Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2025-10-04 12:07 -0400 (Sat, 04 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" 4576
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: 2025-10-03 13:45 -0400 (Fri, 03 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: peakPantheR
Version: 1.23.3
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings peakPantheR_1.23.3.tar.gz
StartedAt: 2025-10-03 10:06:25 -0000 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 10:29:28 -0000 (Fri, 03 Oct 2025)
EllapsedTime: 1382.4 seconds
RetCode: 0
Status:   OK  
CheckDir: peakPantheR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings peakPantheR_1.23.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/peakPantheR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 loading without being on the library search path ... 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                               22.868  0.176  23.126
EICs-peakPantheRAnnotation-method                       14.671  0.602  15.371
peakPantheR_parallelAnnotation                          15.134  0.036  15.199
outputAnnotationDiagnostic-peakPantheRAnnotation-method 14.871  0.068  15.068
outputAnnotationResult-peakPantheRAnnotation-method     14.825  0.024  14.890
retentionTimeCorrection-peakPantheRAnnotation-method     9.977  0.027  10.033
peakPantheR_singleFileSearch                             5.080  0.007   5.102
* 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL peakPantheR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1460 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (/home/biocbuild/tmp/Rtmpo42AVY/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/home/biocbuild/tmp/Rtmpo42AVY/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/home/biocbuild/tmp/Rtmpo42AVY/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/home/biocbuild/tmp/Rtmpo42AVY/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (/home/biocbuild/R/R-4.5.0/site-library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (/home/biocbuild/R/R-4.5.0/site-library/peakPantheR/extdata/test_fakemzML.mzML)
> 
> proc.time()
    user   system  elapsed 
 815.449    9.099 1179.711 

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method14.671 0.60215.371
FIR-peakPantheRAnnotation-method0.0320.0030.035
ROI-peakPantheRAnnotation-method0.0200.0070.028
TIC-peakPantheRAnnotation-method0.0260.0000.026
acquisitionTime-peakPantheRAnnotation-method0.0250.0040.028
annotationDiagnosticPlots-peakPantheRAnnotation-method0.0260.0000.026
annotationParamsDiagnostic-peakPantheRAnnotation-method0.0260.0000.026
annotationTable-peakPantheRAnnotation-method0.0240.0040.028
annotation_diagnostic_multiplot_UI_helper0.2010.0400.241
annotation_fit_summary_UI_helper0.0110.0000.011
annotation_showMethod_UI_helper0.0050.0000.006
annotation_showText_UI_helper0.0000.0000.001
cpdID-peakPantheRAnnotation-method0.0250.0000.026
cpdMetadata-peakPantheRAnnotation-method0.0260.0000.027
cpdName-peakPantheRAnnotation-method0.0260.0000.026
dataPoints-peakPantheRAnnotation-method0.0230.0040.026
filename-peakPantheRAnnotation-method0.0260.0000.026
filepath-peakPantheRAnnotation-method0.0270.0000.027
initialise_annotation_from_files_UI_helper0.0180.0000.018
isAnnotated-peakPantheRAnnotation-method0.0230.0040.027
load_annotation_from_file_UI_helper0.0090.0000.010
nbCompounds-peakPantheRAnnotation-method0.0270.0000.027
nbSamples-peakPantheRAnnotation-method0.0180.0080.027
outputAnnotationDiagnostic-peakPantheRAnnotation-method14.871 0.06815.068
outputAnnotationFeatureMetadata_UI_helper0.0030.0040.007
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0320.0000.033
outputAnnotationResult-peakPantheRAnnotation-method14.825 0.02414.890
outputAnnotationSpectraMetadata_UI_helper0.0080.0000.009
peakFit-peakPantheRAnnotation-method0.0260.0000.027
peakPantheRAnnotation0.0320.0000.032
peakPantheR_ROIStatistics22.868 0.17623.126
peakPantheR_loadAnnotationParamsCSV0.0080.0000.008
peakPantheR_parallelAnnotation15.134 0.03615.199
peakPantheR_plotEICFit0.7770.0000.781
peakPantheR_plotPeakwidth1.2810.0001.285
peakPantheR_quickEIC4.3770.0124.402
peakPantheR_singleFileSearch5.0800.0075.102
peakPantheR_start_GUI000
peakTables-peakPantheRAnnotation-method0.0260.0010.026
resetAnnotation-peakPantheRAnnotation-method0.0320.0000.032
resetFIR-peakPantheRAnnotation-method0.0060.0000.006
retentionTimeCorrection-peakPantheRAnnotation-method 9.977 0.02710.033
spectraMetadata-peakPantheRAnnotation-method0.0260.0000.026
spectraPaths_and_metadata_UI_helper0.0030.0000.003
spectra_metadata_colourScheme_UI_helper0.0070.0000.006
uROI-peakPantheRAnnotation-method0.0270.0000.028
uROIExist-peakPantheRAnnotation-method0.0270.0000.026
useFIR-peakPantheRAnnotation-method0.0250.0000.026
useUROI-peakPantheRAnnotation-method0.0250.0000.025