--- /srv/rebuilderd/tmp/rebuilderdr5C83R/inputs/r-bioc-geoquery_2.80.0+dfsg-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdr5C83R/out/r-bioc-geoquery_2.80.0+dfsg-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-10 15:46:41.000000 debian-binary │ --rw-r--r-- 0 0 0 1920 2026-08-10 15:46:41.000000 control.tar.xz │ --rw-r--r-- 0 0 0 13739876 2026-08-10 15:46:41.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 1872 2026-08-10 15:46:41.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 13741248 2026-08-10 15:46:41.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:46:41.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 1085 2026-08-10 15:46:41.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 941 2026-08-10 15:46:41.000000 ./control │ │ │ -rw-r--r-- 0 root (0) root (0) 3048 2026-08-10 15:46:41.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,14 @@ │ │ │ Package: r-bioc-geoquery │ │ │ Version: 2.80.0+dfsg-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ -Installed-Size: 13540 │ │ │ +Installed-Size: 13541 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-bioc-biobase, r-cran-readr (>= 1.3.1), r-cran-xml2, r-cran-dplyr, r-cran-data.table, r-cran-tidyr, r-cran-magrittr, r-bioc-limma, r-cran-curl, r-cran-rentrez, r-cran-r.utils, r-cran-stringr, r-bioc-summarizedexperiment, r-bioc-s4vectors, r-cran-rvest, r-cran-httr2, r-pkg-team-core-architecture │ │ │ -Suggests: r-cran-knitr, r-cran-rmarkdown, r-bioc-biocgenerics, r-cran-testthat, r-cran-covr, r-cran-markdown, r-cran-quarto, r-bioc-dropletutils, r-bioc-singlecellexperiment │ │ │ +Suggests: r-bioc-biocgenerics │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/GEOquery/ │ │ │ Description: Get data from NCBI Gene Expression Omnibus (GEO) │ │ │ The NCBI Gene Expression Omnibus (GEO) is a public repository of │ │ │ microarray data. Given the rich and varied nature of this resource, it │ │ │ is only natural to want to apply BioConductor tools to these data. │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -14,16 +14,16 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 801 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/Meta/links.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 655 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1577 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/Meta/package.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1229 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 1002 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/NEWS.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/R/GEOquery │ │ │ --rw-r--r-- 0 root (0) root (0) 297235 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/R/GEOquery.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 1928 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/R/GEOquery.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 297245 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/R/GEOquery.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 1933 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/R/GEOquery.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 1572 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/README.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 4256 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/doc/GEOquery.R │ │ │ -rw-r--r-- 0 root (0) root (0) 9615 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/doc/GEOquery.qmd │ │ │ -rw-r--r-- 0 root (0) root (0) 1525 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/doc/index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2015 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/doc/single-cell.R │ │ │ -rw-r--r-- 0 root (0) root (0) 13324 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/doc/single-cell.html │ │ │ @@ -32,18 +32,18 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 1135299 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/extdata/GDS507.soft.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2008407 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/extdata/GPL97.annot.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 0 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/extdata/GPLbroken.soft.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 10142112 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/extdata/GSE781_family.soft.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 119670 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/extdata/GSM11805.txt.gz │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 2074 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/help/AnIndex │ │ │ --rw-r--r-- 0 root (0) root (0) 53328 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/help/GEOquery.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 949 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/help/GEOquery.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 54299 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/help/GEOquery.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 942 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/help/GEOquery.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 624 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 483 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 495 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 7793 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/scripts/ │ │ │ -rw-r--r-- 0 root (0) root (0) 594 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/scripts/buildGEODocsumJson.R │ │ │ -rw-r--r-- 0 root (0) root (0) 7899 2026-08-10 15:46:41.000000 ./usr/lib/R/site-library/GEOquery/scripts/geometa.R │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:46:41.000000 ./usr/share/ │ │ ├── ./usr/lib/R/site-library/GEOquery/R/GEOquery.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -265,15 +265,15 @@ │ │ │ │ "imports" = " tidyr = c(gather = "gather"), tidyr = c(separate = "separate"), " │ │ │ │ "imports" = " tidyr = c(spread = "spread"), utils = c(download.file = "download.file"), " │ │ │ │ "imports" = " xml2 = c(read_html = "read_html"), xml2 = c(read_xml = "read_xml"), " │ │ │ │ "imports" = " xml2 = c(xml_find_all = "xml_find_all"), xml2 = c(xml_text = "xml_text"), " │ │ │ │ "imports" = " Biobase = c(.__C__ExpressionSet = ".__C__ExpressionSet"), " │ │ │ │ "imports" = " limma = c(.__C__MAList = ".__C__MAList"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-geoquery/debian/r-bioc-geoquery/usr/lib/R/site-library/GEOquery"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/debian/r-bioc-geoquery/usr/lib/R/site-library/GEOquery"" │ │ │ │ "spec" = "c(name = "GEOquery", version = "2.80.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/GEOquery/R/GEOquery.rdx │ │ │ ├── GEOquery.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -14,453 +14,453 @@ │ │ │ │ │ $variables$.__C__GSE │ │ │ │ │ [1] 4193 293 │ │ │ │ │ │ │ │ │ │ $variables$.