Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-02-05 11:39 -0500 (Wed, 05 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4717
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4478
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4489
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4442
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 99/2295HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.25.0  (landing page)
David Jimenez-Morales
Snapshot Date: 2025-02-04 13:40 -0500 (Tue, 04 Feb 2025)
git_url: https://git.bioconductor.org/packages/artMS
git_branch: devel
git_last_commit: 10716cd
git_last_commit_date: 2024-10-29 10:32:58 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    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


CHECK results for artMS on nebbiolo1

To the developers/maintainers of the artMS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/artMS.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: artMS
Version: 1.25.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:artMS.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings artMS_1.25.0.tar.gz
StartedAt: 2025-02-04 20:00:28 -0500 (Tue, 04 Feb 2025)
EndedAt: 2025-02-04 20:03:37 -0500 (Tue, 04 Feb 2025)
EllapsedTime: 189.3 seconds
RetCode: 0
Status:   OK  
CheckDir: artMS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:artMS.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings artMS_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/artMS.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘artMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘artMS’ version ‘1.25.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘artMS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

artMS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL artMS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘artMS’ ...
** this is package ‘artMS’ version ‘1.25.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (artMS)

Tests output

artMS.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(artMS)

> 
> test_check("artMS")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  8.628   0.557   9.093 

Example timings

artMS.Rcheck/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.0050.0000.005
artmsAnnotateSpecie0.0050.0010.007
artmsAnnotationUniprot1.2920.0831.375
artmsAvgIntensityRT0.2120.0090.221
artmsChangeColumnName0.0010.0000.000
artmsConvertMetabolomics0.0010.0000.001
artmsDataPlots0.0000.0000.001
artmsEnrichLog2fc000
artmsEnrichProfiler0.0010.0000.000
artmsEvidenceToSAINTq0.0010.0000.001
artmsEvidenceToSaintExpress0.0010.0000.001
artmsFilterEvidenceContaminants0.0090.0000.008
artmsGeneratePhSiteExtended0.0000.0010.000
artmsIsEvidenceNewVersion0.0030.0000.003
artmsIsSpeciesSupported0.0060.0010.006
artmsLeaveOnlyUniprotEntryID0.0010.0000.002
artmsMapUniprot2Entrez0.2790.0030.283
artmsMergeEvidenceAndKeys0.0430.0000.043
artmsMsstatsSummary0.0010.0000.001
artmsPhosfateOutput000
artmsPhotonOutput0.0000.0010.000
artmsPlotHeatmapQuant0.5630.0100.573
artmsProtein2SiteConversion0.0010.0000.001
artmsQualityControlEvidenceBasic0.7380.0050.743
artmsQualityControlEvidenceExtended0.0040.0010.004
artmsQualityControlMetabolomics0.0010.0010.001
artmsQualityControlSummaryExtended0.0020.0000.001
artmsQuantification1.8050.0321.748
artmsResultsWide0.4440.0070.452
artmsSILACtoLong0.0010.0010.001
artmsSpectralCounts0.0400.0030.044
artmsVolcanoPlot0.2990.0020.302
artmsWriteConfigYamlFile000