Arnaud Wolfer
| Snapshot Date: 2025-11-05 13:40 -0500 (Wed, 05 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/peakPantheR |
| git_branch: devel |
| git_last_commit: 5618c13 |
| git_last_commit_date: 2025-10-29 10:54:31 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-06 11:32 -0500 (Thu, 06 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4818 |
| 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 1548/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| peakPantheR 1.25.0 (landing page) Arnaud Wolfer
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
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. |
| Package: peakPantheR |
| Version: 1.25.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings peakPantheR_1.25.0.tar.gz |
| StartedAt: 2025-11-06 02:26:33 -0500 (Thu, 06 Nov 2025) |
| EndedAt: 2025-11-06 02:49:53 -0500 (Thu, 06 Nov 2025) |
| EllapsedTime: 1399.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: peakPantheR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings peakPantheR_1.25.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/peakPantheR.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.25.0’
* 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 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 22.217 0.518 22.744
peakPantheR_parallelAnnotation 15.899 1.238 17.138
outputAnnotationResult-peakPantheRAnnotation-method 15.931 0.672 16.605
outputAnnotationDiagnostic-peakPantheRAnnotation-method 15.648 0.388 16.051
EICs-peakPantheRAnnotation-method 11.512 0.632 12.151
retentionTimeCorrection-peakPantheRAnnotation-method 11.096 0.180 11.277
peakPantheR_singleFileSearch 5.472 0.152 5.624
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
peakPantheR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL peakPantheR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘peakPantheR’ ... ** this is package ‘peakPantheR’ version ‘1.25.0’ ** 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)
peakPantheR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 1.25.0
>
> test_check("peakPantheR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1460 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
closing unused connection 10 (/tmp/Rtmp0o9Tc7/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 9 (/tmp/Rtmp0o9Tc7/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (/tmp/Rtmp0o9Tc7/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (/tmp/Rtmp0o9Tc7/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (/home/biocbuild/bbs-3.23-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (/home/biocbuild/bbs-3.23-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
>
> proc.time()
user system elapsed
763.316 10.936 1076.276
peakPantheR.Rcheck/peakPantheR-Ex.timings
| name | user | system | elapsed | |
| EICs-peakPantheRAnnotation-method | 11.512 | 0.632 | 12.151 | |
| FIR-peakPantheRAnnotation-method | 0.022 | 0.002 | 0.024 | |
| ROI-peakPantheRAnnotation-method | 0.017 | 0.001 | 0.018 | |
| TIC-peakPantheRAnnotation-method | 0.017 | 0.000 | 0.017 | |
| acquisitionTime-peakPantheRAnnotation-method | 0.015 | 0.002 | 0.017 | |
| annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.017 | 0.000 | 0.017 | |
| annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.015 | 0.002 | 0.017 | |
| annotationTable-peakPantheRAnnotation-method | 0.017 | 0.003 | 0.020 | |
| annotation_diagnostic_multiplot_UI_helper | 0.152 | 0.011 | 0.163 | |
| annotation_fit_summary_UI_helper | 0.008 | 0.000 | 0.008 | |
| annotation_showMethod_UI_helper | 0.002 | 0.002 | 0.004 | |
| annotation_showText_UI_helper | 0.001 | 0.000 | 0.001 | |
| cpdID-peakPantheRAnnotation-method | 0.022 | 0.000 | 0.022 | |
| cpdMetadata-peakPantheRAnnotation-method | 0.020 | 0.001 | 0.021 | |
| cpdName-peakPantheRAnnotation-method | 0.02 | 0.00 | 0.02 | |
| dataPoints-peakPantheRAnnotation-method | 0.017 | 0.002 | 0.019 | |
| filename-peakPantheRAnnotation-method | 0.015 | 0.003 | 0.018 | |
| filepath-peakPantheRAnnotation-method | 0.017 | 0.002 | 0.019 | |
| initialise_annotation_from_files_UI_helper | 0.011 | 0.002 | 0.013 | |
| isAnnotated-peakPantheRAnnotation-method | 0.019 | 0.000 | 0.019 | |
| load_annotation_from_file_UI_helper | 0.005 | 0.002 | 0.007 | |
| nbCompounds-peakPantheRAnnotation-method | 0.017 | 0.002 | 0.019 | |
| nbSamples-peakPantheRAnnotation-method | 0.117 | 0.004 | 0.121 | |
| outputAnnotationDiagnostic-peakPantheRAnnotation-method | 15.648 | 0.388 | 16.051 | |
| outputAnnotationFeatureMetadata_UI_helper | 0.005 | 0.001 | 0.006 | |
| outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.022 | 0.005 | 0.027 | |
| outputAnnotationResult-peakPantheRAnnotation-method | 15.931 | 0.672 | 16.605 | |
| outputAnnotationSpectraMetadata_UI_helper | 0.006 | 0.000 | 0.006 | |
| peakFit-peakPantheRAnnotation-method | 0.016 | 0.002 | 0.019 | |
| peakPantheRAnnotation | 0.025 | 0.000 | 0.025 | |
| peakPantheR_ROIStatistics | 22.217 | 0.518 | 22.744 | |
| peakPantheR_loadAnnotationParamsCSV | 0.007 | 0.000 | 0.007 | |
| peakPantheR_parallelAnnotation | 15.899 | 1.238 | 17.138 | |
| peakPantheR_plotEICFit | 0.502 | 0.009 | 0.511 | |
| peakPantheR_plotPeakwidth | 0.923 | 0.062 | 0.985 | |
| peakPantheR_quickEIC | 4.702 | 0.169 | 4.873 | |
| peakPantheR_singleFileSearch | 5.472 | 0.152 | 5.624 | |
| peakPantheR_start_GUI | 0.001 | 0.000 | 0.000 | |
| peakTables-peakPantheRAnnotation-method | 0.016 | 0.002 | 0.018 | |
| resetAnnotation-peakPantheRAnnotation-method | 0.024 | 0.001 | 0.025 | |
| resetFIR-peakPantheRAnnotation-method | 0.005 | 0.000 | 0.005 | |
| retentionTimeCorrection-peakPantheRAnnotation-method | 11.096 | 0.180 | 11.277 | |
| spectraMetadata-peakPantheRAnnotation-method | 0.019 | 0.002 | 0.020 | |
| spectraPaths_and_metadata_UI_helper | 0.001 | 0.001 | 0.003 | |
| spectra_metadata_colourScheme_UI_helper | 0.005 | 0.000 | 0.005 | |
| uROI-peakPantheRAnnotation-method | 0.018 | 0.003 | 0.020 | |
| uROIExist-peakPantheRAnnotation-method | 0.014 | 0.002 | 0.016 | |
| useFIR-peakPantheRAnnotation-method | 0.017 | 0.001 | 0.018 | |
| useUROI-peakPantheRAnnotation-method | 0.017 | 0.001 | 0.018 | |