--- /srv/rebuilderd/tmp/rebuilderd4Hpsj3/inputs/r-bioc-progeny_1.34.0+ds-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderd4Hpsj3/out/r-bioc-progeny_1.34.0+ds-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-07 21:34:54.000000 debian-binary │ --rw-r--r-- 0 0 0 1900 2026-08-07 21:34:54.000000 control.tar.xz │ --rw-r--r-- 0 0 0 8899472 2026-08-07 21:34:54.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 1792 2026-08-07 21:34:54.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 8899424 2026-08-07 21:34:54.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 21:34:54.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 1008 2026-08-07 21:34:54.000000 ./control │ │ │ --rw-r--r-- 0 root (0) root (0) 3180 2026-08-07 21:34:54.000000 ./md5sums │ │ │ +-rw-r--r-- 0 root (0) root (0) 787 2026-08-07 21:34:54.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 3097 2026-08-07 21:34:54.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,14 @@ │ │ │ Package: r-bioc-progeny │ │ │ Version: 1.34.0+ds-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ -Installed-Size: 8787 │ │ │ +Installed-Size: 8786 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-bioc-biobase, r-cran-dplyr, r-cran-tidyr, r-cran-ggplot2, r-cran-ggrepel, r-cran-gridextra, r-bioc-decoupler, r-cran-reshape2, r-pkg-team-core-architecture │ │ │ -Suggests: r-bioc-biomart, r-bioc-biocfilecache, r-cran-broom, r-cran-seurat, r-bioc-singlecellexperiment, r-bioc-deseq2, r-bioc-biocstyle, r-cran-knitr, r-cran-readr, r-cran-readxl, r-cran-pheatmap, r-cran-tibble, r-cran-rmarkdown, r-cran-testthat (>= 2.1.0) │ │ │ +Suggests: r-cran-broom, r-cran-tibble │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/progeny/ │ │ │ Description: activity inference from gene expression │ │ │ This package provides a function to infer pathway activity from gene │ │ │ expression using PROGENy. It contains the linear model which is described │ │ │ in the publication "Perturbation-response genes reveal signaling │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ │ │ │ ├── line order │ │ │ │ @@ -4,15 +4,14 @@ │ │ │ │ usr/lib/R/site-library/progeny/Meta/Rd.rds │ │ │ │ usr/lib/R/site-library/progeny/Meta/data.rds │ │ │ │ usr/lib/R/site-library/progeny/Meta/features.rds │ │ │ │ usr/lib/R/site-library/progeny/Meta/hsearch.rds │ │ │ │ usr/lib/R/site-library/progeny/Meta/links.rds │ │ │ │ usr/lib/R/site-library/progeny/Meta/nsInfo.rds │ │ │ │ usr/lib/R/site-library/progeny/Meta/package.rds │ │ │ │ -usr/lib/R/site-library/progeny/Meta/vignette.rds │ │ │ │ usr/lib/R/site-library/progeny/NAMESPACE │ │ │ │ usr/lib/R/site-library/progeny/NEWS.md │ │ │ │ usr/lib/R/site-library/progeny/R/progeny │ │ │ │ usr/lib/R/site-library/progeny/R/progeny.rdb │ │ │ │ usr/lib/R/site-library/progeny/R/progeny.rdx │ │ │ │ usr/lib/R/site-library/progeny/README.md │ │ │ │ usr/lib/R/site-library/progeny/data/Rdata.rdb ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -11,45 +11,44 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 558 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/Meta/Rd.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 191 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/Meta/data.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 123 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/Meta/features.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 554 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/Meta/hsearch.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 227 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/Meta/links.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 421 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1814 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/Meta/package.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 215 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 598 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 769 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/NEWS.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/R/progeny │ │ │ --rw-r--r-- 0 root (0) root (0) 22781 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/R/progeny.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 414 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/R/progeny.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 22793 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/R/progeny.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 415 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/R/progeny.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 2442 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/README.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/data/ │ │ │ -rw-r--r-- 0 root (0) root (0) 8751157 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/data/Rdata.rdb │ │ │ -rw-r--r-- 0 root (0) root (0) 164 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/data/Rdata.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 199 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/data/Rdata.rdx │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/doc/ │ │ │ --rw-r--r-- 0 root (0) root (0) 1586 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/doc/index.