[ Started: 2026-04-06 20:24:12 CEST ] [ CARNIVAL v2.5.1 for BioC-3.23 from https://github.com/saezlab/CARNIVAL@dev (81a0120 2022-03-17 09:59:10) ] [1] "Libraries: " "/home/omnipath/local/R/4.6-3.23" [3] "/home/omnipath/local/R/4.6" "/opt/R-devel/lib/R/library" Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable) (2026-03-23 r89685) Old packages: 'rlang', 'S4Vectors', 'scuttle', 'wppi' trying URL 'https://cloud.r-project.org/src/contrib/rlang_1.2.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/S4Vectors_0.49.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/scuttle_1.21.2.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/wppi_1.19.0.tar.gz' * installing *source* package ‘rlang’ ... ** this is package ‘rlang’ version ‘1.2.0’ ** package ‘rlang’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c capture.c -o capture.o touch internal.c gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c internal.c -o internal.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c rlang.c -o rlang.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./rlang/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c version.c -o version.o gcc -std=gnu2x -shared -L/usr/local/lib -o rlang.so capture.o internal.o rlang.o version.o installing to /home/omnipath/local/R/4.6-3.23/00LOCK-rlang/00new/rlang/libs ** R ** inst ** 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 ** 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 (rlang) * installing *source* package ‘S4Vectors’ ... ** this is package ‘S4Vectors’ version ‘0.49.1’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c AEbufs.c -o AEbufs.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c DFrame_class.c -o DFrame_class.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Hits_class.c -o Hits_class.o In file included from /usr/include/string.h:548, from /opt/R-devel/lib/R/include/R_ext/RS.h:34, from /opt/R-devel/lib/R/include/Rdefines.h:38, from ../inst/include/S4Vectors_defines.h:18, from S4Vectors.h:1, from Hits_class.c:4: In function ‘memcpy’, inlined from ‘tsort_hits’ at Hits_class.c:113:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:10: warning: ‘__builtin_memcpy’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c LLint_class.c -o LLint_class.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c List_class.c -o List_class.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rle_class.c -o Rle_class.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rle_utils.c -o Rle_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SEXP_utils.c -o SEXP_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SimpleList_class.c -o SimpleList_class.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c character_utils.c -o character_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c eval_utils.c -o eval_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c hash_utils.c -o hash_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c integer_utils.c -o integer_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c logical_utils.c -o logical_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c map_ranges_to_runs.c -o map_ranges_to_runs.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c raw_utils.c -o raw_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c safe_arithm.c -o safe_arithm.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sort_utils.c -o sort_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c subsetting_utils.c -o subsetting_utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c vector_utils.c -o vector_utils.o gcc -std=gnu2x -shared -L/usr/local/lib -o S4Vectors.so AEbufs.o DFrame_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 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/4.6-3.23/00LOCK-S4Vectors/00new/S4Vectors/libs ** R ** inst ** byte-compile and prepare package for lazy loading 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’ 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 ** 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 (S4Vectors) * installing *source* package ‘scuttle’ ... ** this is package ‘scuttle’ version ‘1.21.2’ ** using staged installation ** libs specified C++17 using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ using C++17 g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/Rcpp/include' -I'/home/omnipath/local/R/4.6-3.23/beachmat/include' -I'/home/omnipath/local/R/4.6-3.23/assorthead/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/Rcpp/include' -I'/home/omnipath/local/R/4.6-3.23/beachmat/include' -I'/home/omnipath/local/R/4.6-3.23/assorthead/include' -I/usr/local/include -fpic -g -O2 -c cumulative_prop.cpp -o cumulative_prop.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/Rcpp/include' -I'/home/omnipath/local/R/4.6-3.23/beachmat/include' -I'/home/omnipath/local/R/4.6-3.23/assorthead/include' -I/usr/local/include -fpic -g -O2 -c downsample_counts.cpp -o downsample_counts.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/Rcpp/include' -I'/home/omnipath/local/R/4.6-3.23/beachmat/include' -I'/home/omnipath/local/R/4.6-3.23/assorthead/include' -I/usr/local/include -fpic -g -O2 -c fit_linear_model.cpp -o fit_linear_model.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/Rcpp/include' -I'/home/omnipath/local/R/4.6-3.23/beachmat/include' -I'/home/omnipath/local/R/4.6-3.23/assorthead/include' -I/usr/local/include -fpic -g -O2 -c pool_size_factors.cpp -o pool_size_factors.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/Rcpp/include' -I'/home/omnipath/local/R/4.6-3.23/beachmat/include' -I'/home/omnipath/local/R/4.6-3.23/assorthead/include' -I/usr/local/include -fpic -g -O2 -c sparse_summarize.cpp -o sparse_summarize.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/Rcpp/include' -I'/home/omnipath/local/R/4.6-3.23/beachmat/include' -I'/home/omnipath/local/R/4.6-3.23/assorthead/include' -I/usr/local/include -fpic -g -O2 -c sum_counts.cpp -o sum_counts.