[ Started: 2025-02-13 18:42:56 CET ]
[ CARNIVAL v2.16.0 for BioC-3.20 from https://git.bioconductor.org/packages/CARNIVAL@RELEASE_3_20 (a7305b3 2024-10-29 10:46:30) ]
[1] "Libraries: " "/home/omnipath/local/R/4.4-3.20"
[3] "/home/omnipath/local/R/4.4" "/usr/lib/R/library"
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
Old packages: 'cli', 'wppi'
trying URL 'https://cloud.r-project.org/src/contrib/cli_3.6.4.tar.gz'
Content type 'application/x-gzip' length 637550 bytes (622 KB)
==================================================
downloaded 622 KB
trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/wppi_1.14.0.tar.gz'
Content type 'application/x-gzip' length 663228 bytes (647 KB)
==================================================
downloaded 647 KB
* installing *source* package ‘cli’ ...
** package ‘cli’ 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"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c ansi.c -o ansi.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c cleancall.c -o cleancall.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c diff.c -o diff.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c errors.c -o errors.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c glue.c -o glue.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c init.c -o init.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c inst.c -o inst.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c keypress-unix.c -o keypress-unix.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c keypress-win.c -o keypress-win.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c keypress.c -o keypress.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c md5.c -o md5.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c progress-altrep.c -o progress-altrep.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c progress.c -o progress.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c sha1.c -o sha1.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c sha256.c -o sha256.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c thread.c -o thread.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c tty.c -o tty.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c utf8.c -o utf8.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c utils.c -o utils.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c vt.c -o vt.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c vtparse.c -o vtparse.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c vtparse_table.c -o vtparse_table.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c win-utf8.c -o win-utf8.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c winfiles.c -o winfiles.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c xxhash.c -o xxhash.o
gcc -I"/usr/share/R/include" -DNDEBUG -fvisibility=hidden -I../inst/include -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c xxhash2.c -o xxhash2.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o cli.so ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o xxhash.o xxhash2.o -lpthread -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.4-3.20/00LOCK-cli/00new/cli/libs
** R
** exec
** 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 (cli)
* installing *source* package ‘wppi’ ...
** package ‘wppi’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2025-02-13 18:43:12] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-02-13 18:43:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-13 18:43:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:12] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-13 18:43:12] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-12 19:04:41 UTC; omnipath
[2025-02-13 18:43:12] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-13 18:43:12] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.4.1; ; 2025-02-12 19:04:42 UTC; unix
[2025-02-13 18:43:12] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.8
[2025-02-13 18:43:12] [INFO] [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-13 18:43:12] [INFO] [OmnipathR] Session info: [version=R version 4.4.1 (2024-06-14); 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=2025-02-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-13 18:43:12] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-13 18:43:12] [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
[2025-02-13 18:43:12] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-13 18:43:12] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-13 18:43:12] [TRACE] [OmnipathR] Contains 1 files.
[2025-02-13 18:43:12] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-13 18:43:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-13 18:43:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-13 18:43:12] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-13 18:43:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-13 18:43:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-13 18:43:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-13 18:43:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-13 18:43:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:12] [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
[2025-02-13 18:43:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-13 18:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:15] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-13 18:43:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-12 19:04:41 UTC; omnipath
[2025-02-13 18:43:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-13 18:43:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.4.1; ; 2025-02-12 19:04:42 UTC; unix
[2025-02-13 18:43:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.8
[2025-02-13 18:43:15] [INFO] [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-13 18:43:15] [INFO] [OmnipathR] Session info: [version=R version 4.4.1 (2024-06-14); 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=2025-02-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-13 18:43:15] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-13 18:43:15] [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
[2025-02-13 18:43:15] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-13 18:43:15] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-13 18:43:15] [TRACE] [OmnipathR] Contains 1 files.
[2025-02-13 18:43:15] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-13 18:43:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-13 18:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-13 18:43:15] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-13 18:43:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-13 18:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-13 18:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-13 18:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-13 18:43:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:15] [TRACE] [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-02-13 18:43:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-13 18:43:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:17] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-13 18:43:17] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-12 19:04:41 UTC; omnipath
[2025-02-13 18:43:17] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-13 18:43:17] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.4.1; ; 2025-02-12 19:04:42 UTC; unix
[2025-02-13 18:43:17] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.8
[2025-02-13 18:43:17] [INFO] [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-13 18:43:18] [INFO] [OmnipathR] Session info: [version=R version 4.4.1 (2024-06-14); 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=2025-02-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-13 18:43:18] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-13 18:43:18] [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
[2025-02-13 18:43:18] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-13 18:43:18] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-13 18:43:18] [TRACE] [OmnipathR] Contains 1 files.
[2025-02-13 18:43:18] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-13 18:43:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-13 18:43:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-13 18:43:18] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-13 18:43:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-13 18:43:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-13 18:43:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-13 18:43:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-13 18:43:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 18:43:18] [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/RtmpiT2eUl/downloaded_packages’
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
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: cli, BiocStyle
[ Finished: 2025-02-13 18:43:24 CET ]