ $variables$genSymbols │ │ │ │ │ -[1] 127457 3817 │ │ │ │ │ +[1] 127466 3817 │ │ │ │ │ │ │ │ │ │ $variables$getBioColor │ │ │ │ │ -[1] 131274 1403 │ │ │ │ │ +[1] 131283 1403 │ │ │ │ │ │ │ │ │ │ $variables$getFormalNames │ │ │ │ │ -[1] 132677 866 │ │ │ │ │ +[1] 132686 866 │ │ │ │ │ │ │ │ │ │ $variables$getFragLength │ │ │ │ │ -[1] 133543 420 │ │ │ │ │ +[1] 133552 420 │ │ │ │ │ │ │ │ │ │ $variables$getGaps │ │ │ │ │ -[1] 133963 414 │ │ │ │ │ +[1] 133972 414 │ │ │ │ │ │ │ │ │ │ $variables$getIdeoGR │ │ │ │ │ -[1] 134377 882 │ │ │ │ │ +[1] 134386 882 │ │ │ │ │ │ │ │ │ │ $variables$getIdeogram │ │ │ │ │ -[1] 135259 3343 │ │ │ │ │ +[1] 135268 3343 │ │ │ │ │ │ │ │ │ │ $variables$getScale │ │ │ │ │ -[1] 138602 2470 │ │ │ │ │ +[1] 138611 2470 │ │ │ │ │ │ │ │ │ │ $variables$getXLab │ │ │ │ │ -[1] 141072 415 │ │ │ │ │ +[1] 141081 415 │ │ │ │ │ │ │ │ │ │ $variables$getXScale │ │ │ │ │ -[1] 141487 419 │ │ │ │ │ +[1] 141496 419 │ │ │ │ │ │ │ │ │ │ $variables$getYLab │ │ │ │ │ -[1] 141906 415 │ │ │ │ │ +[1] 141915 415 │ │ │ │ │ │ │ │ │ │ $variables$ggplot2_is.constant │ │ │ │ │ -[1] 142321 401 │ │ │ │ │ +[1] 142330 401 │ │ │ │ │ │ │ │ │ │ $variables$ggplot2_is_calculated_aes │ │ │ │ │ -[1] 142722 432 │ │ │ │ │ +[1] 142731 432 │ │ │ │ │ │ │ │ │ │ $variables$ggplot2_strip_dots │ │ │ │ │ -[1] 143154 640 │ │ │ │ │ +[1] 143163 640 │ │ │ │ │ │ │ │ │ │ $variables$isFacetByOnlySeq │ │ │ │ │ -[1] 143794 532 │ │ │ │ │ +[1] 143803 532 │ │ │ │ │ │ │ │ │ │ $variables$isIdeogram │ │ │ │ │ -[1] 144326 440 │ │ │ │ │ +[1] 144335 440 │ │ │ │ │ │ │ │ │ │ $variables$isJunctionRead │ │ │ │ │ -[1] 144766 240 │ │ │ │ │ +[1] 144775 240 │ │ │ │ │ │ │ │ │ │ $variables$isMatchedWithModel │ │ │ │ │ -[1] 145006 836 │ │ │ │ │ +[1] 145015 836 │ │ │ │ │ │ │ │ │ │ $variables$isSimpleIdeogram │ │ │ │ │ -[1] 145842 495 │ │ │ │ │ +[1] 145851 495 │ │ │ │ │ │ │ │ │ │ $variables$is_coord_genome │ │ │ │ │ -[1] 146337 442 │ │ │ │ │ +[1] 146346 442 │ │ │ │ │ │ │ │ │ │ $variables$is_coord_truncate_gaps │ │ │ │ │ -[1] 146779 443 │ │ │ │ │ +[1] 146788 443 │ │ │ │ │ │ │ │ │ │ $variables$is_homo │ │ │ │ │ -[1] 147222 537 │ │ │ │ │ +[1] 147231 537 │ │ │ │ │ │ │ │ │ │ $variables$maxGap │ │ │ │ │ -[1] 147759 415 │ │ │ │ │ +[1] 147768 415 │ │ │ │ │ │ │ │ │ │ $variables$mold │ │ │ │ │ -[1] 148174 414 │ │ │ │ │ +[1] 148183 414 │ │ │ │ │ │ │ │ │ │ $variables$newDataAfterFacetByGr │ │ │ │ │ -[1] 148588 864 │ │ │ │ │ +[1] 148597 864 │ │ │ │ │ │ │ │ │ │ $variables$parseArgsForAes │ │ │ │ │ -[1] 149452 925 │ │ │ │ │ +[1] 149461 925 │ │ │ │ │ │ │ │ │ │ $variables$parseArgsForNonAes │ │ │ │ │ -[1] 150377 435 │ │ │ │ │ +[1] 150386 435 │ │ │ │ │ │ │ │ │ │ $variables$pileupAsGRanges │ │ │ │ │ -[1] 150812 2007 │ │ │ │ │ +[1] 150821 2007 │ │ │ │ │ │ │ │ │ │ $variables$pileupGRangesAsVariantTable │ │ │ │ │ -[1] 152819 2588 │ │ │ │ │ +[1] 152828 2588 │ │ │ │ │ │ │ │ │ │ $variables$plotColorLegend │ │ │ │ │ -[1] 155407 974 │ │ │ │ │ +[1] 155416 974 │ │ │ │ │ │ │ │ │ │ $variables$pspanGR │ │ │ │ │ -[1] 156381 1782 │ │ │ │ │ +[1] 156390 1782 │ │ │ │ │ │ │ │ │ │ $variables$rectifySeqlevelsStyle │ │ │ │ │ -[1] 158163 327 │ │ │ │ │ +[1] 158172 327 │ │ │ │ │ │ │ │ │ │ $variables$reduceNtruncate │ │ │ │ │ -[1] 158490 2570 │ │ │ │ │ +[1] 158499 2570 │ │ │ │ │ │ │ │ │ │ $variables$rescaleGr │ │ │ │ │ -[1] 161060 2267 │ │ │ │ │ +[1] 161069 2267 │ │ │ │ │ │ │ │ │ │ $variables$scanBamGRanges │ │ │ │ │ -[1] 163327 1665 │ │ │ │ │ +[1] 163336 1665 │ │ │ │ │ │ │ │ │ │ $variables$showColor │ │ │ │ │ -[1] 164992 467 │ │ │ │ │ +[1] 165001 467 │ │ │ │ │ │ │ │ │ │ $variables$show_col2 │ │ │ │ │ -[1] 165459 1492 │ │ │ │ │ +[1] 165468 1492 │ │ │ │ │ │ │ │ │ │ $variables$shrinkageFun │ │ │ │ │ -[1] 166951 419 │ │ │ │ │ +[1] 166960 419 │ │ │ │ │ │ │ │ │ │ $variables$spliceSummary │ │ │ │ │ -[1] 167370 447 │ │ │ │ │ +[1] 167379 447 │ │ │ │ │ │ │ │ │ │ $variables$splitByFacets │ │ │ │ │ -[1] 167817 440 │ │ │ │ │ +[1] 167826 440 │ │ │ │ │ │ │ │ │ │ $variables$strip_formula_dots │ │ │ │ │ -[1] 168257 709 │ │ │ │ │ +[1] 168266 709 │ │ │ │ │ │ │ │ │ │ $variables$subsetArgsByFormals │ │ │ │ │ -[1] 168966 457 │ │ │ │ │ +[1] 168975 457 │ │ │ │ │ │ │ │ │ │ $variables$transformDfToGr │ │ │ │ │ -[1] 169423 3233 │ │ │ │ │ +[1] 169432 3233 │ │ │ │ │ │ │ │ │ │ $variables$transformGRangesForEvenSpace │ │ │ │ │ -[1] 172656 935 │ │ │ │ │ +[1] 172665 935 │ │ │ │ │ │ │ │ │ │ $variables$transformToArch │ │ │ │ │ -[1] 173591 423 │ │ │ │ │ +[1] 173600 423 │ │ │ │ │ │ │ │ │ │ $variables$transformToBarInCircle │ │ │ │ │ -[1] 174014 3939 │ │ │ │ │ +[1] 174023 3939 │ │ │ │ │ │ │ │ │ │ $variables$transformToCircle │ │ │ │ │ -[1] 177953 3032 │ │ │ │ │ +[1] 177962 3032 │ │ │ │ │ │ │ │ │ │ $variables$transformToDf │ │ │ │ │ -[1] 180985 422 │ │ │ │ │ +[1] 180994 422 │ │ │ │ │ │ │ │ │ │ $variables$transformToEven │ │ │ │ │ -[1] 181407 1105 │ │ │ │ │ +[1] 181416 1105 │ │ │ │ │ │ │ │ │ │ $variables$transformToGenome │ │ │ │ │ -[1] 182512 423 │ │ │ │ │ +[1] 182521 423 │ │ │ │ │ │ │ │ │ │ $variables$transformToLinkInCircle │ │ │ │ │ -[1] 182935 3334 │ │ │ │ │ +[1] 182944 3334 │ │ │ │ │ │ │ │ │ │ $variables$transformToRectInCircle │ │ │ │ │ -[1] 186269 4123 │ │ │ │ │ +[1] 186278 4123 │ │ │ │ │ │ │ │ │ │ $variables$transformToSegInCircle │ │ │ │ │ -[1] 190392 3649 │ │ │ │ │ +[1] 190401 3649 │ │ │ │ │ │ │ │ │ │ $variables$transformToSegInCircle2 │ │ │ │ │ -[1] 194041 3707 │ │ │ │ │ +[1] 194050 3707 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 3873 13352 │ │ │ │ │ +[1] 3873 13361 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 31372 260 │ │ │ │ │ +[1] 31381 260 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 21276 5048 │ │ │ │ │ +[1] 21285 5048 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 26324 5048 │ │ │ │ │ +[1] 26333 5048 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 40701 1853 │ │ │ │ │ +[1] 40710 1853 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 40438 263 │ │ │ │ │ +[1] 40447 263 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 36732 1853 │ │ │ │ │ +[1] 36741 1853 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 38585 1853 │ │ │ │ │ +[1] 38594 1853 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 46142 1637 │ │ │ │ │ +[1] 46151 1637 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 45881 261 │ │ │ │ │ +[1] 45890 261 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 42607 1637 │ │ │ │ │ +[1] 42616 1637 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 3582 131 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 44244 1637 │ │ │ │ │ +[1] 44253 1637 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 50925 1417 │ │ │ │ │ +[1] 50934 1417 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 50666 259 │ │ │ │ │ +[1] 50675 259 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 47832 1417 │ │ │ │ │ +[1] 47841 1417 │ │ │ │ │ │ │ │ │ │ $references$`env::24` │ │ │ │ │ -[1] 49249 1417 │ │ │ │ │ +[1] 49258 1417 │ │ │ │ │ │ │ │ │ │ $references$`env::25` │ │ │ │ │ -[1] 54468 907 │ │ │ │ │ +[1] 54477 907 │ │ │ │ │ │ │ │ │ │ $references$`env::26` │ │ │ │ │ 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707 │ │ │ │ │ +[1] 59638 707 │ │ │ │ │ │ │ │ │ │ $references$`env::37` │ │ │ │ │ -[1] 62748 565 │ │ │ │ │ +[1] 62757 565 │ │ │ │ │ │ │ │ │ │ $references$`env::38` │ │ │ │ │ -[1] 62486 262 │ │ │ │ │ +[1] 62495 262 │ │ │ │ │ │ │ │ │ │ $references$`env::39` │ │ │ │ │ -[1] 61356 565 │ │ │ │ │ +[1] 61365 565 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 17277 131 │ │ │ │ │ +[1] 17286 131 │ │ │ │ │ │ │ │ │ │ $references$`env::40` │ │ │ │ │ -[1] 61921 565 │ │ │ │ │ +[1] 61930 565 │ │ │ │ │ │ │ │ │ │ $references$`env::41` │ │ │ │ │ -[1] 68913 2644 │ │ │ │ │ +[1] 68922 2644 │ │ │ │ │ │ │ │ │ │ $references$`env::42` │ │ │ │ │ -[1] 68654 259 │ │ │ │ │ +[1] 68663 259 │ │ │ │ │ │ │ │ │ │ $references$`env::43` │ │ │ │ │ -[1] 63366 2644 │ │ │ │ │ +[1] 63375 2644 │ │ │ │ │ │ │ │ │ │ $references$`env::44` │ │ │ │ │ -[1] 66010 2644 │ │ │ │ │ +[1] 66019 2644 │ │ │ │ │ │ │ │ │ │ $references$`env::45` │ │ │ │ │ -[1] 73793 961 │ │ │ │ │ +[1] 73802 961 │ │ │ │ │ │ │ │ │ │ $references$`env::46` │ │ │ │ │ -[1] 73532 261 │ │ │ │ │ +[1] 73541 261 │ │ │ │ │ │ │ │ │ │ $references$`env::47` │ │ │ │ │ -[1] 71610 961 │ │ │ │ │ +[1] 71619 961 │ │ │ │ │ │ │ │ │ │ $references$`env::48` │ │ │ │ │ -[1] 72571 961 │ │ │ │ │ +[1] 72580 961 │ │ │ │ │ │ │ │ │ │ $references$`env::49` │ │ │ │ │ -[1] 79090 2008 │ │ │ │ │ +[1] 79099 2008 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 20056 1168 │ │ │ │ │ +[1] 20065 1168 │ │ │ │ │ │ │ │ │ │ $references$`env::50` │ │ │ │ │ -[1] 78823 267 │ │ │ │ │ +[1] 78832 267 │ │ │ │ │ │ │ │ │ │ $references$`env::51` │ │ │ │ │ -[1] 74807 2008 │ │ │ │ │ +[1] 74816 2008 │ │ │ │ │ │ │ │ │ │ $references$`env::52` │ │ │ │ │ -[1] 76815 2008 │ │ │ │ │ +[1] 76824 2008 │ │ │ │ │ │ │ │ │ │ $references$`env::53` │ │ │ │ │ -[1] 83955 1269 │ │ │ │ │ +[1] 83964 1269 │ │ │ │ │ │ │ │ │ │ $references$`env::54` │ │ │ │ │ -[1] 83689 266 │ │ │ │ │ +[1] 83698 266 │ │ │ │ │ │ │ │ │ │ $references$`env::55` │ │ │ │ │ -[1] 81151 1269 │ │ │ │ │ +[1] 81160 1269 │ │ │ │ │ │ │ │ │ │ $references$`env::56` │ │ │ │ │ -[1] 82420 1269 │ │ │ │ │ +[1] 82429 1269 │ │ │ │ │ │ │ │ │ │ $references$`env::57` │ │ │ │ │ -[1] 87680 1069 │ │ │ │ │ +[1] 87689 1069 │ │ │ │ │ │ │ │ │ │ $references$`env::58` │ │ │ │ │ -[1] 87415 265 │ │ │ │ │ +[1] 87424 265 │ │ │ │ │ │ │ │ │ │ $references$`env::59` │ │ │ │ │ -[1] 85277 1069 │ │ │ │ │ +[1] 85286 1069 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 19796 260 │ │ │ │ │ +[1] 19805 260 │ │ │ │ │ │ │ │ │ │ $references$`env::60` │ │ │ │ │ -[1] 86346 1069 │ │ │ │ │ +[1] 86355 1069 │ │ │ │ │ │ │ │ │ │ $references$`env::61` │ │ │ │ │ -[1] 90959 946 │ │ │ │ │ +[1] 90968 946 │ │ │ │ │ │ │ │ │ │ $references$`env::62` │ │ │ │ │ -[1] 90694 265 │ │ │ │ │ +[1] 90703 265 │ │ │ │ │ │ │ │ │ │ $references$`env::63` │ │ │ │ │ -[1] 88802 946 │ │ │ │ │ +[1] 88811 946 │ │ │ │ │ │ │ │ │ │ $references$`env::64` │ │ │ │ │ -[1] 89748 946 │ │ │ │ │ +[1] 89757 946 │ │ │ │ │ │ │ │ │ │ $references$`env::65` │ │ │ │ │ -[1] 95986 1881 │ │ │ │ │ +[1] 95995 1881 │ │ │ │ │ │ │ │ │ │ $references$`env::66` │ │ │ │ │ -[1] 95720 266 │ │ │ │ │ +[1] 95729 266 │ │ │ │ │ │ │ │ │ │ $references$`env::67` │ │ │ │ │ -[1] 91958 1881 │ │ │ │ │ +[1] 91967 1881 │ │ │ │ │ │ │ │ │ │ $references$`env::68` │ │ │ │ │ -[1] 93839 1881 │ │ │ │ │ +[1] 93848 1881 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 17460 1168 │ │ │ │ │ +[1] 17469 1168 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 18628 1168 │ │ │ │ │ +[1] 18637 1168 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 31632 5048 │ │ │ │ │ +[1] 31641 5048 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/biovizBase/help/biovizBase.