Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-31 17:02:49 -0400 (Fri, 31 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4753
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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

Package 95/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.22.0  (landing page)
David Jimenez-Morales
Snapshot Date: 2024-05-30 18:28:32 -0400 (Thu, 30 May 2024)
git_url: https://git.bioconductor.org/packages/artMS
git_branch: RELEASE_3_19
git_last_commit: b75f560
git_last_commit_date: 2024-04-30 11:10:48 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for artMS on nebbiolo1


To the developers/maintainers of the artMS package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: artMS
Version: 1.22.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:artMS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings artMS_1.22.0.tar.gz
StartedAt: 2024-05-31 01:14:35 -0400 (Fri, 31 May 2024)
EndedAt: 2024-05-31 01:17:39 -0400 (Fri, 31 May 2024)
EllapsedTime: 184.4 seconds
RetCode: 0
Status:   OK  
CheckDir: artMS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:artMS.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings artMS_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/artMS.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘artMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘artMS’ version ‘1.22.0’
* 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 code 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 loading without being on the library search path ... 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

artMS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL artMS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  8.141   0.533   8.580 

Example timings

artMS.Rcheck/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.0050.0000.006
artmsAnnotateSpecie0.0030.0040.007
artmsAnnotationUniprot1.1280.0681.197
artmsAvgIntensityRT0.2040.0000.204
artmsChangeColumnName0.0010.0000.000
artmsConvertMetabolomics0.0010.0000.000
artmsDataPlots000
artmsEnrichLog2fc0.0000.0000.001
artmsEnrichProfiler000
artmsEvidenceToSAINTq0.0020.0000.001
artmsEvidenceToSaintExpress0.0010.0000.001
artmsFilterEvidenceContaminants0.0400.0000.041
artmsGeneratePhSiteExtended000
artmsIsEvidenceNewVersion0.0010.0040.003
artmsIsSpeciesSupported0.0050.0000.006
artmsLeaveOnlyUniprotEntryID0.0010.0000.002
artmsMapUniprot2Entrez0.2700.0040.275
artmsMergeEvidenceAndKeys0.0180.0000.018
artmsMsstatsSummary0.0010.0000.000
artmsPhosfateOutput000
artmsPhotonOutput000
artmsPlotHeatmapQuant0.5300.0150.545
artmsProtein2SiteConversion0.0000.0020.001
artmsQualityControlEvidenceBasic0.7850.0140.799
artmsQualityControlEvidenceExtended0.0050.0000.005
artmsQualityControlMetabolomics0.0010.0000.001
artmsQualityControlSummaryExtended0.0020.0000.001
artmsQuantification1.1240.0521.122
artmsResultsWide0.9750.0761.051
artmsSILACtoLong000
artmsSpectralCounts0.0410.0000.040
artmsVolcanoPlot0.2470.0000.247
artmsWriteConfigYamlFile0.0000.0000.001