[ Started: 2024-11-01 13:06:22 CET ] [ cosmosR v1.9.1 for BioC-3.20 from https://github.com/saezlab/cosmosR@master (81d1a7f 2024-07-23 10:15:19) ] [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: 'OmnipathR' 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 ‘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 [2024-11-01 13:06:36] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-11-01 13:06:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-01 13:06:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-01 13:06:36] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-01 13:06:36] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-01 13:06:36] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-01 13:06:36] [TRACE] [OmnipathR] Contains 1 files. [2024-11-01 13:06:36] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-01 13:06:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-01 13:06:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-01 13:06:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-01 13:06:36] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-01 13:06:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-01 13:06:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-01 13:06:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-01 13:06:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-01 13:06:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-01 13:06:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-01 13:06:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-01 13:06:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-01 13:06:36] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-11-01 13:06:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-01 13:06:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-01 13:06:38] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-11-01 13:06:38] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-01 13:06:38] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-11-01 13:06:38] [TRACE] [OmnipathR] Contains 1 files. [2024-11-01 13:06:38] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-01 13:06:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-01 13:06:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-01 13:06:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-11-01 13:06:38] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2024-11-01 13:06:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-01 13:06:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-01 13:06:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-01 13:06:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-01 13:06:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-01 13:06:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-01 13:06:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-01 13:06:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-01 13:06:38] [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/Rtmpam5Hsi/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' 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 14 packages ahead of CRAN: BiocParallel, limma, BiocGenerics, zlibbioc, GenomeInfoDbData, Biobase, fgsea, marray, graph, decoupleR, bcellViper, piano, 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/Rtmpam5Hsi/downloaded_packages’ Warning messages: 1: In i.p(...) : installation of package ‘S4Vectors’ had non-zero exit status 2: In i.p(...) : installation of package ‘IRanges’ had non-zero exit status 3: In i.p(...) : installation of package ‘GenomeInfoDb’ had non-zero exit status 4: In i.p(...) : installation of package ‘XVector’ had non-zero exit status 5: In i.p(...) : installation of package ‘Biostrings’ had non-zero exit status 6: In i.p(...) : installation of package ‘KEGGREST’ had non-zero exit status 7: In i.p(...) : installation of package ‘AnnotationDbi’ had non-zero exit status 8: In i.p(...) : installation of package ‘annotate’ had non-zero exit status 9: In i.p(...) : installation of package ‘GSEABase’ had non-zero exit status [ Finished: 2024-11-01 13:06:58 CET ]