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ structure(list(structure("mut.gr", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion sample data set", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("data(CRC)", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("The data used in\n", Rd_tag = "TEXT"), │ │ │ │ structure("this study is from this a\n", Rd_tag = "TEXT"), │ │ │ │ structure("paper http://www.nature.com/ng/journal/v43/n10/full/ng.936.html.", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ - structure(list(structure("data(CRC)", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/CRC.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("data(CRC)", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/CRC.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ GCcontent (list) = structure(list(structure(list(structure("GC content computation for BSgenome", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("GCcontent", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("GCcontent", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Compute GC content in a certain region of a BSgenome object", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("GCcontent(obj, ..., view.width, as.prob = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -52,15 +52,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" if the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("view.width", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" is specified, the GC content will be computed\n", Rd_tag = "TEXT"), │ │ │ │ structure(" in the sliding view", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("Numeric value indicate count or percentage", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("library(BSgenome.Hsapiens.UCSC.hg19)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("GCcontent(Hsapiens, GRanges(\"chr1\", IRanges(1e6, 1e6 + 1000)))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/GCcontent.Rd", class = "Rd", meta = list( │ │ │ │ + structure("GCcontent(Hsapiens, GRanges(\"chr1\", IRanges(1e6, 1e6 + 1000)))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/GCcontent.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ addStepping-method (list) = structure(list(structure(list(structure("Adding disjoint levels to a GenomicRanges object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("addStepping-method", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("addStepping", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("addStepping,GenomicRanges-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Adding disjoint levels to a GenomicRanges object", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -128,15 +128,15 @@ │ │ │ │ structure(" pair = sample(letters, size = N,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" replace = TRUE))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## grouping and extending\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(addStepping(gr))\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(addStepping(gr, group.name = \"pair\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("gr.close <- GRanges(c(\"chr1\", \"chr1\"), IRanges(c(10, 20), width = 9))\n", Rd_tag = "RCODE"), │ │ │ │ structure("addStepping(gr.close)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("addStepping(gr.close, extend.size = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/addStepping-method.Rd", class = "Rd", meta = list( │ │ │ │ + structure("addStepping(gr.close, extend.size = 5)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/addStepping-method.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ aes-utils (list) = structure(list(structure(list(structure("Utils for parsing (un)evaluated arguments", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("parseArgsForAes", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("parseArgsForAes", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("parseArgsForNonAes", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Utilities for parsing (un)evaluated arguments\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -151,30 +151,30 @@ │ │ │ │ structure(list(structure("parseArgsForAes", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" return a unevaluated arguments.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" For ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("parseArgsNonForAes", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" return a evaluated/quoted arguments.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("args <- alist(a = color, b = \"b\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# parseArgsForAes(args)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/aes-utils.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# parseArgsForAes(args)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/aes-utils.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ biovizBase-package (list) = structure(list(structure(list(structure("biovizBase is a package which provides utilities and color scheme...", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("biovizBase-package", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("biovizBase-package", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("biovizBase-package", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("biovizBase", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("biovizBase is a package which provides utilities and color scheme\n", Rd_tag = "TEXT"), │ │ │ │ structure("for higher level graphic package which aim to visualize biological\n", Rd_tag = "TEXT"), │ │ │ │ structure("data especially genetic data.", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("This package provides default color scheme for nucleotide, strand,\n", Rd_tag = "TEXT"), │ │ │ │ structure("amino acid, try to pass colorblind checking as possible as we can.\n", Rd_tag = "TEXT"), │ │ │ │ structure("And also provide giemsa stain result color scheme used to show\n", Rd_tag = "TEXT"), │ │ │ │ structure("cytoband. This package also provides utilites to manipulate and\n", Rd_tag = "TEXT"), │ │ │ │ - structure("summarize raw data to get them ready to be visualized.", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/biovizBase-package.Rd", class = "Rd", meta = list( │ │ │ │ + structure("summarize raw data to get them ready to be visualized.", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/biovizBase-package.Rd", class = "Rd", meta = list( │ │ │ │ docType = "package", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ colorBlindSafePal (list) = structure(list(structure(list(structure("Color blind safe palette generator", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("colorBlindSafePal", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("colorBlindSafePal", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("genBrewerBlindPalInfo", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("genDichromatPalInfo", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -277,15 +277,15 @@ │ │ │ │ structure("mypal <- colorBlindSafePal(20)\n", Rd_tag = "VERB"), │ │ │ │ structure("## or pass character name\n", Rd_tag = "VERB"), │ │ │ │ structure("mypal <- colorBlindSafePal(\"Set2\")\n", Rd_tag = "VERB"), │ │ │ │ structure("mypal12 <- colorBlindSafePal(22)\n", Rd_tag = "VERB"), │ │ │ │ structure("show_col(mypal(12, repeatable = FALSE)) # warning\n", Rd_tag = "VERB"), │ │ │ │ structure("show_col(mypal(11, repeatable = TRUE)) # no warning, and repeat\n", Rd_tag = "VERB"), │ │ │ │ structure("show_col(mypal12(12))\n", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/colorBlindSafePal.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/colorBlindSafePal.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ containLetters (list) = structure(list(structure(list(structure("Checking if string contains letters or not", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("containLetters", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("containLetters", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Test if a string contain any letters", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("containLetters(obj, all=FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -296,29 +296,29 @@ │ │ │ │ structure("if all is set to TRUE, return TRUE only when the string is composed\n", Rd_tag = "TEXT"), │ │ │ │ structure("of just letters.