--- /srv/rebuilderd/tmp/rebuilderdwPpp0G/inputs/r-bioc-gsvadata_1.48.1-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdwPpp0G/out/r-bioc-gsvadata_1.48.1-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-12 01:01:17.000000 debian-binary │ -rw-r--r-- 0 0 0 2096 2026-08-12 01:01:17.000000 control.tar.xz │ --rw-r--r-- 0 0 0 16518632 2026-08-12 01:01:17.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 16518900 2026-08-12 01:01:17.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -13,15 +13,15 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 822 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/Meta/hsearch.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 393 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/Meta/links.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 312 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1155 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/Meta/package.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 303 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/NAMESPACE │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/R/GSVAdata │ │ │ --rw-r--r-- 0 root (0) root (0) 6660 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/R/GSVAdata.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 6663 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/R/GSVAdata.rdb │ │ │ -rw-r--r-- 0 root (0) root (0) 270 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/R/GSVAdata.rdx │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/data/ │ │ │ -rw-r--r-- 0 root (0) root (0) 236904 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/data/annotEntrez220212.RData │ │ │ -rw-r--r-- 0 root (0) root (0) 1823 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/data/brainTxDbSets.RData │ │ │ -rw-r--r-- 0 root (0) root (0) 673912 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/data/c2BroadSets.RData │ │ │ -rw-r--r-- 0 root (0) root (0) 5044371 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/data/commonPickrellHuang.RData │ │ │ -rw-r--r-- 0 root (0) root (0) 309 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/data/datalist │ │ │ @@ -36,18 +36,18 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 595742 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/extdata/human_cerebellum_lowres.png │ │ │ -rw-r--r-- 0 root (0) root (0) 998675 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/extdata/human_cerebellum_norm_logcounts_250x4816.mtx.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 2402 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/extdata/human_cerebellum_rowdata_250x4816.csv.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 54266 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/extdata/human_cerebellum_spatialcoords_250x4816.csv.gz │ │ │ -rw-r--r-- 0 root (0) root (0) 1550 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/extdata/pbmc_cell_type_gene_set_signatures.gmt.gz │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 702 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/help/AnIndex │ │ │ --rw-r--r-- 0 root (0) root (0) 25744 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/help/GSVAdata.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 25918 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/help/GSVAdata.rdb │ │ │ -rw-r--r-- 0 root (0) root (0) 430 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/help/GSVAdata.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 337 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 280 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 286 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 3839 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/scripts/ │ │ │ -rw-r--r-- 0 root (0) root (0) 2288 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/scripts/prepare_HumanBrain_snRNAseq.R │ │ │ -rw-r--r-- 0 root (0) root (0) 2928 2026-08-12 01:01:17.000000 ./usr/lib/R/site-library/GSVAdata/scripts/prepare_HumanCerebellumSubset.R │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 01:01:17.000000 ./usr/share/ │ │ ├── ./usr/lib/R/site-library/GSVAdata/R/GSVAdata.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -316,15 +316,15 @@ │ │ │ │ "imports" = ""metadata<-" = "metadata<-", resize = "resize", mcols = "mcols", " │ │ │ │ "imports" = "".__T__length<-:base" = ".__T__length<-:base", ".__T__mcols:S4Vectors" = ".__T__mcols:S4Vectors", " │ │ │ │ "imports" = "promoters = "promoters", ".__T__start<-:BiocGenerics" = ".__T__start<-:BiocGenerics"" │ │ │ │ "imports" = "), Matrix = c(readMM = "readMM"), SpatialExperiment = c(SpatialExperiment = "SpatialExperiment"), " │ │ │ │ "imports" = " SpatialExperiment = c(addImg = "addImg"), methods = c(as = "as"), " │ │ │ │ "imports" = " utils = c(read.csv = "read.csv"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-gsvadata/debian/r-bioc-gsvadata/usr/lib/R/site-library/GSVAdata"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-gsvadata-1.48.1/debian/r-bioc-gsvadata/usr/lib/R/site-library/GSVAdata"" │ │ │ │ "spec" = "c(name = "GSVAdata", version = "1.48.1")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/GSVAdata/R/GSVAdata.rdx │ │ │ ├── GSVAdata.