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CHECK report for artMS on merida1

This page was generated on 2020-08-10 12:43:28 -0400 (Mon, 10 Aug 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 83/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.7.5
David Jimenez-Morales
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/artMS
Branch: master
Last Commit: 4ab9bd7
Last Changed Date: 2020-05-21 01:16:54 -0400 (Thu, 21 May 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: artMS
Version: 1.7.5
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_1.7.5.tar.gz
StartedAt: 2020-08-10 04:05:34 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 04:09:59 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 264.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: artMS.Rcheck
Warnings: 1

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_1.7.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/artMS.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.7.5’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘ComplexHeatmap::pheatmap’ by ‘pheatmap::pheatmap’ when loading ‘artMS’
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/artMS.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.9Mb
  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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-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
Warning: replacing previous import ‘ComplexHeatmap::pheatmap’ by ‘pheatmap::pheatmap’ when loading ‘artMS’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘ComplexHeatmap::pheatmap’ by ‘pheatmap::pheatmap’ when loading ‘artMS’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘ComplexHeatmap::pheatmap’ by ‘pheatmap::pheatmap’ when loading ‘artMS’
** testing if installed package keeps a record of temporary installation path
* DONE (artMS)

Tests output

artMS.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
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)


Warning message:
replacing previous import 'ComplexHeatmap::pheatmap' by 'pheatmap::pheatmap' when loading 'artMS' 
> 
> test_check("artMS")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 11.579   0.597  12.168 

Example timings

artMS.Rcheck/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.0060.0010.007
artmsAnnotateSpecie0.0020.0040.006
artmsAnnotationUniprot3.5520.5244.081
artmsAvgIntensityRT2.8750.0422.920
artmsChangeColumnName0.0010.0010.001
artmsConvertMetabolomics0.0010.0010.002
artmsDataPlots0.0000.0000.001
artmsEnrichLog2fc0.5610.0104.413
artmsEnrichProfiler0.4040.0081.959
artmsEvidenceToSAINTq0.0030.0000.003
artmsEvidenceToSaintExpress0.0020.0000.003
artmsFilterEvidenceContaminants0.0370.0050.043
artmsGeneratePhSiteExtended0.0010.0000.000
artmsIsEvidenceNewVersion0.0020.0000.003
artmsIsSpeciesSupported0.0980.0010.100
artmsLeaveOnlyUniprotEntryID0.0030.0000.003
artmsMapUniprot2Entrez0.2630.0030.267
artmsMergeEvidenceAndKeys0.1060.0050.111
artmsMsstatsSummary0.0010.0000.002
artmsPhosfateOutput0.0000.0010.000
artmsPhotonOutput0.0010.0000.000
artmsPlotHeatmapQuant0.4250.0070.432
artmsProtein2SiteConversion0.0030.0000.003
artmsQualityControlEvidenceBasic1.5600.0301.594
artmsQualityControlEvidenceExtended0.0080.0010.009
artmsQualityControlMetabolomics0.0020.0010.003
artmsQualityControlSummaryExtended0.0040.0010.005
artmsQuantification0.0010.0000.001
artmsResultsWide0.4390.0080.448
artmsSILACtoLong000
artmsSpectralCounts0.1110.0020.114
artmsVolcanoPlot0.3100.0040.316
artmsWriteConfigYamlFile0.0000.0000.001