Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-16 11:04:39 -0400 (Mon, 16 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4153
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for artMS on nebbiolo1


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? 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 82/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.14.0  (landing page)
David Jimenez-Morales
Snapshot Date: 2022-05-15 13:55:12 -0400 (Sun, 15 May 2022)
git_url: https://git.bioconductor.org/packages/artMS
git_branch: RELEASE_3_15
git_last_commit: 6bdad67
git_last_commit_date: 2022-04-26 11:51:59 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: artMS
Version: 1.14.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:artMS.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings artMS_1.14.0.tar.gz
StartedAt: 2022-05-15 18:24:15 -0400 (Sun, 15 May 2022)
EndedAt: 2022-05-15 18:26:57 -0400 (Sun, 15 May 2022)
EllapsedTime: 162.7 seconds
RetCode: 0
Status:   OK  
CheckDir: artMS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:artMS.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings artMS_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/artMS.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (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 ‘1.14.0’
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL artMS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  8.790   0.552   9.260 

Example timings

artMS.Rcheck/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.0020.0030.006
artmsAnnotateSpecie0.6190.0150.635
artmsAnnotationUniprot1.4960.2071.705
artmsAvgIntensityRT0.2160.0000.215
artmsChangeColumnName0.0010.0000.001
artmsConvertMetabolomics0.0010.0000.001
artmsDataPlots000
artmsEnrichLog2fc000
artmsEnrichProfiler000
artmsEvidenceToSAINTq0.0010.0000.001
artmsEvidenceToSaintExpress0.0010.0000.001
artmsFilterEvidenceContaminants0.0080.0000.008
artmsGeneratePhSiteExtended000
artmsIsEvidenceNewVersion0.0000.0030.003
artmsIsSpeciesSupported0.1050.0000.104
artmsLeaveOnlyUniprotEntryID0.0020.0000.002
artmsMapUniprot2Entrez0.1940.0000.194
artmsMergeEvidenceAndKeys0.0170.0000.017
artmsMsstatsSummary0.0000.0000.001
artmsPhosfateOutput000
artmsPhotonOutput000
artmsPlotHeatmapQuant0.4510.0110.463
artmsProtein2SiteConversion0.0000.0020.002
artmsQualityControlEvidenceBasic0.7550.0010.758
artmsQualityControlEvidenceExtended0.0010.0040.005
artmsQualityControlMetabolomics0.0010.0000.001
artmsQualityControlSummaryExtended0.0410.0000.041
artmsQuantification1.0890.0721.120
artmsResultsWide0.9730.0321.005
artmsSILACtoLong000
artmsSpectralCounts0.0440.0020.046
artmsVolcanoPlot0.2660.0030.268
artmsWriteConfigYamlFile0.0010.0000.000