[ Started: 2025-02-22 00:05:09 CET ] [ CARNIVAL v2.7.2 for BioC-3.21 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.5-3.21" [3] "/home/omnipath/local/R/4.5" "/opt/R-devel/lib/R/library" Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Old packages: 'BiocCheck', 'processx', 'wppi' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/BiocCheck_1.43.11.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/processx_3.8.6.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.15.0.tar.gz' * installing *source* package ‘BiocCheck’ ... ** this is package ‘BiocCheck’ version ‘1.43.11’ ** 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 (BiocCheck) * installing *source* package ‘processx’ ... ** this is package ‘processx’ version ‘3.8.6’ ** package ‘processx’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -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 -g -O2 -L/usr/local/lib -I../inst/include -Wall tools/sock.c -o tools/sock gcc -g -O2 -L/usr/local/lib supervisor/supervisor.c \ supervisor/utils.c -o supervisor/supervisor gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c base64.c -o base64.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c client.c -o client.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c errors.c -o errors.o gcc -shared -L/usr/local/lib -o client.so base64.o client.o errors.o \ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c poll.c -o poll.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c processx-connection.c -o processx-connection.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c processx-vector.c -o processx-vector.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c create-time.c -o create-time.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/childlist.c -o unix/childlist.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/connection.c -o unix/connection.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/processx.c -o unix/processx.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/sigchld.c -o unix/sigchld.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c unix/utils.c -o unix/utils.o gcc -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 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c cleancall.c -o cleancall.o gcc -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/4.5-3.21/00LOCK-processx/00new/processx ** R ** inst ** byte-compile and prepare package for lazy loading R6Class process: finalize() method is public, but it should be private as of R6 2.4.0. This code will continue to work, but in a future version of R6, finalize() will be required to be private. ** 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 ‘1.15.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2025-02-22 00:05:27] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-02-22 00:05:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-22 00:05:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:27] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-22 00:05:27] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 00:14:46 UTC; omnipath [2025-02-22 00:05:27] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-22 00:05:27] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 00:14:47 UTC; unix [2025-02-22 00:05:27] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-22 00:05:27] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-22 00:05:27] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-22 00:05:27] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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] [2025-02-22 00:05:27] [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 [2025-02-22 00:05:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-22 00:05:27] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-22 00:05:27] [TRACE] [OmnipathR] Contains 1 files. [2025-02-22 00:05:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-22 00:05:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-22 00:05:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-22 00:05:27] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-22 00:05:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-22 00:05:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-22 00:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-22 00:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-22 00:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:28] [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 [2025-02-22 00:05:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-22 00:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:30] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-22 00:05:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 00:14:46 UTC; omnipath [2025-02-22 00:05:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-22 00:05:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 00:14:47 UTC; unix [2025-02-22 00:05:30] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-22 00:05:30] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-22 00:05:30] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-22 00:05:30] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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] [2025-02-22 00:05:30] [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 [2025-02-22 00:05:30] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-22 00:05:30] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-22 00:05:30] [TRACE] [OmnipathR] Contains 1 files. [2025-02-22 00:05:30] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-22 00:05:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-22 00:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-22 00:05:30] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-22 00:05:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-22 00:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-22 00:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-22 00:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-22 00:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:31] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-02-22 00:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-22 00:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:33] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-22 00:05:33] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 00:14:46 UTC; omnipath [2025-02-22 00:05:33] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-22 00:05:33] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 00:14:47 UTC; unix [2025-02-22 00:05:33] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-22 00:05:33] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-22 00:05:33] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-22; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-22 00:05:33] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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] [2025-02-22 00:05:33] [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 [2025-02-22 00:05:33] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-22 00:05:33] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-22 00:05:33] [TRACE] [OmnipathR] Contains 1 files. [2025-02-22 00:05:33] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-22 00:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-22 00:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-22 00:05:33] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-22 00:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-22 00:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-22 00:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-22 00:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-22 00:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-22 00:05:33] [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/Rtmptlcyui/downloaded_packages’ Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) 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: processx [ Finished: 2025-02-22 00:05:36 CET ]