Multiple platform build/check report for BioC 3.21 - BUILD BIN results for gINTomics on palomino7

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"	4719
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4480
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4491
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4444
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*

BUILD BIN results for gINTomics on palomino7

To the developers/maintainers of the gINTomics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gINTomics.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: gINTomics

Version: 1.3.0

Command: rm -rf gINTomics.buildbin-libdir && mkdir gINTomics.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=gINTomics.buildbin-libdir gINTomics_1.3.0.tar.gz

StartedAt: 2025-02-06 08:09:00 -0500 (Thu, 06 Feb 2025)

EndedAt: 2025-02-06 08:12:26 -0500 (Thu, 06 Feb 2025)

EllapsedTime: 206.0 seconds

RetCode: 0

Status: OK

PackageFile: gINTomics_1.3.0.zip

PackageFileSize: 3.811 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf gINTomics.buildbin-libdir && mkdir gINTomics.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=gINTomics.buildbin-libdir gINTomics_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'gINTomics' ...
** this is package 'gINTomics' version '1.3.0'
** using staged installation
** R
[2025-02-06 08:09:20] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-06 08:09:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:09:20] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-06 08:09:20] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-06 08:09:20] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-05
[2025-02-06 08:09:20] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-05 21:06:33 UTC; windows
[2025-02-06 08:09:20] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-06 08:09:20] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-06 08:09:29] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-21 r87610 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=2025-02-06; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-02-06 08:09:36] [INFO]    [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.44; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.13; curl=8.10.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.22; PCRE=10.44 2024-06-07; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.0]
[2025-02-06 08:09:36] [INFO]    [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) 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; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-06 08:09:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-06 08:09:36] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-06 08:09:36] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-06 08:09:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-06 08:09:36] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-06 08:09:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:09:36] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-06 08:09:36] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-06 08:09:36] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-06 08:09:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:09:38] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-06 08:09:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:09:39] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-06 08:09:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:09:39] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-06 08:09:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:09:39] [TRACE]   [OmnipathR] Cache locked: FALSE



** data
** inst
** byte-compile and prepare package for lazy loading
[2025-02-06 08:11:07] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-06 08:11:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:11:07] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-06 08:11:07] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-06 08:11:07] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-05
[2025-02-06 08:11:07] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-05 21:06:33 UTC; windows
[2025-02-06 08:11:07] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-06 08:11:07] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-06 08:11:09] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-21 r87610 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=2025-02-06; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-02-06 08:11:09] [INFO]    [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.44; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.13; curl=8.10.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.22; PCRE=10.44 2024-06-07; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.0]
[2025-02-06 08:11:09] [INFO]    [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) 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; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:11:09] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:11:09] [TRACE]   [OmnipathR] Cache locked: FALSE
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-02-06 08:12:02] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-06 08:12:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:12:02] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-06 08:12:02] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-06 08:12:02] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-05
[2025-02-06 08:12:02] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-05 21:06:33 UTC; windows
[2025-02-06 08:12:02] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-06 08:12:02] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-06 08:12:03] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-21 r87610 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=2025-02-06; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-02-06 08:12:03] [INFO]    [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.44; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.13; curl=8.10.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.22; PCRE=10.44 2024-06-07; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.0]
[2025-02-06 08:12:03] [INFO]    [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) 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; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:12:03] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-06 08:12:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:12:04] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-02-06 08:12:20] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-06 08:12:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:12:20] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-06 08:12:20] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-06 08:12:20] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-05
[2025-02-06 08:12:20] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-05 21:06:33 UTC; windows
[2025-02-06 08:12:20] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-06 08:12:20] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-06 08:12:21] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-21 r87610 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=2025-02-06; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-02-06 08:12:21] [INFO]    [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.44; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.13; curl=8.10.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.22; PCRE=10.44 2024-06-07; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.0]
[2025-02-06 08:12:21] [INFO]    [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) 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; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:12:21] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-06 08:12:21] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'gINTomics' as gINTomics_1.3.0.zip
* DONE (gINTomics)