[ Started: 2024-04-07 16:57:12 CEST ] [ CARNIVAL v2.7.2 for BioC-3.19 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.19" [3] "/home/omnipath/local/R/4.4" "/opt/R-alpha/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/knitr_1.46.tar.gz' Content type 'application/x-gzip' length 471553 bytes (460 KB) ================================================== downloaded 460 KB * installing *source* package ‘knitr’ ... ** package ‘knitr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** 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 (knitr) The downloaded source packages are in ‘/tmp/Rtmp1GznYu/downloaded_packages’ Warning message: package ‘remotes’ was built under R version 4.5.0 Warning message: package ‘BiocManager’ was built under R version 4.5.0 Bioconductor version 3.19 (BiocManager 1.30.22), R 4.4.0 alpha (2024-04-04 r86334) Old packages: 'AnnotationHub', 'GenomeInfoDb', 'S4Vectors', 'SpatialExperiment', 'wppi' also installing the dependency ‘UCSC.utils’ trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/UCSC.utils_0.99.5.tar.gz' Content type 'application/x-gzip' length 235727 bytes (230 KB) ================================================== downloaded 230 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/AnnotationHub_3.11.4.tar.gz' Content type 'application/x-gzip' length 997488 bytes (974 KB) ================================================== downloaded 974 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/GenomeInfoDb_1.39.12.tar.gz' Content type 'application/x-gzip' length 3582169 bytes (3.4 MB) ================================================== downloaded 3.4 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/S4Vectors_0.41.6.tar.gz' Content type 'application/x-gzip' length 881795 bytes (861 KB) ================================================== downloaded 861 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/SpatialExperiment_1.13.2.tar.gz' Content type 'application/x-gzip' length 5406891 bytes (5.2 MB) ================================================== downloaded 5.2 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/wppi_1.11.0.tar.gz' Content type 'application/x-gzip' length 662120 bytes (646 KB) ================================================== downloaded 646 KB * installing *source* package ‘S4Vectors’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c AEbufs.c -o AEbufs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c DataFrame_class.c -o DataFrame_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Hits_class.c -o Hits_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c LLint_class.c -o LLint_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c List_class.c -o List_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rle_class.c -o Rle_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rle_utils.c -o Rle_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SEXP_utils.c -o SEXP_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SimpleList_class.c -o SimpleList_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c anyMissing.c -o anyMissing.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c character_utils.c -o character_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c eval_utils.c -o eval_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c hash_utils.c -o hash_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c integer_utils.c -o integer_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c logical_utils.c -o logical_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c map_ranges_to_runs.c -o map_ranges_to_runs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c raw_utils.c -o raw_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c safe_arithm.c -o safe_arithm.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sort_utils.c -o sort_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c subsetting_utils.c -o subsetting_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c vector_utils.c -o vector_utils.o gcc -shared -L/usr/local/lib -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-S4Vectors/00new/S4Vectors/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning message: package ‘BiocGenerics’ was built under R version 4.5.0 in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List” Creating a new generic function for ‘unname’ in package ‘S4Vectors’ Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’ Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’ Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame” Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table” Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (S4Vectors) * installing *source* package ‘wppi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2024-04-07 16:57:42] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-04-07 16:57:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-07 16:57:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:42] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-04-07 16:57:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-07 16:57:42] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-04-07 16:57:42] [TRACE] [OmnipathR] Contains 1 files. [2024-04-07 16:57:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-07 16:57:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-07 16:57:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-04-07 16:57:42] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-04-07 16:57:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-07 16:57:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-07 16:57:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-07 16:57:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-07 16:57:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:42] [TRACE] [OmnipathR] Cache locked: FALSE Note: wrong number of arguments to '/' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-04-07 16:57:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-07 16:57:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:44] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-04-07 16:57:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-07 16:57:44] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-04-07 16:57:44] [TRACE] [OmnipathR] Contains 1 files. [2024-04-07 16:57:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-07 16:57:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-07 16:57:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-04-07 16:57:44] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-04-07 16:57:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-07 16:57:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-07 16:57:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-07 16:57:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-07 16:57:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:44] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-04-07 16:57:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-07 16:57:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:46] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-04-07 16:57:46] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-07 16:57:46] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-04-07 16:57:46] [TRACE] [OmnipathR] Contains 1 files. [2024-04-07 16:57:46] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-07 16:57:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-07 16:57:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-04-07 16:57:46] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-04-07 16:57:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-07 16:57:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-07 16:57:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-07 16:57:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-07 16:57:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-07 16:57:46] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) * installing *source* package ‘UCSC.utils’ ... ** 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 (UCSC.utils) * installing *source* package ‘AnnotationHub’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: package ‘BiocGenerics’ was built under R version 4.5.0 2: package ‘BiocFileCache’ was built under R version 4.5.0 3: package ‘dbplyr’ was built under R version 4.5.0 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘BiocFileCache’ was built under R version 4.5.0 Warning: package ‘dbplyr’ was built under R version 4.5.0 ** testing if installed package can be loaded from final location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘BiocFileCache’ was built under R version 4.5.0 Warning: package ‘dbplyr’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (AnnotationHub) * installing *source* package ‘SpatialExperiment’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: package ‘SingleCellExperiment’ was built under R version 4.5.0 2: package ‘SummarizedExperiment’ was built under R version 4.5.0 3: package ‘MatrixGenerics’ was built under R version 4.5.0 4: package ‘matrixStats’ was built under R version 4.5.0 5: package ‘GenomicRanges’ was built under R version 4.5.0 6: package ‘BiocGenerics’ was built under R version 4.5.0 7: package ‘IRanges’ was built under R version 4.5.0 8: package ‘Biobase’ was built under R version 4.5.0 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: package ‘SingleCellExperiment’ was built under R version 4.5.0 Warning: package ‘SummarizedExperiment’ was built under R version 4.5.0 Warning: package ‘MatrixGenerics’ was built under R version 4.5.0 Warning: package ‘matrixStats’ was built under R version 4.5.0 Warning: package ‘GenomicRanges’ was built under R version 4.5.0 Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 Warning: package ‘Biobase’ was built under R version 4.5.0 ** testing if installed package can be loaded from final location Warning: package ‘SingleCellExperiment’ was built under R version 4.5.0 Warning: package ‘SummarizedExperiment’ was built under R version 4.5.0 Warning: package ‘MatrixGenerics’ was built under R version 4.5.0 Warning: package ‘matrixStats’ was built under R version 4.5.0 Warning: package ‘GenomicRanges’ was built under R version 4.5.0 Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 Warning: package ‘Biobase’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (SpatialExperiment) * installing *source* package ‘GenomeInfoDb’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: package ‘BiocGenerics’ was built under R version 4.5.0 2: package ‘IRanges’ was built under R version 4.5.0 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 ** testing if installed package can be loaded from final location Warning: package ‘BiocGenerics’ was built under R version 4.5.0 Warning: package ‘IRanges’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (GenomeInfoDb) The downloaded source packages are in ‘/tmp/Rtmp1GznYu/downloaded_packages’ Bioconductor version 3.19 (BiocManager 1.30.22), R 4.4.0 alpha (2024-04-04 r86334) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 1 packages ahead of CRAN: BiocStyle [ Finished: 2024-04-07 16:58:27 CEST ]