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This page was generated on 2024-04-18 11:32:06 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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 94/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
artMS 1.20.0  (landing page)
David Jimenez-Morales
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/artMS
git_branch: RELEASE_3_18
git_last_commit: cc581a0
git_last_commit_date: 2023-10-24 11:09:13 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for artMS on kjohnson1


To the developers/maintainers of the artMS package:
- 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: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2024-04-17 05:52:42 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 05:56:12 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 209.8 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/artMS.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘artMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘artMS’ version ‘1.20.0’
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL artMS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
 10.971   0.510  11.490 

Example timings

artMS.Rcheck/artMS-Ex.timings

nameusersystemelapsed
artmsAnalysisQuantifications0.0080.0010.009
artmsAnnotateSpecie0.0100.0020.012
artmsAnnotationUniprot2.7580.5413.309
artmsAvgIntensityRT0.2420.0040.247
artmsChangeColumnName0.0000.0000.001
artmsConvertMetabolomics0.0000.0010.001
artmsDataPlots0.0000.0000.001
artmsEnrichLog2fc0.0000.0000.001
artmsEnrichProfiler000
artmsEvidenceToSAINTq0.0010.0000.002
artmsEvidenceToSaintExpress0.0010.0000.002
artmsFilterEvidenceContaminants0.0120.0020.014
artmsGeneratePhSiteExtended000
artmsIsEvidenceNewVersion0.0050.0000.005
artmsIsSpeciesSupported0.1130.0030.116
artmsLeaveOnlyUniprotEntryID0.0020.0000.002
artmsMapUniprot2Entrez0.3120.0050.317
artmsMergeEvidenceAndKeys0.0210.0000.021
artmsMsstatsSummary0.0010.0000.002
artmsPhosfateOutput000
artmsPhotonOutput000
artmsPlotHeatmapQuant0.5770.0150.596
artmsProtein2SiteConversion0.0020.0000.002
artmsQualityControlEvidenceBasic0.8120.0240.849
artmsQualityControlEvidenceExtended0.0070.0000.008
artmsQualityControlMetabolomics0.0020.0010.002
artmsQualityControlSummaryExtended0.0020.0000.003
artmsQuantification1.3230.0461.377
artmsResultsWide0.6130.0210.640
artmsSILACtoLong0.0000.0010.000
artmsSpectralCounts0.0550.0030.058
artmsVolcanoPlot0.2520.0090.265
artmsWriteConfigYamlFile000