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CHECK report for artMS on merida1

This page was generated on 2019-04-16 12:13:58 -0400 (Tue, 16 Apr 2019).

Package 77/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.0.12
David Jimenez-Morales
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/artMS
Branch: RELEASE_3_8
Last Commit: cb3b4fc
Last Changed Date: 2019-04-07 21:39:33 -0400 (Sun, 07 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: 1.0.12
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_1.0.12.tar.gz
StartedAt: 2019-04-15 22:24:58 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:28:15 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 197.7 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_1.0.12.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/artMS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.12’
* 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/3.5/Resources/library’
* installing *source* package ‘artMS’ ...
** 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
* DONE (artMS)

Tests output

artMS.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  6.995   0.419   7.444 

Example timings

artMS.Rcheck/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.0070.0020.009
artmsAnnotateSpecie0.0030.0030.007
artmsAnnotationUniprot2.4710.2322.730
artmsAvgIntensityRT2.0690.0562.137
artmsChangeColumnName0.0010.0010.001
artmsConvertMetabolomics0.0010.0000.001
artmsDataPlots000
artmsEnrichLog2fc0.2910.0103.895
artmsEnrichProfiler0.3670.0112.304
artmsEvidenceToSAINTq0.0020.0000.002
artmsEvidenceToSaintExpress0.0010.0000.002
artmsFilterEvidenceContaminants0.0340.0070.042
artmsGeneratePhSiteExtended000
artmsIsEvidenceNewVersion0.0030.0000.003
artmsIsSpeciesSupported0.0900.0070.096
artmsMapUniprot2Entrez0.1730.0040.176
artmsMergeEvidenceAndKeys0.0720.0060.078
artmsMsstatsSummary0.0010.0000.001
artmsPhosfateOutput0.0010.0000.000
artmsPhotonOutput0.0010.0000.000
artmsPlotHeatmapQuant0.3910.0120.404
artmsProtein2SiteConversion0.0020.0000.002
artmsQualityControlEvidenceBasic1.8670.0461.927
artmsQualityControlEvidenceExtended0.0050.0010.006
artmsQualityControlMetabolomics0.0010.0000.002
artmsQualityControlSummaryExtended0.0030.0000.002
artmsQuantification0.0000.0000.001
artmsReplicatePlots0.2210.0210.244
artmsResultsWide0.3500.0140.369
artmsSILACtoLong0.0010.0000.000
artmsSpectralCounts0.1250.0060.131
artmsVolcanoPlot0.3310.0020.335
artmsWriteConfigYamlFile0.0010.0010.000