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/Rcpp/include' -I'/home/omnipath/local/R/4.6-3.23/beachmat/include' -I'/home/omnipath/local/R/4.6-3.23/assorthead/include' -I/usr/local/include -fpic -g -O2 -c utils.cpp -o utils.o g++ -std=gnu++17 -shared -L/usr/local/lib -o scuttle.so RcppExports.o cumulative_prop.o downsample_counts.o fit_linear_model.o pool_size_factors.o sparse_summarize.o sum_counts.o utils.o -llapack -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.6-3.23/00LOCK-scuttle/00new/scuttle/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 (scuttle) * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.19.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2026-04-06 20:25:33] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. 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[2026-04-06 20:25:33] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-05 20:03:20 UTC; omnipath [2026-04-06 20:25:33] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-06 20:25:33] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-05 20:03:22 UTC; unix [2026-04-06 20:25:33] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.11 [2026-04-06 20:25:33] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-06 20:25:34] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-06; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-06 20:25:34] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-06 20:25:34] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.11(2026-04-05); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); wppi 1.19.0(2025-11-18); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-04-06 20:25:34] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-06 20:25:34] [TRACE] [OmnipathR] Running on a build server, wiping cache. 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[2026-04-06 20:25:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-06 20:25:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-06 20:25:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:34] [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 [2026-04-06 20:25:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-06 20:25:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:36] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-06 20:25:36] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-05 20:03:20 UTC; omnipath [2026-04-06 20:25:36] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-06 20:25:36] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-05 20:03:22 UTC; unix [2026-04-06 20:25:36] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.11 [2026-04-06 20:25:36] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-06 20:25:37] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-06; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-06 20:25:37] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-06 20:25:37] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.11(2026-04-05); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); wppi 1.19.0(2025-11-18); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-04-06 20:25:37] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-06 20:25:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-06 20:25:37] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-06 20:25:37] [TRACE] [OmnipathR] Contains 1 files. [2026-04-06 20:25:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-06 20:25:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-06 20:25:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-06 20:25:37] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-06 20:25:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-06 20:25:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-06 20:25:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-06 20:25:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-06 20:25:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:37] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-04-06 20:25:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-06 20:25:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:39] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-06 20:25:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-04-05 20:03:20 UTC; omnipath [2026-04-06 20:25:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-06 20:25:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-05 20:03:22 UTC; unix [2026-04-06 20:25:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.11 [2026-04-06 20:25:39] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-06 20:25:39] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-04-06; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-06 20:25:39] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-04-06 20:25:40] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.11(2026-04-05); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); wppi 1.19.0(2025-11-18); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-04-06 20:25:40] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-04-06 20:25:40] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-06 20:25:40] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-06 20:25:40] [TRACE] [OmnipathR] Contains 1 files. [2026-04-06 20:25:40] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-06 20:25:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-06 20:25:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-06 20:25:40] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-06 20:25:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-06 20:25:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-06 20:25:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-06 20:25:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-06 20:25:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-06 20:25:40] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) The downloaded source packages are in ‘/tmp/RtmpdixZZ6/downloaded_packages’ Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable) (2026-03-23 r89685) 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: rlang [ Finished: 2026-04-06 20:25:43 CEST ]