[ Started: 2025-05-01 22:25:10 CEST ] [ 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/reformulas_0.4.1.tar.gz' Content type 'application/x-gzip' length 75934 bytes (74 KB) ================================================== downloaded 74 KB * installing *source* package ‘reformulas’ ... ** this is package ‘reformulas’ version ‘0.4.1’ ** package ‘reformulas’ 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 (reformulas) The downloaded source packages are in ‘/tmp/RtmpQ6j6bz/downloaded_packages’ Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Old packages: 'enrichplot', 'SummarizedExperiment', 'textshaping', 'utf8', 'wppi' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/enrichplot_1.28.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/SummarizedExperiment_1.38.1.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/textshaping_1.0.1.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/utf8_1.2.5.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.16.0.tar.gz' * installing *source* package ‘enrichplot’ ... ** this is package ‘enrichplot’ version ‘1.28.1’ ** 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 (enrichplot) * installing *source* package ‘SummarizedExperiment’ ... ** this is package ‘SummarizedExperiment’ version ‘1.38.1’ ** 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 (SummarizedExperiment) * installing *source* package ‘textshaping’ ... ** this is package ‘textshaping’ version ‘1.0.1’ ** package ‘textshaping’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi Using PKG_LIBS=-lharfbuzz -lfreetype -lfribidi ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ rm -f textshaping.so cpp11.o face_feature.o hb_shaper.o init.o string_bidi.o string_metrics.o string_shape.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -DNDEBUG -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I'/home/omnipath/local/R/4.5-3.21/systemfonts/include' -I/usr/local/include -fpic -g -O2 -c cpp11.cpp -o cpp11.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -DNDEBUG -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I'/home/omnipath/local/R/4.5-3.21/systemfonts/include' -I/usr/local/include -fpic -g -O2 -c face_feature.cpp -o face_feature.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -DNDEBUG -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I'/home/omnipath/local/R/4.5-3.21/systemfonts/include' -I/usr/local/include -fpic -g -O2 -c hb_shaper.cpp -o hb_shaper.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -DNDEBUG -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I'/home/omnipath/local/R/4.5-3.21/systemfonts/include' -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -DNDEBUG -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I'/home/omnipath/local/R/4.5-3.21/systemfonts/include' -I/usr/local/include -fpic -g -O2 -c string_bidi.cpp -o string_bidi.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -DNDEBUG -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I'/home/omnipath/local/R/4.5-3.21/systemfonts/include' -I/usr/local/include -fpic -g -O2 -c string_metrics.cpp -o string_metrics.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -DNDEBUG -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/fribidi -I'/home/omnipath/local/R/4.5-3.21/cpp11/include' -I'/home/omnipath/local/R/4.5-3.21/systemfonts/include' -I/usr/local/include -fpic -g -O2 -c string_shape.cpp -o string_shape.o g++ -std=gnu++17 -shared -L/usr/local/lib -o textshaping.so cpp11.o face_feature.o hb_shaper.o init.o string_bidi.o string_metrics.o string_shape.o -lharfbuzz -lfreetype -lfribidi installing to /home/omnipath/local/R/4.5-3.21/00LOCK-textshaping/00new/textshaping/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (textshaping) * installing *source* package ‘utf8’ ... ** this is package ‘utf8’ version ‘1.2.5’ ** package ‘utf8’ 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 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c as_utf8.c -o as_utf8.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c bytes.c -o bytes.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c context.c -o context.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c render.c -o render.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c render_table.c -o render_table.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c string.c -o string.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c text.c -o text.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8_encode.c -o utf8_encode.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8_format.c -o utf8_format.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8_normalize.c -o utf8_normalize.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8_valid.c -o utf8_valid.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8_width.c -o utf8_width.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c util.c -o util.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/array.c -o utf8lite/src/array.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/char.c -o utf8lite/src/char.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/encode.c -o utf8lite/src/encode.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/error.c -o utf8lite/src/error.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/escape.c -o utf8lite/src/escape.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/graph.c -o utf8lite/src/graph.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/graphscan.c -o utf8lite/src/graphscan.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/normalize.c -o utf8lite/src/normalize.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/render.c -o utf8lite/src/render.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/text.c -o utf8lite/src/text.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/textassign.c -o utf8lite/src/textassign.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/textiter.c -o utf8lite/src/textiter.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -c utf8lite/src/textmap.c -o utf8lite/src/textmap.o ar rcs libcutf8lite.a utf8lite/src/array.o utf8lite/src/char.o utf8lite/src/encode.o utf8lite/src/error.o utf8lite/src/escape.o utf8lite/src/graph.o utf8lite/src/graphscan.o utf8lite/src/normalize.o utf8lite/src/render.o utf8lite/src/text.o utf8lite/src/textassign.o utf8lite/src/textiter.o utf8lite/src/textmap.o gcc -shared -L/usr/local/lib -o utf8.so as_utf8.o bytes.o context.o init.o render.o render_table.o string.o text.o utf8_encode.o utf8_format.o utf8_normalize.o utf8_valid.o utf8_width.o util.o -L. -lcutf8lite installing to /home/omnipath/local/R/4.5-3.21/00LOCK-utf8/00new/utf8/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 (utf8) * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.16.