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("Useful when processing/sorting seqnames", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("Logical value", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("tengfei", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("containLetters(\"XYZ123\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("containLetters(\"XYZ123\", TRUE)", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/containLetters.Rd", class = "Rd", meta = list( │ │ │ │ + structure("containLetters(\"XYZ123\", TRUE)", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/containLetters.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ crc1.GeRL (list) = structure(list(structure(list(structure("crc1.GeRL", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("crc1.GeRL", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("crc1.GeRL", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("crc1.GeRL", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("CRC-1 mutation and structural rearrangment", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("data(crc1.GeRL)", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" GenomicRangesList contains somatic mutation, reaarangment etc for a\n", Rd_tag = "TEXT"), │ │ │ │ structure(" tumor sample, please check the reference for detials.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("data(crc1.GeRL)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("crc1.GeRL\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/crc1.GeRL.Rd", class = "Rd", meta = list( │ │ │ │ + structure("crc1.GeRL\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/crc1.GeRL.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ crunch-method (list) = structure(list(structure(list(structure("Fetching GRanges from various data source", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("crunch", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("crunch", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("crunch,TxDb-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("crunch,EnsDb-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -413,30 +413,30 @@ │ │ │ │ structure("gr <- genesymbol[\"BRCA1\"]\n", Rd_tag = "RCODE"), │ │ │ │ structure("seqlevels(gr) <- sub(seqlevels(gr), pattern=\"chr\", replacement=\"\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("temp <- crunch(edb, which = gr)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Alternatively, use the GenenameFilter from the AnnotationFilter package:\n", Rd_tag = "RCODE"), │ │ │ │ structure("temp <- crunch(edb, which = GenenameFilter(\"BRCA1\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Or a filter expression\n", Rd_tag = "RCODE"), │ │ │ │ structure("temp <- crunch(edb, which = ~ genename == \"BRCA1\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/crunch-method.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/crunch-method.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ darned_hg19_subset500 (list) = structure(list(structure(list(structure("Subset of RNA editing sites in hg19...", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("darned_hg19_subset500", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("darned_hg19_subset500", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("darned_hg19_subset500", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("Subset of RNA editing sites in hg19", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("data(darned_hg19_subset500)", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("This data set provides a subset(500 sites only) of hg19 RNA editing sites, and\n", Rd_tag = "TEXT"), │ │ │ │ structure("originally from DARNED ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("http://darned.ucc.ie/", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure(" for the hg19\n", Rd_tag = "TEXT"), structure("assembly.", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("data(darned_hg19_subset500)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("darned_hg19_subset500", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/darned_hg19_subset500.Rd", class = "Rd", meta = list( │ │ │ │ + structure("darned_hg19_subset500", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/darned_hg19_subset500.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ estimateCoverage-method (list) = structure(list(structure(list(structure("Estimation of Coverage", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("estimateCoverage", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("estimateCoverage", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("estimateCoverage,BamFile-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Estimation of Coverage\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -453,15 +453,15 @@ │ │ │ │ structure(list(list(structure("maxBinSize", Rd_tag = "TEXT")), │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure(" Max bin size.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("GRanges", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" object.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("Michael Lawrence", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/estimateCoverage-method.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Michael Lawrence", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/estimateCoverage-method.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ flatGrl (list) = structure(list(structure(list(structure("Transform GRangesList to GRanges", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("flatGrl", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("flatGrl", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Transform GRangesList to GRanges.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("flatGrl(object, indName = \"grl_name\")\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -488,28 +488,28 @@ │ │ │ │ structure(" object.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("library(GenomicRanges)\n", Rd_tag = "RCODE"), │ │ │ │ structure("gr1 <- GRanges(\"chr1\", IRanges(1:10, width = 5))\n", Rd_tag = "RCODE"), │ │ │ │ structure("gr2 <- GRanges(\"chr2\", IRanges(1:10, width = 5))\n", Rd_tag = "RCODE"), │ │ │ │ structure("obj <- GRangesList(gr1, gr2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("values(obj) <- data.frame(a = 1:2, b = letters[1:2])\n", Rd_tag = "RCODE"), │ │ │ │ - structure("stack(obj)\n", Rd_tag = "RCODE"), structure("flatGrl(obj)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/flatGrl.Rd", class = "Rd", meta = list( │ │ │ │ + structure("stack(obj)\n", Rd_tag = "RCODE"), structure("flatGrl(obj)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/flatGrl.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ genesymbol (list) = structure(list(structure(list(structure("Gene symbols with position...", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("genesymbol", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("genesymbol", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("genesymbol", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("Gene symbols with position", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("data(genesymbol)", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("This data set provides genen symbols in human with position\n", Rd_tag = "TEXT"), │ │ │ │ structure("and starnd information, stored as GRanges object.", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(genesymbol)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("head(genesymbol)\n", Rd_tag = "RCODE"), structure("genesymbol[\"RBM17\"]\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/genesymbol.Rd", class = "Rd", meta = list( │ │ │ │ + structure("head(genesymbol)\n", Rd_tag = "RCODE"), structure("genesymbol[\"RBM17\"]\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/genesymbol.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ getBioColor (list) = structure(list(structure(list(structure("Color scheme getter for biological data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getBioColor", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getBioColor", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" This function tries to get default color scheme either from fixed\n", Rd_tag = "TEXT"), │ │ │ │ structure(" palette or options for specified data set, usually just biological\n", Rd_tag = "TEXT"), │ │ │ │ @@ -649,15 +649,15 @@ │ │ │ │ structure("options(biovizBase = opts)\n", Rd_tag = "RCODE"), │ │ │ │ structure("## get from option(default)\n", Rd_tag = "RCODE"), │ │ │ │ structure("getBioColor(\"DNA_BASES_N\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("## get default fixed color\n", Rd_tag = "RCODE"), │ │ │ │ structure("getBioColor(\"DNA_BASES_N\", source = \"default\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("seqs <- c(\"A\", \"C\", \"T\", \"G\", \"G\", \"G\", \"C\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("## get colors for a sequence.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("getBioColor(\"DNA_BASES_N\")[seqs]\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/getBioColor.Rd", class = "Rd", meta = list( │ │ │ │ + structure("getBioColor(\"DNA_BASES_N\")[seqs]\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/getBioColor.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ getFormalNames (list) = structure(list(structure(list(structure("Get formals from functions", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getFormalNames", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getFormalNames", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Get formals from functions, used for dispatching arguments inside.