Multiple platform build/check report for BioC 3.21 - INSTALL results for wppi on kjohnson3

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*

INSTALL results for wppi on kjohnson3

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

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL wppi

StartedAt: 2025-02-05 15:17:17 -0500 (Wed, 05 Feb 2025)

EndedAt: 2025-02-05 15:17:23 -0500 (Wed, 05 Feb 2025)

EllapsedTime: 6.6 seconds

RetCode: 0

Status: OK

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘wppi’ ...
** this is package ‘wppi’ version ‘1.15.0’
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:18] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 15:17:18] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-05 15:17:18] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-05
[2025-02-05 15:17:18] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-05 20:16:53 UTC; unix
[2025-02-05 15:17:18] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-05 15:17:18] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-05 15:17:18] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-20 r87609); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-05; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.552 @ /usr/local/bin/quarto]
[2025-02-05 15:17:18] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.42 2022-12-11; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-02-05 15:17:18] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-05 15:17:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:18] [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
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:20] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 15:17:20] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-05 15:17:20] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-05
[2025-02-05 15:17:20] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-05 20:16:53 UTC; unix
[2025-02-05 15:17:20] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-05 15:17:20] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-05 15:17:20] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-20 r87609); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-05; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.552 @ /usr/local/bin/quarto]
[2025-02-05 15:17:20] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.42 2022-12-11; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-02-05 15:17:20] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:20] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:22] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 15:17:22] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-05 15:17:22] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-05
[2025-02-05 15:17:22] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-05 20:16:53 UTC; unix
[2025-02-05 15:17:22] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-05 15:17:22] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-05 15:17:22] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-20 r87609); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-05; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.552 @ /usr/local/bin/quarto]
[2025-02-05 15:17:22] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.42 2022-12-11; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-02-05 15:17:22] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 15:17:22] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)