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CHECK report for artMS on celaya2

This page was generated on 2020-01-16 13:52:46 -0500 (Thu, 16 Jan 2020).

Package 85/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.5.1
David Jimenez-Morales
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/artMS
Branch: master
Last Commit: 294217f
Last Changed Date: 2019-12-06 19:29:34 -0500 (Fri, 06 Dec 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: artMS
Version: 1.5.1
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_1.5.1.tar.gz
StartedAt: 2020-01-16 01:48:32 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 01:53:40 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 308.0 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_1.5.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/artMS.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.5.1’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
artmsAnnotationUniprot 5.136  0.609    5.75
* 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/Versions/Current/Resources/bin/R CMD INSTALL artMS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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)


> 
> test_check("artMS")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 12.722   1.203  13.881 

Example timings

artMS.Rcheck/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.0060.0010.006
artmsAnnotateSpecie0.0040.0050.008
artmsAnnotationUniprot5.1360.6095.750
artmsAvgIntensityRT2.7340.1382.872
artmsChangeColumnName0.0010.0000.001
artmsConvertMetabolomics0.0010.0010.001
artmsDataPlots0.0010.0000.000
artmsEnrichLog2fc0.6820.0274.404
artmsEnrichProfiler0.3160.0082.141
artmsEvidenceToSAINTq0.0010.0000.002
artmsEvidenceToSaintExpress0.0010.0010.001
artmsFilterEvidenceContaminants0.0920.0100.101
artmsGeneratePhSiteExtended0.0010.0000.001
artmsIsEvidenceNewVersion0.0030.0000.003
artmsIsSpeciesSupported0.0820.0010.082
artmsLeaveOnlyUniprotEntryID0.0030.0010.003
artmsMapUniprot2Entrez0.2660.0060.272
artmsMergeEvidenceAndKeys0.1500.0150.165
artmsMsstatsSummary0.0020.0010.001
artmsPhosfateOutput000
artmsPhotonOutput000
artmsPlotHeatmapQuant0.4680.0170.487
artmsProtein2SiteConversion0.0020.0010.002
artmsQualityControlEvidenceBasic2.4470.1152.563
artmsQualityControlEvidenceExtended0.0050.0010.005
artmsQualityControlMetabolomics0.0010.0000.001
artmsQualityControlSummaryExtended0.0020.0000.003
artmsQuantification000
artmsResultsWide0.3910.0100.402
artmsSILACtoLong000
artmsSpectralCounts0.1500.0090.159
artmsVolcanoPlot0.3300.0170.347
artmsWriteConfigYamlFile0.0010.0000.000