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getFormalNames(..., remove.dots = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -669,15 +669,15 @@ │ │ │ │ structure(list(list(structure("remove.dots", Rd_tag = "TEXT")), │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure(" logical value, indicate remove dots in formals or not, default is ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("TRUE", Rd_tag = "RCODE")), 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 = "TEXT"), structure(" A character vector for formal arguments.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("getFormalNames(plot, sapply)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/getFormalNames.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("getFormalNames(plot, sapply)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/getFormalNames.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ getGaps (list) = structure(list(structure(list(structure("get gaps for a stepping transformed GRanges object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getGaps", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getGaps", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("getGaps,GRanges-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Get gaps for a stepping transformed GRanges object, for visualization\n", Rd_tag = "TEXT"), │ │ │ │ @@ -731,15 +731,15 @@ │ │ │ │ structure(" value = rnorm(N, 10, 3), score = rnorm(N, 100, 30),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" sample = sample(c(\"Normal\", \"Tumor\"), \n", Rd_tag = "RCODE"), │ │ │ │ structure(" size = N, replace = TRUE),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" pair = sample(letters, size = N, \n", Rd_tag = "RCODE"), │ │ │ │ structure(" replace = TRUE))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("grl <- splitByFacets(gr, sample ~ seqnames)\n", Rd_tag = "RCODE"), │ │ │ │ structure("gr <- unlist(endoapply(grl, addStepping))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("gr.gaps <- getGaps(gr, group.name = \"stepping\", facets = sample ~ seqnames)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/getGaps.Rd", class = "Rd", meta = list( │ │ │ │ + structure("gr.gaps <- getGaps(gr, group.name = \"stepping\", facets = sample ~ seqnames)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/getGaps.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ getIdeoGR (list) = structure(list(structure(list(structure("Get ideogram information", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getIdeoGR", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getIdeoGR", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" This function tries to parse ideogram information from\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure("seqlengths", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ @@ -769,15 +769,15 @@ │ │ │ │ structure(" getIdeoGR(hg19IdeogramCyto)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" ## with seqlengths\n", Rd_tag = "RCODE"), │ │ │ │ structure(" gr <- GRanges(\"chr1\", IRanges(1,3))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" seqlevels(gr) <- c(\"chr1\", \"chr2\", \"chr3\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" nms <- c(100, 200, 300)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" names(nms) <- c(\"chr1\", \"chr2\", \"chr3\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" seqlengths(gr) <- nms\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" gr\n", Rd_tag = "RCODE"), structure(" getIdeoGR(gr)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/getIdeoGR.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" gr\n", Rd_tag = "RCODE"), structure(" getIdeoGR(gr)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/getIdeoGR.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ getIdeogram (list) = structure(list(structure(list(structure("Get ideogram.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getIdeogram", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getIdeogram", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Get ideogram w/o cytoband for certain genome", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("getIdeogram(genome, subchr, cytobands=TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -800,15 +800,15 @@ │ │ │ │ structure(list(structure("http://genome.ucsc.edu/cgi-bin/hgTables", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure(" in UCSC genome\n", Rd_tag = "TEXT"), structure("browser.This is useful for visualization of the whole genome or\n", Rd_tag = "TEXT"), │ │ │ │ structure("single chromosome, you can see some examples in ggbio package.", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("A GRanges object.", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(list( │ │ │ │ structure("hg19IdeogramCyto <- getIdeogram(\"hg19\", cytoband = TRUE)", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/getIdeogram.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/getIdeogram.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ getScale (list) = structure(list(structure(list(structure("Get scale information from a GRanges", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getScale", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getScale", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Trying to get scale information from a ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("GRanges", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ @@ -838,67 +838,67 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("GRanges", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" object, with extra column: \"type\" indicate it's longer\n", Rd_tag = "TEXT"), │ │ │ │ structure(" major ticks or shorter minor ticks. \"scale.y\" indicates y height for\n", Rd_tag = "TEXT"), │ │ │ │ structure(" major and minor ticks. Default ratio is 3:1.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/getScale.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/getScale.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ hg19Ideogram (list) = structure(list(structure(list(structure("Hg19 ideogram without cytoband information...", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("hg19Ideogram", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("hg19Ideogram", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("hg19Ideogram", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("Hg19 ideogram without cytoband information", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("data(hg19Ideogram)", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("This data set provides hg19 genome information wihout cytoband\n", Rd_tag = "TEXT"), │ │ │ │ structure("information.", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("data(hg19Ideogram)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("hg19Ideogram", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/hg19Ideogram.Rd", class = "Rd", meta = list( │ │ │ │ + structure("hg19Ideogram", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/hg19Ideogram.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ hg19IdeogramCyto (list) = structure(list(structure(list(structure("Hg19 ideogram with cytoband information...", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("hg19IdeogramCyto", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("hg19IdeogramCyto", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("hg19IdeogramCyto", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("Hg19 ideogram with cytoband information", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("data(hg19IdeogramCyto)", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("This data set provides hg19 genome information with cytoband\n", Rd_tag = "TEXT"), │ │ │ │ structure("information.", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("data(hg19IdeogramCyto)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("hg19IdeogramCyto", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/hg19IdeogramCyto.Rd", class = "Rd", meta = list( │ │ │ │ + structure("hg19IdeogramCyto", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/hg19IdeogramCyto.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ ideo (list) = structure(list(structure(list(structure("ideogram without cytoband information", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("ideo", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("ideo", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("ideogram without cytoband information", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("data(ideo)", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("This data set provides hg19, hg18, mm10, mm9 genome information wihout cytoband\n", Rd_tag = "TEXT"), │ │ │ │ structure("information as a lit.", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("data(ideo)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("ideo", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/ideo.Rd", class = "Rd", meta = list( │ │ │ │ + structure("ideo", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/ideo.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ ideoCyto (list) = structure(list(structure(list(structure("ideogram with cytoband information", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("ideoCyto", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("ideoCyto", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("ideogram with cytoband information", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("data(ideoCyto)", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("This data set provides hg19, hg18, mm10, mm9 genome information with cytoband\n", Rd_tag = "TEXT"), │ │ │ │ structure("information as a lit.", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("data(ideoCyto)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("ideoCyto", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/ideoCyto.Rd", class = "Rd", meta = list( │ │ │ │ + structure("ideoCyto", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/ideoCyto.