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This page was generated on 2024-03-04 11:39:37 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1437/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.11.3  (landing page)
Denes Turei
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 4183d8d
git_last_commit_date: 2024-02-16 10:54:02 -0500 (Fri, 16 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

INSTALL 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: 3.11.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR
StartedAt: 2024-03-01 16:03:34 -0500 (Fri, 01 Mar 2024)
EndedAt: 2024-03-01 16:04:13 -0500 (Fri, 01 Mar 2024)
EllapsedTime: 38.5 seconds
RetCode: 0
Status:   OK  

Command output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: OmnipathR.Rd:3: docType ‘_PACKAGE’ is unrecognized
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2024-03-01 16:04:03] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-01 16:04:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:03] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:03] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-01 16:04:03] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:08] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)