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,31 +1,31 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 4992 52 │ │ │ │ │ +[1] 4995 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 5175 52 │ │ │ │ │ +[1] 5178 52 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 5227 53 │ │ │ │ │ +[1] 5230 53 │ │ │ │ │ │ │ │ │ │ $variables$HumanCerebellumNormSubset │ │ │ │ │ -[1] 5280 1380 │ │ │ │ │ +[1] 5283 1380 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 290 4702 │ │ │ │ │ +[1] 290 4705 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 0 131 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ [1] 131 159 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 5044 131 │ │ │ │ │ +[1] 5047 131 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/GSVAdata/help/GSVAdata.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -91,15 +91,15 @@ │ │ │ │ structure("expression profiles. ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Proc. Natl. Acad. Sci. USA", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(", 102(43):15545-50, 2005.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("R.G.W. Verhaak, K.A. Hoadley, E. Purdom, V. Wang, Y. Qi, et al.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Integrated genomic analysis identifies clinically relevant subtypes of\n", Rd_tag = "TEXT"), │ │ │ │ structure("glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and\n", Rd_tag = "TEXT"), │ │ │ │ structure("NF1. ", Rd_tag = "TEXT"), structure(list(structure("Cancer Cell", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ - structure(", 17:98-110, 2010.\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-gsvadata/man/GSVAdata-package.Rd", class = "Rd", meta = list( │ │ │ │ + structure(", 17:98-110, 2010.\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/GSVAdata-package.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ HumanCerebellumNormSubset (list) = structure(list(structure(list(structure("HumanCerebellumSubset", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("HumanCerebellumNormSubset", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("HumanCerebellumNormSubset", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A subset of the Visium spatial 10X Genomics spatial gene\n", Rd_tag = "TEXT"), │ │ │ │ structure("expression data for the human cerebellum, after quality control filtering\n", Rd_tag = "TEXT"), │ │ │ │ @@ -110,15 +110,15 @@ │ │ │ │ structure("quality control filtering and normalization, and to save the resulting\n", Rd_tag = "TEXT"), │ │ │ │ structure("subsetted data in different files in the `inst/extdata` directory.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("HumanCerebellumNormSubset()\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A `SpatialExperiment` object containing the subsetted normalized\n", Rd_tag = "TEXT"), │ │ │ │ structure("human cerebellum spatial transcriptomics data.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("spe <- HumanCerebellumNormSubset()\n", Rd_tag = "RCODE"), │ │ │ │ - structure("spe\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gsvadata/man/HumanCerebellumNormSubset.Rd", class = "Rd", meta = list( │ │ │ │ + structure("spe\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/HumanCerebellumNormSubset.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ annotEntrez220212 (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("Annotation data on gene length and G+C content from NCBI\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("annotEntrez220212", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("annotEntrez220212", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -145,15 +145,15 @@ │ │ │ │ structure(" whose row names indicate the corresponding Entrez \n", Rd_tag = "TEXT"), │ │ │ │ structure("Gene identifier.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" NCBI: ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("http://www.ncbi.nlm.nih.gov", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\source"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(annotEntrez220212)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dim(annotEntrez220212)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("head(annotEntrez220212)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gsvadata/man/annotEntrez220212.Rd", class = "Rd", meta = list( │ │ │ │ + structure("head(annotEntrez220212)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/annotEntrez220212.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ brainTxDbSets (list) = structure(list(structure(list(structure("Gene sets signatures of brain cell types", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("brainTxDbSets", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("brainTxDbSets", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Gene sets signatures specific to four different brain cell types (astrocytes,\n", Rd_tag = "TEXT"), │ │ │ │ @@ -167,15 +167,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" obtained from the Brain Transcriptome Database (Cahoy et al., 2008).\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Cahoy, J.D., Emery, B., Kaushal, A., Foo, L.C., Zamanian, J.L. et al.\n", Rd_tag = "TEXT"), │ │ │ │ structure("A transcriptome database for astrocytes, neurons, and oligodendrocytes: a\n", Rd_tag = "TEXT"), │ │ │ │ structure("new resource for understanding brain development and function.\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("J Neurosci", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(", 28:264-278, 2008.