Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R 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 1552/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.22.1  (landing page)
Arnaud Wolfer
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/peakPantheR
git_branch: RELEASE_3_21
git_last_commit: bf87a9e
git_last_commit_date: 2025-09-27 17:27:28 -0400 (Sat, 27 Sep 2025)
nebbiolo1Linux (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    ERROR    OK  
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


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: 1.22.1
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_1.22.1.tar.gz
StartedAt: 2025-10-14 08:03:50 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 08:38:29 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 2078.8 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_1.22.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/peakPantheR.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.22.1’
* 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                               30.879  0.373  32.161
EICs-peakPantheRAnnotation-method                       21.646  1.091  22.831
peakPantheR_parallelAnnotation                          19.240  0.119  19.469
outputAnnotationDiagnostic-peakPantheRAnnotation-method 18.094  0.163  18.380
outputAnnotationResult-peakPantheRAnnotation-method     17.647  0.122  17.860
retentionTimeCorrection-peakPantheRAnnotation-method    11.763  0.061  11.838
peakPantheR_singleFileSearch                             6.123  0.055   6.199
peakPantheR_quickEIC                                     5.434  0.040   5.479
* 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 ‘1.22.1’
** 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 RC (2025-06-05 r88288) -- "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 1.22.1 

> 
> test_check("peakPantheR")
2025-10-14 08:17:09.739 R[99885:7165893] XType: com.apple.fonts is not accessible.
2025-10-14 08:17:09.740 R[99885:7165893] XType: XTFontStaticRegistry is enabled.
2025-10-14 08:17:54.689 R[17935:7211147] XType: com.apple.fonts is not accessible.
2025-10-14 08:17:54.689 R[17935:7211147] XType: XTFontStaticRegistry is enabled.
2025-10-14 08:18:20.242 R[20065:7214841] XType: com.apple.fonts is not accessible.
2025-10-14 08:18:20.242 R[20065:7214841] XType: XTFontStaticRegistry is enabled.
2025-10-14 08:25:15.270 R[34774:7254422] XType: com.apple.fonts is not accessible.
2025-10-14 08:25:15.270 R[34774:7254422] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1480 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (/private/tmp/Rtmp0ymxZS/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/private/tmp/Rtmp0ymxZS/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/private/tmp/Rtmp0ymxZS/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/private/tmp/Rtmp0ymxZS/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 
1181.144    9.803 1756.367 

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method21.646 1.09122.831
FIR-peakPantheRAnnotation-method0.0540.0040.057
ROI-peakPantheRAnnotation-method0.0390.0030.041
TIC-peakPantheRAnnotation-method0.0370.0020.039
acquisitionTime-peakPantheRAnnotation-method0.0380.0020.041
annotationDiagnosticPlots-peakPantheRAnnotation-method0.0350.0030.038
annotationParamsDiagnostic-peakPantheRAnnotation-method0.0360.0020.042
annotationTable-peakPantheRAnnotation-method0.0400.0030.042
annotation_diagnostic_multiplot_UI_helper0.3430.0260.369
annotation_fit_summary_UI_helper0.0180.0040.021
annotation_showMethod_UI_helper0.0090.0020.012
annotation_showText_UI_helper0.0010.0020.002
cpdID-peakPantheRAnnotation-method0.0310.0030.035
cpdMetadata-peakPantheRAnnotation-method0.0380.0040.044
cpdName-peakPantheRAnnotation-method0.0290.0040.032
dataPoints-peakPantheRAnnotation-method0.0350.0040.038
filename-peakPantheRAnnotation-method0.0360.0040.042
filepath-peakPantheRAnnotation-method0.0360.0050.041
initialise_annotation_from_files_UI_helper0.0290.0060.035
isAnnotated-peakPantheRAnnotation-method0.0350.0040.039
load_annotation_from_file_UI_helper0.0140.0050.018
nbCompounds-peakPantheRAnnotation-method0.0340.0040.038
nbSamples-peakPantheRAnnotation-method0.0330.0040.037
outputAnnotationDiagnostic-peakPantheRAnnotation-method18.094 0.16318.380
outputAnnotationFeatureMetadata_UI_helper0.0110.0010.011
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0500.0020.051
outputAnnotationResult-peakPantheRAnnotation-method17.647 0.12217.860
outputAnnotationSpectraMetadata_UI_helper0.0120.0010.013
peakFit-peakPantheRAnnotation-method0.0350.0030.037
peakPantheRAnnotation0.0560.0050.061
peakPantheR_ROIStatistics30.879 0.37332.161
peakPantheR_loadAnnotationParamsCSV0.0120.0020.015
peakPantheR_parallelAnnotation19.240 0.11919.469
peakPantheR_plotEICFit1.2600.0081.270
peakPantheR_plotPeakwidth2.1440.0532.200
peakPantheR_quickEIC5.4340.0405.479
peakPantheR_singleFileSearch6.1230.0556.199
peakPantheR_start_GUI0.0000.0000.001
peakTables-peakPantheRAnnotation-method0.0350.0040.039
resetAnnotation-peakPantheRAnnotation-method0.0440.0040.049
resetFIR-peakPantheRAnnotation-method0.0100.0020.011
retentionTimeCorrection-peakPantheRAnnotation-method11.763 0.06111.838
spectraMetadata-peakPantheRAnnotation-method0.0330.0030.036
spectraPaths_and_metadata_UI_helper0.0040.0030.007
spectra_metadata_colourScheme_UI_helper0.0100.0010.012
uROI-peakPantheRAnnotation-method0.0390.0030.043
uROIExist-peakPantheRAnnotation-method0.0320.0020.033
useFIR-peakPantheRAnnotation-method0.0310.0030.033
useUROI-peakPantheRAnnotation-method0.0320.0030.035