__C__GSM │ │ │ │ │ [1] 4486 1220 │ │ │ │ │ │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 8441 52 │ │ │ │ │ +[1] 8451 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 8624 52 │ │ │ │ │ +[1] 8634 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__Accession:GEOquery` │ │ │ │ │ -[1] 10350 52 │ │ │ │ │ +[1] 10360 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__Columns:GEOquery` │ │ │ │ │ -[1] 12336 52 │ │ │ │ │ +[1] 12346 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__GPL:GEOquery` │ │ │ │ │ -[1] 13847 53 │ │ │ │ │ +[1] 13857 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__GPLList:GEOquery` │ │ │ │ │ -[1] 15370 53 │ │ │ │ │ +[1] 15380 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__GSM:GEOquery` │ │ │ │ │ -[1] 16113 53 │ │ │ │ │ +[1] 16123 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__GSMList:GEOquery` │ │ │ │ │ -[1] 17634 53 │ │ │ │ │ +[1] 17644 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__Meta:GEOquery` │ │ │ │ │ -[1] 19342 53 │ │ │ │ │ +[1] 19352 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__Table:GEOquery` │ │ │ │ │ -[1] 21306 53 │ │ │ │ │ +[1] 21316 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__dataTable:GEOquery` │ │ │ │ │ -[1] 22832 53 │ │ │ │ │ +[1] 22842 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__show:methods` │ │ │ │ │ -[1] 224315 53 │ │ │ │ │ +[1] 224325 53 │ │ │ │ │ │ │ │ │ │ $variables$.genericGEOTableParser │ │ │ │ │ -[1] 224368 1323 │ │ │ │ │ +[1] 224378 1323 │ │ │ │ │ │ │ │ │ │ $variables$.na_strings │ │ │ │ │ -[1] 225691 63 │ │ │ │ │ +[1] 225701 63 │ │ │ │ │ │ │ │ │ │ $variables$.onLoad │ │ │ │ │ -[1] 225754 403 │ │ │ │ │ +[1] 225764 403 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 226157 53 │ │ │ │ │ +[1] 226167 53 │ │ │ │ │ │ │ │ │ │ $variables$.parseGPLTxt │ │ │ │ │ -[1] 226210 686 │ │ │ │ │ +[1] 226220 686 │ │ │ │ │ │ │ │ │ │ $variables$.parseGPLWithLimits │ │ │ │ │ -[1] 226896 2230 │ │ │ │ │ +[1] 226906 2230 │ │ │ │ │ │ │ │ │ │ $variables$.parseGSMTxt │ │ │ │ │ -[1] 229126 686 │ │ │ │ │ +[1] 229136 686 │ │ │ │ │ │ │ │ │ │ $variables$.parseGSMWithLimits │ │ │ │ │ -[1] 229812 2098 │ │ │ │ │ +[1] 229822 2098 │ │ │ │ │ │ │ │ │ │ $variables$.read_lines │ │ │ │ │ -[1] 231910 329 │ │ │ │ │ +[1] 231920 329 │ │ │ │ │ │ │ │ │ │ $variables$Accession │ │ │ │ │ -[1] 232239 401 │ │ │ │ │ +[1] 232249 401 │ │ │ │ │ │ │ │ │ │ $variables$Columns │ │ │ │ │ -[1] 232640 402 │ │ │ │ │ +[1] 232650 402 │ │ │ │ │ │ │ │ │ │ $variables$GDS2MA │ │ │ │ │ -[1] 233042 1655 │ │ │ │ │ +[1] 233052 1655 │ │ │ │ │ │ │ │ │ │ $variables$GDS2eSet │ │ │ │ │ -[1] 234697 3239 │ │ │ │ │ +[1] 234707 3239 │ │ │ │ │ │ │ │ │ │ $variables$GPL │ │ │ │ │ -[1] 237936 401 │ │ │ │ │ +[1] 237946 401 │ │ │ │ │ │ │ │ │ │ $variables$GPLList │ │ │ │ │ -[1] 238337 403 │ │ │ │ │ +[1] 238347 403 │ │ │ │ │ │ │ │ │ │ $variables$GPLcache │ │ │ │ │ -[1] 238871 53 │ │ │ │ │ +[1] 238881 53 │ │ │ │ │ │ │ │ │ │ $variables$GSM │ │ │ │ │ -[1] 238924 401 │ │ │ │ │ +[1] 238934 401 │ │ │ │ │ │ │ │ │ │ $variables$GSMList │ │ │ │ │ -[1] 239325 403 │ │ │ │ │ +[1] 239335 403 │ │ │ │ │ │ │ │ │ │ $variables$Meta │ │ │ │ │ -[1] 239728 400 │ │ │ │ │ +[1] 239738 400 │ │ │ │ │ │ │ │ │ │ $variables$Table │ │ │ │ │ -[1] 240128 401 │ │ │ │ │ +[1] 240138 401 │ │ │ │ │ │ │ │ │ │ $variables$browseGEOAccession │ │ │ │ │ -[1] 240529 263 │ │ │ │ │ +[1] 240539 263 │ │ │ │ │ │ │ │ │ │ $variables$browseWebsiteRNASeqSearch │ │ │ │ │ -[1] 240792 262 │ │ │ │ │ +[1] 240802 262 │ │ │ │ │ │ │ │ │ │ $variables$chopColumns │ │ │ │ │ -[1] 241054 311 │ │ │ │ │ +[1] 241064 311 │ │ │ │ │ │ │ │ │ │ $variables$dataTable │ │ │ │ │ -[1] 241365 404 │ │ │ │ │ +[1] 241375 404 │ │ │ │ │ │ │ │ │ │ $variables$downloadFile │ │ │ │ │ -[1] 241769 1589 │ │ │ │ │ +[1] 241779 1589 │ │ │ │ │ │ │ │ │ │ $variables$extractFilenameFromDownloadURL │ │ │ │ │ -[1] 243358 623 │ │ │ │ │ +[1] 243368 623 │ │ │ │ │ │ │ │ │ │ $variables$fastTabRead │ │ │ │ │ -[1] 243981 1795 │ │ │ │ │ +[1] 243991 1795 │ │ │ │ │ │ │ │ │ │ $variables$fileOpen │ │ │ │ │ -[1] 245776 737 │ │ │ │ │ +[1] 245786 737 │ │ │ │ │ │ │ │ │ │ $variables$filegrep │ │ │ │ │ -[1] 246513 1028 │ │ │ │ │ +[1] 246523 1028 │ │ │ │ │ │ │ │ │ │ $variables$findFirstEntity │ │ │ │ │ -[1] 247541 1429 │ │ │ │ │ +[1] 247551 1429 │ │ │ │ │ │ │ │ │ │ $variables$getAndParseGSEMatrices │ │ │ │ │ -[1] 248970 1601 │ │ │ │ │ +[1] 248980 1601 │ │ │ │ │ │ │ │ │ │ $variables$getDirListing │ │ │ │ │ -[1] 250571 526 │ │ │ │ │ +[1] 250581 526 │ │ │ │ │ │ │ │ │ │ $variables$getGEO │ │ │ │ │ -[1] 251097 1342 │ │ │ │ │ +[1] 251107 1342 │ │ │ │ │ │ │ │ │ │ $variables$getGEORaw │ │ │ │ │ -[1] 252439 298 │ │ │ │ │ +[1] 252449 298 │ │ │ │ │ │ │ │ │ │ $variables$getGEOSeriesFileListing │ │ │ │ │ -[1] 252737 632 │ │ │ │ │ +[1] 252747 632 │ │ │ │ │ │ │ │ │ │ $variables$getGEOSuppFileURL │ │ │ │ │ -[1] 253369 879 │ │ │ │ │ +[1] 253379 879 │ │ │ │ │ │ │ │ │ │ $variables$getGEOSuppFiles │ │ │ │ │ -[1] 254248 2558 │ │ │ │ │ +[1] 254258 2558 │ │ │ │ │ │ │ │ │ │ $variables$getGEOfile │ │ │ │ │ -[1] 256806 3044 │ │ │ │ │ +[1] 256816 3044 │ │ │ │ │ │ │ │ │ │ $variables$getGSEDataTables │ │ │ │ │ -[1] 259850 1178 │ │ │ │ │ +[1] 259860 1178 │ │ │ │ │ │ │ │ │ │ $variables$getGSEDownloadPageURLs │ │ │ │ │ -[1] 261028 1068 │ │ │ │ │ +[1] 261038 1068 │ │ │ │ │ │ │ │ │ │ $variables$getRNAQuantAnnotationURL │ │ │ │ │ -[1] 262096 543 │ │ │ │ │ +[1] 262106 543 │ │ │ │ │ │ │ │ │ │ $variables$getRNAQuantRawCountsURL │ │ │ │ │ -[1] 262639 540 │ │ │ │ │ +[1] 262649 540 │ │ │ │ │ │ │ │ │ │ $variables$getRNASeqData │ │ │ │ │ -[1] 263179 1337 │ │ │ │ │ +[1] 263189 1337 │ │ │ │ │ │ │ │ │ │ $variables$getRNASeqQuantGenomeInfo │ │ │ │ │ -[1] 264516 452 │ │ │ │ │ +[1] 264526 452 │ │ │ │ │ │ │ │ │ │ $variables$getRNASeqQuantResults │ │ │ │ │ -[1] 264968 863 │ │ │ │ │ +[1] 264978 863 │ │ │ │ │ │ │ │ │ │ $variables$hasRNASeqQuantifications │ │ │ │ │ -[1] 265831 504 │ │ │ │ │ +[1] 265841 504 │ │ │ │ │ │ │ │ │ │ $variables$parseGDS │ │ │ │ │ -[1] 266335 871 │ │ │ │ │ +[1] 266345 871 │ │ │ │ │ │ │ │ │ │ $variables$parseGDSSubsets │ │ │ │ │ -[1] 267206 2671 │ │ │ │ │ +[1] 267216 2671 │ │ │ │ │ │ │ │ │ │ $variables$parseGEO │ │ │ │ │ -[1] 269877 990 │ │ │ │ │ +[1] 269887 990 │ │ │ │ │ │ │ │ │ │ $variables$parseGPL │ │ │ │ │ -[1] 270867 1083 │ │ │ │ │ +[1] 270877 1083 │ │ │ │ │ │ │ │ │ │ $variables$parseGSE │ │ │ │ │ -[1] 271950 2158 │ │ │ │ │ +[1] 271960 2158 │ │ │ │ │ │ │ │ │ │ $variables$parseGSEMatrix │ │ │ │ │ -[1] 274108 8516 │ │ │ │ │ +[1] 274118 8516 │ │ │ │ │ │ │ │ │ │ $variables$parseGSM │ │ │ │ │ -[1] 282624 505 │ │ │ │ │ +[1] 282634 505 │ │ │ │ │ │ │ │ │ │ $variables$parseGeoColumns │ │ │ │ │ -[1] 283129 769 │ │ │ │ │ +[1] 283139 769 │ │ │ │ │ │ │ │ │ │ $variables$parseGeoMeta │ │ │ │ │ -[1] 283898 923 │ │ │ │ │ +[1] 283908 923 │ │ │ │ │ │ │ │ │ │ $variables$parse_name_value_pairs │ │ │ │ │ -[1] 284821 1557 │ │ │ │ │ +[1] 284831 1557 │ │ │ │ │ │ │ │ │ │ $variables$preprocess_records │ │ │ │ │ -[1] 286378 806 │ │ │ │ │ +[1] 286388 806 │ │ │ │ │ │ │ │ │ │ $variables$printHead │ │ │ │ │ -[1] 287184 4116 │ │ │ │ │ +[1] 287194 4116 │ │ │ │ │ │ │ │ │ │ $variables$readRNAQuantAnnotation │ │ │ │ │ -[1] 291300 562 │ │ │ │ │ +[1] 291310 562 │ │ │ │ │ │ │ │ │ │ $variables$readRNAQuantRawCounts │ │ │ │ │ -[1] 291862 667 │ │ │ │ │ +[1] 291872 667 │ │ │ │ │ │ │ │ │ │ $variables$searchFieldsGEO │ │ │ │ │ -[1] 292529 500 │ │ │ │ │ +[1] 292539 500 │ │ │ │ │ │ │ │ │ │ $variables$searchGEO │ │ │ │ │ -[1] 293029 1507 │ │ │ │ │ +[1] 293039 1507 │ │ │ │ │ │ │ │ │ │ $variables$splitOnFirst │ │ │ │ │ -[1] 294536 708 │ │ │ │ │ +[1] 294546 708 │ │ │ │ │ │ │ │ │ │ $variables$str_split │ │ │ │ │ -[1] 295244 390 │ │ │ │ │ +[1] 295254 390 │ │ │ │ │ │ │ │ │ │ $variables$txtGrab │ │ │ │ │ -[1] 295634 528 │ │ │ │ │ +[1] 295644 528 │ │ │ │ │ │ │ │ │ │ $variables$urlExtractRNASeqQuantGenomeInfo │ │ │ │ │ -[1] 296162 788 │ │ │ │ │ +[1] 296172 788 │ │ │ │ │ │ │ │ │ │ $variables$urlForAccession │ │ │ │ │ -[1] 296950 285 │ │ │ │ │ +[1] 296960 285 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 5997 2444 │ │ │ │ │ +[1] 5997 2454 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 11516 263 │ │ │ │ │ +[1] 11526 263 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 10402 557 │ │ │ │ │ +[1] 10412 557 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 10959 557 │ │ │ │ │ +[1] 10969 557 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 13448 399 │ │ │ │ │ +[1] 13458 399 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 13186 262 │ │ │ │ │ +[1] 13196 262 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 12388 399 │ │ │ │ │ +[1] 12398 399 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 12787 399 │ │ │ │ │ +[1] 12797 