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ isIdeogram (list) = structure(list(structure(list(structure("Ideogram checking", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("isIdeogram", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("isIdeogram", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Check if an object is ideogram or not", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("isIdeogram(obj)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -911,15 +911,15 @@ │ │ │ │ structure(list(structure("GRanges", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" and with extra column", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("A logical value to indicate it's a ideogram or not.", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("data(hg19IdeogramCyto)\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(hg19Ideogram)\n", Rd_tag = "RCODE"), │ │ │ │ structure("isIdeogram(hg19IdeogramCyto)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("isIdeogram(hg19Ideogram)", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/isIdeogram.Rd", class = "Rd", meta = list( │ │ │ │ + structure("isIdeogram(hg19Ideogram)", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/isIdeogram.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ isMatchedWithModel (list) = structure(list(structure(list(structure("Utils for Splicing Summary", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("isMatchedWithModel", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("isMatchedWithModel", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("isJunctionRead", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Utilities used for summarizing isoforms\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -967,15 +967,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("library(GenomicAlignments)\n", Rd_tag = "RCODE"), │ │ │ │ structure("bamfile <- system.file(\"extdata\", \"SRR027894subRBM17.bam\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package=\"biovizBase\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("## get index of junction read\n", Rd_tag = "RCODE"), │ │ │ │ structure("which(isJunctionRead(cigar(readGAlignments(bamfile))))\n", Rd_tag = "RCODE"), │ │ │ │ structure("##\n", Rd_tag = "RCODE"), structure("model <- GRanges(\"chr1\", IRanges(c(10, 20, 30, 40), width = 5))\n", Rd_tag = "RCODE"), │ │ │ │ structure("gr <- GRanges(\"chr1\", IRanges(c(10, 10, 12, 22, 33), c(31, 40, 22, 32,\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" 44)))\n", Rd_tag = "RCODE"), structure("isMatchedWithModel(model, gr)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/isMatchedWithModel.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" 44)))\n", Rd_tag = "RCODE"), structure("isMatchedWithModel(model, gr)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/isMatchedWithModel.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ isSimpleIdeogram (list) = structure(list(structure(list(structure("Simple ideogram checking", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("isSimpleIdeogram", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("isSimpleIdeogram", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Check if an object is a simple ideogram or not", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("isSimpleIdeogram(obj)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -986,15 +986,15 @@ │ │ │ │ structure("information. But it double check to see if there is only one entry\n", Rd_tag = "TEXT"), │ │ │ │ structure("per chromosome", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("A logical value to indicate it's a simple ideogram or not.", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("tengfei", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("data(hg19IdeogramCyto)\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(hg19Ideogram)\n", Rd_tag = "RCODE"), │ │ │ │ structure("isSimpleIdeogram(hg19IdeogramCyto)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("isSimpleIdeogram(hg19Ideogram)", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/isSimpleIdeogram.Rd", class = "Rd", meta = list( │ │ │ │ + structure("isSimpleIdeogram(hg19Ideogram)", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/isSimpleIdeogram.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ labs (list) = structure(list(structure(list(structure("parse x and y label information from a specific object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getYLab-method", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getYLab", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("getYLab,TxDb-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("getXLab-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1018,15 +1018,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("obj", Rd_tag = "TEXT")), │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure(" A ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("TxDb", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" object.\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" a string.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/labs.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/labs.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ maxGap-method (list) = structure(list(structure(list(structure("Estimated max gaps", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("maxGap-method", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("maxGap", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("maxGap,GenomicRanges-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Compute an estimated max gap information, which could\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1050,15 +1050,15 @@ │ │ │ │ structure("gr1 <- GRanges(\"chr1\", IRanges(start = c(100, 300, 600),\n", Rd_tag = "RCODE"), │ │ │ │ structure("end = c(200, 400, 800)))\n", Rd_tag = "RCODE"), │ │ │ │ structure("gr2 <- GRanges(\"chr1\", IRanges(start = c(100, 350, 550),\n", Rd_tag = "RCODE"), │ │ │ │ structure("end = c(220, 500, 900)))\n", Rd_tag = "RCODE"), │ │ │ │ structure("gaps.gr <- intersect(gaps(gr1, start = min(start(gr1))),\n", Rd_tag = "RCODE"), │ │ │ │ structure("gaps(gr2, start = min(start(gr2))))\n", Rd_tag = "RCODE"), │ │ │ │ structure("shrink.fun <- shrinkageFun(gaps.gr, max.gap = maxGap(gaps.gr))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("shrink.fun(gr1)\n", Rd_tag = "RCODE"), structure("shrink.fun(gr2)", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/maxGap-method.Rd", class = "Rd", meta = list( │ │ │ │ + structure("shrink.fun(gr1)\n", Rd_tag = "RCODE"), structure("shrink.fun(gr2)", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/maxGap-method.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ mold-method (list) = structure(list(structure(list(structure("mold data into data.frame", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mold", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mold", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("mold,IRanges-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("mold,GRanges-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1117,15 +1117,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("assay.id", Rd_tag = "TEXT")), │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure(" define the assay id you want to convert into a ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("data.frame", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ 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 = "TEXT"), structure(" a data.frame object.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/mold-method.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/mold-method.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ pileupAsGRanges (list) = structure(list(structure(list(structure("Summarize reads for certain region", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("pileupAsGRanges", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("pileupAsGRanges", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("This function summarize reads from bam files for nucleotides on\n", Rd_tag = "TEXT"), │ │ │ │ structure("single base unit in a given region, this allows the downstream\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1170,15 +1170,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(list( │ │ │ │ structure("\n", Rd_tag = "VERB"), structure("library(Rsamtools)\n", Rd_tag = "VERB"), │ │ │ │ structure("data(genesymbol)\n", Rd_tag = "VERB"), structure("library(BSgenome.Hsapiens.UCSC.hg19) \n", Rd_tag = "VERB"), │ │ │ │ structure("bamfile <- system.file(\"extdata\", \"SRR027894subRBM17.bam\", package=\"biovizBase\")\n", Rd_tag = "VERB"), │ │ │ │ structure("test <- pileupAsGRanges(bamfile, region = genesymbol[\"RBM17\"])\n", Rd_tag = "VERB"), │ │ │ │ structure("test.match <- pileupGRangesAsVariantTable(test, Hsapiens)\n", Rd_tag = "VERB"), │ │ │ │ structure("head(test[,-7])\n", Rd_tag = "VERB"), structure("head(test.match[,-5])\n", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/pileupAsGRanges.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/pileupAsGRanges.