\n", Rd_tag = "TEXT")), Rd_tag = "\\source"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(brainTxDbSets)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("head(lapply(brainTxDbSets, head))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gsvadata/man/brainTxDbSets.Rd", class = "Rd", meta = list( │ │ │ │ + structure("head(lapply(brainTxDbSets, head))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/brainTxDbSets.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ c2BroadSets (list) = structure(list(structure(list(structure("C2 collection of canonical pathways from MSigDB 3.0", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("c2BroadSets", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("c2BroadSets", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("C2 Broad Sets.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -196,15 +196,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Subramanian, Tamayo, et al. ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("PNAS", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(", 102:15545-15550, 2005.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("Mootha, Lindgren, et al. ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Nat Genet", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(", 34:267-273, 2003.\n", Rd_tag = "TEXT")), Rd_tag = "\\source"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(c2BroadSets)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("c2BroadSets\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gsvadata/man/c2BroadSets.Rd", class = "Rd", meta = list( │ │ │ │ + structure("c2BroadSets\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/c2BroadSets.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ commonPickrellHuang (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("Matching microarray and RNA-seq data from human lymphoblastoid cell lines\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("commonPickrellHuang", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("commonPickrellHuang", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("huangArrayRMAnoBatchCommon_eset", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -338,15 +338,15 @@ │ │ │ │ structure("dim(pickrellCountsYaleCQNcommon_eset)\n", Rd_tag = "RCODE"), │ │ │ │ structure("table(huangArrayRMAnoBatchCommon_eset$Gender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("table(pickrellCountsArgonneCQNcommon_eset$Gender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("table(pickrellCountsYaleCQNcommon_eset$Gender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" featureNames(pickrellCountsArgonneCQNcommon_eset)))\n", Rd_tag = "RCODE"), │ │ │ │ structure("stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" sampleNames(pickrellCountsArgonneCQNcommon_eset)))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gsvadata/man/commonPickrellHuang.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" sampleNames(pickrellCountsArgonneCQNcommon_eset)))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/commonPickrellHuang.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ gbm_VerhaakEtAl (list) = structure(list(structure(list(structure("Glioblastoma Multiforme (GBM) Data by Verhaak et al. (2010)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("gbm_eset", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("gbm_VerhaakEtAl", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("gbm_eset", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -370,15 +370,15 @@ │ │ │ │ structure(", 17:98-110, 2010.\n", Rd_tag = "TEXT")), Rd_tag = "\\source"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U., and Speed, T.P.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Exploration, normalization, and summaries of high density oligonucleotide array probe level data.\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Biostatistics", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(", 4(2):249--64, 2003.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(gbm_VerhaakEtAl)\n", Rd_tag = "RCODE"), │ │ │ │ structure("gbm_eset\n", Rd_tag = "RCODE"), structure("head(pData(gbm_eset))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("table(gbm_eset$subtype)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gsvadata/man/gbm_VerhaakEtAl.Rd", class = "Rd", meta = list( │ │ │ │ + structure("table(gbm_eset$subtype)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/gbm_VerhaakEtAl.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ genderGenesEntrez (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("Entrez genes with documented sex-specific expression\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("genderGenesEntrez", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("genderGenesEntrez", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("msYgenesEntrez", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -410,15 +410,15 @@ │ │ │ │ structure(", 423:825--837, 2003.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("L. Carrel and H.F. Willard. X-inactivation profile reveals extensive\n", Rd_tag = "TEXT"), │ │ │ │ structure("variability in X-linked gene expression in females.\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Nature", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(", 434:400--404, 2005.