[ Started: 2026-04-01 20:25:13 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: 'DelayedArray', 'GSVA', 'pkgload', 'processx', 'wppi' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/DelayedArray_0.37.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/GSVA_2.5.20.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/pkgload_1.5.1.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/processx_3.8.7.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/wppi_1.19.0.tar.gz' * installing *source* package ‘DelayedArray’ ... ** this is package ‘DelayedArray’ version ‘0.37.1’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘apply’ in package ‘DelayedArray’ Creating a new generic function for ‘sweep’ in package ‘DelayedArray’ Creating a new generic function for ‘scale’ in package ‘DelayedArray’ Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qpois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’ ** 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 (DelayedArray) * installing *source* package ‘processx’ ... ** this is package ‘processx’ version ‘3.8.7’ ** package ‘processx’ 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 -g -O2 -L/usr/local/lib -Wall tools/px.c -o tools/px In file included from /usr/include/features.h:502, from /usr/include/unistd.h:25, from tools/px.c:11: In function ‘read’, inlined from ‘echo_from_fd’ at tools/px.c:93:9: /usr/include/x86_64-linux-gnu/bits/unistd.h:28:10: warning: ‘__read_alias’ specified size 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 28 | return __glibc_fortify (read, __nbytes, sizeof (char), | ^~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/unistd-decl.h: In function ‘echo_from_fd’: /usr/include/x86_64-linux-gnu/bits/unistd-decl.h:29:16: note: in a call to function ‘__read_alias’ declared with attribute ‘access (write_only, 2, 3)’ 29 | extern ssize_t __REDIRECT_FORTIFY (__read_alias, (int __fd, void *__buf, | ^~~~~~~~~~~~~~~~~~ gcc -std=gnu2x -g -O2 -L/usr/local/lib -I../inst/include -Wall tools/sock.c -o tools/sock gcc -std=gnu2x -g -O2 -L/usr/local/lib supervisor/supervisor.c \ supervisor/utils.c -o supervisor/supervisor gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c base64.c -o base64.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c client.c -o client.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c errors.c -o errors.o gcc -std=gnu2x -shared -L/usr/local/lib -o client.so base64.o client.o errors.o \ gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c poll.c -o poll.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c processx-connection.c -o processx-connection.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c processx-vector.c -o processx-vector.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c create-time.c -o create-time.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/childlist.c -o unix/childlist.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/connection.c -o unix/connection.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/processx.c -o unix/processx.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/sigchld.c -o unix/sigchld.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/utils.c -o unix/utils.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/named_pipe.c -o unix/named_pipe.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c cleancall.c -o cleancall.o gcc -std=gnu2x -shared -L/usr/local/lib -o processx.so init.o poll.o errors.o processx-connection.o processx-vector.o create-time.o base64.o unix/childlist.o unix/connection.o unix/processx.o unix/sigchld.o unix/utils.o unix/named_pipe.o cleancall.o installing via 'install.libs.R' to /home/omnipath/local/R/4.6-3.23/00LOCK-processx/00new/processx ** 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 (processx) * 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 [2026-04-01 20:25:48] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2026-04-01 20:25:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-01 20:25:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:48] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-01 20:25:48] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-31 19:48:27 UTC; omnipath [2026-04-01 20:25:48] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-01 20:25:48] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-31 19:48:29 UTC; unix [2026-04-01 20:25:48] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.11 [2026-04-01 20:25:48] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-01 20:25:48] [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=2026-04-01; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-01 20:25:48] [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] [2026-04-01 20:25:48] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); 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 1.2.0(2026-02-03); 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 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.11(2026-03-31); 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 1.1.7(2026-01-09); 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) [2026-04-01 20:25:48] [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 [2026-04-01 20:25:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-01 20:25:48] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-01 20:25:48] [TRACE] [OmnipathR] Contains 1 files. [2026-04-01 20:25:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-01 20:25:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-01 20:25:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-01 20:25:48] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-01 20:25:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-01 20:25:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-01 20:25:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-01 20:25:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-01 20:25:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:48] [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 [2026-04-01 20:25:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-01 20:25:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:51] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-01 20:25:51] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-31 19:48:27 UTC; omnipath [2026-04-01 20:25:51] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-01 20:25:51] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-31 19:48:29 UTC; unix [2026-04-01 20:25:51] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.11 [2026-04-01 20:25:51] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-01 20:25:51] [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=2026-04-01; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-01 20:25:51] [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] [2026-04-01 20:25:52] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); 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 1.2.0(2026-02-03); 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 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.11(2026-03-31); 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 1.1.7(2026-01-09); 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) [2026-04-01 20:25:52] [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 [2026-04-01 20:25:52] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-01 20:25:52] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-01 20:25:52] [TRACE] [OmnipathR] Contains 1 files. [2026-04-01 20:25:52] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-01 20:25:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-01 20:25:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-01 20:25:52] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-01 20:25:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-01 20:25:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-01 20:25:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-01 20:25:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-01 20:25:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:52] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-04-01 20:25:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-01 20:25:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:54] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-04-01 20:25:54] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-31 19:48:27 UTC; omnipath [2026-04-01 20:25:54] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-04-01 20:25:54] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-31 19:48:29 UTC; unix [2026-04-01 20:25:54] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.11 [2026-04-01 20:25:54] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-04-01 20:25:54] [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=2026-04-01; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-04-01 20:25:54] [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] [2026-04-01 20:25:54] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); 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 1.2.0(2026-02-03); 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 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.11(2026-03-31); 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 1.1.7(2026-01-09); 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) [2026-04-01 20:25:54] [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 [2026-04-01 20:25:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-01 20:25:54] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-04-01 20:25:54] [TRACE] [OmnipathR] Contains 1 files. [2026-04-01 20:25:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-01 20:25:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-01 20:25:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-04-01 20:25:54] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-04-01 20:25:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-01 20:25:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-01 20:25:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-01 20:25:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-01 20:25:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-01 20:25:55] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) * installing *source* package ‘GSVA’ ... ** this is package ‘GSVA’ version ‘2.5.20’ ** 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'/home/omnipath/local/R/4.6-3.23/cli/include' -I/usr/local/include -fpic -g -O2 -c ecdfvals.c -o ecdfvals.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/cli/include' -I/usr/local/include -fpic -g -O2 -c kcdfvals.c -o kcdfvals.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/cli/include' -I/usr/local/include -fpic -g -O2 -c kernel_estimation.c -o kernel_estimation.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/cli/include' -I/usr/local/include -fpic -g -O2 -c ks_test.c -o ks_test.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/cli/include' -I/usr/local/include -fpic -g -O2 -c register_cmethods.c -o register_cmethods.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/cli/include' -I/usr/local/include -fpic -g -O2 -c row_rngs_nzrngs.c -o row_rngs_nzrngs.o gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.6-3.23/cli/include' -I/usr/local/include -fpic -g -O2 -c utils.c -o utils.o gcc -std=gnu2x -shared -L/usr/local/lib -o GSVA.so ecdfvals.o kcdfvals.o kernel_estimation.o ks_test.o register_cmethods.o row_rngs_nzrngs.o utils.o installing to /home/omnipath/local/R/4.6-3.23/00LOCK-GSVA/00new/GSVA/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 (GSVA) * installing *source* package ‘pkgload’ ... ** this is package ‘pkgload’ version ‘1.5.1’ ** package ‘pkgload’ 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 (pkgload) The downloaded source packages are in ‘/tmp/RtmpjPm870/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 2 packages ahead of CRAN: processx, pkgload [ Finished: 2026-04-01 20:26:31 CEST ]