Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-09-22 11:35:27 -0400 (Fri, 22 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4394
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 94/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.18.0  (landing page)
David Jimenez-Morales
Snapshot Date: 2023-09-21 14:00:15 -0400 (Thu, 21 Sep 2023)
git_url: https://git.bioconductor.org/packages/artMS
git_branch: RELEASE_3_17
git_last_commit: 06049bc
git_last_commit_date: 2023-04-25 11:06:01 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  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: 1.18.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:artMS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings artMS_1.18.0.tar.gz
StartedAt: 2023-09-21 19:11:40 -0400 (Thu, 21 Sep 2023)
EndedAt: 2023-09-21 19:14:56 -0400 (Thu, 21 Sep 2023)
EllapsedTime: 195.9 seconds
RetCode: 0
Status:   OK  
CheckDir: artMS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:artMS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings artMS_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/artMS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘artMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘artMS’ version ‘1.18.0’
* 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘artMS_vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

artMS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL artMS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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 
  8.706   0.517   9.172 

Example timings

artMS.Rcheck/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.0060.0000.007
artmsAnnotateSpecie0.0040.0040.007
artmsAnnotationUniprot0.930.081.01
artmsAvgIntensityRT0.1970.0040.201
artmsChangeColumnName000
artmsConvertMetabolomics000
artmsDataPlots000
artmsEnrichLog2fc0.0000.0010.001
artmsEnrichProfiler0.0000.0010.000
artmsEvidenceToSAINTq0.0000.0010.001
artmsEvidenceToSaintExpress0.0000.0010.001
artmsFilterEvidenceContaminants0.0010.0100.011
artmsGeneratePhSiteExtended000
artmsIsEvidenceNewVersion0.0030.0000.004
artmsIsSpeciesSupported0.0060.0000.006
artmsLeaveOnlyUniprotEntryID0.0010.0000.001
artmsMapUniprot2Entrez0.1590.0000.159
artmsMergeEvidenceAndKeys0.0180.0000.018
artmsMsstatsSummary0.0010.0000.001
artmsPhosfateOutput0.0010.0000.000
artmsPhotonOutput000
artmsPlotHeatmapQuant0.3400.0000.341
artmsProtein2SiteConversion0.0020.0000.002
artmsQualityControlEvidenceBasic0.7570.0000.757
artmsQualityControlEvidenceExtended0.0050.0000.005
artmsQualityControlMetabolomics0.0020.0000.002
artmsQualityControlSummaryExtended0.0020.0000.002
artmsQuantification1.2050.0681.234
artmsResultsWide0.2550.0040.258
artmsSILACtoLong0.0010.0000.000
artmsSpectralCounts0.0710.0040.074
artmsVolcanoPlot0.2620.0000.261
artmsWriteConfigYamlFile0.0010.0000.000