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 1198 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/doc/index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 889 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/doc/progeny.R │ │ │ -rw-r--r-- 0 root (0) root (0) 3933 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/doc/progeny.Rmd │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/extdata/ │ │ │ -rw-r--r-- 0 root (0) root (0) 2256 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/extdata/human_def_expected.csv │ │ │ -rw-r--r-- 0 root (0) root (0) 17466 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/extdata/human_input.csv │ │ │ -rw-r--r-- 0 root (0) root (0) 2249 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/extdata/human_perm_expected.csv │ │ │ -rw-r--r-- 0 root (0) root (0) 2191 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/extdata/mouse_def_expected.csv │ │ │ -rw-r--r-- 0 root (0) root (0) 12672 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/extdata/mouse_input.csv │ │ │ -rw-r--r-- 0 root (0) root (0) 2192 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/extdata/mouse_perm_expected.csv │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 218 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/help/AnIndex │ │ │ -rw-r--r-- 0 root (0) root (0) 162 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/help/aliases.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/help/figures/ │ │ │ -rw-r--r-- 0 root (0) root (0) 95705 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/help/figures/tool_logo.png │ │ │ --rw-r--r-- 0 root (0) root (0) 209 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/help/paths.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 18150 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/help/progeny.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 351 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/help/progeny.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 226 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 18327 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/help/progeny.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 343 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/help/progeny.rdx │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 2338 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-07 21:34:54.000000 ./usr/lib/R/site-library/progeny/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 21:34:54.000000 ./usr/share/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 21:34:54.000000 ./usr/share/doc/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-07 21:34:54.000000 ./usr/share/doc/r-bioc-progeny/ │ │ │ -rw-r--r-- 0 root (0) root (0) 910 2026-08-07 21:34:54.000000 ./usr/share/doc/r-bioc-progeny/changelog.Debian.gz │ │ ├── ./usr/lib/R/site-library/progeny/R/progeny.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -285,15 +285,15 @@ │ │ │ │ "imports" = "gtable_rbind = "gtable_rbind", ellipseGrob = "ellipseGrob"), " │ │ │ │ "imports" = " dplyr = c(group_by = "group_by"), dplyr = c(select = "select"), " │ │ │ │ "imports" = " dplyr = c(top_n = "top_n"), dplyr = c(ungroup = "ungroup"), " │ │ │ │ "imports" = " reshape2 = c(melt = "melt"), stats = c(complete.cases = "complete.cases"), " │ │ │ │ "imports" = " stats = c(ecdf = "ecdf"), stats = c(sd = "sd"), tidyr = c("%>%" = "%>%"), " │ │ │ │ "imports" = " tidyr = c(spread = "spread"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-progeny/debian/r-bioc-progeny/usr/lib/R/site-library/progeny"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-progeny-1.34.0+ds/debian/r-bioc-progeny/usr/lib/R/site-library/progeny"" │ │ │ │ "spec" = "c(name = "progeny", version = "1.34.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/progeny/R/progeny.rdx │ │ │ ├── progeny.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,58 +1,58 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 5044 52 │ │ │ │ │ +[1] 5056 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 5227 52 │ │ │ │ │ +[1] 5239 52 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 5279 52 │ │ │ │ │ +[1] 5291 52 │ │ │ │ │ │ │ │ │ │ $variables$getModel │ │ │ │ │ -[1] 5331 2074 │ │ │ │ │ +[1] 5343 2074 │ │ │ │ │ │ │ │ │ │ $variables$progeny │ │ │ │ │ -[1] 7405 308 │ │ │ │ │ +[1] 7417 308 │ │ │ │ │ │ │ │ │ │ $variables$progeny.ExpressionSet │ │ │ │ │ -[1] 7713 512 │ │ │ │ │ +[1] 7725 512 │ │ │ │ │ │ │ │ │ │ $variables$progeny.Seurat │ │ │ │ │ -[1] 8225 1581 │ │ │ │ │ +[1] 8237 1581 │ │ │ │ │ │ │ │ │ │ $variables$progeny.SingleCellExperiment │ │ │ │ │ -[1] 9806 613 │ │ │ │ │ +[1] 9818 613 │ │ │ │ │ │ │ │ │ │ $variables$progeny.default │ │ │ │ │ -[1] 10419 387 │ │ │ │ │ +[1] 10431 387 │ │ │ │ │ │ │ │ │ │ $variables$progeny.matrix │ │ │ │ │ -[1] 10806 2959 │ │ │ │ │ +[1] 10818 2959 │ │ │ │ │ │ │ │ │ │ $variables$progenyPerm │ │ │ │ │ -[1] 13765 3558 │ │ │ │ │ +[1] 13777 3558 │ │ │ │ │ │ │ │ │ │ $variables$progenyScatter │ │ │ │ │ -[1] 17323 4468 │ │ │ │ │ +[1] 17335 4468 │ │ │ │ │ │ │ │ │ │ $variables$saveProgenyPlots │ │ │ │ │ -[1] 21791 990 │ │ │ │ │ +[1] 21803 990 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 289 4755 │ │ │ │ │ +[1] 289 4767 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 0 131 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ [1] 131 158 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 5096 131 │ │ │ │ │ +[1] 5108 131 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/progeny/doc/index.html │ │ │ @@ -10,28 +10,17 @@ │ │ │ │ │ │