\n", Rd_tag = "TEXT")), Rd_tag = "\\source"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(genderGenesEntrez)\n", Rd_tag = "RCODE"), │ │ │ │ structure("length(msYgenesEntrez)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("length(XiEgenesEntrez)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gsvadata/man/genderGenesEntrez.Rd", class = "Rd", meta = list( │ │ │ │ + structure("length(XiEgenesEntrez)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/genderGenesEntrez.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ geneprotExpCostaEtAl2021 (list) = structure(list(structure(list(structure("RNA-seq Data by Costa et al. (2021)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("geneprotExpCostaEtAl2021", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("geneprotExpCostaEtAl2021", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("geneExpCostaEtAl2021", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("protExpCostaEtAl2021", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -499,15 +499,15 @@ │ │ │ │ structure(", 29:15--21, 2013.\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for\n", Rd_tag = "TEXT"), │ │ │ │ structure("differential expression analysis of digital gene expression data.\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("Bioinformatics", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(", 26:139--140, 2010.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(geneprotExpCostaEtAl2021)\n", Rd_tag = "RCODE"), │ │ │ │ structure("geneExpCostaEtAl2021\n", Rd_tag = "RCODE"), │ │ │ │ - structure("protExpCostaEtAl2021\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-gsvadata/man/geneprotExpCostaEtAl2021.Rd", class = "Rd", meta = list( │ │ │ │ + structure("protExpCostaEtAl2021\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/geneprotExpCostaEtAl2021.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ ├── ./usr/lib/R/site-library/GSVAdata/help/GSVAdata.rdx │ │ │ ├── GSVAdata.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,61 +1,61 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$`GSVAdata-package` │ │ │ │ │ -[1] 288 4337 │ │ │ │ │ +[1] 295 4346 │ │ │ │ │ │ │ │ │ │ $variables$HumanCerebellumNormSubset │ │ │ │ │ -[1] 4920 1112 │ │ │ │ │ +[1] 4944 1125 │ │ │ │ │ │ │ │ │ │ $variables$annotEntrez220212 │ │ │ │ │ -[1] 6321 1649 │ │ │ │ │ +[1] 6367 1659 │ │ │ │ │ │ │ │ │ │ $variables$brainTxDbSets │ │ │ │ │ -[1] 8254 1241 │ │ │ │ │ +[1] 8321 1252 │ │ │ │ │ │ │ │ │ │ $variables$c2BroadSets │ │ │ │ │ -[1] 9778 1376 │ │ │ │ │ +[1] 9866 1385 │ │ │ │ │ │ │ │ │ │ $variables$commonPickrellHuang │ │ │ │ │ -[1] 11442 5888 │ │ │ │ │ +[1] 11550 5897 │ │ │ │ │ │ │ │ │ │ $variables$gbm_VerhaakEtAl │ │ │ │ │ -[1] 17617 1753 │ │ │ │ │ +[1] 17744 1762 │ │ │ │ │ │ │ │ │ │ $variables$genderGenesEntrez │ │ │ │ │ -[1] 19659 1905 │ │ │ │ │ +[1] 19804 1916 │ │ │ │ │ │ │ │ │ │ $variables$geneprotExpCostaEtAl2021 │ │ │ │ │ -[1] 21859 3885 │ │ │ │ │ +[1] 22024 3894 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 288 │ │ │ │ │ +[1] 0 295 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 4625 295 │ │ │ │ │ +[1] 4641 303 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 6032 289 │ │ │ │ │ +[1] 6069 298 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 7970 284 │ │ │ │ │ +[1] 8026 295 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 9495 283 │ │ │ │ │ +[1] 9573 293 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 11154 288 │ │ │ │ │ +[1] 11251 299 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 17330 287 │ │ │ │ │ +[1] 17447 297 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 19370 289 │ │ │ │ │ +[1] 19506 298 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 21564 295 │ │ │ │ │ +[1] 21720 304 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/GSVAdata/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,11 +1,11 @@ │ │ │ │ │ -[1] "/home/moeller/Salsa/r-bioc-gsvadata/man/GSVAdata-package.Rd" │ │ │ │ │ -[2] "/home/moeller/Salsa/r-bioc-gsvadata/man/HumanCerebellumNormSubset.Rd" │ │ │ │ │ -[3] "/home/moeller/Salsa/r-bioc-gsvadata/man/annotEntrez220212.Rd" │ │ │ │ │ -[4] "/home/moeller/Salsa/r-bioc-gsvadata/man/brainTxDbSets.Rd" │ │ │ │ │ -[5] "/home/moeller/Salsa/r-bioc-gsvadata/man/c2BroadSets.Rd" │ │ │ │ │ -[6] "/home/moeller/Salsa/r-bioc-gsvadata/man/commonPickrellHuang.Rd" │ │ │ │ │ -[7] "/home/moeller/Salsa/r-bioc-gsvadata/man/gbm_VerhaakEtAl.Rd" │ │ │ │ │ -[8] "/home/moeller/Salsa/r-bioc-gsvadata/man/genderGenesEntrez.Rd" │ │ │ │ │ -[9] "/home/moeller/Salsa/r-bioc-gsvadata/man/geneprotExpCostaEtAl2021.Rd" │ │ │ │ │ +[1] "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/GSVAdata-package.Rd" │ │ │ │ │ +[2] "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/HumanCerebellumNormSubset.Rd" │ │ │ │ │ +[3] "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/annotEntrez220212.Rd" │ │ │ │ │ +[4] "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/brainTxDbSets.Rd" │ │ │ │ │ +[5] "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/c2BroadSets.Rd" │ │ │ │ │ +[6] "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/commonPickrellHuang.Rd" │ │ │ │ │ +[7] "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/gbm_VerhaakEtAl.Rd" │ │ │ │ │ +[8] "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/genderGenesEntrez.Rd" │ │ │ │ │ +[9] "/build/reproducible-path/r-bioc-gsvadata-1.48.1/man/geneprotExpCostaEtAl2021.Rd" │ │ │ │ │ attr(,"first") │ │ │ │ │ -[1] 41 │ │ │ │ │ +[1] 53