399 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 14968 402 │ │ │ │ │ +[1] 14978 402 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 14704 264 │ │ │ │ │ +[1] 14714 264 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 13900 402 │ │ │ │ │ +[1] 13910 402 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 5706 131 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 14302 402 │ │ │ │ │ +[1] 14312 402 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 15970 143 │ │ │ │ │ +[1] 15980 143 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 15709 261 │ │ │ │ │ +[1] 15719 261 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 15423 143 │ │ │ │ │ +[1] 15433 143 │ │ │ │ │ │ │ │ │ │ $references$`env::24` │ │ │ │ │ -[1] 15566 143 │ │ │ │ │ +[1] 15576 143 │ │ │ │ │ │ │ │ │ │ $references$`env::25` │ │ │ │ │ -[1] 17232 402 │ │ │ │ │ +[1] 17242 402 │ │ │ │ │ │ │ │ │ │ $references$`env::26` │ │ │ │ │ -[1] 16970 262 │ │ │ │ │ +[1] 16980 262 │ │ │ │ │ │ │ │ │ │ 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Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"))), Rd_tag = "\\section"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sean Davis\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("GEOData-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/GDS-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/GDS-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ GEOData-accessors (list) = structure(list(structure(list(structure("Generic functions for GEOquery", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("GEOData-accessors", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("GEOData-accessors", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("dataTable", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Accession", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -24,15 +24,15 @@ │ │ │ │ structure(list(structure("Meta", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Table", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("IO", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The main documentation is in the Class documentation\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sean Davis\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("GEOData-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/GEOData-accessors.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/GEOData-accessors.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ GEOData-class (list) = structure(list(structure(list(structure("Class 'GEOData'", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("GEOData-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("GEOData-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Accession,GEOData-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Columns,GEOData-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -51,15 +51,15 @@ │ │ │ │ structure(list(structure("GDS-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("GPL-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",\n", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("GSM-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("GEODataTable-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure(",\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/GEOData-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure(",\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/GEOData-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ GEODataTable-class (list) = structure(list(structure(list(structure("Class 'GEODataTable'", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("GEODataTable-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("GEODataTable-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Accession,GEODataTable-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Columns,GEODataTable-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -70,15 +70,15 @@ │ │ │ │ structure(list(structure("classes", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Contains the column descriptions and data for the datatable part of a GEO\n", Rd_tag = "TEXT"), │ │ │ │ structure("object\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(list(structure("Objects from the Class", Rd_tag = "TEXT")), │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure(" Objects can be created by calls of the form\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("new('GEODataTable', ...)", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT"))), Rd_tag = "\\section"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sean Davis\n", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/GEODataTable-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sean Davis\n", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/GEODataTable-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ GPL-class (list) = structure(list(structure(list(structure("Class 'GPL'", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("GPL-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("GPL-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("GPL", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("GPL,GDS-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -87,15 +87,15 @@ │ │ │ │ structure(list(list(structure("Objects from the Class", Rd_tag = "TEXT")), │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure(" Objects can be created by calls of the form\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("new('GPL', ...)", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT"))), Rd_tag = "\\section"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sean Davis\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("GEOData-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/GPL-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/GPL-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ GSE-class (list) = structure(list(structure(list(structure("Class 'GSE'", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("GSE-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("GSE-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("GPLList,GSE-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("GSMList,GSE-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -107,30 +107,30 @@ │ │ │ │ structure(list(structure("new('GSE', ...)", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT"))), Rd_tag = "\\section"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sean Davis\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("GPL-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(",", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("GSM-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/GSE-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/GSE-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ GSM-class (list) = structure(list(structure(list(structure("Class 'GSM'", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("GSM-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("GSM-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("classes", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A class containing a GEO Sample entity\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(list(structure("Objects from the Class", Rd_tag = "TEXT")), │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure(" Objects can be created by calls of the form\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("new('GSM', ...)", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT"))), Rd_tag = "\\section"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sean Davis\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("GEOData-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/GSM-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/GSM-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ browseGEOAccession (list) = structure(list(structure(list(structure("Open the GEO page for a given accession", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("browseGEOAccession", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("browseGEOAccession", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sometimes, you just need to see the GEO website page for a\n", Rd_tag = "TEXT"), │ │ │ │ structure("GEO accession. This function opens the GEO page for a given\n", Rd_tag = "TEXT"), │ │ │ │ @@ -140,28 +140,28 @@ │ │ │ │ list(structure("geo", Rd_tag = "TEXT")), list(structure("A GEO accession number", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("urlForAccession", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(list( │ │ │ │ structure("\n", Rd_tag = "VERB"), structure("browseGEOAccession(\"GSE262484\")\n", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/browseGEOAccession.