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2025-05-01 22:26:12] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-05-01 22:26:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-01 22:26:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:12] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-05-01 22:26:12] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 22:40:50 UTC; biocbuild [2025-05-01 22:26:12] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16 [2025-05-01 22:26:12] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-30 21:34:50 UTC; unix [2025-05-01 22:26:12] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-05-01 22:26:12] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-05-01 22:26:12] [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=2025-05-01; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-05-01 22:26:12] [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] [2025-05-01 22:26:12] [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 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-16); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-04-15); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-05-01 22:26:12] [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 [2025-05-01 22:26:12] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-05-01 22:26:12] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-05-01 22:26:12] [TRACE] [OmnipathR] Contains 1 files. [2025-05-01 22:26:12] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-05-01 22:26:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-01 22:26:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-05-01 22:26:12] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-05-01 22:26:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-05-01 22:26:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-05-01 22:26:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-05-01 22:26:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-05-01 22:26:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:12] [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 [2025-05-01 22:26:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-01 22:26:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:15] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-05-01 22:26:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 22:40:50 UTC; biocbuild [2025-05-01 22:26:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16 [2025-05-01 22:26:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-30 21:34:50 UTC; unix [2025-05-01 22:26:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-05-01 22:26:15] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-05-01 22:26:15] [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=2025-05-01; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-05-01 22:26:15] [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] [2025-05-01 22:26:15] [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 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-16); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-04-15); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-05-01 22:26:15] [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 [2025-05-01 22:26:15] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-05-01 22:26:15] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-05-01 22:26:15] [TRACE] [OmnipathR] Contains 1 files. [2025-05-01 22:26:15] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-05-01 22:26:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-01 22:26:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-05-01 22:26:15] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-05-01 22:26:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-05-01 22:26:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-05-01 22:26:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-05-01 22:26:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-05-01 22:26:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:15] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-05-01 22:26:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-01 22:26:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:17] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-05-01 22:26:17] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 22:40:50 UTC; biocbuild [2025-05-01 22:26:17] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16 [2025-05-01 22:26:17] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-30 21:34:50 UTC; unix [2025-05-01 22:26:17] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-05-01 22:26:17] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-05-01 22:26:17] [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=2025-05-01; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-05-01 22:26:17] [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] [2025-05-01 22:26:18] [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 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-16); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-04-15); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-05-01 22:26:18] [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 [2025-05-01 22:26:18] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-05-01 22:26:18] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-05-01 22:26:18] [TRACE] [OmnipathR] Contains 1 files. [2025-05-01 22:26:18] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-05-01 22:26:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-01 22:26:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-05-01 22:26:18] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-05-01 22:26:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-05-01 22:26:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-05-01 22:26:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-05-01 22:26:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-05-01 22:26:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-01 22:26:18] [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/RtmpQ6j6bz/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: utf8 [ Finished: 2025-05-01 22:26:21 CEST ]