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This page was generated on 2025-08-09 12:08 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 1538/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.23.0  (landing page)
Arnaud Wolfer
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/peakPantheR
git_branch: devel
git_last_commit: c81e5f2
git_last_commit_date: 2025-04-15 11:50:16 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    ERROR    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: 1.23.0
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_1.23.0.tar.gz
StartedAt: 2025-08-08 23:01:45 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 23:24:38 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 1372.7 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_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/peakPantheR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.23.0’
* 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                               21.571  0.513  22.534
outputAnnotationDiagnostic-peakPantheRAnnotation-method 16.013  0.157  16.249
peakPantheR_parallelAnnotation                          15.612  0.157  15.895
outputAnnotationResult-peakPantheRAnnotation-method     15.490  0.126  15.679
EICs-peakPantheRAnnotation-method                       13.777  0.754  14.654
retentionTimeCorrection-peakPantheRAnnotation-method    10.947  0.112  11.158
peakPantheR_singleFileSearch                             5.467  0.064   5.570
* 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 ‘1.23.0’
** 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 4.5.1 (2025-06-13) -- "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 1.23.0 

> 
> test_check("peakPantheR")
2025-08-08 23:10:47.855 R[95757:418532286] XType: com.apple.fonts is not accessible.
2025-08-08 23:10:47.856 R[95757:418532286] XType: XTFontStaticRegistry is enabled.
2025-08-08 23:11:03.327 R[20658:418594159] XType: com.apple.fonts is not accessible.
2025-08-08 23:11:03.327 R[20658:418594159] XType: XTFontStaticRegistry is enabled.
2025-08-08 23:11:12.962 R[20834:418594682] XType: com.apple.fonts is not accessible.
2025-08-08 23:11:12.962 R[20834:418594682] XType: XTFontStaticRegistry is enabled.
2025-08-08 23:15:32.108 R[41356:418637183] XType: com.apple.fonts is not accessible.
2025-08-08 23:15:32.109 R[41356:418637183] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1478 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1478 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (/private/tmp/RtmpKEhQOc/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/private/tmp/RtmpKEhQOc/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/private/tmp/RtmpKEhQOc/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/private/tmp/RtmpKEhQOc/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 
 828.985    8.922 1160.432

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method13.777 0.75414.654
FIR-peakPantheRAnnotation-method0.0300.0040.034
ROI-peakPantheRAnnotation-method0.0280.0030.032
TIC-peakPantheRAnnotation-method0.0250.0020.027
acquisitionTime-peakPantheRAnnotation-method0.0290.0030.032
annotationDiagnosticPlots-peakPantheRAnnotation-method0.0240.0030.027
annotationParamsDiagnostic-peakPantheRAnnotation-method0.0220.0030.024
annotationTable-peakPantheRAnnotation-method0.0240.0030.026
annotation_diagnostic_multiplot_UI_helper0.1210.0170.139
annotation_fit_summary_UI_helper0.0090.0010.011
annotation_showMethod_UI_helper0.0040.0010.005
annotation_showText_UI_helper0.0010.0000.002
cpdID-peakPantheRAnnotation-method0.0250.0020.027
cpdMetadata-peakPantheRAnnotation-method0.0290.0030.032
cpdName-peakPantheRAnnotation-method0.0260.0030.029
dataPoints-peakPantheRAnnotation-method0.0280.0030.030
filename-peakPantheRAnnotation-method0.0260.0030.029
filepath-peakPantheRAnnotation-method0.0250.0030.029
initialise_annotation_from_files_UI_helper0.0140.0030.016
isAnnotated-peakPantheRAnnotation-method0.0250.0020.029
load_annotation_from_file_UI_helper0.0080.0020.010
nbCompounds-peakPantheRAnnotation-method0.0250.0020.027
nbSamples-peakPantheRAnnotation-method0.0260.0030.029
outputAnnotationDiagnostic-peakPantheRAnnotation-method16.013 0.15716.249
outputAnnotationFeatureMetadata_UI_helper0.0040.0010.005
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0240.0010.024
outputAnnotationResult-peakPantheRAnnotation-method15.490 0.12615.679
outputAnnotationSpectraMetadata_UI_helper0.0060.0010.006
peakFit-peakPantheRAnnotation-method0.0280.0020.029
peakPantheRAnnotation0.0380.0030.041
peakPantheR_ROIStatistics21.571 0.51322.534
peakPantheR_loadAnnotationParamsCSV0.0060.0020.008
peakPantheR_parallelAnnotation15.612 0.15715.895
peakPantheR_plotEICFit0.3700.0050.376
peakPantheR_plotPeakwidth0.6390.0180.662
peakPantheR_quickEIC4.6770.0644.790
peakPantheR_singleFileSearch5.4670.0645.570
peakPantheR_start_GUI000
peakTables-peakPantheRAnnotation-method0.0280.0020.030
resetAnnotation-peakPantheRAnnotation-method0.0340.0020.037
resetFIR-peakPantheRAnnotation-method0.0050.0010.006
retentionTimeCorrection-peakPantheRAnnotation-method10.947 0.11211.158
spectraMetadata-peakPantheRAnnotation-method0.0250.0020.028
spectraPaths_and_metadata_UI_helper0.0030.0010.004
spectra_metadata_colourScheme_UI_helper0.0050.0010.006
uROI-peakPantheRAnnotation-method0.0280.0020.032
uROIExist-peakPantheRAnnotation-method0.0230.0010.026
useFIR-peakPantheRAnnotation-method0.0250.0020.027
useUROI-peakPantheRAnnotation-method0.0210.0010.023