[ Started: 2024-11-04 13:15:01 CET ] [ MetaProViz v2.1.2 for BioC-3.20 from https://github.com/saezlab/MetaProViz@development (1a3ec3e 2024-10-31 15:00:57) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.20" [3] "/home/omnipath/local/R/4.4" "/usr/lib/R/library" 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) Old packages: 'decoupleR', 'OmnipathR' trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/decoupleR_2.12.0.tar.gz' Content type 'application/x-gzip' length 5238810 bytes (5.0 MB) ================================================== downloaded 5.0 MB trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/OmnipathR_3.14.0.tar.gz' Content type 'application/x-gzip' length 3715601 bytes (3.5 MB) ================================================== downloaded 3.5 MB * installing *source* package ‘decoupleR’ ... ** package ‘decoupleR’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (decoupleR) * installing *source* package ‘OmnipathR’ ... ** package ‘OmnipathR’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-11-04 13:15:20] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-11-04 13:15:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-04 13:15:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:15:20] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-04 13:15:20] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-04 13:15:20] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-04 13:15:20] [TRACE] [OmnipathR] Contains 1 files. [2024-11-04 13:15:20] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-04 13:15:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-04 13:15:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:15:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-04 13:15:20] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-04 13:15:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-04 13:15:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:15:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-04 13:15:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:15:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-04 13:15:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:15:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-04 13:15:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:15:20] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-11-04 13:15:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-04 13:15:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:15:21] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-04 13:15:21] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-04 13:15:21] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-04 13:15:21] [TRACE] [OmnipathR] Contains 1 files. [2024-11-04 13:15:21] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-04 13:15:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-04 13:15:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:15:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-04 13:15:21] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-04 13:15:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-04 13:15:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:15:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-04 13:15:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:15:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-04 13:15:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:15:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-04 13:15:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:15:21] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR) The downloaded source packages are in ‘/tmp/RtmpenzDmD/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' OmnipathR (3.14.0 -> 400729939...) [GitHub] cosmosR (NA -> 81d1a7fe7...) [GitHub] NA (NA -> b0cd237f3...) [Git] GenomeInfoDb (NA -> 1.38.8 ) [CRAN] XVector (NA -> 0.42.0 ) [CRAN] IRanges (NA -> 2.36.0 ) [CRAN] S4Vectors (NA -> 0.40.2 ) [CRAN] admisc (NA -> 0.36 ) [CRAN] gridGraphics (NA -> 0.5-1 ) [CRAN] yulab.utils (NA -> 0.1.7 ) [CRAN] ggplotify (NA -> 0.1.2 ) [CRAN] ggfun (NA -> 0.1.7 ) [CRAN] nloptr (NA -> 2.1.1 ) [CRAN] lme4 (NA -> 1.1-35.5 ) [CRAN] pbkrtest (NA -> 0.5.3 ) [CRAN] car (NA -> 3.1-3 ) [CRAN] rstatix (NA -> 0.7.2 ) [CRAN] Biostrings (NA -> 2.70.3 ) [CRAN] KEGGREST (NA -> 1.42.0 ) [CRAN] Annotatio... (NA -> 1.64.1 ) [CRAN] annotate (NA -> 1.80.0 ) [CRAN] GO.db (NA -> 3.18.0 ) [CRAN] treeio (NA -> 1.26.0 ) [CRAN] tidytree (NA -> 0.4.6 ) [CRAN] qvalue (NA -> 2.34.0 ) [CRAN] HDO.db (NA -> 0.99.1 ) [CRAN] ggtree (NA -> 3.10.1 ) [CRAN] GOSemSim (NA -> 2.28.1 ) [CRAN] shadowtext (NA -> 0.1.4 ) [CRAN] scatterpie (NA -> 0.2.4 ) [CRAN] ggnewscale (NA -> 0.5.0 ) [CRAN] DOSE (NA -> 3.28.2 ) [CRAN] aplot (NA -> 0.2.3 ) [CRAN] venn (NA -> 1.12 ) [CRAN] ggpubr (NA -> 0.6.0 ) [CRAN] FactoMineR (NA -> 2.11 ) [CRAN] GSEABase (NA -> 1.64.0 ) [CRAN] gson (NA -> 0.1.0 ) [CRAN] enrichplot (NA -> 1.22.0 ) [CRAN] downloader (NA -> 0.4 ) [CRAN] kableExtra (NA -> 1.4.0 ) [CRAN] ggVennDia... (NA -> 1.5.2 ) [CRAN] factoextra (NA -> 1.0.7 ) [CRAN] EnhancedV... (NA -> 1.20.0 ) [CRAN] clusterPr... (NA -> 4.10.1 ) [CRAN] Downloading GitHub repo saezlab/cosmosR@HEAD GenomeInfoDb (NA -> 1.38.8) [CRAN] XVector (NA -> 0.42.0) [CRAN] Biostrings (NA -> 2.70.3) [CRAN] KEGGREST (NA -> 1.42.0) [CRAN] S4Vectors (NA -> 0.40.2) [CRAN] IRanges (NA -> 2.36.0) [CRAN] Annotatio... (NA -> 1.64.1) [CRAN] annotate (NA -> 1.80.0) [CRAN] GSEABase (NA -> 1.64.0) [CRAN] Skipping 9 packages ahead of CRAN: zlibbioc, GenomeInfoDbData, Biobase, BiocGenerics, graph, decoupleR, bcellViper, dorothea, CARNIVAL Installing 9 packages: GenomeInfoDb, XVector, Biostrings, KEGGREST, S4Vectors, IRanges, AnnotationDbi, annotate, GSEABase trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomeInfoDb_1.38.8.tar.gz' Content type 'application/gzip' length 3581806 bytes (3.4 MB) ================================================== downloaded 3.4 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/XVector_0.42.0.tar.gz' Content type 'application/gzip' length 67825 bytes (66 KB) ================================================== downloaded 66 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/Biostrings_2.70.3.tar.gz' Content type 'application/gzip' length 12740728 bytes (12.2 MB) ================================================== downloaded 12.2 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/KEGGREST_1.42.0.tar.gz' Content type 'application/gzip' length 22412 bytes (21 KB) ================================================== downloaded 21 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/S4Vectors_0.40.2.tar.gz' Content type 'application/gzip' length 838187 bytes (818 KB) ================================================== downloaded 818 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/IRanges_2.36.0.tar.gz' Content type 'application/gzip' length 481055 bytes (469 KB) ================================================== downloaded 469 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/AnnotationDbi_1.64.1.tar.gz' Content type 'application/gzip' length 4359564 bytes (4.2 MB) ================================================== downloaded 4.2 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/annotate_1.80.0.tar.gz' Content type 'application/gzip' length 1497628 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GSEABase_1.64.0.tar.gz' Content type 'application/gzip' length 299035 bytes (292 KB) ================================================== downloaded 292 KB * installing *source* package ‘S4Vectors’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c AEbufs.c -o AEbufs.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c DataFrame_class.c -o DataFrame_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Hits_class.c -o Hits_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c LLint_class.c -o LLint_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c List_class.c -o List_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Rle_class.c -o Rle_class.o Rle_class.c: In function ‘_subset_Rle_by_ranges’: Rle_class.c:1136:17: error: format not a string literal and no format arguments [-Werror=format-security] 1136 | error(errmsg); | ^~~~~ Rle_class.c: In function ‘_subset_Rle_by_positions’: Rle_class.c:1161:17: error: format not a string literal and no format arguments [-Werror=format-security] 1161 | error(errmsg); | ^~~~~ Rle_class.c: In function ‘Rle_extract_range’: Rle_class.c:1190:17: error: format not a string literal and no format arguments [-Werror=format-security] 1190 | error(errmsg); | ^~~~~ cc1: some warnings being treated as errors make: *** [/usr/lib/R/etc/Makeconf:195: Rle_class.o] Error 1 ERROR: compilation failed for package ‘S4Vectors’ * removing ‘/home/omnipath/local/R/4.4-3.20/S4Vectors’ ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’ * removing ‘/home/omnipath/local/R/4.4-3.20/IRanges’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘GenomeInfoDb’ * removing ‘/home/omnipath/local/R/4.4-3.20/GenomeInfoDb’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘XVector’ * removing ‘/home/omnipath/local/R/4.4-3.20/XVector’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘GenomeInfoDb’ are not available for package ‘Biostrings’ * removing ‘/home/omnipath/local/R/4.4-3.20/Biostrings’ ERROR: dependency ‘Biostrings’ is not available for package ‘KEGGREST’ * removing ‘/home/omnipath/local/R/4.4-3.20/KEGGREST’ ERROR: dependencies ‘IRanges’, ‘S4Vectors’, ‘KEGGREST’ are not available for package ‘AnnotationDbi’ * removing ‘/home/omnipath/local/R/4.4-3.20/AnnotationDbi’ ERROR: dependency ‘AnnotationDbi’ is not available for package ‘annotate’ * removing ‘/home/omnipath/local/R/4.4-3.20/annotate’ ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘GSEABase’ * removing ‘/home/omnipath/local/R/4.4-3.20/GSEABase’ The downloaded source packages are in ‘/tmp/RtmpenzDmD/downloaded_packages’ ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpenzDmD/remotes17d57317d35aed/saezlab-cosmosR-81d1a7f/DESCRIPTION’ ... OK * preparing ‘cosmosR’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘cosmosR_1.9.1.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘cosmosR/vignettes/net_compr_MOON_files/figure-markdown_strict/extract_subnetwork_from_scored_MOON_network_1.png’ ERROR: dependency ‘GSEABase’ is not available for package ‘cosmosR’ * removing ‘/home/omnipath/local/R/4.4-3.20/cosmosR’ Downloading git repo https://git.bioconductor.org/packages/limma.git '/usr/bin/git' clone --depth 1 --no-hardlinks https://git.bioconductor.org/packages/limma.git /tmp/RtmpenzDmD/file17d5735a62b647 Cloning into '/tmp/RtmpenzDmD/file17d5735a62b647'... ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpenzDmD/file17d5735a62b647/DESCRIPTION’ ... OK * preparing ‘limma’: * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘limma_3.63.1.tar.gz’ * installing *source* package ‘limma’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c normexp.c -o normexp.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c weighted_lowess.c -o weighted_lowess.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o limma.so init.o normexp.o weighted_lowess.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-limma/00new/limma/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (limma) Skipping 13 packages ahead of CRAN: zlibbioc, GenomeInfoDbData, BiocGenerics, graph, Biobase, decoupleR, bcellViper, fgsea, BiocParallel, dorothea, CARNIVAL, BiocStyle, limma Installing 42 packages: GenomeInfoDb, XVector, IRanges, S4Vectors, admisc, gridGraphics, yulab.utils, ggplotify, ggfun, nloptr, lme4, pbkrtest, car, rstatix, Biostrings, KEGGREST, AnnotationDbi, annotate, GO.db, treeio, tidytree, qvalue, HDO.db, ggtree, GOSemSim, shadowtext, scatterpie, ggnewscale, DOSE, aplot, venn, ggpubr, FactoMineR, GSEABase, gson, enrichplot, downloader, kableExtra, ggVennDiagram, factoextra, EnhancedVolcano, clusterProfiler trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomeInfoDb_1.38.8.tar.gz' Content type 'application/gzip' length 3581806 bytes (3.4 MB) ================================================== downloaded 3.4 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/XVector_0.42.0.tar.gz' Content type 'application/gzip' length 67825 bytes (66 KB) ================================================== downloaded 66 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/IRanges_2.36.0.tar.gz' Content type 'application/gzip' length 481055 bytes (469 KB) ================================================== downloaded 469 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/S4Vectors_0.40.2.tar.gz' Content type 'application/gzip' length 838187 bytes (818 KB) ================================================== downloaded 818 KB trying URL 'https://cran.uni-muenster.de/src/contrib/admisc_0.36.tar.gz' Content type 'application/x-gzip' length 70620 bytes (68 KB) ================================================== downloaded 68 KB trying URL 'https://cran.uni-muenster.de/src/contrib/gridGraphics_0.5-1.tar.gz' Content type 'application/x-gzip' length 69207 bytes (67 KB) ================================================== downloaded 67 KB trying URL 'https://cran.uni-muenster.de/src/contrib/yulab.utils_0.1.7.tar.gz' Content type 'application/x-gzip' length 23777 bytes (23 