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/browseGEOAccession.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ browseWebsiteRNASeqSearch (list) = structure(list(structure(list(structure("Browse GEO search website for RNA-seq datasets", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("browseWebsiteRNASeqSearch", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("browseWebsiteRNASeqSearch", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function opens a browser window to the NCBI GEO website\n", Rd_tag = "TEXT"), │ │ │ │ structure("with a search for RNA-seq datasets. It is included as a convenience\n", Rd_tag = "TEXT"), │ │ │ │ structure("function to remind users of how to search for RNA-seq datasets using\n", Rd_tag = "TEXT"), │ │ │ │ structure("the NCBI GEO website and an \"rnaseq counts\" filter.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("browseWebsiteRNASeqSearch()\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(list( │ │ │ │ structure("\n", Rd_tag = "VERB"), structure("browseWebsiteRNASeqSearch()\n", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/browseWebsiteRNASeqSearch.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/browseWebsiteRNASeqSearch.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ coercion (list) = structure(list(structure(list(structure("Convert a GDS data structure to a BioConductor data structure", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("coercion", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("coercion", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("GDS2MA", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("GDS2eSet", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -213,15 +213,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sean Davis\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("See the limma and ExpressionSet help in the appropriate packages\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(list(structure("gds505 <- getGEO('GDS505')", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(list(structure("MA <- GDS2MA(gds505)", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(list(structure("eset <- GDS2eSet(gds505)", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/coercion.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/coercion.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractFilenameFromDownloadURL (list) = structure(list(structure(list(structure("Extract filename from a GEO download URL", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractFilenameFromDownloadURL", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractFilenameFromDownloadURL", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function extracts the filename from a GEO download URL.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -231,27 +231,27 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("url", Rd_tag = "TEXT")), list(structure("A GEO download URL", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The idea is to use this function to extract filenames that\n", Rd_tag = "TEXT"), │ │ │ │ structure("contain important metadata from the GEO RNA-seq quantification.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("In particular, the filename is expected to contain the genome build\n", Rd_tag = "TEXT"), │ │ │ │ structure("and species information that we can attach to the SummarizedExperiment.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("A character vector with the filename\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/extractFilenameFromDownloadURL.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("A character vector with the filename\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/extractFilenameFromDownloadURL.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getDirListing (list) = structure(list(structure(list(structure("get a directory listing from NCBI GEO", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getDirListing", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getDirListing", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This one makes some assumptions about the structure of the HTML response\n", Rd_tag = "TEXT"), │ │ │ │ structure("returned.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getDirListing(url)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("url", Rd_tag = "TEXT")), list(structure("A URL, assumed to return an NCBI-formatted\n", Rd_tag = "TEXT"), │ │ │ │ structure("index page", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/getDirListing.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/getDirListing.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getGEO (list) = structure(list(structure(list(structure("Get a GEO object from NCBI or file", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getGEO", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getGEO", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("IO", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function is the main user-level function in the GEOquery package. It\n", Rd_tag = "TEXT"), │ │ │ │ @@ -375,15 +375,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("gds <- getGEO('GDS10')\n", Rd_tag = "RCODE"), │ │ │ │ structure("gds\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("gse <- getGEO('GSE10')\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Returns a list, so look at first item\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("gse[[1]]\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/getGEO.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/getGEO.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getGEOSeriesFileListing (list) = structure(list(structure(list(structure("GSE Supplemental file listing", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getGEOSeriesFileListing", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getGEOSeriesFileListing", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The GEO Series records often have one or more supplemental files.\n", Rd_tag = "TEXT"), │ │ │ │ structure("In most cases, those files are archived as '.tar' files, the contents\n", Rd_tag = "TEXT"), │ │ │ │ @@ -393,15 +393,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("GSE", Rd_tag = "TEXT")), list(structure("character(1) the GSE accession", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function reads that file listing file and returns the results\n", Rd_tag = "TEXT"), │ │ │ │ structure("as a data.frame.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A data.frame with 5 columns. See example.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getGEOSeriesFileListing('GSE288770')\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/getGEOSeriesFileListing.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/getGEOSeriesFileListing.