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This page was generated on 2021-11-29 15:05:47 -0500 (Mon, 29 Nov 2021).

CHECK results for artMS on machv2

To the developers/maintainers of the artMS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/artMS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 84/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.12.0  (landing page)
David Jimenez-Morales
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/artMS
git_branch: RELEASE_3_14
git_last_commit: 58efc32
git_last_commit_date: 2021-10-26 12:47:58 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: artMS
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:artMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings artMS_1.12.0.tar.gz
StartedAt: 2021-11-28 13:37:15 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 13:41:27 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 252.4 seconds
RetCode: 0
Status:   OK  
CheckDir: artMS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:artMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings artMS_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/artMS.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.12.0’
* 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 LazyData ... 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/Resources/bin/R CMD INSTALL artMS
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
 13.077   0.628  13.731 

Example timings

artMS.Rcheck/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.0060.0010.007
artmsAnnotateSpecie0.0070.0020.009
artmsAnnotationUniprot3.0670.5283.600
artmsAvgIntensityRT0.4140.0120.426
artmsChangeColumnName0.0010.0010.001
artmsConvertMetabolomics0.0010.0010.001
artmsDataPlots0.0010.0010.001
artmsEnrichLog2fc0.0000.0010.001
artmsEnrichProfiler0.0000.0010.001
artmsEvidenceToSAINTq0.0020.0000.002
artmsEvidenceToSaintExpress0.0020.0000.001
artmsFilterEvidenceContaminants0.0150.0010.016
artmsGeneratePhSiteExtended000
artmsIsEvidenceNewVersion0.0040.0000.005
artmsIsSpeciesSupported0.0740.0010.076
artmsLeaveOnlyUniprotEntryID0.0020.0010.002
artmsMapUniprot2Entrez0.3370.0070.343
artmsMergeEvidenceAndKeys0.0300.0010.031
artmsMsstatsSummary0.0010.0000.001
artmsPhosfateOutput000
artmsPhotonOutput0.0010.0000.000
artmsPlotHeatmapQuant0.7370.0120.750
artmsProtein2SiteConversion0.0020.0010.003
artmsQualityControlEvidenceBasic1.1440.0251.172
artmsQualityControlEvidenceExtended0.0090.0000.009
artmsQualityControlMetabolomics0.0020.0000.003
artmsQualityControlSummaryExtended0.0030.0010.004
artmsQuantification2.7120.0652.778
artmsResultsWide0.6870.0090.697
artmsSILACtoLong000
artmsSpectralCounts0.0480.0010.050
artmsVolcanoPlot0.3590.0100.369
artmsWriteConfigYamlFile0.0000.0000.001