│ │ │
│ │ │ [Up] │ │ │ [Top] │ │ │
│ │ │

Vignettes from package 'progeny'

│ │ │ - │ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
progeny::PROGENy pathway signaturessource
│ │ │ +The package contains no vignette meta-information. │ │ │

Other files in the doc directory

│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │
progeny.R
progeny.Rmd
│ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,7 +1,8 @@ │ │ │ │ ************ VViiggnneetttteess aanndd ootthheerr ddooccuummeennttaattiioonn[[[[RR llooggoo]]]] ************ │ │ │ │ =============================================================================== │ │ │ │ _[_[_U_p_]_]_[_[_T_o_p_]_] │ │ │ │ ********** VViiggnneetttteess ffrroomm ppaacckkaaggee ''pprrooggeennyy'' ********** │ │ │ │ -_p_r_o_g_e_n_y_:_: PROGENy pathway signatures _s_o_u_r_c_e │ │ │ │ +The package contains no vignette meta-information. │ │ │ │ ********** OOtthheerr ffiilleess iinn tthhee ddoocc ddiirreeccttoorryy ********** │ │ │ │ _p_r_o_g_e_n_y_._R │ │ │ │ + _p_r_o_g_e_n_y_._R_m_d │ │ ├── ./usr/lib/R/site-library/progeny/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,10 +1,10 @@ │ │ │ │ │ -[1] "/home/moeller/Salsa/r-bioc-progeny/man/getModel.Rd" │ │ │ │ │ -[2] "/home/moeller/Salsa/r-bioc-progeny/man/model_human_full.Rd" │ │ │ │ │ -[3] "/home/moeller/Salsa/r-bioc-progeny/man/model_mouse_full.Rd" │ │ │ │ │ -[4] "/home/moeller/Salsa/r-bioc-progeny/man/progeny.Rd" │ │ │ │ │ -[5] "/home/moeller/Salsa/r-bioc-progeny/man/progenyPerm.Rd" │ │ │ │ │ -[6] "/home/moeller/Salsa/r-bioc-progeny/man/progenyScatter.Rd" │ │ │ │ │ -[7] "/home/moeller/Salsa/r-bioc-progeny/man/saveProgenyPlots.Rd" │ │ │ │ │ -[8] "/home/moeller/Salsa/r-bioc-progeny/man/vignette_data.Rd" │ │ │ │ │ +[1] "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/getModel.Rd" │ │ │ │ │ +[2] "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/model_human_full.Rd" │ │ │ │ │ +[3] "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/model_mouse_full.Rd" │ │ │ │ │ +[4] "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/progeny.Rd" │ │ │ │ │ +[5] "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/progenyPerm.Rd" │ │ │ │ │ +[6] "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/progenyScatter.Rd" │ │ │ │ │ +[7] "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/saveProgenyPlots.Rd" │ │ │ │ │ +[8] "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/vignette_data.Rd" │ │ │ │ │ attr(,"first") │ │ │ │ │ -[1] 40 │ │ │ │ │ +[1] 55 │ │ ├── ./usr/lib/R/site-library/progeny/help/progeny.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -14,15 +14,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("decoupleR", Rd_tag = "TEXT")), │ │ │ │ list(structure("if TRUE, the model matrix is goign to be generated with a format \n", Rd_tag = "TEXT"), │ │ │ │ structure("makes it directlz compatible with the decoupleR package", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function returns model matrix according to the top n significant\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("#getting a model matrix according to the desired top n significant \n", Rd_tag = "RCODE"), │ │ │ │ - structure("model <- getModel(\"Human\", top=100)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-progeny/man/getModel.Rd", class = "Rd", meta = list( │ │ │ │ + structure("model <- getModel(\"Human\", top=100)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/getModel.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ model_human_full (list) = structure(list(structure(list(structure("The full human linear model underlying PROGENy", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("model_human_full", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("model_human_full", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -44,15 +44,15 @@ │ │ │ │ structure(list(list(structure("p.value", Rd_tag = "TEXT")), │ │ │ │ list(structure("significance of gene in pathway", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\describe"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\format"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("https://www.nature.com/articles/s41467-017-02391-6", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\source"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("get(\"model_human_full\", envir = .GlobalEnv)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-progeny/man/model_human_full.