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getGEOSuppFileURL (list) = structure(list(structure(list(structure("Get GEO supplemental file URL for a given GEO accession", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getGEOSuppFileURL", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getGEOSuppFileURL", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Get GEO supplemental file URL for a given GEO accession\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getGEOSuppFileURL(GEO)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -409,15 +409,15 @@ │ │ │ │ list(structure("GEO", Rd_tag = "TEXT")), list()), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# an example of a GEO supplemental file URL\n", Rd_tag = "RCODE"), │ │ │ │ structure("# with a set of single-cell RNA-seq data\n", Rd_tag = "RCODE"), │ │ │ │ structure("url = getGEOSuppFileURL(\"GSE161228\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("url\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure(list(structure("\n", Rd_tag = "VERB"), structure(" browseURL(url)\n", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/getGEOSuppFileURL.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/getGEOSuppFileURL.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getGEOSuppFiles (list) = structure(list(structure(list(structure("Get Supplemental Files from GEO", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getGEOSuppFiles", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getGEOSuppFiles", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("IO", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("database", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -466,15 +466,15 @@ │ │ │ │ list(structure("sdavis2@mail.nih.gov", Rd_tag = "TEXT"))), Rd_tag = "\\href"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("a <- getGEOSuppFiles('GSM1137', fetch_files = FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("a\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("# with a set of single-cell RNA-seq data\n", Rd_tag = "RCODE"), │ │ │ │ structure("a <- getGEOSuppFiles('GSE161228', fetch_files = FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("a\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/getGEOSuppFiles.Rd", class = "Rd", meta = list( │ │ │ │ + structure("a\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/getGEOSuppFiles.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getGEOfile (list) = structure(list(structure(list(structure("Download a file from GEO soft file to the local machine", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getGEOfile", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getGEOfile", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("IO", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function simply downloads a SOFT format file associated with the GEO\n", Rd_tag = "TEXT"), │ │ │ │ @@ -516,15 +516,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sean Davis\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("getGEO", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("# myfile <- getGEOfile('GDS10')\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/getGEOfile.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/getGEOfile.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getGSEDataTables (list) = structure(list(structure(list(structure("Get GSE data tables from GEO into R data structures.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getGSEDataTables", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getGSEDataTables", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("IO", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("In some cases, instead of individual sample records (GSM) containing\n", Rd_tag = "TEXT"), │ │ │ │ @@ -546,53 +546,53 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("getGEO", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("dfl = getGSEDataTables('GSE3494')\n", Rd_tag = "RCODE"), │ │ │ │ structure("lapply(dfl,head)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/getGSEDataTables.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/getGSEDataTables.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getGSEDownloadPageURLs (list) = structure(list(structure(list(structure("get all download links from a GEO accession", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getGSEDownloadPageURLs", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getGSEDownloadPageURLs", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function gets all download links from a GEO accession number.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getGSEDownloadPageURLs(gse)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("gse", Rd_tag = "TEXT")), list(structure("GEO accession number", 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 with all download links\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/getGSEDownloadPageURLs.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("A character vector with all download links\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/getGSEDownloadPageURLs.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getRNAQuantAnnotationURL (list) = structure(list(structure(list(structure("Get the RNA-seq quantification annotation link", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getRNAQuantAnnotationURL", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getRNAQuantAnnotationURL", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function extracts the link to the RNA-seq quantification annotation\n", Rd_tag = "TEXT"), │ │ │ │ structure("file from a geoDownloadLinks object.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getRNAQuantAnnotationURL(links)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("links", Rd_tag = "TEXT")), list(structure("A geoDownloadLinks object", 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 with the link to the annotation file\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/getRNAQuantAnnotationURL.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("A character vector with the link to the annotation file\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/getRNAQuantAnnotationURL.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getRNAQuantRawCountsURL (list) = structure(list(structure(list(structure("Get the link to the raw counts file from GEO", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getRNAQuantRawCountsURL", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getRNAQuantRawCountsURL", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function extracts the link to the raw counts file from a\n", Rd_tag = "TEXT"), │ │ │ │ structure("geoDownloadLinks object.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getRNAQuantRawCountsURL(links)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("links", Rd_tag = "TEXT")), list(structure("A geoDownloadLinks object", 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 with the link to the raw counts file\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/getRNAQuantRawCountsURL.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("A character vector with the link to the raw counts file\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/getRNAQuantRawCountsURL.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getRNASeqData (list) = structure(list(structure(list(structure("Get GEO RNA-seq quantifications as a SummarizedExperiment object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getRNASeqData", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getRNASeqData", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("For human and mouse GEO datasets, NCBI GEO attempts to process\n", Rd_tag = "TEXT"), │ │ │ │ structure("the raw data and provide quantifications in the form of raw counts\n", Rd_tag = "TEXT"), │ │ │ │ @@ -616,43 +616,43 @@ │ │ │ │ structure(list(list(structure("https://ncbi.nlm.nih.gov/geo/info/rnaseqcounts.html", Rd_tag = "VERB")), │ │ │ │ list(structure("GEO documentation", Rd_tag = "TEXT"))), Rd_tag = "\\href"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("for more details.