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ pileupGRangesAsVariantTable (list) = structure(list(structure(list(structure("Mismatch summary", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("pileupGRangesAsVariantTable", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("pileupGRangesAsVariantTable", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Compare to reference genome and compute mismatch summary for\n", Rd_tag = "TEXT"), │ │ │ │ structure("certain region of reads.", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1226,15 +1226,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(list( │ │ │ │ structure("\n", Rd_tag = "VERB"), structure("library(Rsamtools)\n", Rd_tag = "VERB"), │ │ │ │ structure("data(genesymbol)\n", Rd_tag = "VERB"), structure("library(BSgenome.Hsapiens.UCSC.hg19) \n", Rd_tag = "VERB"), │ │ │ │ structure("bamfile <- system.file(\"extdata\", \"SRR027894subRBM17.bam\", package=\"biovizBase\")\n", Rd_tag = "VERB"), │ │ │ │ structure("test <- pileupAsGRanges(bamfile, region = genesymbol[\"RBM17\"])\n", Rd_tag = "VERB"), │ │ │ │ structure("test.match <- pileupGRangesAsVariantTable(test, Hsapiens)\n", Rd_tag = "VERB"), │ │ │ │ structure("head(test[,-7])\n", Rd_tag = "VERB"), structure("head(test.match[,-5])\n", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/pileupGRangesAsVariantTable.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/pileupGRangesAsVariantTable.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ plotColorLegend (list) = structure(list(structure(list(structure("Show colors", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotColorLegend", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotColorLegend", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Plot color legend, simple way to check your default color scheme", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("plotColorLegend(colors, labels, title)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1247,15 +1247,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(list(list( │ │ │ │ structure("title", Rd_tag = "TEXT")), list(structure("Title for the color legend.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("Show color sheme as a legend style, labels", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("A graphic device showing color legend.", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("cols <- getOption(\"biovizBase\")$baseColor\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plotColorLegend(cols, title = \"strand legend\")", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/plotColorLegend.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plotColorLegend(cols, title = \"strand legend\")", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/plotColorLegend.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ │ │ @@ -1294,15 +1294,15 @@ │ │ │ │ structure("shrink.fun2 <- shrinkageFun(gaps(gr1), max.gap = 0)\n", Rd_tag = "RCODE"), │ │ │ │ structure("s1 <- shrink.fun1(gr1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("getXScale(s1)\n", Rd_tag = "RCODE"), structure("# coord:genome\n", Rd_tag = "RCODE"), │ │ │ │ structure("set.seed(1)\n", Rd_tag = "RCODE"), structure("gr1 <- GRanges(\"chr1\", IRanges(start = as.integer(runif(20, 1, 100)),\n", Rd_tag = "RCODE"), │ │ │ │ structure("width = 5))\n", Rd_tag = "RCODE"), structure("gr2 <- GRanges(\"chr2\", IRanges(start = as.integer(runif(20, 1, 100)),\n", Rd_tag = "RCODE"), │ │ │ │ structure("width = 5))\n", Rd_tag = "RCODE"), structure("gr <- c(gr1, gr2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("gr.t <- transformToGenome(gr, space.skip = 1)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("getXScale(gr.t)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/scale.Rd", class = "Rd", meta = list( │ │ │ │ + structure("getXScale(gr.t)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/scale.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ showColor (list) = structure(list(structure(list(structure("Show colors", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("showColor", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("showColor", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Show colors with color string or names of color vectors.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("showColor(colors, label = c(\"color\", \"name\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1316,15 +1316,15 @@ │ │ │ │ structure(" with names of the vectors.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A plot.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(list( │ │ │ │ structure("\n", Rd_tag = "VERB"), structure("showColor(getBioColor(\"CYTOBAND\"))\n", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/showColor.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/showColor.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ shrinkageFun-method (list) = structure(list(structure(list(structure("Shrinkage function", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("shrinkageFun-method", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("shrinkageFun", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("is_coord_truncate_gaps", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("shrinkageFun,GenomicRanges-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1369,15 +1369,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("shrink.fun1 <- shrinkageFun(gaps(gr1), max.gap = maxGap(gaps(gr1), 0.1))\n", Rd_tag = "RCODE"), │ │ │ │ structure("shrink.fun2 <- shrinkageFun(gaps(gr1, start(gr1), end(gr1)), max.gap = maxGap(gaps(gr1), 0.1))\n", Rd_tag = "RCODE"), │ │ │ │ structure("shrink.fun3 <- shrinkageFun(gaps(gr1), max.gap = 0)\n", Rd_tag = "RCODE"), │ │ │ │ structure("s1 <- shrink.fun1(gr1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("s2 <- shrink.fun2(gr1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("s3 <- shrink.fun3(gr1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("metadata(s1)$coord\n", Rd_tag = "RCODE"), │ │ │ │ - structure("values(s1)$.ori\n", Rd_tag = "RCODE"), structure("is_coord_truncate_gaps(s1)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/shrinkageFun-method.Rd", class = "Rd", meta = list( │ │ │ │ + structure("values(s1)$.ori\n", Rd_tag = "RCODE"), structure("is_coord_truncate_gaps(s1)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/shrinkageFun-method.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ splitByFacets-method (list) = structure(list(structure(list(structure("split a GRanges by formula", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("splitByFacets", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("splitByFacets", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("splitByFacets,GRanges,formula-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("splitByFacets,GRanges,GRanges-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1440,15 +1440,15 @@ │ │ │ │ structure(" sample = sample(c(\"Normal\", \"Tumor\"), \n", Rd_tag = "RCODE"), │ │ │ │ structure(" size = N, replace = TRUE),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" pair = sample(letters, size = N, \n", Rd_tag = "RCODE"), │ │ │ │ structure(" replace = TRUE))\n", Rd_tag = "RCODE"), │ │ │ │ structure("facets <- sample ~ seqnames\n", Rd_tag = "RCODE"), │ │ │ │ structure("splitByFacets(gr, facets)\n", Rd_tag = "RCODE"), │ │ │ │ structure("splitByFacets(gr)\n", Rd_tag = "RCODE"), structure("gr.sub <- GRanges(\"chr1\", IRanges(c(1, 200, 250), width = c(50, 10,\n", Rd_tag = "RCODE"), │ │ │ │ - structure("30)))\n", Rd_tag = "RCODE"), structure("splitByFacets(gr, gr.sub)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/splitByFacets-method.Rd", class = "Rd", meta = list( │ │ │ │ + structure("30)))\n", Rd_tag = "RCODE"), structure("splitByFacets(gr, gr.sub)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/splitByFacets-method.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ strip_formula_dots (list) = structure(list(structure(list(structure("strip dots around a formula variables", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("strip_formula_dots", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("strip_formula_dots", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" strip dots around variables in a formula.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(" strip_formula_dots(formula)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1456,15 +1456,15 @@ │ │ │ │ structure(list(list(structure("formula", Rd_tag = "TEXT")), │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure(" A formula. such as coverage ~ seqnames, or ..coverage.. ~ seqnames.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A formula wihout \"..\" around for all variables.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("obj <- ..coverage.. ~ seqnames\n", Rd_tag = "RCODE"), │ │ │ │ - structure("strip_formula_dots(obj)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/strip_formula_dots.Rd", class = "Rd", meta = list( │ │ │ │ + structure("strip_formula_dots(obj)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/strip_formula_dots.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ subsetArgsByFormals (list) = structure(list(structure(list(structure("Subset list of arguments by functions", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("subsetArgsByFormals", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("subsetArgsByFormals", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" find arguments matched by formals of passed functions, \n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("subsetArgsByFormals(args, ..., remove.dots = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1480,15 +1480,15 @@ │ │ │ │ structure(list(list(structure("remove.dots", Rd_tag = "TEXT")), │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure(" logical value indicate whether to include dots in formals or not.