| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 100/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| artMS 1.26.0 (landing page) David Jimenez-Morales
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: artMS |
| Version: 1.26.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:artMS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings artMS_1.26.0.tar.gz |
| StartedAt: 2025-10-14 06:16:25 -0000 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 06:20:56 -0000 (Tue, 14 Oct 2025) |
| EllapsedTime: 271.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: artMS.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:artMS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings artMS_1.26.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/artMS.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘artMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘artMS’ version ‘1.26.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
artMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL artMS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘artMS’ ... ** this is package ‘artMS’ version ‘1.26.0’ ** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
12.430 0.534 13.315
artMS.Rcheck/artMS-Ex.timings
| name | user | system | elapsed | |
| artmsAnalysisQuantifications | 0.003 | 0.003 | 0.006 | |
| artmsAnnotateSpecie | 0.004 | 0.004 | 0.008 | |
| artmsAnnotationUniprot | 0.824 | 0.052 | 0.942 | |
| artmsAvgIntensityRT | 0.877 | 0.040 | 1.482 | |
| artmsChangeColumnName | 0 | 0 | 0 | |
| artmsConvertMetabolomics | 0.000 | 0.000 | 0.001 | |
| artmsDataPlots | 0.001 | 0.000 | 0.000 | |
| artmsEnrichLog2fc | 0 | 0 | 0 | |
| artmsEnrichProfiler | 0.001 | 0.000 | 0.000 | |
| artmsEvidenceToSAINTq | 0.001 | 0.000 | 0.001 | |
| artmsEvidenceToSaintExpress | 0.001 | 0.000 | 0.001 | |
| artmsFilterEvidenceContaminants | 0.013 | 0.000 | 0.025 | |
| artmsGeneratePhSiteExtended | 0 | 0 | 0 | |
| artmsIsEvidenceNewVersion | 0.003 | 0.000 | 0.003 | |
| artmsIsSpeciesSupported | 0.006 | 0.001 | 0.016 | |
| artmsLeaveOnlyUniprotEntryID | 0.002 | 0.000 | 0.001 | |
| artmsMapUniprot2Entrez | 0.336 | 0.004 | 0.505 | |
| artmsMergeEvidenceAndKeys | 0.021 | 0.000 | 0.021 | |
| artmsMsstatsSummary | 0.001 | 0.000 | 0.001 | |
| artmsPhosfateOutput | 0.000 | 0.000 | 0.001 | |
| artmsPhotonOutput | 0 | 0 | 0 | |
| artmsPlotHeatmapQuant | 0.620 | 0.016 | 0.636 | |
| artmsProtein2SiteConversion | 0.002 | 0.000 | 0.001 | |
| artmsQualityControlEvidenceBasic | 1.437 | 0.039 | 1.533 | |
| artmsQualityControlEvidenceExtended | 0.005 | 0.000 | 0.005 | |
| artmsQualityControlMetabolomics | 0.001 | 0.000 | 0.002 | |
| artmsQualityControlSummaryExtended | 0.002 | 0.000 | 0.002 | |
| artmsQuantification | 1.692 | 0.024 | 1.719 | |
| artmsResultsWide | 0.682 | 0.020 | 0.703 | |
| artmsSILACtoLong | 0 | 0 | 0 | |
| artmsSpectralCounts | 0.050 | 0.000 | 0.051 | |
| artmsVolcanoPlot | 0.502 | 0.004 | 0.512 | |
| artmsWriteConfigYamlFile | 0.001 | 0.000 | 0.001 | |