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("get(\"model_human_full\", envir = .GlobalEnv)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/model_human_full.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ model_mouse_full (list) = structure(list(structure(list(structure("The full mouse linear model underlying PROGENy", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("model_mouse_full", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("model_mouse_full", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("MGI gene symbols in rows, pathways in columns. Pathway activity inference\n", Rd_tag = "TEXT"), │ │ │ │ @@ -72,15 +72,15 @@ │ │ │ │ structure(list(list(structure("p.value", Rd_tag = "TEXT")), │ │ │ │ list(structure("significance of gene in a pathway", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\describe"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\format"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("https://www.ncbi.nlm.nih.gov/pubmed/31525460", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\source"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("get(\"model_mouse_full\", envir = .GlobalEnv)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-progeny/man/model_mouse_full.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("get(\"model_mouse_full\", envir = .GlobalEnv)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/model_mouse_full.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ progeny (list) = structure(list(structure(list(structure("Calculate PROGENy pathway scores from gene expression", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("progeny", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("progeny", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function uses the linear model of pathway-responsive genes underlying\n", Rd_tag = "TEXT"), │ │ │ │ structure("the PROGENy method. It transforms a gene expression matrix with HGNC/MGI gene\n", Rd_tag = "TEXT"), │ │ │ │ @@ -178,15 +178,15 @@ │ │ │ │ structure(list(structure("progenyPerm", 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("# use example gene expression matrix here, this is just for illustration\n", Rd_tag = "RCODE"), │ │ │ │ structure("gene_expression <- as.matrix(read.csv(system.file(\"extdata\", \n", Rd_tag = "RCODE"), │ │ │ │ structure("\"human_input.csv\", package = \"progeny\"), row.names = 1))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# calculate pathway activities\n", Rd_tag = "RCODE"), │ │ │ │ structure("pathways <- progeny(gene_expression, scale=TRUE, \n", Rd_tag = "RCODE"), │ │ │ │ - structure(" organism=\"Human\", top = 100, perm = 1)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-progeny/man/progeny.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" organism=\"Human\", top = 100, perm = 1)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/progeny.Rd", class = "Rd", meta = list( │ │ │ │ docType = "package", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ progenyPerm (list) = structure(list(structure(list(structure("Compute progeny pathway scores and assesses significance based on permutations", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("progenyPerm", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("progenyPerm", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Compute progeny pathway scores and assesses significance based on permutations\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("progenyPerm(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -230,15 +230,15 @@ │ │ │ │ structure("1-p.value two-sided test over an empirical distribution) with the sign \n", Rd_tag = "TEXT"), │ │ │ │ structure("indicating the direction of the regulation. The second element is the null \n", Rd_tag = "TEXT"), │ │ │ │ structure("distribution list (a null distribution is generated for each sample/contrast).\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("# use example gene expression matrix\n", Rd_tag = "RCODE"), │ │ │ │ structure("gene_expression <- as.matrix(read.csv(system.file(\"extdata\", \n", Rd_tag = "RCODE"), │ │ │ │ structure("\"human_input.csv\", package = \"progeny\"), row.names = 1))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# calculate pathway activities\n", Rd_tag = "RCODE"), │ │ │ │ - structure("progeny(gene_expression, scale=TRUE, organism=\"Human\", top=100, perm=10000)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-progeny/man/progenyPerm.Rd", class = "Rd", meta = list( │ │ │ │ + structure("progeny(gene_expression, scale=TRUE, organism=\"Human\", top=100, perm=10000)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/progenyPerm.