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This page was generated on 2021-10-20 12:05:33 -0400 (Wed, 20 Oct 2021).

CHECK results for artMS on merida1

To the developers/maintainers of the artMS package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 84/2072HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.11.2  (landing page)
David Jimenez-Morales
Snapshot Date: 2021-10-19 14:50:04 -0400 (Tue, 19 Oct 2021)
git_url: https://git.bioconductor.org/packages/artMS
git_branch: master
git_last_commit: 5fd14f8
git_last_commit_date: 2021-07-14 02:53:05 -0400 (Wed, 14 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: artMS
Version: 1.11.2
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_1.11.2.tar.gz
StartedAt: 2021-10-20 00:41:48 -0400 (Wed, 20 Oct 2021)
EndedAt: 2021-10-20 00:45:53 -0400 (Wed, 20 Oct 2021)
EllapsedTime: 245.4 seconds
RetCode: 0
Status:   OK  
CheckDir: artMS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.11.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/artMS.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘artMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘artMS’ version ‘1.11.2’
* 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 R 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 in ‘inst/doc’ ... 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 
 12.713   0.656  13.327 

Example timings

artMS.Rcheck/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.0060.0010.006
artmsAnnotateSpecie0.0070.0010.008
artmsAnnotationUniprot2.7980.4563.258
artmsAvgIntensityRT0.3660.0070.374
artmsChangeColumnName0.0000.0000.001
artmsConvertMetabolomics0.0010.0000.001
artmsDataPlots000
artmsEnrichLog2fc0.0000.0000.001
artmsEnrichProfiler0.0010.0010.000
artmsEvidenceToSAINTq0.0020.0000.003
artmsEvidenceToSaintExpress0.0010.0000.002
artmsFilterEvidenceContaminants0.0200.0030.023
artmsGeneratePhSiteExtended0.0000.0000.001
artmsIsEvidenceNewVersion0.0050.0000.005
artmsIsSpeciesSupported0.1020.0030.104
artmsLeaveOnlyUniprotEntryID0.0020.0000.003
artmsMapUniprot2Entrez0.3270.0050.333
artmsMergeEvidenceAndKeys0.0230.0010.024
artmsMsstatsSummary0.0010.0000.001
artmsPhosfateOutput000
artmsPhotonOutput000
artmsPlotHeatmapQuant0.6420.0140.657
artmsProtein2SiteConversion0.0020.0000.002
artmsQualityControlEvidenceBasic1.2210.0331.266
artmsQualityControlEvidenceExtended0.0060.0000.006
artmsQualityControlMetabolomics0.0020.0000.002
artmsQualityControlSummaryExtended0.0030.0000.003
artmsQuantification2.5610.0742.638
artmsResultsWide0.6310.0080.641
artmsSILACtoLong0.0000.0000.001
artmsSpectralCounts0.0630.0030.065
artmsVolcanoPlot0.3570.0070.364
artmsWriteConfigYamlFile0.0010.0000.001