[ Started: 2025-02-17 00:05:11 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: 'wppi'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.15.0.tar.gz'
Content type 'application/x-gzip' length 662577 bytes (647 KB)
==================================================
downloaded 647 KB

* 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
[2025-02-17 00:05:17] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-02-17 00:05:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-17 00:05:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:17] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-17 00:05:17] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-16 00:18:34 UTC; omnipath
[2025-02-17 00:05:17] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-17 00:05:17] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-16 00:18:35 UTC; unix
[2025-02-17 00:05:17] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-17 00:05:17] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-17 00:05:17] [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=2025-02-17; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-17 00:05:18] [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]
[2025-02-17 00:05:18] [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
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-17 00:05:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:18] [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
[2025-02-17 00:05:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-17 00:05:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:20] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-17 00:05:20] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-16 00:18:34 UTC; omnipath
[2025-02-17 00:05:20] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-17 00:05:20] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-16 00:18:35 UTC; unix
[2025-02-17 00:05:20] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-17 00:05:20] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-17 00:05:20] [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=2025-02-17; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-17 00:05:20] [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]
[2025-02-17 00:05:20] [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
[2025-02-17 00:05:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-17 00:05:20] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-17 00:05:20] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-17 00:05:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-17 00:05:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-17 00:05:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-17 00:05:20] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-17 00:05:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-17 00:05:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-17 00:05:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-17 00:05:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-17 00:05:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:21] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:23] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-17 00:05:23] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-16 00:18:34 UTC; omnipath
[2025-02-17 00:05:23] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-17 00:05:23] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-16 00:18:35 UTC; unix
[2025-02-17 00:05:23] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-17 00:05:23] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-17 00:05:23] [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=2025-02-17; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-17 00:05:23] [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]
[2025-02-17 00:05:23] [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
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-17 00:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-17 00:05:23] [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/RtmpvD1PTs/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: 2025-02-17 00:05:26 CET ]