Multiple platform build/check report for BioC 3.21 - INSTALL results for OmnipathR on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4720
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4482
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4493
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4446
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

INSTALL results for OmnipathR on nebbiolo1

To the developers/maintainers of the OmnipathR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: OmnipathR

Version: 3.15.9

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL OmnipathR

StartedAt: 2025-02-14 15:08:18 -0500 (Fri, 14 Feb 2025)

EndedAt: 2025-02-14 15:08:36 -0500 (Fri, 14 Feb 2025)

EllapsedTime: 17.3 seconds

RetCode: 0

Status: OK

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* 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
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-02-14 15:08:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-14 15:08:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-14 15:08:32] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-02-14 15:08:32] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-14 15:08:32] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-14
[2025-02-14 15:08:32] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-14 20:08:19 UTC; unix
[2025-02-14 15:08:32] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-14 15:08:32] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-14 15:08:33] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-20 r87609); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-14; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-02-14 15:08:33] [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=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-14 15:08:33] [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
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] Contains 8 files.
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-14 15:08:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-14 15:08:33] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-14 15:08:35] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-02-14 15:08:35] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-14 15:08:35] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-14
[2025-02-14 15:08:35] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-14 20:08:19 UTC; unix
[2025-02-14 15:08:35] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-14 15:08:35] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-14 15:08:35] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-20 r87609); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-14; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-02-14 15:08:35] [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=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-14 15:08:35] [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
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-14 15:08:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-14 15:08:35] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)