KB) ================================================== downloaded 23 KB trying URL 'https://cran.uni-muenster.de/src/contrib/ggplotify_0.1.2.tar.gz' Content type 'application/x-gzip' length 117886 bytes (115 KB) ================================================== downloaded 115 KB trying URL 'https://cran.uni-muenster.de/src/contrib/ggfun_0.1.7.tar.gz' Content type 'application/x-gzip' length 106366 bytes (103 KB) ================================================== downloaded 103 KB trying URL 'https://cran.uni-muenster.de/src/contrib/nloptr_2.1.1.tar.gz' Content type 'application/x-gzip' length 2236635 bytes (2.1 MB) 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bytes (609 KB) ================================================== downloaded 609 KB * installing *source* package ‘S4Vectors’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c AEbufs.c -o AEbufs.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c DataFrame_class.c -o DataFrame_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Hits_class.c -o Hits_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c LLint_class.c -o LLint_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c List_class.c -o List_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Rle_class.c -o Rle_class.o Rle_class.c: In function ‘_subset_Rle_by_ranges’: Rle_class.c:1136:17: error: format not a string literal and no format arguments [-Werror=format-security] 1136 | error(errmsg); | ^~~~~ Rle_class.c: In function ‘_subset_Rle_by_positions’: Rle_class.c:1161:17: error: format not a string literal and no format arguments [-Werror=format-security] 1161 | error(errmsg); | ^~~~~ Rle_class.c: In function ‘Rle_extract_range’: Rle_class.c:1190:17: error: format not a string literal and no format arguments [-Werror=format-security] 1190 | error(errmsg); | ^~~~~ cc1: some warnings being treated as errors make: *** [/usr/lib/R/etc/Makeconf:195: Rle_class.o] Error 1 ERROR: compilation failed for package ‘S4Vectors’ * removing ‘/home/omnipath/local/R/4.4-3.20/S4Vectors’ * installing *source* package ‘admisc’ ... ** package ‘admisc’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c admisc.c -o admisc.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c registerDynamicSymbol.c -o registerDynamicSymbol.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o admisc.so admisc.o registerDynamicSymbol.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-admisc/00new/admisc/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (admisc) * installing *source* package ‘gridGraphics’ ... ** package ‘gridGraphics’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gridGraphics) * installing *source* package ‘yulab.utils’ ... ** package ‘yulab.utils’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (yulab.utils) * installing *source* package ‘nloptr’ ... ** package ‘nloptr’ successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -std=gnu++17 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++17 accepts -g... (cached) yes checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed checking for pkg-config... /usr/bin/pkg-config checking if pkg-config knows NLopt... no checking for cmake... no ------------------ CMAKE NOT FOUND -------------------- CMake was not found on the PATH. Please install CMake: - sudo yum install cmake (Fedora/CentOS; inside a terminal) - sudo apt install cmake (Debian/Ubuntu; inside a terminal). - sudo pacman -S cmake (Arch Linux; inside a terminal). - brew install --cask cmake (MacOS; inside a terminal with Homebrew) - sudo port install cmake (MacOS; inside a terminal with MacPorts) Alternatively install CMake from: ------------------------------------------------------- ERROR: configuration failed for package ‘nloptr’ * removing ‘/home/omnipath/local/R/4.4-3.20/nloptr’ * installing *source* package ‘qvalue’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (qvalue) * installing *source* package ‘shadowtext’ ... ** package ‘shadowtext’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (shadowtext) * installing *source* package ‘ggnewscale’ ... ** package ‘ggnewscale’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggnewscale) * installing *source* package ‘gson’ ... ** package ‘gson’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gson) * installing *source* package ‘downloader’ ... ** package ‘downloader’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (downloader) * installing *source* package ‘kableExtra’ ... ** package ‘kableExtra’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (kableExtra) * installing *source* package ‘EnhancedVolcano’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (EnhancedVolcano) ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’ * removing ‘/home/omnipath/local/R/4.4-3.20/IRanges’ * installing *source* package ‘ggplotify’ ... ** package ‘ggplotify’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggplotify) * installing *source* package ‘ggfun’ ... ** package ‘ggfun’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggfun) ERROR: dependency ‘nloptr’ is not available for package ‘lme4’ * removing ‘/home/omnipath/local/R/4.4-3.20/lme4’ * installing *source* package ‘tidytree’ ... ** package ‘tidytree’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tidytree) * installing *source* package ‘venn’ ... ** package ‘venn’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (venn) ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘GenomeInfoDb’ * removing ‘/home/omnipath/local/R/4.4-3.20/GenomeInfoDb’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘XVector’ * removing ‘/home/omnipath/local/R/4.4-3.20/XVector’ ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’ * removing ‘/home/omnipath/local/R/4.4-3.20/pbkrtest’ * installing *source* package ‘treeio’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (treeio) * installing *source* package ‘scatterpie’ ... ** package ‘scatterpie’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scatterpie) * installing *source* package ‘aplot’ ... ** package ‘aplot’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (aplot) ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’ * removing ‘/home/omnipath/local/R/4.4-3.20/car’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘GenomeInfoDb’ are not available for package ‘Biostrings’ * removing ‘/home/omnipath/local/R/4.4-3.20/Biostrings’ * installing *source* package ‘ggtree’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggtree) * installing *source* package ‘ggVennDiagram’ ... ** package ‘ggVennDiagram’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggVennDiagram) ERROR: dependency ‘car’ is not available for package ‘rstatix’ * removing ‘/home/omnipath/local/R/4.4-3.20/rstatix’ ERROR: dependency ‘Biostrings’ is not available for package ‘KEGGREST’ * removing ‘/home/omnipath/local/R/4.4-3.20/KEGGREST’ ERROR: dependency ‘car’ is not available for package ‘FactoMineR’ * removing ‘/home/omnipath/local/R/4.4-3.20/FactoMineR’ ERROR: dependencies ‘IRanges’, ‘S4Vectors’, ‘KEGGREST’ are not available for package ‘AnnotationDbi’ * removing ‘/home/omnipath/local/R/4.4-3.20/AnnotationDbi’ ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’ * removing ‘/home/omnipath/local/R/4.4-3.20/ggpubr’ ERROR: dependency ‘AnnotationDbi’ is not available for package ‘annotate’ * removing ‘/home/omnipath/local/R/4.4-3.20/annotate’ ERROR: dependency ‘AnnotationDbi’ is not available for package ‘GO.db’ * removing ‘/home/omnipath/local/R/4.4-3.20/GO.db’ ERROR: dependency ‘AnnotationDbi’ is not available for package ‘HDO.db’ * removing ‘/home/omnipath/local/R/4.4-3.20/HDO.db’ ERROR: dependencies ‘FactoMineR’, ‘ggpubr’ are not available for package ‘factoextra’ * removing ‘/home/omnipath/local/R/4.4-3.20/factoextra’ ERROR: dependencies ‘AnnotationDbi’, ‘GO.db’ are not available for package ‘GOSemSim’ * removing ‘/home/omnipath/local/R/4.4-3.20/GOSemSim’ ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘GSEABase’ * removing ‘/home/omnipath/local/R/4.4-3.20/GSEABase’ ERROR: dependencies ‘AnnotationDbi’, ‘HDO.db’, ‘GOSemSim’ are not available for package ‘DOSE’ * removing ‘/home/omnipath/local/R/4.4-3.20/DOSE’ ERROR: dependencies ‘DOSE’, ‘GOSemSim’ are not available for package ‘enrichplot’ * removing ‘/home/omnipath/local/R/4.4-3.20/enrichplot’ ERROR: dependencies ‘AnnotationDbi’, ‘DOSE’, ‘enrichplot’, ‘GO.db’, ‘GOSemSim’ are not available for package ‘clusterProfiler’ * removing ‘/home/omnipath/local/R/4.4-3.20/clusterProfiler’ The downloaded source packages are in ‘/tmp/RtmpenzDmD/downloaded_packages’ Downloading GitHub repo saezlab/OmnipathR@HEAD ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpenzDmD/remotes17d57331fad08e/saezlab-OmnipathR-4007299/DESCRIPTION’ ... OK * preparing ‘OmnipathR’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Removed empty directory ‘OmnipathR/.github’ * looking to see if a ‘data/datalist’ file should be added * building ‘OmnipathR_3.13.28.tar.gz’ * installing *source* package ‘OmnipathR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-11-04 13:17:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-04 13:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:17:49] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-04 13:17:49] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-04 13:17:49] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-04 13:17:49] [TRACE] [OmnipathR] Contains 1 files. [2024-11-04 13:17:49] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-04 13:17:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-04 13:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:17:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-04 13:17:49] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-04 13:17:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-04 13:17:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:17:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-04 13:17:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:17:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-04 13:17:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:17:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-04 13:17:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:17:50] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-11-04 13:17:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-04 13:17:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:17:51] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-04 13:17:51] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-04 13:17:51] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-04 13:17:51] [TRACE] [OmnipathR] Contains 1 files. [2024-11-04 13:17:51] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-04 13:17:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-04 13:17:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:17:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-04 13:17:51] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-04 13:17:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-04 13:17:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:17:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-04 13:17:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:17:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-04 13:17:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:17:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-04 13:17:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-04 13:17:51] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR) Downloading GitHub repo saezlab/cosmosR@HEAD GenomeInfoDb (NA -> 1.38.8) [CRAN] XVector (NA -> 0.42.0) [CRAN] Biostrings (NA -> 2.70.3) [CRAN] KEGGREST (NA -> 1.42.0) [CRAN] S4Vectors (NA -> 0.40.2) [CRAN] IRanges (NA -> 2.36.0) [CRAN] Annotatio... (NA -> 1.64.1) [CRAN] annotate (NA -> 1.80.0) [CRAN] GSEABase (NA -> 1.64.0) [CRAN] Skipping 9 packages ahead of CRAN: zlibbioc, GenomeInfoDbData, Biobase, BiocGenerics, graph, decoupleR, bcellViper, dorothea, CARNIVAL Installing 9 packages: GenomeInfoDb, XVector, Biostrings, KEGGREST, S4Vectors, IRanges, AnnotationDbi, annotate, GSEABase trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomeInfoDb_1.38.8.tar.gz' Content type 'application/gzip' length 3581806 bytes (3.4 MB) ================================================== downloaded 3.4 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/XVector_0.42.0.tar.gz' Content type 'application/gzip' length 67825 bytes (66 KB) ================================================== downloaded 66 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/Biostrings_2.70.3.tar.gz' Content type 'application/gzip' length 12740728 bytes (12.2 MB) ================================================== downloaded 12.2 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/KEGGREST_1.42.0.tar.gz' Content type 'application/gzip' length 22412 bytes (21 KB) ================================================== downloaded 21 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/S4Vectors_0.40.2.tar.gz' Content type 'application/gzip' length 838187 bytes (818 KB) ================================================== downloaded 818 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/IRanges_2.36.0.tar.gz' Content type 'application/gzip' length 481055 bytes (469 KB) ================================================== downloaded 