| Back to Multiple platform build/check report for BioC 3.11 |
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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 86/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| artMS 1.6.5 David Jimenez-Morales
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK |
| 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 |
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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_1.6.5.tar.gz
###
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* 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.
artMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
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
artMS.Rcheck/artMS-Ex.timings
| name | user | system | elapsed | |
| artmsAnalysisQuantifications | 0.006 | 0.001 | 0.007 | |
| artmsAnnotateSpecie | 0.002 | 0.004 | 0.005 | |
| artmsAnnotationUniprot | 3.504 | 0.512 | 4.018 | |
| artmsAvgIntensityRT | 2.620 | 0.035 | 2.657 | |
| artmsChangeColumnName | 0.001 | 0.000 | 0.001 | |
| artmsConvertMetabolomics | 0.001 | 0.001 | 0.001 | |
| artmsDataPlots | 0 | 0 | 0 | |
| artmsEnrichLog2fc | 0.510 | 0.009 | 4.610 | |
| artmsEnrichProfiler | 0.392 | 0.013 | 2.041 | |
| artmsEvidenceToSAINTq | 0.001 | 0.001 | 0.002 | |
| artmsEvidenceToSaintExpress | 0.001 | 0.000 | 0.001 | |
| artmsFilterEvidenceContaminants | 0.104 | 0.007 | 0.113 | |
| artmsGeneratePhSiteExtended | 0.001 | 0.000 | 0.000 | |
| artmsIsEvidenceNewVersion | 0.002 | 0.001 | 0.002 | |
| artmsIsSpeciesSupported | 0.074 | 0.002 | 0.076 | |
| artmsLeaveOnlyUniprotEntryID | 0.002 | 0.000 | 0.002 | |
| artmsMapUniprot2Entrez | 0.242 | 0.007 | 0.253 | |
| artmsMergeEvidenceAndKeys | 0.110 | 0.005 | 0.115 | |
| artmsMsstatsSummary | 0.002 | 0.001 | 0.002 | |
| artmsPhosfateOutput | 0.000 | 0.001 | 0.000 | |
| artmsPhotonOutput | 0.000 | 0.000 | 0.001 | |
| artmsPlotHeatmapQuant | 0.411 | 0.014 | 0.431 | |
| artmsProtein2SiteConversion | 0.002 | 0.000 | 0.002 | |
| artmsQualityControlEvidenceBasic | 1.368 | 0.061 | 1.447 | |
| artmsQualityControlEvidenceExtended | 0.007 | 0.001 | 0.008 | |
| artmsQualityControlMetabolomics | 0.003 | 0.000 | 0.002 | |
| artmsQualityControlSummaryExtended | 0.042 | 0.002 | 0.044 | |
| artmsQuantification | 0 | 0 | 0 | |
| artmsResultsWide | 0.337 | 0.008 | 0.348 | |
| artmsSILACtoLong | 0.001 | 0.000 | 0.001 | |
| artmsSpectralCounts | 0.176 | 0.010 | 0.186 | |
| artmsVolcanoPlot | 0.263 | 0.004 | 0.270 | |
| artmsWriteConfigYamlFile | 0.000 | 0.000 | 0.001 | |