\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(" argumnets that matched with passed function.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("args <- list(x = 1:3, simplify = TRUE, b = \"b\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("subsetArgsByFormals(args, plot, sapply)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/subsetArgsByFormals.Rd", class = "Rd", meta = list( │ │ │ │ + structure("subsetArgsByFormals(args, plot, sapply)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/subsetArgsByFormals.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ transform (list) = structure(list(structure(list(structure("Transform GRanges to different coordinates and layout", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("transformToGenome", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("transformToGenome", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("transformToGenome,GRanges-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("transformToGenome,GRangesList-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1698,15 +1698,15 @@ │ │ │ │ structure("width = 5))\n", Rd_tag = "RCODE"), structure("gr <- c(gr1, gr2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("gr.t <- transformToGenome(gr, space.skip = 0.1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("is_coord_genome(gr.t)\n", Rd_tag = "RCODE"), │ │ │ │ structure("transformToCircle(gr.t)\n", Rd_tag = "RCODE"), │ │ │ │ structure("transformToRectInCircle(gr)\n", Rd_tag = "RCODE"), │ │ │ │ structure("transformToSegInCircle(gr)\n", Rd_tag = "RCODE"), │ │ │ │ structure("values(gr1)$to.gr <- gr2\n", Rd_tag = "RCODE"), │ │ │ │ - structure("transformToLinkInCircle(gr1, linked.to = \"to.gr\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/transform.Rd", class = "Rd", meta = list( │ │ │ │ + structure("transformToLinkInCircle(gr1, linked.to = \"to.gr\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/transform.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ transformGRangesForEvenSpace (list) = structure(list(structure(list(structure("Transform GRanges with New Coordinates", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("transformGRangesForEvenSpace", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("transformGRangesForEvenSpace", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" For graphics, like linked plot, e.g. generated by\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure("qplotRangesLinkedToData", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ @@ -1725,10 +1725,10 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" A GRanges object as passed in, with new column x.new which indicate\n", Rd_tag = "TEXT"), │ │ │ │ structure(" the static track coordinates, in this way, we could map the new\n", Rd_tag = "TEXT"), │ │ │ │ structure(" coordinates with the old one.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Tengfei Yin", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("library(GenomicRanges)\n", Rd_tag = "RCODE"), │ │ │ │ structure("gr <- GRanges(\"chr1\", IRanges(seq(1,100, length.out = 10), width = 5))\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(biovizBase)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("transformGRangesForEvenSpace(gr)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-biovizbase/man/transformGRangesForEvenSpace.Rd", class = "Rd", meta = list( │ │ │ │ + structure("transformGRangesForEvenSpace(gr)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/transformGRangesForEvenSpace.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/biovizBase/help/biovizBase.rdx │ │ │ ├── biovizBase.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,247 +1,247 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$CRC │ │ │ │ │ -[1] 273 836 │ │ │ │ │ +[1] 286 850 │ │ │ │ │ │ │ │ │ │ $variables$GCcontent │ │ │ │ │ -[1] 1387 2024 │ │ │ │ │ +[1] 1425 2039 │ │ │ │ │ │ │ │ │ │ $variables$`addStepping-method` │ │ │ │ │ -[1] 3698 2900 │ │ │ │ │ +[1] 3759 2912 │ │ │ │ │ │ │ │ │ │ $variables$`aes-utils` │ │ │ │ │ -[1] 6875 1033 │ │ │ │ │ +[1] 6958 1051 │ │ │ │ │ │ │ │ │ │ $variables$`biovizBase-package` │ │ │ │ │ -[1] 8192 872 │ │ │ │ │ +[1] 8302 884 │ │ │ │ │ │ │ │ │ │ $variables$colorBlindSafePal │ │ │ │ │ -[1] 9349 3852 │ │ │ │ │ +[1] 9481 3866 │ │ │ │ │ │ │ │ │ │ $variables$containLetters │ │ │ │ │ -[1] 13484 983 │ │ │ │ │ +[1] 13640 997 │ │ │ │ │ │ │ │ │ │ $variables$crc1.GeRL │ │ │ │ │ -[1] 14747 859 │ │ │ │ │ +[1] 14928 873 │ │ │ │ │ │ │ │ │ │ $variables$`crunch-method` │ │ │ │ │ -[1] 15889 3434 │ │ │ │ │ +[1] 16093 3447 │ │ │ │ │ │ │ │ │ │ $variables$darned_hg19_subset500 │ │ │ │ │ -[1] 19615 838 │ │ │ │ │ +[1] 19840 852 │ │ │ │ │ │ │ │ │ │ $variables$`estimateCoverage-method` │ │ │ │ │ -[1] 20742 1040 │ │ │ │ │ +[1] 20991 1056 │ │ │ │ │ │ │ │ │ │ $variables$flatGrl │ │ │ │ │ -[1] 22059 1512 │ │ │ │ │ +[1] 22335 1526 │ │ │ │ │ │ │ │ │ │ $variables$genesymbol │ │ │ │ │ -[1] 23851 753 │ │ │ │ │ +[1] 24151 766 │ │ │ │ │ │ │ │ │ │ $variables$getBioColor │ │ │ │ │ -[1] 24885 4995 │ │ │ │ │ +[1] 25208 5010 │ │ │ │ │ │ │ │ │ │ $variables$getFormalNames │ │ │ │ │ -[1] 30163 1045 │ │ │ │ │ +[1] 30512 1060 │ │ │ │ │ │ │ │ │ │ $variables$getGaps │ │ │ │ │ -[1] 31485 2489 │ │ │ │ │ +[1] 31859 2500 │ │ │ │ │ │ │ │ │ │ $variables$getIdeoGR │ │ │ │ │ -[1] 34252 1570 │ │ │ │ │ +[1] 34649 1585 │ │ │ │ │ │ │ │ │ │ $variables$getIdeogram │ │ │ │ │ -[1] 36102 1592 │ │ │ │ │ +[1] 36525 1609 │ │ │ │ │ │ │ │ │ │ $variables$getScale │ │ │ │ │ -[1] 37971 1529 │ │ │ │ │ +[1] 38422 1543 │ │ │ │ │ │ │ │ │ │ $variables$hg19Ideogram │ │ │ │ │ -[1] 39783 696 │ │ │ │ │ +[1] 40258 709 │ │ │ │ │ │ │ │ │ │ $variables$hg19IdeogramCyto │ │ │ │ │ -[1] 40767 702 │ │ │ │ │ +[1] 41264 718 │ │ │ │ │ │ │ │ │ │ $variables$ideo │ │ │ │ │ -[1] 41742 689 │ │ │ │ │ +[1] 42267 703 │ │ │ │ │ │ │ │ │ │ $variables$ideoCyto │ │ │ │ │ -[1] 42708 693 │ │ │ │ │ +[1] 43259 706 │ │ │ │ │ │ │ │ │ │ $variables$isIdeogram │ │ │ │ │ -[1] 43681 1021 │ │ │ │ │ +[1] 44255 1037 │ │ │ │ │ │ │ │ │ │ $variables$isMatchedWithModel │ │ │ │ │ -[1] 44988 2175 │ │ │ │ │ +[1] 45588 2189 │ │ │ │ │ │ │ │ │ │ $variables$isSimpleIdeogram │ │ │ │ │ -[1] 47448 964 │ │ │ │ │ +[1] 48070 980 │ │ │ │ │ │ │ │ │ │ $variables$labs │ │ │ │ │ -[1] 48685 1202 │ │ │ │ │ +[1] 49334 1216 │ │ │ │ │ │ │ │ │ │ $variables$`maxGap-method` │ │ │ │ │ -[1] 50171 1491 │ │ │ │ │ +[1] 50843 1504 │ │ │ │ │ │ │ │ │ │ $variables$`mold-method` │ │ │ │ │ -[1] 51942 2253 │ │ │ │ │ +[1] 52638 2269 │ │ │ │ │ │ │ │ │ │ $variables$pileupAsGRanges │ │ │ │ │ -[1] 54481 2303 │ │ │ │ │ +[1] 55202 2317 │ │ │ │ │ │ │ │ │ │ $variables$pileupGRangesAsVariantTable │ │ │ │ │ -[1] 57077 2449 │ │ │ │ │ +[1] 57821 2463 │ │ │ │ │ │ │ │ │ │ $variables$plotColorLegend │ │ │ │ │ -[1] 59810 1122 │ │ │ │ │ +[1] 60578 1136 │ │ │ │ │ │ │ │ │ │ $variables$scale │ │ │ │ │ -[1] 61206 1640 │ │ │ │ │ +[1] 61999 1654 │ │ │ │ │ │ │ │ │ │ $variables$showColor │ │ │ │ │ -[1] 63124 1042 │ │ │ │ │ +[1] 63943 1062 │ │ │ │ │ │ │ │ │ │ $variables$`shrinkageFun-method` │ │ │ │ │ -[1] 64453 2155 │ │ │ │ │ +[1] 65302 2168 │ │ │ │ │ │ │ │ │ │ $variables$`splitByFacets-method` │ │ │ │ │ -[1] 66896 2454 │ │ │ │ │ +[1] 67767 2467 │ │ │ │ │ │ │ │ │ │ $variables$strip_formula_dots │ │ │ │ │ -[1] 69637 899 │ │ │ │ │ +[1] 70530 913 │ │ │ │ │ │ │ │ │ │ $variables$subsetArgsByFormals │ │ │ │ │ -[1] 70823 1155 │ │ │ │ │ +[1] 71741 1168 │ │ │ │ │ │ │ │ │ │ $variables$transform │ │ │ │ │ -[1] 72254 6154 │ │ │ │ │ +[1] 73198 6167 │ │ │ │ │ │ │ │ │ │ $variables$transformGRangesForEvenSpace │ │ │ │ │ -[1] 78700 1365 │ │ │ │ │ +[1] 79669 1379 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 273 │ │ │ │ │ +[1] 0 286 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 19323 292 │ │ │ │ │ +[1] 19540 300 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 20453 289 │ │ │ │ │ +[1] 20692 299 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 21782 277 │ │ │ │ │ +[1] 22047 288 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 23571 280 │ │ │ │ │ +[1] 23861 290 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 24604 281 │ │ │ │ │ +[1] 24917 291 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 29880 283 │ │ │ │ │ +[1] 30218 294 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 31208 277 │ │ │ │ │ +[1] 31572 287 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 33974 278 │ │ │ │ │ +[1] 34359 290 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 35822 280 │ │ │ │ │ +[1] 36234 291 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 37694 277 │ │ │ │ │ +[1] 38134 288 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 1109 278 │ │ │ │ │ +[1] 1136 289 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 39500 283 │ │ │ │ │ +[1] 39965 293 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 40479 288 │ │ │ │ │ +[1] 40967 297 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 41469 273 │ │ │ │ │ +[1] 41982 285 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 42431 277 │ │ │ │ │ +[1] 42970 289 │ │ │ │ │ │ │ │ │ │ $references$`env::24` │ │ │ │ │ -[1] 43401 280 │ │ │ │ │ +[1] 43965 290 │ │ │ │ │ │ │ │ │ │ $references$`env::25` │ │ │ │ │ -[1] 44702 286 │ │ │ │ │ +[1] 45292 296 │ │ │ │ │ │ │ │ │ │ $references$`env::26` │ │ │ │ │ -[1] 47163 285 │ │ │ │ │ +[1] 47777 293 │ │ │ │ │ │ │ │ │ │ $references$`env::27` │ │ │ │ │ -[1] 48412 273 │ │ │ │ │ +[1] 49050 284 │ │ │ │ │ │ │ │ │ │ $references$`env::28` │ │ │ │ │ -[1] 49887 284 │ │ │ │ │ +[1] 50550 293 │ │ │ │ │ │ │ │ │ │ $references$`env::29` │ │ │ │ │ -[1] 51662 280 │ │ │ │ │ +[1] 52347 291 