469 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/AnnotationDbi_1.64.1.tar.gz' Content type 'application/gzip' length 4359564 bytes (4.2 MB) ================================================== downloaded 4.2 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/annotate_1.80.0.tar.gz' Content type 'application/gzip' length 1497628 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GSEABase_1.64.0.tar.gz' Content type 'application/gzip' length 299035 bytes (292 KB) ================================================== downloaded 292 KB * installing *source* package ‘S4Vectors’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c AEbufs.c -o AEbufs.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c DataFrame_class.c -o DataFrame_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Hits_class.c -o Hits_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c LLint_class.c -o LLint_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c List_class.c -o List_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Rle_class.c -o Rle_class.o Rle_class.c: In function ‘_subset_Rle_by_ranges’: Rle_class.c:1136:17: error: format not a string literal and no format arguments [-Werror=format-security] 1136 | error(errmsg); | ^~~~~ Rle_class.c: In function ‘_subset_Rle_by_positions’: Rle_class.c:1161:17: error: format not a string literal and no format arguments [-Werror=format-security] 1161 | error(errmsg); | ^~~~~ Rle_class.c: In function ‘Rle_extract_range’: Rle_class.c:1190:17: error: format not a string literal and no format arguments [-Werror=format-security] 1190 | error(errmsg); | ^~~~~ cc1: some warnings being treated as errors make: *** [/usr/lib/R/etc/Makeconf:195: Rle_class.o] Error 1 ERROR: compilation failed for package ‘S4Vectors’ * removing ‘/home/omnipath/local/R/4.4-3.20/S4Vectors’ ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’ * removing ‘/home/omnipath/local/R/4.4-3.20/IRanges’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘GenomeInfoDb’ * removing ‘/home/omnipath/local/R/4.4-3.20/GenomeInfoDb’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘XVector’ * removing ‘/home/omnipath/local/R/4.4-3.20/XVector’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘GenomeInfoDb’ are not available for package ‘Biostrings’ * removing ‘/home/omnipath/local/R/4.4-3.20/Biostrings’ ERROR: dependency ‘Biostrings’ is not available for package ‘KEGGREST’ * removing ‘/home/omnipath/local/R/4.4-3.20/KEGGREST’ ERROR: dependencies ‘IRanges’, ‘S4Vectors’, ‘KEGGREST’ are not available for package ‘AnnotationDbi’ * removing ‘/home/omnipath/local/R/4.4-3.20/AnnotationDbi’ ERROR: dependency ‘AnnotationDbi’ is not available for package ‘annotate’ * removing ‘/home/omnipath/local/R/4.4-3.20/annotate’ ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘GSEABase’ * removing ‘/home/omnipath/local/R/4.4-3.20/GSEABase’ The downloaded source packages are in ‘/tmp/RtmpenzDmD/downloaded_packages’ ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpenzDmD/remotes17d573398f7a50/saezlab-cosmosR-81d1a7f/DESCRIPTION’ ... OK * preparing ‘cosmosR’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘cosmosR_1.9.1.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘cosmosR/vignettes/net_compr_MOON_files/figure-markdown_strict/extract_subnetwork_from_scored_MOON_network_1.png’ ERROR: dependency ‘GSEABase’ is not available for package ‘cosmosR’ * removing ‘/home/omnipath/local/R/4.4-3.20/cosmosR’ Downloading git repo https://git.bioconductor.org/packages/limma.git '/usr/bin/git' clone --depth 1 --no-hardlinks https://git.bioconductor.org/packages/limma.git /tmp/RtmpenzDmD/file17d5737d94a0cf Cloning into '/tmp/RtmpenzDmD/file17d5737d94a0cf'... ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpenzDmD/file17d5737d94a0cf/DESCRIPTION’ ... OK * preparing ‘limma’: * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘limma_3.63.1.tar.gz’ * installing *source* package ‘limma’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c normexp.c -o normexp.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c weighted_lowess.c -o weighted_lowess.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o limma.so init.o normexp.o weighted_lowess.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-limma/00new/limma/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (limma) There were 43 warnings (use warnings() to see them) [ Finished: 2024-11-04 13:18:27 CET ]