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A SummarizedExperiment object with the raw counts as the counts\n", Rd_tag = "TEXT"), │ │ │ │ structure("assay, the annotation as the rowData, and the metadata from GEO as\n", Rd_tag = "TEXT"), │ │ │ │ structure("the colData.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("se <- getRNASeqData(\"GSE164073\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("se\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/getRNASeqData.Rd", class = "Rd", meta = list( │ │ │ │ + structure("se\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/getRNASeqData.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getRNASeqQuantGenomeInfo (list) = structure(list(structure(list(structure("Extract genome build and species for GEO RNA-seq quantification", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getRNASeqQuantGenomeInfo", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getRNASeqQuantGenomeInfo", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function extracts the genome build and species information\n", Rd_tag = "TEXT"), │ │ │ │ structure("for a GEO RNA-seq quantification.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getRNASeqQuantGenomeInfo(gse)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("gse", Rd_tag = "TEXT")), list(structure("GEO accession number", 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 with the genome build and species information\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getRNASeqQuantGenomeInfo(\"GSE164073\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/getRNASeqQuantGenomeInfo.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/getRNASeqQuantGenomeInfo.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getRNASeqQuantResults (list) = structure(list(structure(list(structure("Get RNA-seq quantification and annotation from GEO", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getRNASeqQuantResults", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getRNASeqQuantResults", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function downloads the raw counts and annotation files from GEO\n", Rd_tag = "TEXT"), │ │ │ │ structure("for a given GEO accession number.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getRNASeqQuantResults(gse)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("gse", Rd_tag = "TEXT")), list(structure("GEO accession number", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A list with two elements: quants (a matrix of raw counts) and\n", Rd_tag = "TEXT"), │ │ │ │ - structure("annotation (a data frame of annotation information).\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/getRNASeqQuantResults.Rd", class = "Rd", meta = list( │ │ │ │ + structure("annotation (a data frame of annotation information).\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/getRNASeqQuantResults.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ hasRNASeqQuantifications (list) = structure(list(structure(list(structure("Does a GEO accession have RNA-seq quantifications?", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("hasRNASeqQuantifications", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("hasRNASeqQuantifications", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function checks if a GEO accession number has RNA-seq quantifications\n", Rd_tag = "TEXT"), │ │ │ │ structure("available. It does this by checking if the GEO accession number has a\n", Rd_tag = "TEXT"), │ │ │ │ @@ -660,15 +660,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("hasRNASeqQuantifications(accession)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("accession", Rd_tag = "TEXT")), list(structure("GEO accession number", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("TRUE if the GEO accession number has RNA-seq quantifications\n", Rd_tag = "TEXT"), │ │ │ │ structure("available, FALSE otherwise.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("hasRNASeqQuantifications(\"GSE164073\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/hasRNASeqQuantifications.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/hasRNASeqQuantifications.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ parseGEO (list) = structure(list(structure(list(structure("Parse GEO text", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("parseGEO", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("parseGEO", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -707,15 +707,15 @@ │ │ │ │ structure("There should be no reason to use the parseGPL, parseGDS, parseGSE, or\n", Rd_tag = "TEXT"), │ │ │ │ structure("parseGSM functions directly.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("parseGEO returns an object of the associated type. For example, if\n", Rd_tag = "TEXT"), │ │ │ │ structure("it is passed the text from a GDS entry, a GDS object is returned.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sean Davis\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("getGEO", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/parseGEO.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/parseGEO.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ parseGSEMatrix (list) = structure(list(structure(list(structure("Parse a GSE mstrix file", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("parseGSEMatrix", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("parseGSEMatrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Not meant for user calling, but parses\n", Rd_tag = "TEXT"), │ │ │ │ @@ -735,30 +735,30 @@ │ │ │ │ list(structure("the destdination directory for download", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("getGPL", Rd_tag = "TEXT")), │ │ │ │ list(structure("whether or not to get the GPL associated", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("parseCharacteristics", Rd_tag = "TEXT")), │ │ │ │ list(structure("Whether or not to do full 'characteristic' parsing", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/parseGSEMatrix.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/parseGSEMatrix.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ readRNAQuantAnnotation (list) = structure(list(structure(list(structure("Read RNA-seq quantification annotation from GEO", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("readRNAQuantAnnotation", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("readRNAQuantAnnotation", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function reads the annotation file from a GEO link. The annotation\n", Rd_tag = "TEXT"), │ │ │ │ structure("file is expected to be a tab-separated file with the first column\n", Rd_tag = "TEXT"), │ │ │ │ structure("containing the gene IDs and the remaining columns containing the\n", Rd_tag = "TEXT"), │ │ │ │ structure("annotation information.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("readRNAQuantAnnotation(link)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("link", Rd_tag = "TEXT")), list(structure("A link to the annotation file", 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 of annotation information with gene IDs as row names\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/readRNAQuantAnnotation.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("A data frame of annotation information with gene IDs as row names\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/readRNAQuantAnnotation.