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This page was generated on 2025-08-08 12:07 -0400 (Fri, 08 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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

Package 1471/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.17.4  (landing page)
Denes Turei
Snapshot Date: 2025-08-07 13:45 -0400 (Thu, 07 Aug 2025)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: a7f3b9d
git_last_commit_date: 2025-07-16 10:03:35 -0400 (Wed, 16 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


BUILD BIN results for OmnipathR on palomino8

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: 3.17.4
Command: rm -rf OmnipathR.buildbin-libdir && mkdir OmnipathR.buildbin-libdir && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL --build --library=OmnipathR.buildbin-libdir OmnipathR_3.17.4.tar.gz
StartedAt: 2025-08-08 09:48:58 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 09:52:01 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 182.7 seconds
RetCode: 0
Status:   OK  
PackageFile: OmnipathR_3.17.4.zip
PackageFileSize: 3.322 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf OmnipathR.buildbin-libdir && mkdir OmnipathR.buildbin-libdir && F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL --build --library=OmnipathR.buildbin-libdir OmnipathR_3.17.4.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'OmnipathR' ...
** this is package 'OmnipathR' version '3.17.4'
** 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
[2025-08-08 09:51:49] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-08 09:51:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-08 09:51:49] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-08 09:51:49] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-08-08 01:09:58 UTC; biocbuild
[2025-08-08 09:51:49] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-07
[2025-08-08 09:51:49] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 13:49:00 UTC; windows
[2025-08-08 09:51:49] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-08 09:51:49] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpgX7Dp8/file8981f775061". Did you mean command "update"?
Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
  running command '"quarto" TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpgX7Dp8/file8981f775061 -V' had status 1
[2025-08-08 09:51:51] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-08-08; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-08 09:51:51] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-08-08 09:51:51] [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); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); 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); 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); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-07); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); 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 2.4.2(2025-07-18); 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 3.3.0(2025-06-08); 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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); 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 2.3.3(2025-05-13)
[2025-08-08 09:51:51] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] Contains 1 files.
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-08 09:51:51] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-08 09:51:51] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-08-08 09:51:54] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-08 09:51:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-08 09:51:54] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-08 09:51:54] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-08-08 01:09:58 UTC; biocbuild
[2025-08-08 09:51:54] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-07
[2025-08-08 09:51:54] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 13:49:00 UTC; windows
[2025-08-08 09:51:54] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-08 09:51:54] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpE7709r/file135644d10384a". Did you mean command "update"?
Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
  running command '"quarto" TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpE7709r/file135644d10384a -V' had status 1
[2025-08-08 09:51:55] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-08-08; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-08 09:51:55] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-08-08 09:51:56] [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); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); 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); 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); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-07); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); 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 2.4.2(2025-07-18); 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 3.3.0(2025-06-08); 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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); 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 2.3.3(2025-05-13)
[2025-08-08 09:51:56] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] Contains 1 files.
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-08 09:51:56] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/meat/OmnipathR.buildbin-libdir/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/meat/OmnipathR.buildbin-libdir/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/meat/OmnipathR.buildbin-libdir/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/meat/OmnipathR.buildbin-libdir/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-08 09:51:56] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'OmnipathR' as OmnipathR_3.17.4.zip
* DONE (OmnipathR)