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ progenyScatter (list) = structure(list(structure(list(structure("Calculate Progeny Scores with Permutations", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("progenyScatter", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("progenyScatter", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function generate a series of scatter plot with marginal distribution\n", Rd_tag = "TEXT"), │ │ │ │ structure("(in the form of an arrangeGrob object), for each progeny pathway and\n", Rd_tag = "TEXT"), │ │ │ │ @@ -293,15 +293,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("gene_expression <- read.csv(system.file(\"extdata\", \n", Rd_tag = "RCODE"), │ │ │ │ structure("\"human_input.csv\", package = \"progeny\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# getting a model matrix with 100 top significant genes and converting to df\n", Rd_tag = "RCODE"), │ │ │ │ structure("weight_matrix <- getModel(\"Human\", top=100)\n", Rd_tag = "RCODE"), │ │ │ │ structure("weight_matrix <- data.frame(names = row.names(weight_matrix), \n", Rd_tag = "RCODE"), │ │ │ │ structure(" row.names = NULL, weight_matrix)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("#use progenyScatter function\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plots <- progenyScatter(gene_expression, weight_matrix)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-progeny/man/progenyScatter.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plots <- progenyScatter(gene_expression, weight_matrix)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/progenyScatter.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) { │ │ │ │ @@ -340,15 +340,15 @@ │ │ │ │ structure(" row.names = NULL, weight_matrix) \n", Rd_tag = "RCODE"), │ │ │ │ structure("plots <- progenyScatter(gene_expression, weight_matrix)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("#create a list with contrast names\n", Rd_tag = "RCODE"), │ │ │ │ structure("contrast_names <- names(gene_expression[2:ncol(gene_expression)])\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("#assign a path to store your plots\n", Rd_tag = "RCODE"), │ │ │ │ structure("dirpath <- \"./progeny_plots/\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# save it\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# saveProgenyPlots(plots, contrast_names, dirpath)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-progeny/man/saveProgenyPlots.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# saveProgenyPlots(plots, contrast_names, dirpath)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/saveProgenyPlots.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ vignette_data (list) = structure(list(structure(list(structure("The RNA data used in the progeny vignette", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("vignette_data", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("vignette_data", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("datasets", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("List with three elements: the gene counts, the experimental design and \n", Rd_tag = "TEXT"), │ │ │ │ @@ -365,10 +365,10 @@ │ │ │ │ structure(list(list(structure("limma_ttop", Rd_tag = "TEXT")), │ │ │ │ list(structure("differential analysis result using limma", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\describe"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\format"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119931", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\source"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(\"vignette_data\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-progeny/man/vignette_data.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(\"vignette_data\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-progeny-1.34.0+ds/man/vignette_data.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/progeny/help/progeny.rdx │ │ │ ├── progeny.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,55 +1,55 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$getModel │ │ │ │ │ -[1] 284 1239 │ │ │ │ │ +[1] 294 1254 │ │ │ │ │ │ │ │ │ │ $variables$model_human_full │ │ │ │ │ -[1] 1814 1324 │ │ │ │ │ +[1] 1847 1336 │ │ │ │ │ │ │ │ │ │ $variables$model_mouse_full │ │ │ │ │ -[1] 3428 1326 │ │ │ │ │ +[1] 3482 1337 │ │ │ │ │ │ │ │ │ │ $variables$progeny │ │ │ │ │ -[1] 5033 4101 │ │ │ │ │ +[1] 5108 4112 │ │ │ │ │ │ │ │ │ │ $variables$progenyPerm │ │ │ │ │ -[1] 9415 2284 │ │ │ │ │ +[1] 9512 2295 │ │ │ │ │ │ │ │ │ │ $variables$progenyScatter │ │ │ │ │ -[1] 11981 2702 │ │ │ │ │ +[1] 12100 2714 │ │ │ │ │ │ │ │ │ │ $variables$saveProgenyPlots │ │ │ │ │ -[1] 14969 1749 │ │ │ │ │ +[1] 15111 1760 │ │ │ │ │ │ │ │ │ │ $variables$vignette_data │ │ │ │ │ -[1] 17005 1145 │ │ │ │ │ +[1] 17168 1159 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 284 │ │ │ │ │ +[1] 0 294 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 1523 291 │ │ │ │ │ +[1] 1548 299 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 3138 290 │ │ │ │ │ +[1] 3183 299 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 4754 279 │ │ │ │ │ +[1] 4819 289 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 9134 281 │ │ │ │ │ +[1] 9220 292 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 11699 282 │ │ │ │ │ +[1] 11807 293 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 14683 286 │ │ │ │ │ +[1] 14814 297 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 16718 287 │ │ │ │ │ +[1] 16871 297 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE