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This page was generated on 2025-09-29 12:05 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4833
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4621
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4566
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 1551/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.23.3  (landing page)
Arnaud Wolfer
Snapshot Date: 2025-09-28 13:45 -0400 (Sun, 28 Sep 2025)
git_url: https://git.bioconductor.org/packages/peakPantheR
git_branch: devel
git_last_commit: 0d1b221
git_last_commit_date: 2025-09-27 18:38:06 -0400 (Sat, 27 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for peakPantheR on lconway

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.

raw results


Summary

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: 2025-09-28 23:15:10 -0400 (Sun, 28 Sep 2025)
EndedAt: 2025-09-28 23:38:30 -0400 (Sun, 28 Sep 2025)
EllapsedTime: 1400.1 seconds
RetCode: 0
Status:   OK  
CheckDir: peakPantheR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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                               23.336  0.271  23.722
outputAnnotationDiagnostic-peakPantheRAnnotation-method 17.026  0.185  17.348
peakPantheR_parallelAnnotation                          17.022  0.152  17.288
outputAnnotationResult-peakPantheRAnnotation-method     16.499  0.126  16.683
EICs-peakPantheRAnnotation-method                       13.419  0.760  14.325
retentionTimeCorrection-peakPantheRAnnotation-method    10.836  0.341  11.517
peakPantheR_singleFileSearch                             5.691  0.125   5.903
* 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


Installation output

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)

Tests output

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")
2025-09-28 23:24:36.443 R[74469:404447057] XType: com.apple.fonts is not accessible.
2025-09-28 23:24:36.443 R[74469:404447057] XType: XTFontStaticRegistry is enabled.
2025-09-28 23:24:56.306 R[1215:404521207] XType: com.apple.fonts is not accessible.
2025-09-28 23:24:56.306 R[1215:404521207] XType: XTFontStaticRegistry is enabled.
2025-09-28 23:25:08.602 R[2067:404523050] XType: com.apple.fonts is not accessible.
2025-09-28 23:25:08.602 R[2067:404523050] XType: XTFontStaticRegistry is enabled.
2025-09-28 23:29:44.277 R[24459:404570066] XType: com.apple.fonts is not accessible.
2025-09-28 23:29:44.277 R[24459:404570066] 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/RtmpJtbGIP/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/private/tmp/RtmpJtbGIP/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/private/tmp/RtmpJtbGIP/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/private/tmp/RtmpJtbGIP/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 
 837.515    8.929 1185.349 

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method13.419 0.76014.325
FIR-peakPantheRAnnotation-method0.0320.0030.035
ROI-peakPantheRAnnotation-method0.0290.0020.031
TIC-peakPantheRAnnotation-method0.0240.0020.028
acquisitionTime-peakPantheRAnnotation-method0.0270.0030.030
annotationDiagnosticPlots-peakPantheRAnnotation-method0.0270.0020.029
annotationParamsDiagnostic-peakPantheRAnnotation-method0.0260.0030.029
annotationTable-peakPantheRAnnotation-method0.0260.0030.029
annotation_diagnostic_multiplot_UI_helper0.1910.0220.216
annotation_fit_summary_UI_helper0.0080.0010.010
annotation_showMethod_UI_helper0.0050.0010.006
annotation_showText_UI_helper0.0010.0010.001
cpdID-peakPantheRAnnotation-method0.0280.0030.030
cpdMetadata-peakPantheRAnnotation-method0.0280.0030.030
cpdName-peakPantheRAnnotation-method0.0260.0030.030
dataPoints-peakPantheRAnnotation-method0.0260.0030.029
filename-peakPantheRAnnotation-method0.0240.0030.026
filepath-peakPantheRAnnotation-method0.0260.0030.028
initialise_annotation_from_files_UI_helper0.0160.0040.019
isAnnotated-peakPantheRAnnotation-method0.0260.0030.030
load_annotation_from_file_UI_helper0.0070.0020.010
nbCompounds-peakPantheRAnnotation-method0.0250.0030.028
nbSamples-peakPantheRAnnotation-method0.0260.0030.029
outputAnnotationDiagnostic-peakPantheRAnnotation-method17.026 0.18517.348
outputAnnotationFeatureMetadata_UI_helper0.0060.0010.006
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0250.0010.025
outputAnnotationResult-peakPantheRAnnotation-method16.499 0.12616.683
outputAnnotationSpectraMetadata_UI_helper0.0050.0010.006
peakFit-peakPantheRAnnotation-method0.0240.0020.026
peakPantheRAnnotation0.0340.0030.036
peakPantheR_ROIStatistics23.336 0.27123.722
peakPantheR_loadAnnotationParamsCSV0.0060.0010.007
peakPantheR_parallelAnnotation17.022 0.15217.288
peakPantheR_plotEICFit0.6170.0050.626
peakPantheR_plotPeakwidth1.1320.0351.177
peakPantheR_quickEIC4.7740.0544.853
peakPantheR_singleFileSearch5.6910.1255.903
peakPantheR_start_GUI0.0010.0000.000
peakTables-peakPantheRAnnotation-method0.0300.0030.032
resetAnnotation-peakPantheRAnnotation-method0.0350.0030.038
resetFIR-peakPantheRAnnotation-method0.0050.0010.006
retentionTimeCorrection-peakPantheRAnnotation-method10.836 0.34111.517
spectraMetadata-peakPantheRAnnotation-method0.0230.0020.026
spectraPaths_and_metadata_UI_helper0.0020.0010.003
spectra_metadata_colourScheme_UI_helper0.0040.0010.005
uROI-peakPantheRAnnotation-method0.0270.0020.029
uROIExist-peakPantheRAnnotation-method0.0240.0020.026
useFIR-peakPantheRAnnotation-method0.0250.0020.027
useUROI-peakPantheRAnnotation-method0.0290.0020.033