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

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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

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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)

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 

name	user	system	elapsed
artmsAnalysisQuantifications	0.005	0.001	0.006
artmsAnnotateSpecie	0.003	0.003	0.006
artmsAnnotationUniprot	3.966	0.566	4.536
artmsAvgIntensityRT	3.425	0.100	3.525
artmsChangeColumnName	0.001	0.001	0.001
artmsConvertMetabolomics	0.000	0.001	0.001
artmsDataPlots	0.001	0.000	0.001
artmsEnrichLog2fc	0.477	0.038	4.809
artmsEnrichProfiler	0.418	0.011	2.493
artmsEvidenceToSAINTq	0.003	0.001	0.003
artmsEvidenceToSaintExpress	0.001	0.001	0.001
artmsFilterEvidenceContaminants	0.042	0.004	0.047
artmsGeneratePhSiteExtended	0	0	0
artmsIsEvidenceNewVersion	0.002	0.001	0.002
artmsIsSpeciesSupported	0.085	0.004	0.090
artmsLeaveOnlyUniprotEntryID	0.002	0.000	0.003
artmsMapUniprot2Entrez	0.258	0.010	0.267
artmsMergeEvidenceAndKeys	0.119	0.012	0.132
artmsMsstatsSummary	0.001	0.000	0.002
artmsPhosfateOutput	0.001	0.000	0.001
artmsPhotonOutput	0.000	0.000	0.001
artmsPlotHeatmapQuant	0.439	0.015	0.455
artmsProtein2SiteConversion	0.001	0.000	0.001
artmsQualityControlEvidenceBasic	2.654	0.111	2.766
artmsQualityControlEvidenceExtended	0.005	0.001	0.006
artmsQualityControlMetabolomics	0.002	0.001	0.003
artmsQualityControlSummaryExtended	0.003	0.000	0.003
artmsQuantification	0.000	0.000	0.001
artmsResultsWide	0.420	0.012	0.432
artmsSILACtoLong	0	0	0
artmsSpectralCounts	0.112	0.006	0.118
artmsVolcanoPlot	0.504	0.064	0.570
artmsWriteConfigYamlFile	0.001	0.000	0.001