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 3411 287 │ │ │ │ │ +[1] 3464 295 │ │ │ │ │ │ │ │ │ │ $references$`env::30` │ │ │ │ │ -[1] 54195 286 │ │ │ │ │ +[1] 54907 295 │ │ │ │ │ │ │ │ │ │ $references$`env::31` │ │ │ │ │ -[1] 56784 293 │ │ │ │ │ +[1] 57519 302 │ │ │ │ │ │ │ │ │ │ $references$`env::32` │ │ │ │ │ -[1] 59526 284 │ │ │ │ │ +[1] 60284 294 │ │ │ │ │ │ │ │ │ │ $references$`env::33` │ │ │ │ │ -[1] 60932 274 │ │ │ │ │ +[1] 61714 285 │ │ │ │ │ │ │ │ │ │ $references$`env::34` │ │ │ │ │ -[1] 62846 278 │ │ │ │ │ +[1] 63653 290 │ │ │ │ │ │ │ │ │ │ $references$`env::35` │ │ │ │ │ -[1] 64166 287 │ │ │ │ │ +[1] 65005 297 │ │ │ │ │ │ │ │ │ │ $references$`env::36` │ │ │ │ │ -[1] 66608 288 │ │ │ │ │ +[1] 67470 297 │ │ │ │ │ │ │ │ │ │ $references$`env::37` │ │ │ │ │ -[1] 69350 287 │ │ │ │ │ +[1] 70234 296 │ │ │ │ │ │ │ │ │ │ $references$`env::38` │ │ │ │ │ -[1] 70536 287 │ │ │ │ │ +[1] 71443 298 │ │ │ │ │ │ │ │ │ │ $references$`env::39` │ │ │ │ │ -[1] 71978 276 │ │ │ │ │ +[1] 72909 289 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 6598 277 │ │ │ │ │ +[1] 6671 287 │ │ │ │ │ │ │ │ │ │ $references$`env::40` │ │ │ │ │ -[1] 78408 292 │ │ │ │ │ +[1] 79365 304 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 7908 284 │ │ │ │ │ +[1] 8009 293 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 9064 285 │ │ │ │ │ +[1] 9186 295 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 13201 283 │ │ │ │ │ +[1] 13347 293 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 14467 280 │ │ │ │ │ +[1] 14637 291 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 15606 283 │ │ │ │ │ +[1] 15801 292 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/biovizBase/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,42 +1,42 @@ │ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-biovizbase/man/CRC.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-biovizbase/man/GCcontent.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-biovizbase/man/addStepping-method.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-biovizbase/man/aes-utils.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-biovizbase/man/biovizBase-package.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-biovizbase/man/colorBlindSafePal.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-biovizbase/man/containLetters.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-biovizbase/man/crc1.GeRL.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-biovizbase/man/crunch-method.Rd" │ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-biovizbase/man/darned_hg19_subset500.Rd" │ │ │ │ │ -[11] "/home/moeller/Salsa/r-bioc-biovizbase/man/estimateCoverage-method.Rd" │ │ │ │ │ -[12] "/home/moeller/Salsa/r-bioc-biovizbase/man/flatGrl.Rd" │ │ │ │ │ -[13] "/home/moeller/Salsa/r-bioc-biovizbase/man/genesymbol.Rd" │ │ │ │ │ -[14] "/home/moeller/Salsa/r-bioc-biovizbase/man/getBioColor.Rd" │ │ │ │ │ -[15] "/home/moeller/Salsa/r-bioc-biovizbase/man/getFormalNames.Rd" │ │ │ │ │ -[16] "/home/moeller/Salsa/r-bioc-biovizbase/man/getGaps.Rd" │ │ │ │ │ -[17] "/home/moeller/Salsa/r-bioc-biovizbase/man/getIdeoGR.Rd" │ │ │ │ │ -[18] "/home/moeller/Salsa/r-bioc-biovizbase/man/getIdeogram.Rd" │ │ │ │ │ -[19] "/home/moeller/Salsa/r-bioc-biovizbase/man/getScale.Rd" │ │ │ │ │ -[20] "/home/moeller/Salsa/r-bioc-biovizbase/man/hg19Ideogram.Rd" │ │ │ │ │ -[21] "/home/moeller/Salsa/r-bioc-biovizbase/man/hg19IdeogramCyto.Rd" │ │ │ │ │ -[22] "/home/moeller/Salsa/r-bioc-biovizbase/man/ideo.Rd" │ │ │ │ │ -[23] "/home/moeller/Salsa/r-bioc-biovizbase/man/ideoCyto.Rd" │ │ │ │ │ -[24] "/home/moeller/Salsa/r-bioc-biovizbase/man/isIdeogram.Rd" │ │ │ │ │ -[25] "/home/moeller/Salsa/r-bioc-biovizbase/man/isMatchedWithModel.Rd" │ │ │ │ │ -[26] "/home/moeller/Salsa/r-bioc-biovizbase/man/isSimpleIdeogram.Rd" │ │ │ │ │ -[27] "/home/moeller/Salsa/r-bioc-biovizbase/man/labs.Rd" │ │ │ │ │ -[28] "/home/moeller/Salsa/r-bioc-biovizbase/man/maxGap-method.Rd" │ │ │ │ │ -[29] "/home/moeller/Salsa/r-bioc-biovizbase/man/mold-method.Rd" │ │ │ │ │ -[30] "/home/moeller/Salsa/r-bioc-biovizbase/man/pileupAsGRanges.Rd" │ │ │ │ │ -[31] "/home/moeller/Salsa/r-bioc-biovizbase/man/pileupGRangesAsVariantTable.Rd" │ │ │ │ │ -[32] "/home/moeller/Salsa/r-bioc-biovizbase/man/plotColorLegend.Rd" │ │ │ │ │ -[33] "/home/moeller/Salsa/r-bioc-biovizbase/man/scale.Rd" │ │ │ │ │ -[34] "/home/moeller/Salsa/r-bioc-biovizbase/man/showColor.Rd" │ │ │ │ │ -[35] "/home/moeller/Salsa/r-bioc-biovizbase/man/shrinkageFun-method.Rd" │ │ │ │ │ -[36] "/home/moeller/Salsa/r-bioc-biovizbase/man/splitByFacets-method.Rd" │ │ │ │ │ -[37] "/home/moeller/Salsa/r-bioc-biovizbase/man/strip_formula_dots.Rd" │ │ │ │ │ -[38] "/home/moeller/Salsa/r-bioc-biovizbase/man/subsetArgsByFormals.Rd" │ │ │ │ │ -[39] "/home/moeller/Salsa/r-bioc-biovizbase/man/transform.Rd" │ │ │ │ │ -[40] "/home/moeller/Salsa/r-bioc-biovizbase/man/transformGRangesForEvenSpace.Rd" │ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/CRC.Rd" │ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/GCcontent.Rd" │ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/addStepping-method.Rd" │ │ │ │ │ + [4] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/aes-utils.Rd" │ │ │ │ │ + [5] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/biovizBase-package.Rd" │ │ │ │ │ + [6] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/colorBlindSafePal.Rd" │ │ │ │ │ + [7] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/containLetters.Rd" │ │ │ │ │ + [8] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/crc1.GeRL.Rd" │ │ │ │ │ + [9] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/crunch-method.Rd" │ │ │ │ │ +[10] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/darned_hg19_subset500.Rd" │ │ │ │ │ +[11] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/estimateCoverage-method.Rd" │ │ │ │ │ +[12] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/flatGrl.Rd" │ │ │ │ │ +[13] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/genesymbol.Rd" │ │ │ │ │ +[14] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/getBioColor.Rd" │ │ │ │ │ +[15] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/getFormalNames.Rd" │ │ │ │ │ +[16] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/getGaps.Rd" │ │ │ │ │ +[17] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/getIdeoGR.Rd" │ │ │ │ │ +[18] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/getIdeogram.Rd" │ │ │ │ │ +[19] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/getScale.Rd" │ │ │ │ │ +[20] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/hg19Ideogram.Rd" │ │ │ │ │ +[21] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/hg19IdeogramCyto.Rd" │ │ │ │ │ +[22] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/ideo.Rd" │ │ │ │ │ +[23] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/ideoCyto.Rd" │ │ │ │ │ +[24] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/isIdeogram.Rd" │ │ │ │ │ +[25] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/isMatchedWithModel.Rd" │ │ │ │ │ +[26] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/isSimpleIdeogram.Rd" │ │ │ │ │ +[27] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/labs.Rd" │ │ │ │ │ +[28] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/maxGap-method.Rd" │ │ │ │ │ +[29] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/mold-method.Rd" │ │ │ │ │ +[30] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/pileupAsGRanges.Rd" │ │ │ │ │ +[31] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/pileupGRangesAsVariantTable.Rd" │ │ │ │ │ +[32] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/plotColorLegend.Rd" │ │ │ │ │ +[33] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/scale.Rd" │ │ │ │ │ +[34] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/showColor.Rd" │ │ │ │ │ +[35] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/shrinkageFun-method.Rd" │ │ │ │ │ +[36] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/splitByFacets-method.Rd" │ │ │ │ │ +[37] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/strip_formula_dots.Rd" │ │ │ │ │ +[38] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/subsetArgsByFormals.Rd" │ │ │ │ │ +[39] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/transform.Rd" │ │ │ │ │ +[40] "/build/reproducible-path/r-bioc-biovizbase-1.60.0+ds/man/transformGRangesForEvenSpace.Rd" │ │ │ │ │ attr(,"first") │ │ │ │ │ -[1] 43 │ │ │ │ │ +[1] 58 │ │ ├── ./usr/lib/R/site-library/biovizBase/libs/biovizBase.so │ │ │┄ File has been modified after NT_GNU_BUILD_ID has been applied. │ │ │ ├── readelf --wide --notes {} │ │ │ │ @@ -1,4 +1,4 @@ │ │ │ │ │ │ │ │ Displaying notes found in: .note.gnu.build-id │ │ │ │ Owner Data size Description │ │ │ │ - GNU 0x00000014 NT_GNU_BUILD_ID (unique build ID bitstring) Build ID: 0335980f1f4efd02ed8e6a7eb768184931e514cf │ │ │ │ + GNU 0x00000014 NT_GNU_BUILD_ID (unique build ID bitstring) Build ID: 6c203d5e9ecd52e5d79d937b7503bcc2240255f0 │ │ │ ├── readelf --wide --decompress --hex-dump=.gnu_debuglink {} │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ │ │ │ │ Hex dump of section '.gnu_debuglink': │ │ │ │ - 0x00000000 33353938 30663166 34656664 30326564 35980f1f4efd02ed │ │ │ │ - 0x00000010 38653661 37656237 36383138 34393331 8e6a7eb768184931 │ │ │ │ - 0x00000020 65353134 63662e64 65627567 00000000 e514cf.debug.... │ │ │ │ - 0x00000030 3cb4e88e <... │ │ │ │ + 0x00000000 32303364 35653965 63643532 65356437 203d5e9ecd52e5d7 │ │ │ │ + 0x00000010 39643933 37623735 30336263 63323234 9d937b7503bcc224 │ │ │ │ + 0x00000020 30323535 66302e64 65627567 00000000 0255f0.debug.... │ │ │ │ + 0x00000030 a8b8e7b6 ....