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CHECK report for artMS on merida1

This page was generated on 2020-04-15 12:48:20 -0400 (Wed, 15 Apr 2020).

Package 85/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.4.3
David Jimenez-Morales
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/artMS
Branch: RELEASE_3_10
Last Commit: 539d4cb
Last Changed Date: 2020-02-08 19:43:48 -0400 (Sat, 08 Feb 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: artMS
Version: 1.4.3
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_1.4.3.tar.gz
StartedAt: 2020-04-15 00:27:23 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:30:58 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 215.4 seconds
RetCode: 0
Status:  OK 
CheckDir: artMS.Rcheck
Warnings: 0

Command output

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### Running 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_1.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/artMS.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.4.3’
* 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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL artMS
###
##############################################################################
##############################################################################


* 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
** 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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 
  8.645   0.549   9.208 

Example timings

artMS.Rcheck/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.0350.0010.036
artmsAnnotateSpecie0.0020.0030.005
artmsAnnotationUniprot3.2160.2793.533
artmsAvgIntensityRT2.6690.0562.750
artmsChangeColumnName0.0010.0000.001
artmsConvertMetabolomics0.0010.0000.001
artmsDataPlots000
artmsEnrichLog2fc0.4510.0094.313
artmsEnrichProfiler0.3510.0053.018
artmsEvidenceToSAINTq0.0020.0000.002
artmsEvidenceToSaintExpress0.0020.0010.002
artmsFilterEvidenceContaminants0.0670.0050.073
artmsGeneratePhSiteExtended0.0000.0000.001
artmsIsEvidenceNewVersion0.0010.0000.002
artmsIsSpeciesSupported0.0620.0000.062
artmsLeaveOnlyUniprotEntryID0.0020.0010.002
artmsMapUniprot2Entrez0.3030.0080.315
artmsMergeEvidenceAndKeys0.0680.0040.072
artmsMsstatsSummary0.0010.0000.001
artmsPhosfateOutput0.0010.0000.000
artmsPhotonOutput000
artmsPlotHeatmapQuant0.3940.0070.405
artmsProtein2SiteConversion0.0020.0000.002
artmsQualityControlEvidenceBasic2.1220.0492.195
artmsQualityControlEvidenceExtended0.0060.0000.008
artmsQualityControlMetabolomics0.0020.0000.002
artmsQualityControlSummaryExtended0.0020.0000.002
artmsQuantification000
artmsResultsWide0.3720.0050.381
artmsSILACtoLong000
artmsSpectralCounts0.1800.0060.187
artmsVolcanoPlot0.3120.0030.317
artmsWriteConfigYamlFile000