[ Started: 2025-02-16 00:05:10 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" trying URL 'https://cran.uni-muenster.de/src/contrib/R6_2.6.1.tar.gz' Content type 'application/x-gzip' length 64507 bytes (62 KB) ================================================== downloaded 62 KB * installing *source* package ‘R6’ ... ** this is package ‘R6’ version ‘2.6.1’ ** package ‘R6’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (R6) The downloaded source packages are in ‘/tmp/RtmpbXsVsD/downloaded_packages’ Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Old packages: 'assorthead', 'DelayedArray', 'HDF5Array', 'wppi' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/assorthead_1.1.14.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/DelayedArray_0.33.6.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/HDF5Array_1.35.13.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.15.0.tar.gz' * installing *source* package ‘assorthead’ ... ** this is package ‘assorthead’ version ‘1.1.14’ ** using staged installation ** inst ** help No man pages found in package ‘assorthead’ *** 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 (assorthead) * installing *source* package ‘DelayedArray’ ... ** this is package ‘DelayedArray’ version ‘0.33.6’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c R_init_DelayedArray.c -o R_init_DelayedArray.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c compress_atomic_vector.c -o compress_atomic_vector.o gcc -shared -L/usr/local/lib -o DelayedArray.so R_init_DelayedArray.o S4Vectors_stubs.o compress_atomic_vector.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-DelayedArray/00new/DelayedArray/libs ** 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 ** 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 (DelayedArray) * 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 [2025-02-16 00:05:42] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. 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[2025-02-16 00:05:42] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-15 00:05:22 UTC; omnipath [2025-02-16 00:05:42] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-16 00:05:42] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-15 00:05:23 UTC; unix [2025-02-16 00:05:42] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-16 00:05:42] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-16 00:05:43] [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=2025-02-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-16 00:05:43] [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] [2025-02-16 00:05:43] [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 [2025-02-16 00:05:43] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-16 00:05:43] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-16 00:05:43] [TRACE] [OmnipathR] Contains 1 files. [2025-02-16 00:05:43] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-16 00:05:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-16 00:05:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-16 00:05:43] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-16 00:05:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-16 00:05:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-16 00:05:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-16 00:05:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-16 00:05:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:43] [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 [2025-02-16 00:05:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-16 00:05:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:45] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-16 00:05:45] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-15 00:05:22 UTC; omnipath [2025-02-16 00:05:45] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-16 00:05:45] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-15 00:05:23 UTC; unix [2025-02-16 00:05:45] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-16 00:05:45] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-16 00:05:46] [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=2025-02-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-16 00:05:46] [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] [2025-02-16 00:05:46] [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 [2025-02-16 00:05:46] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-16 00:05:46] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-16 00:05:46] [TRACE] [OmnipathR] Contains 1 files. [2025-02-16 00:05:46] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-16 00:05:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-16 00:05:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-16 00:05:46] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-16 00:05:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-16 00:05:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-16 00:05:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-16 00:05:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-16 00:05:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:46] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-02-16 00:05:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-16 00:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:48] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-16 00:05:48] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-15 00:05:22 UTC; omnipath [2025-02-16 00:05:48] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-16 00:05:48] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-15 00:05:23 UTC; unix [2025-02-16 00:05:48] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-16 00:05:48] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-16 00:05:48] [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=2025-02-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-16 00:05:48] [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=8.6.14; 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] [2025-02-16 00:05:48] [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 [2025-02-16 00:05:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-16 00:05:48] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-16 00:05:48] [TRACE] [OmnipathR] Contains 1 files. [2025-02-16 00:05:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-16 00:05:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-16 00:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-16 00:05:48] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-16 00:05:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-16 00:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-16 00:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-16 00:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-16 00:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-16 00:05:48] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) * installing *source* package ‘HDF5Array’ ... ** this is package ‘HDF5Array’ version ‘1.35.13’ ** 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 (HDF5Array) The downloaded source packages are in ‘/tmp/RtmpbXsVsD/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' [ Finished: 2025-02-16 00:06:06 CET ]