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This page was generated on 2025-10-07 12:05 -0400 (Tue, 07 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 1555/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.23.3  (landing page)
Arnaud Wolfer
Snapshot Date: 2025-10-06 13:45 -0400 (Mon, 06 Oct 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  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 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 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: 2025-10-06 23:43:50 -0400 (Mon, 06 Oct 2025)
EndedAt: 2025-10-07 00:06:59 -0400 (Tue, 07 Oct 2025)
EllapsedTime: 1388.8 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                               23.327  0.278  23.706
outputAnnotationDiagnostic-peakPantheRAnnotation-method 16.629  0.186  16.954
peakPantheR_parallelAnnotation                          16.359  0.149  16.619
outputAnnotationResult-peakPantheRAnnotation-method     15.982  0.147  16.211
EICs-peakPantheRAnnotation-method                       13.719  0.937  15.005
retentionTimeCorrection-peakPantheRAnnotation-method    10.757  0.145  11.027
peakPantheR_singleFileSearch                             5.778  0.065   5.875
* 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")
2025-10-06 23:53:13.303 R[11358:474342034] XType: com.apple.fonts is not accessible.
2025-10-06 23:53:13.303 R[11358:474342034] XType: XTFontStaticRegistry is enabled.
2025-10-06 23:53:33.201 R[38177:474414318] XType: com.apple.fonts is not accessible.
2025-10-06 23:53:33.201 R[38177:474414318] XType: XTFontStaticRegistry is enabled.
2025-10-06 23:53:45.728 R[39120:474416401] XType: com.apple.fonts is not accessible.
2025-10-06 23:53:45.728 R[39120:474416401] XType: XTFontStaticRegistry is enabled.
2025-10-06 23:58:20.568 R[62486:474465243] XType: com.apple.fonts is not accessible.
2025-10-06 23:58:20.568 R[62486:474465243] 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/Rtmpkcash7/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/private/tmp/Rtmpkcash7/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/private/tmp/Rtmpkcash7/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/private/tmp/Rtmpkcash7/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 
 823.855    9.385 1171.364 

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method13.719 0.93715.005
FIR-peakPantheRAnnotation-method0.0340.0030.037
ROI-peakPantheRAnnotation-method0.0280.0030.031
TIC-peakPantheRAnnotation-method0.0250.0030.027
acquisitionTime-peakPantheRAnnotation-method0.0260.0030.029
annotationDiagnosticPlots-peakPantheRAnnotation-method0.0260.0030.029
annotationParamsDiagnostic-peakPantheRAnnotation-method0.0270.0030.030
annotationTable-peakPantheRAnnotation-method0.0280.0030.030
annotation_diagnostic_multiplot_UI_helper0.1790.0220.203
annotation_fit_summary_UI_helper0.0090.0020.011
annotation_showMethod_UI_helper0.0050.0010.007
annotation_showText_UI_helper0.0010.0000.001
cpdID-peakPantheRAnnotation-method0.0260.0030.028
cpdMetadata-peakPantheRAnnotation-method0.0270.0030.031
cpdName-peakPantheRAnnotation-method0.0250.0030.028
dataPoints-peakPantheRAnnotation-method0.0270.0020.030
filename-peakPantheRAnnotation-method0.0260.0020.028
filepath-peakPantheRAnnotation-method0.0260.0030.029
initialise_annotation_from_files_UI_helper0.0170.0030.020
isAnnotated-peakPantheRAnnotation-method0.0230.0030.026
load_annotation_from_file_UI_helper0.0070.0020.008
nbCompounds-peakPantheRAnnotation-method0.0250.0030.028
nbSamples-peakPantheRAnnotation-method0.0250.0020.028
outputAnnotationDiagnostic-peakPantheRAnnotation-method16.629 0.18616.954
outputAnnotationFeatureMetadata_UI_helper0.0070.0000.007
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0220.0010.024
outputAnnotationResult-peakPantheRAnnotation-method15.982 0.14716.211
outputAnnotationSpectraMetadata_UI_helper0.0070.0000.007
peakFit-peakPantheRAnnotation-method0.0260.0020.028
peakPantheRAnnotation0.0350.0030.037
peakPantheR_ROIStatistics23.327 0.27823.706
peakPantheR_loadAnnotationParamsCSV0.0070.0020.008
peakPantheR_parallelAnnotation16.359 0.14916.619
peakPantheR_plotEICFit0.6050.0050.613
peakPantheR_plotPeakwidth1.0590.0321.101
peakPantheR_quickEIC4.6930.0654.783
peakPantheR_singleFileSearch5.7780.0655.875
peakPantheR_start_GUI000
peakTables-peakPantheRAnnotation-method0.0290.0030.033
resetAnnotation-peakPantheRAnnotation-method0.0340.0040.038
resetFIR-peakPantheRAnnotation-method0.0070.0010.007
retentionTimeCorrection-peakPantheRAnnotation-method10.757 0.14511.027
spectraMetadata-peakPantheRAnnotation-method0.0200.0020.023
spectraPaths_and_metadata_UI_helper0.0020.0020.006
spectra_metadata_colourScheme_UI_helper0.0040.0010.005
uROI-peakPantheRAnnotation-method0.0210.0030.027
uROIExist-peakPantheRAnnotation-method0.0200.0020.022
useFIR-peakPantheRAnnotation-method0.0200.0020.024
useUROI-peakPantheRAnnotation-method0.0170.0020.019