[ Started: 2025-02-18 00:16:42 CET ]
[ OmnipathR v3.15.9 for BioC-3.21 from https://github.com/saezlab/OmnipathR@devel (0a92537 2025-02-13 19:46:14) ]

* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.15.9’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'download_to_cache(url_key = url_key, ': unused argument (http_param = http_param) 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:16:52] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:16:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-17 23:16:41 UTC; omnipath
[2025-02-18 00:16:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-18 00:16:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-17 23:16:42 UTC; unix
[2025-02-18 00:16:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-18 00:16:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-18 00:16:52] [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=2025-02-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-18 00:16:52] [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]
[2025-02-18 00:16:52] [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
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] Contains 45 files.
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:16:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:16:52] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-02-18 00:16:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:16:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:16:53] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:16:54] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-17 23:16:41 UTC; omnipath
[2025-02-18 00:16:54] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-18 00:16:54] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-17 23:16:42 UTC; unix
[2025-02-18 00:16:54] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-18 00:16:54] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-18 00:16:54] [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=2025-02-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-18 00:16:54] [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=8.6.14; 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]
[2025-02-18 00:16:54] [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
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:16:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-18 00:16:54] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
[ Finished: 2025-02-18 00:16:54 CET ]