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ readRNAQuantRawCounts (list) = structure(list(structure(list(structure("Read raw counts from GEO", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("readRNAQuantRawCounts", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("readRNAQuantRawCounts", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function reads the raw counts from a GEO link. The raw counts\n", Rd_tag = "TEXT"), │ │ │ │ @@ -768,15 +768,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("readRNAQuantRawCounts(link)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("link", Rd_tag = "TEXT")), list(structure("A link to the raw counts file", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function reads the raw counts and returns a matrix with the\n", Rd_tag = "TEXT"), │ │ │ │ structure("gene IDs as the row names, ready for use in creating a\n", Rd_tag = "TEXT"), │ │ │ │ structure("SummarizedExperiment.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("A matrix of raw counts with gene IDs as row names\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/readRNAQuantRawCounts.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("A matrix of raw counts with gene IDs as row names\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/readRNAQuantRawCounts.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ │ │ @@ -792,15 +792,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("a data.frame with names of possible search fields for GEO search\n", Rd_tag = "TEXT"), │ │ │ │ structure("as well as descriptions, data types, etc. for each field. Fields are\n", Rd_tag = "TEXT"), │ │ │ │ structure("in rows and their properties are in columns.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("searchGEO", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("searchFieldsGEO()\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/searchFieldsGEO.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/searchFieldsGEO.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ searchGEO (list) = structure(list(structure(list(structure("Search GEO database", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("searchGEO", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("searchGEO", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function searches the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("https://www.ncbi.nlm.nih.gov/gds", Rd_tag = "VERB")), │ │ │ │ @@ -837,29 +837,29 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("a data.frame contains the search results\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("searchFieldsGEO", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(list( │ │ │ │ structure("\n", Rd_tag = "VERB"), structure("searchGEO(\"diabetes[ALL] AND Homo sapiens[ORGN] AND GSE[ETYP]\")\n", Rd_tag = "VERB")), Rd_tag = "\\dontrun"), │ │ │ │ - structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/searchGEO.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/searchGEO.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ urlExtractRNASeqQuantGenomeInfo (list) = structure(list(structure(list(structure("Extract genome build and species from a GEO download URL", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("urlExtractRNASeqQuantGenomeInfo", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("urlExtractRNASeqQuantGenomeInfo", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("internal", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function extracts the genome build and species information\n", Rd_tag = "TEXT"), │ │ │ │ structure("from a GEO download URL. The genome build and species information\n", Rd_tag = "TEXT"), │ │ │ │ structure("is expected to be in the filename of the download URL.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("urlExtractRNASeqQuantGenomeInfo(url)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("url", Rd_tag = "TEXT")), list(structure("A GEO annotation file download URL", 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 with the genome build and species information\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/urlExtractRNASeqQuantGenomeInfo.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("A character vector with the genome build and species information\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/urlExtractRNASeqQuantGenomeInfo.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ urlForAccession (list) = structure(list(structure(list(structure("The URL for a GEO accession", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("urlForAccession", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("urlForAccession", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Sometimes, you just need the URL for a GEO accession. This function\n", Rd_tag = "TEXT"), │ │ │ │ structure("returns the URL for a given GEO accession number that\n", Rd_tag = "TEXT"), │ │ │ │ @@ -870,10 +870,10 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A character vector with the URL for the GEO accession\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("browseGEOAccession", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("urlForAccession(\"GSE262484\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-geoquery/man/urlForAccession.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/urlForAccession.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/GEOquery/help/GEOquery.rdx │ │ │ ├── GEOquery.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,205 +1,205 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$`GDS-class` │ │ │ │ │ -[1] 282 842 │ │ │ │ │ +[1] 295 858 │ │ │ │ │ │ │ │ │ │ $variables$`GEOData-accessors` │ │ │ │ │ -[1] 1411 895 │ │ │ │ │ +[1] 1454 910 │ │ │ │ │ │ │ │ │ │ $variables$`GEOData-class` │ │ │ │ │ -[1] 2590 1202 │ │ │ │ │ +[1] 2662 1218 │ │ │ │ │ │ │ │ │ │ $variables$`GEODataTable-class` │ │ │ │ │ -[1] 4080 992 │ │ │ │ │ +[1] 4181 1006 │ │ │ │ │ │ │ │ │ │ $variables$`GPL-class` │ │ │ │ │ -[1] 5353 924 │ │ │ │ │ +[1] 5483 940 │ │ │ │ │ │ │ │ │ │ $variables$`GSE-class` │ │ │ │ │ -[1] 6557 981 │ │ │ │ │ +[1] 6718 996 │ │ │ │ │ │ │ │ │ │ $variables$`GSM-class` │ │ │ │ │ -[1] 7819 855 │ │ │ │ │ +[1] 8009 871 │ │ │ │ │ │ │ │ │ │ $variables$browseGEOAccession │ │ │ │ │ -[1] 8962 978 │ │ │ │ │ +[1] 9183 992 │ │ │ │ │ │ │ │ │ │ $variables$browseWebsiteRNASeqSearch │ │ │ │ │ -[1] 10234 826 │ │ │ │ │ +[1] 10483 841 │ │ │ │ │ │ │ │ │ │ $variables$coercion │ │ │ │ │ -[1] 11339 2598 │ │ │ │ │ +[1] 11618 2612 │ │ │ │ │ │ │ │ │ │ $variables$extractFilenameFromDownloadURL │ │ │ │ │ -[1] 14232 1121 │ │ │ │ │ +[1] 14539 1135 │ │ │ │ │ │ │ │ │ │ $variables$getDirListing │ │ │ │ │ -[1] 15637 769 │ │ │ │ │ +[1] 15972 784 │ │ │ │ │ │ │ │ │ │ $variables$getGEO │ │ │ │ │ -[1] 16686 5580 │ │ │ │ │ +[1] 17049 5595 │ │ │ │ │ │ │ │ │ │ $variables$getGEOSeriesFileListing │ │ │ │ │ -[1] 22560 1085 │ │ │ │ │ +[1] 22950 1100 │ │ │ │ │ │ │ │ │ │ $variables$getGEOSuppFileURL │ │ │ │ │ -[1] 23938 901 │ │ │ │ │ +[1] 24354 916 │ │ │ │ │ │ │ │ │ │ $variables$getGEOSuppFiles │ │ │ │ │ -[1] 25127 2388 │ │ │ │ │ +[1] 25571 2402 │ │ │ │ │ │ │ │ │ │ $variables$getGEOfile │ │ │ │ │ -[1] 27796 2347 │ │ │ │ │ +[1] 28269 2361 │ │ │ │ │ │ │ │ │ │ $variables$getGSEDataTables │ │ │ │ │ -[1] 30430 1525 │ │ │ │ │ +[1] 30931 1541 │ │ │ │ │ │ │ │ │ │ $variables$getGSEDownloadPageURLs │ │ │ │ │ -[1] 32248 791 │ │ │ │ │ +[1] 32779 806 │ │ │ │ │ │ │ │ │ │ $variables$getRNAQuantAnnotationURL │ │ │ │ │ -[1] 33334 844 │ │ │ │ │ +[1] 33894 859 │ │ │ │ │ │ │ │ │ │ $variables$getRNAQuantRawCountsURL │ │ │ │ │ -[1] 34473 828 │ │ │ │ │ +[1] 35062 844 │ │ │ │ │ │ │ │ │ │ $variables$getRNASeqData │ │ │ │ │ -[1] 35586 1765 │ │ │ │ │ +[1] 36206 1779 │ │ │ │ │ │ │ │ │ │ $variables$getRNASeqQuantGenomeInfo │ │ │ │ │ -[1] 37645 871 │ │ │ │ │ +[1] 38294 885 │ │ │ │ │ │ │ │ │ │ $variables$getRNASeqQuantResults │ │ │ │ │ -[1] 