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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 95/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.22.0  (landing page)
David Jimenez-Morales
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/artMS
git_branch: RELEASE_3_19
git_last_commit: b75f560
git_last_commit_date: 2024-04-30 11:10:48 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for artMS on kjohnson3

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: 1.22.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:artMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings artMS_1.22.0.tar.gz
StartedAt: 2024-06-10 07:31:30 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 07:35:59 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 268.6 seconds
RetCode: 0
Status:   OK  
CheckDir: artMS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:artMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings artMS_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/artMS.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘artMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘artMS’ version ‘1.22.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

artMS.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘artMS’ ...
** 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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
 10.879   0.585  15.790 

Example timings

artMS.Rcheck/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.0060.0010.012
artmsAnnotateSpecie0.9180.0071.325
artmsAnnotationUniprot2.1590.6353.810
artmsAvgIntensityRT0.2330.0060.240
artmsChangeColumnName000
artmsConvertMetabolomics0.0010.0010.000
artmsDataPlots000
artmsEnrichLog2fc000
artmsEnrichProfiler0.0000.0000.001
artmsEvidenceToSAINTq0.0010.0000.002
artmsEvidenceToSaintExpress0.0010.0000.001
artmsFilterEvidenceContaminants0.0540.0030.093
artmsGeneratePhSiteExtended0.0000.0000.001
artmsIsEvidenceNewVersion0.0050.0000.007
artmsIsSpeciesSupported0.0810.0020.134
artmsLeaveOnlyUniprotEntryID0.0010.0000.002
artmsMapUniprot2Entrez0.5830.0120.732
artmsMergeEvidenceAndKeys0.0230.0010.025
artmsMsstatsSummary0.0010.0010.001
artmsPhosfateOutput000
artmsPhotonOutput000
artmsPlotHeatmapQuant0.9440.0200.965
artmsProtein2SiteConversion0.0020.0010.002
artmsQualityControlEvidenceBasic1.7890.0462.582
artmsQualityControlEvidenceExtended0.0050.0010.010
artmsQualityControlMetabolomics0.0010.0000.003
artmsQualityControlSummaryExtended0.0020.0000.005
artmsQuantification1.2710.0211.871
artmsResultsWide0.8010.0161.163
artmsSILACtoLong000
artmsSpectralCounts0.0460.0010.047
artmsVolcanoPlot0.2670.0100.276
artmsWriteConfigYamlFile000