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This page was generated on 2024-05-30 12:37:10 -0400 (Thu, 30 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4669
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4404
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4431
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4384
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 1422/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.13.1  (landing page)
Denes Turei
Snapshot Date: 2024-05-29 11:04:14 -0400 (Wed, 29 May 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 1cdbb59
git_last_commit_date: 2024-05-29 08:38:09 -0400 (Wed, 29 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  

BUILD BIN results for OmnipathR on merida1


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: 3.13.1
Command: rm -rf OmnipathR.buildbin-libdir && mkdir OmnipathR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh OmnipathR_3.13.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R OmnipathR.buildbin-libdir
StartedAt: 2024-05-30 10:55:38 -0400 (Thu, 30 May 2024)
EndedAt: 2024-05-30 10:56:17 -0400 (Thu, 30 May 2024)
EllapsedTime: 38.4 seconds
RetCode: 0
Status:   OK  
PackageFile: OmnipathR_3.13.1.tgz
PackageFileSize: 2.898 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf OmnipathR.buildbin-libdir && mkdir OmnipathR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh OmnipathR_3.13.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R OmnipathR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=OmnipathR.buildbin-libdir OmnipathR_3.13.1.tar.gz'
>>>>>>> 

* installing *source* package ‘OmnipathR’ ...
** 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
[2024-05-30 10:56:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 10:56:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 10:56:10] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 10:56:10] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 10:56:10] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 10:56:10] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 10:56:10] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 10:56:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 10:56:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 10:56:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 10:56:11] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 10:56:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 10:56:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 10:56:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 10:56:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 10:56:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 10:56:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 10:56:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 10:56:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 10:56:11] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 10:56:15] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 10:56:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.buildbin-libdir/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.buildbin-libdir/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.buildbin-libdir/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.buildbin-libdir/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 10:56:15] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)