38806 900 │ │ │ │ │ +[1] 39485 916 │ │ │ │ │ │ │ │ │ │ $variables$hasRNASeqQuantifications │ │ │ │ │ -[1] 40000 943 │ │ │ │ │ +[1] 40709 959 │ │ │ │ │ │ │ │ │ │ $variables$parseGEO │ │ │ │ │ -[1] 41224 1959 │ │ │ │ │ +[1] 41963 1975 │ │ │ │ │ │ │ │ │ │ $variables$parseGSEMatrix │ │ │ │ │ -[1] 43469 1212 │ │ │ │ │ +[1] 44237 1229 │ │ │ │ │ │ │ │ │ │ $variables$readRNAQuantAnnotation │ │ │ │ │ -[1] 44972 932 │ │ │ │ │ +[1] 45772 948 │ │ │ │ │ │ │ │ │ │ $variables$readRNAQuantRawCounts │ │ │ │ │ -[1] 46196 1036 │ │ │ │ │ +[1] 47026 1053 │ │ │ │ │ │ │ │ │ │ $variables$searchFieldsGEO │ │ │ │ │ -[1] 47518 849 │ │ │ │ │ +[1] 48380 865 │ │ │ │ │ │ │ │ │ │ $variables$searchGEO │ │ │ │ │ -[1] 48648 2208 │ │ │ │ │ +[1] 49540 2222 │ │ │ │ │ │ │ │ │ │ $variables$urlExtractRNASeqQuantGenomeInfo │ │ │ │ │ -[1] 51155 886 │ │ │ │ │ +[1] 52077 901 │ │ │ │ │ │ │ │ │ │ $variables$urlForAccession │ │ │ │ │ -[1] 52326 1002 │ │ │ │ │ +[1] 53278 1021 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 282 │ │ │ │ │ +[1] 0 295 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 11060 279 │ │ │ │ │ +[1] 11324 294 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 13937 295 │ │ │ │ │ +[1] 14230 309 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 15353 284 │ │ │ │ │ +[1] 15674 298 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 16406 280 │ │ │ │ │ +[1] 16756 293 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 22266 294 │ │ │ │ │ +[1] 22644 306 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 23645 293 │ │ │ │ │ +[1] 24050 304 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 24839 288 │ │ │ │ │ +[1] 25270 301 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 27515 281 │ │ │ │ │ +[1] 27973 296 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 30143 287 │ │ │ │ │ +[1] 30630 301 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 31955 293 │ │ │ │ │ +[1] 32472 307 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 1124 287 │ │ │ │ │ +[1] 1153 301 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 33039 295 │ │ │ │ │ +[1] 33585 309 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 34178 295 │ │ │ │ │ +[1] 34753 309 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 35301 285 │ │ │ │ │ +[1] 35906 300 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 37351 294 │ │ │ │ │ +[1] 37985 309 │ │ │ │ │ │ │ │ │ │ $references$`env::24` │ │ │ │ │ -[1] 38516 290 │ │ │ │ │ +[1] 39179 306 │ │ │ │ │ │ │ │ │ │ $references$`env::25` │ │ │ │ │ -[1] 39706 294 │ │ │ │ │ +[1] 40401 308 │ │ │ │ │ │ │ │ │ │ $references$`env::26` │ │ │ │ │ -[1] 40943 281 │ │ │ │ │ +[1] 41668 295 │ │ │ │ │ │ │ │ │ │ $references$`env::27` │ │ │ │ │ -[1] 43183 286 │ │ │ │ │ +[1] 43938 299 │ │ │ │ │ │ │ │ │ │ $references$`env::28` │ │ │ │ │ -[1] 44681 291 │ │ │ │ │ +[1] 45466 306 │ │ │ │ │ │ │ │ │ │ $references$`env::29` │ │ │ │ │ -[1] 45904 292 │ │ │ │ │ +[1] 46720 306 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 2306 284 │ │ │ │ │ +[1] 2364 298 │ │ │ │ │ │ │ │ │ │ $references$`env::30` │ │ │ │ │ -[1] 47232 286 │ │ │ │ │ +[1] 48079 301 │ │ │ │ │ │ │ │ │ │ $references$`env::31` │ │ │ │ │ -[1] 48367 281 │ │ │ │ │ +[1] 49245 295 │ │ │ │ │ │ │ │ │ │ $references$`env::32` │ │ │ │ │ -[1] 50856 299 │ │ │ │ │ +[1] 51762 315 │ │ │ │ │ │ │ │ │ │ $references$`env::33` │ │ │ │ │ -[1] 52041 285 │ │ │ │ │ +[1] 52978 300 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 3792 288 │ │ │ │ │ +[1] 3880 301 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 5072 281 │ │ │ │ │ +[1] 5187 296 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 6277 280 │ │ │ │ │ +[1] 6423 295 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 7538 281 │ │ │ │ │ +[1] 7714 295 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 8674 288 │ │ │ │ │ +[1] 8880 303 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 9940 294 │ │ │ │ │ +[1] 10175 308 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/GEOquery/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,35 +1,35 @@ │ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-geoquery/man/GDS-class.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-geoquery/man/GEOData-accessors.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-geoquery/man/GEOData-class.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-geoquery/man/GEODataTable-class.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-geoquery/man/GPL-class.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-geoquery/man/GSE-class.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-geoquery/man/GSM-class.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-geoquery/man/browseGEOAccession.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-geoquery/man/browseWebsiteRNASeqSearch.Rd" │ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-geoquery/man/coercion.Rd" │ │ │ │ │ -[11] "/home/moeller/Salsa/r-bioc-geoquery/man/extractFilenameFromDownloadURL.Rd" │ │ │ │ │ -[12] "/home/moeller/Salsa/r-bioc-geoquery/man/getDirListing.Rd" │ │ │ │ │ -[13] "/home/moeller/Salsa/r-bioc-geoquery/man/getGEO.Rd" │ │ │ │ │ -[14] "/home/moeller/Salsa/r-bioc-geoquery/man/getGEOSeriesFileListing.Rd" │ │ │ │ │ -[15] "/home/moeller/Salsa/r-bioc-geoquery/man/getGEOSuppFileURL.Rd" │ │ │ │ │ -[16] "/home/moeller/Salsa/r-bioc-geoquery/man/getGEOSuppFiles.Rd" │ │ │ │ │ -[17] "/home/moeller/Salsa/r-bioc-geoquery/man/getGEOfile.Rd" │ │ │ │ │ -[18] "/home/moeller/Salsa/r-bioc-geoquery/man/getGSEDataTables.Rd" │ │ │ │ │ -[19] "/home/moeller/Salsa/r-bioc-geoquery/man/getGSEDownloadPageURLs.Rd" │ │ │ │ │ -[20] "/home/moeller/Salsa/r-bioc-geoquery/man/getRNAQuantAnnotationURL.Rd" │ │ │ │ │ -[21] "/home/moeller/Salsa/r-bioc-geoquery/man/getRNAQuantRawCountsURL.Rd" │ │ │ │ │ -[22] "/home/moeller/Salsa/r-bioc-geoquery/man/getRNASeqData.Rd" │ │ │ │ │ -[23] "/home/moeller/Salsa/r-bioc-geoquery/man/getRNASeqQuantGenomeInfo.Rd" │ │ │ │ │ -[24] "/home/moeller/Salsa/r-bioc-geoquery/man/getRNASeqQuantResults.Rd" │ │ │ │ │ -[25] "/home/moeller/Salsa/r-bioc-geoquery/man/hasRNASeqQuantifications.Rd" │ │ │ │ │ -[26] "/home/moeller/Salsa/r-bioc-geoquery/man/parseGEO.Rd" │ │ │ │ │ -[27] "/home/moeller/Salsa/r-bioc-geoquery/man/parseGSEMatrix.Rd" │ │ │ │ │ -[28] "/home/moeller/Salsa/r-bioc-geoquery/man/readRNAQuantAnnotation.Rd" │ │ │ │ │ -[29] "/home/moeller/Salsa/r-bioc-geoquery/man/readRNAQuantRawCounts.Rd" │ │ │ │ │ -[30] "/home/moeller/Salsa/r-bioc-geoquery/man/searchFieldsGEO.Rd" │ │ │ │ │ -[31] "/home/moeller/Salsa/r-bioc-geoquery/man/searchGEO.Rd" │ │ │ │ │ -[32] "/home/moeller/Salsa/r-bioc-geoquery/man/urlExtractRNASeqQuantGenomeInfo.Rd" │ │ │ │ │ -[33] "/home/moeller/Salsa/r-bioc-geoquery/man/urlForAccession.Rd" │ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/GDS-class.Rd" │ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/GEOData-accessors.Rd" │ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/GEOData-class.Rd" │ │ │ │ │ + [4] "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/GEODataTable-class.Rd" │ │ │ │ │ + [5] "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/GPL-class.Rd" │ │ │ │ │ + [6] "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/GSE-class.Rd" │ │ │ │ │ + [7] "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/GSM-class.Rd" │ │ │ │ │ + [8] "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/browseGEOAccession.Rd" │ │ │ │ │ + [9] "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/browseWebsiteRNASeqSearch.Rd" │ │ │ │ │ +[10] "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/coercion.Rd" │ │ │ │ │ +[11] "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/extractFilenameFromDownloadURL.Rd" │ │ │ │ │ +[12] "/build/reproducible-path/r-bioc-geoquery-2.80.0+dfsg/man/getDirListing.Rd" │ │ │ │ │ +[13] 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