| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-29 12:06 -0400 (Wed, 29 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 1571/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| peakPantheR 1.23.3 (landing page) Arnaud Wolfer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
|
To the developers/maintainers of the peakPantheR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/peakPantheR.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. |
| Package: peakPantheR |
| Version: 1.23.3 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings peakPantheR_1.23.3.tar.gz |
| StartedAt: 2025-10-28 23:10:52 -0400 (Tue, 28 Oct 2025) |
| EndedAt: 2025-10-28 23:33:37 -0400 (Tue, 28 Oct 2025) |
| EllapsedTime: 1365.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: peakPantheR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings peakPantheR_1.23.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/peakPantheR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.23.3’
* 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 ‘peakPantheR’ 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 whether startup messages can be suppressed ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
peakPantheR_ROIStatistics 23.420 0.350 23.960
peakPantheR_parallelAnnotation 16.786 0.351 17.525
outputAnnotationResult-peakPantheRAnnotation-method 15.685 0.122 15.875
outputAnnotationDiagnostic-peakPantheRAnnotation-method 15.402 0.148 15.661
EICs-peakPantheRAnnotation-method 13.513 0.740 14.383
retentionTimeCorrection-peakPantheRAnnotation-method 10.633 0.081 10.775
peakPantheR_singleFileSearch 5.478 0.062 5.592
* 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
peakPantheR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL peakPantheR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘peakPantheR’ ... ** this is package ‘peakPantheR’ version ‘1.23.3’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (peakPantheR)
peakPantheR.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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(peakPantheR)
This is peakPantheR version 1.23.3
>
> test_check("peakPantheR")
2025-10-28 23:19:59.977 R[47089:666698253] XType: com.apple.fonts is not accessible.
2025-10-28 23:19:59.977 R[47089:666698253] XType: XTFontStaticRegistry is enabled.
2025-10-28 23:20:19.307 R[72305:666769533] XType: com.apple.fonts is not accessible.
2025-10-28 23:20:19.308 R[72305:666769533] XType: XTFontStaticRegistry is enabled.
2025-10-28 23:20:31.268 R[72938:666771287] XType: com.apple.fonts is not accessible.
2025-10-28 23:20:31.268 R[72938:666771287] XType: XTFontStaticRegistry is enabled.
2025-10-28 23:25:06.633 R[94976:666817346] XType: com.apple.fonts is not accessible.
2025-10-28 23:25:06.633 R[94976:666817346] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1460 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
closing unused connection 10 (/private/tmp/Rtmp1c5HJM/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 9 (/private/tmp/Rtmp1c5HJM/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (/private/tmp/Rtmp1c5HJM/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (/private/tmp/Rtmp1c5HJM/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
>
> proc.time()
user system elapsed
819.021 8.686 1157.398
peakPantheR.Rcheck/peakPantheR-Ex.timings
| name | user | system | elapsed | |
| EICs-peakPantheRAnnotation-method | 13.513 | 0.740 | 14.383 | |
| FIR-peakPantheRAnnotation-method | 0.032 | 0.003 | 0.035 | |
| ROI-peakPantheRAnnotation-method | 0.029 | 0.002 | 0.031 | |
| TIC-peakPantheRAnnotation-method | 0.027 | 0.002 | 0.030 | |
| acquisitionTime-peakPantheRAnnotation-method | 0.028 | 0.003 | 0.031 | |
| annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.024 | 0.002 | 0.026 | |
| annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.025 | 0.002 | 0.028 | |
| annotationTable-peakPantheRAnnotation-method | 0.026 | 0.002 | 0.027 | |
| annotation_diagnostic_multiplot_UI_helper | 0.169 | 0.012 | 0.182 | |
| annotation_fit_summary_UI_helper | 0.008 | 0.001 | 0.009 | |
| annotation_showMethod_UI_helper | 0.004 | 0.000 | 0.005 | |
| annotation_showText_UI_helper | 0.000 | 0.000 | 0.001 | |
| cpdID-peakPantheRAnnotation-method | 0.022 | 0.002 | 0.025 | |
| cpdMetadata-peakPantheRAnnotation-method | 0.025 | 0.003 | 0.028 | |
| cpdName-peakPantheRAnnotation-method | 0.024 | 0.003 | 0.027 | |
| dataPoints-peakPantheRAnnotation-method | 0.024 | 0.003 | 0.027 | |
| filename-peakPantheRAnnotation-method | 0.027 | 0.002 | 0.029 | |
| filepath-peakPantheRAnnotation-method | 0.025 | 0.003 | 0.029 | |
| initialise_annotation_from_files_UI_helper | 0.013 | 0.003 | 0.016 | |
| isAnnotated-peakPantheRAnnotation-method | 0.023 | 0.002 | 0.025 | |
| load_annotation_from_file_UI_helper | 0.006 | 0.002 | 0.008 | |
| nbCompounds-peakPantheRAnnotation-method | 0.023 | 0.002 | 0.025 | |
| nbSamples-peakPantheRAnnotation-method | 0.130 | 0.004 | 0.134 | |
| outputAnnotationDiagnostic-peakPantheRAnnotation-method | 15.402 | 0.148 | 15.661 | |
| outputAnnotationFeatureMetadata_UI_helper | 0.006 | 0.000 | 0.006 | |
| outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.021 | 0.001 | 0.022 | |
| outputAnnotationResult-peakPantheRAnnotation-method | 15.685 | 0.122 | 15.875 | |
| outputAnnotationSpectraMetadata_UI_helper | 0.006 | 0.000 | 0.006 | |
| peakFit-peakPantheRAnnotation-method | 0.021 | 0.001 | 0.023 | |
| peakPantheRAnnotation | 0.030 | 0.002 | 0.031 | |
| peakPantheR_ROIStatistics | 23.42 | 0.35 | 23.96 | |
| peakPantheR_loadAnnotationParamsCSV | 0.007 | 0.001 | 0.008 | |
| peakPantheR_parallelAnnotation | 16.786 | 0.351 | 17.525 | |
| peakPantheR_plotEICFit | 0.550 | 0.006 | 0.559 | |
| peakPantheR_plotPeakwidth | 1.084 | 0.045 | 1.140 | |
| peakPantheR_quickEIC | 4.645 | 0.067 | 4.741 | |
| peakPantheR_singleFileSearch | 5.478 | 0.062 | 5.592 | |
| peakPantheR_start_GUI | 0 | 0 | 0 | |
| peakTables-peakPantheRAnnotation-method | 0.027 | 0.002 | 0.029 | |
| resetAnnotation-peakPantheRAnnotation-method | 0.035 | 0.006 | 0.044 | |
| resetFIR-peakPantheRAnnotation-method | 0.006 | 0.001 | 0.006 | |
| retentionTimeCorrection-peakPantheRAnnotation-method | 10.633 | 0.081 | 10.775 | |
| spectraMetadata-peakPantheRAnnotation-method | 0.024 | 0.002 | 0.026 | |
| spectraPaths_and_metadata_UI_helper | 0.003 | 0.002 | 0.004 | |
| spectra_metadata_colourScheme_UI_helper | 0.006 | 0.001 | 0.007 | |
| uROI-peakPantheRAnnotation-method | 0.026 | 0.002 | 0.028 | |
| uROIExist-peakPantheRAnnotation-method | 0.023 | 0.002 | 0.024 | |
| useFIR-peakPantheRAnnotation-method | 0.027 | 0.002 | 0.028 | |
| useUROI-peakPantheRAnnotation-method | 0.025 | 0.002 | 0.028 | |