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This page was generated on 2025-11-24 12:05 -0500 (Mon, 24 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4873
merida1macOS 12.7.6 Montereyx86_644.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" 4654
kjohnson1macOS 13.7.5 Venturaarm644.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" 4600
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4668
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 1571/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.24.0  (landing page)
Arnaud Wolfer
Snapshot Date: 2025-11-20 15:01 -0500 (Thu, 20 Nov 2025)
git_url: https://git.bioconductor.org/packages/peakPantheR
git_branch: RELEASE_3_22
git_last_commit: 9bede65
git_last_commit_date: 2025-10-29 10:54:31 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for peakPantheR on merida1

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: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2025-11-21 09:25:38 -0500 (Fri, 21 Nov 2025)
EndedAt: 2025-11-21 10:00:29 -0500 (Fri, 21 Nov 2025)
EllapsedTime: 2090.8 seconds
RetCode: 0
Status:   OK  
CheckDir: peakPantheR.Rcheck
Warnings: 0

Command output

##############################################################################
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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_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/peakPantheR.Rcheck’
* using R version 4.5.2 Patched (2025-11-05 r88990)
* 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 ‘1.24.0’
* 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 ‘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                               30.560  0.515  31.464
EICs-peakPantheRAnnotation-method                       23.436  1.165  25.166
peakPantheR_parallelAnnotation                          19.722  0.160  20.015
outputAnnotationDiagnostic-peakPantheRAnnotation-method 18.433  0.151  19.104
outputAnnotationResult-peakPantheRAnnotation-method     18.123  0.125  18.510
retentionTimeCorrection-peakPantheRAnnotation-method    12.633  0.099  12.957
peakPantheR_singleFileSearch                             6.409  0.069   6.593
peakPantheR_quickEIC                                     5.712  0.075   6.024
* 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 ‘1.24.0’
** 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 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"
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 1.24.0 

> 
> test_check("peakPantheR")
2025-11-21 09:39:20.805 R[16397:38227338] XType: com.apple.fonts is not accessible.
2025-11-21 09:39:20.805 R[16397:38227338] XType: XTFontStaticRegistry is enabled.
2025-11-21 09:40:06.011 R[33687:38264819] XType: com.apple.fonts is not accessible.
2025-11-21 09:40:06.011 R[33687:38264819] XType: XTFontStaticRegistry is enabled.
2025-11-21 09:40:31.088 R[35019:38267820] XType: com.apple.fonts is not accessible.
2025-11-21 09:40:31.088 R[35019:38267820] XType: XTFontStaticRegistry is enabled.
2025-11-21 09:47:51.053 R[50895:38308732] XType: com.apple.fonts is not accessible.
2025-11-21 09:47:51.053 R[50895:38308732] 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/RtmpRzfUmq/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/private/tmp/RtmpRzfUmq/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/private/tmp/RtmpRzfUmq/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/private/tmp/RtmpRzfUmq/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 
1160.086   10.215 1772.248

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method23.436 1.16525.166
FIR-peakPantheRAnnotation-method0.0480.0030.051
ROI-peakPantheRAnnotation-method0.0390.0030.043
TIC-peakPantheRAnnotation-method0.0360.0030.039
acquisitionTime-peakPantheRAnnotation-method0.0380.0040.043
annotationDiagnosticPlots-peakPantheRAnnotation-method0.0370.0030.040
annotationParamsDiagnostic-peakPantheRAnnotation-method0.0380.0030.041
annotationTable-peakPantheRAnnotation-method0.0380.0030.042
annotation_diagnostic_multiplot_UI_helper0.3800.0310.413
annotation_fit_summary_UI_helper0.0180.0040.022
annotation_showMethod_UI_helper0.0090.0020.012
annotation_showText_UI_helper0.0010.0010.002
cpdID-peakPantheRAnnotation-method0.0360.0050.041
cpdMetadata-peakPantheRAnnotation-method0.0380.0040.042
cpdName-peakPantheRAnnotation-method0.0360.0050.041
dataPoints-peakPantheRAnnotation-method0.0380.0050.043
filename-peakPantheRAnnotation-method0.0370.0040.042
filepath-peakPantheRAnnotation-method0.0360.0050.042
initialise_annotation_from_files_UI_helper0.0300.0060.041
isAnnotated-peakPantheRAnnotation-method0.0360.0040.040
load_annotation_from_file_UI_helper0.0150.0040.020
nbCompounds-peakPantheRAnnotation-method0.0370.0050.043
nbSamples-peakPantheRAnnotation-method0.1560.0040.161
outputAnnotationDiagnostic-peakPantheRAnnotation-method18.433 0.15119.104
outputAnnotationFeatureMetadata_UI_helper0.0130.0010.016
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0580.0020.063
outputAnnotationResult-peakPantheRAnnotation-method18.123 0.12518.510
outputAnnotationSpectraMetadata_UI_helper0.0140.0010.015
peakFit-peakPantheRAnnotation-method0.0380.0020.041
peakPantheRAnnotation0.0570.0050.063
peakPantheR_ROIStatistics30.560 0.51531.464
peakPantheR_loadAnnotationParamsCSV0.0140.0030.016
peakPantheR_parallelAnnotation19.722 0.16020.015
peakPantheR_plotEICFit1.3270.0081.339
peakPantheR_plotPeakwidth2.3780.1022.571
peakPantheR_quickEIC5.7120.0756.024
peakPantheR_singleFileSearch6.4090.0696.593
peakPantheR_start_GUI0.0000.0010.001
peakTables-peakPantheRAnnotation-method0.0390.0040.044
resetAnnotation-peakPantheRAnnotation-method0.0510.0050.056
resetFIR-peakPantheRAnnotation-method0.0110.0010.014
retentionTimeCorrection-peakPantheRAnnotation-method12.633 0.09912.957
spectraMetadata-peakPantheRAnnotation-method0.0370.0040.051
spectraPaths_and_metadata_UI_helper0.0050.0040.085
spectra_metadata_colourScheme_UI_helper0.0130.0030.017
uROI-peakPantheRAnnotation-method0.0400.0060.047
uROIExist-peakPantheRAnnotation-method0.0380.0050.070
useFIR-peakPantheRAnnotation-method0.0350.0040.045
useUROI-peakPantheRAnnotation-method0.0370.0040.044