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CHECK report for artMS on celaya2

This page was generated on 2019-10-16 13:03:43 -0400 (Wed, 16 Oct 2019).

Package 82/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.2.7
David Jimenez-Morales
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/artMS
Branch: RELEASE_3_9
Last Commit: 6399484
Last Changed Date: 2019-10-15 02:09:49 -0400 (Tue, 15 Oct 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK YES, new version is higher than in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK YES, new version is higher than in internal repository

Summary

Package: artMS
Version: 1.2.7
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:artMS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings artMS_1.2.7.tar.gz
StartedAt: 2019-10-16 00:37:19 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:41:40 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 261.7 seconds
RetCode: 0
Status:  OK 
CheckDir: artMS.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:artMS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings artMS_1.2.7.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/artMS.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.7’
* 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 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:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL artMS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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
Warning: replacing previous import ‘MASS::select’ by ‘dplyr::select’ when loading ‘MSstats’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘MASS::select’ by ‘dplyr::select’ when loading ‘MSstats’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘MASS::select’ by ‘dplyr::select’ when loading ‘MSstats’
** testing if installed package keeps a record of temporary installation path
* DONE (artMS)

Tests output

artMS.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)


Warning message:
replacing previous import 'MASS::select' by 'dplyr::select' when loading 'MSstats' 
> 
> test_check("artMS")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 10.266   1.074  11.292 

Example timings

artMS.Rcheck/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.0050.0010.006
artmsAnnotateSpecie0.0030.0030.006
artmsAnnotationUniprot3.9660.5664.536
artmsAvgIntensityRT3.4250.1003.525
artmsChangeColumnName0.0010.0010.001
artmsConvertMetabolomics0.0000.0010.001
artmsDataPlots0.0010.0000.001
artmsEnrichLog2fc0.4770.0384.809
artmsEnrichProfiler0.4180.0112.493
artmsEvidenceToSAINTq0.0030.0010.003
artmsEvidenceToSaintExpress0.0010.0010.001
artmsFilterEvidenceContaminants0.0420.0040.047
artmsGeneratePhSiteExtended000
artmsIsEvidenceNewVersion0.0020.0010.002
artmsIsSpeciesSupported0.0850.0040.090
artmsLeaveOnlyUniprotEntryID0.0020.0000.003
artmsMapUniprot2Entrez0.2580.0100.267
artmsMergeEvidenceAndKeys0.1190.0120.132
artmsMsstatsSummary0.0010.0000.002
artmsPhosfateOutput0.0010.0000.001
artmsPhotonOutput0.0000.0000.001
artmsPlotHeatmapQuant0.4390.0150.455
artmsProtein2SiteConversion0.0010.0000.001
artmsQualityControlEvidenceBasic2.6540.1112.766
artmsQualityControlEvidenceExtended0.0050.0010.006
artmsQualityControlMetabolomics0.0020.0010.003
artmsQualityControlSummaryExtended0.0030.0000.003
artmsQuantification0.0000.0000.001
artmsResultsWide0.4200.0120.432
artmsSILACtoLong000
artmsSpectralCounts0.1120.0060.118
artmsVolcanoPlot0.5040.0640.570
artmsWriteConfigYamlFile0.0010.0000.001