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CHECK report for artMS on machv2

This page was generated on 2020-10-17 11:58:04 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE artMS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 86/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.6.5
David Jimenez-Morales
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/artMS
Branch: RELEASE_3_11
Last Commit: ba1bbb1
Last Changed Date: 2020-05-21 13:44:10 -0400 (Thu, 21 May 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: artMS
Version: 1.6.5
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_1.6.5.tar.gz
StartedAt: 2020-10-16 22:43:39 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 22:52:02 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 503.5 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_1.6.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/artMS.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.6.5’
* 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 ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/artMS.Rcheck/00check.log’
for details.



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 version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  9.620   0.649  32.534 

Example timings

artMS.Rcheck/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.0060.0010.007
artmsAnnotateSpecie0.0020.0040.005
artmsAnnotationUniprot3.5040.5124.018
artmsAvgIntensityRT2.6200.0352.657
artmsChangeColumnName0.0010.0000.001
artmsConvertMetabolomics0.0010.0010.001
artmsDataPlots000
artmsEnrichLog2fc0.5100.0094.610
artmsEnrichProfiler0.3920.0132.041
artmsEvidenceToSAINTq0.0010.0010.002
artmsEvidenceToSaintExpress0.0010.0000.001
artmsFilterEvidenceContaminants0.1040.0070.113
artmsGeneratePhSiteExtended0.0010.0000.000
artmsIsEvidenceNewVersion0.0020.0010.002
artmsIsSpeciesSupported0.0740.0020.076
artmsLeaveOnlyUniprotEntryID0.0020.0000.002
artmsMapUniprot2Entrez0.2420.0070.253
artmsMergeEvidenceAndKeys0.1100.0050.115
artmsMsstatsSummary0.0020.0010.002
artmsPhosfateOutput0.0000.0010.000
artmsPhotonOutput0.0000.0000.001
artmsPlotHeatmapQuant0.4110.0140.431
artmsProtein2SiteConversion0.0020.0000.002
artmsQualityControlEvidenceBasic1.3680.0611.447
artmsQualityControlEvidenceExtended0.0070.0010.008
artmsQualityControlMetabolomics0.0030.0000.002
artmsQualityControlSummaryExtended0.0420.0020.044
artmsQuantification000
artmsResultsWide0.3370.0080.348
artmsSILACtoLong0.0010.0000.001
artmsSpectralCounts0.1760.0100.186
artmsVolcanoPlot0.2630.0040.270
artmsWriteConfigYamlFile0.0000.0000.001