Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-01 12:05 -0400 (Mon, 01 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 1541/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
peakPantheR 1.23.0 (landing page) Arnaud Wolfer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.23.0 |
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: 2025-08-31 22:44:19 -0400 (Sun, 31 Aug 2025) |
EndedAt: 2025-08-31 23:06:23 -0400 (Sun, 31 Aug 2025) |
EllapsedTime: 1324.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: peakPantheR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 21.063 0.256 21.416 outputAnnotationDiagnostic-peakPantheRAnnotation-method 16.609 0.146 16.830 peakPantheR_parallelAnnotation 16.222 0.135 16.431 outputAnnotationResult-peakPantheRAnnotation-method 15.406 0.118 15.589 EICs-peakPantheRAnnotation-method 12.986 0.703 13.782 retentionTimeCorrection-peakPantheRAnnotation-method 10.431 0.089 10.632 peakPantheR_singleFileSearch 5.513 0.064 5.614 * 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
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)
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") 2025-08-31 22:53:01.712 R[56995:167165783] XType: com.apple.fonts is not accessible. 2025-08-31 22:53:01.713 R[56995:167165783] XType: XTFontStaticRegistry is enabled. 2025-08-31 22:53:16.319 R[81993:167236380] XType: com.apple.fonts is not accessible. 2025-08-31 22:53:16.319 R[81993:167236380] XType: XTFontStaticRegistry is enabled. 2025-08-31 22:53:25.665 R[82168:167236886] XType: com.apple.fonts is not accessible. 2025-08-31 22:53:25.665 R[82168:167236886] XType: XTFontStaticRegistry is enabled. 2025-08-31 22:57:32.473 R[2748:167279229] XType: com.apple.fonts is not accessible. 2025-08-31 22:57:32.473 R[2748:167279229] 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/Rtmp35uIvl/notValidXML.mzML) 2: In .Internal(gc(verbose, reset, full)) : closing unused connection 9 (/private/tmp/Rtmp35uIvl/notValidXML.mzML) 3: In .Internal(gc(verbose, reset, full)) : closing unused connection 8 (/private/tmp/Rtmp35uIvl/notValidXML.mzML) 4: In .Internal(gc(verbose, reset, full)) : closing unused connection 7 (/private/tmp/Rtmp35uIvl/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 799.467 8.429 1121.374
peakPantheR.Rcheck/peakPantheR-Ex.timings
name | user | system | elapsed | |
EICs-peakPantheRAnnotation-method | 12.986 | 0.703 | 13.782 | |
FIR-peakPantheRAnnotation-method | 0.038 | 0.004 | 0.042 | |
ROI-peakPantheRAnnotation-method | 0.029 | 0.003 | 0.032 | |
TIC-peakPantheRAnnotation-method | 0.026 | 0.003 | 0.029 | |
acquisitionTime-peakPantheRAnnotation-method | 0.030 | 0.003 | 0.033 | |
annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.030 | 0.003 | 0.033 | |
annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.030 | 0.003 | 0.032 | |
annotationTable-peakPantheRAnnotation-method | 0.031 | 0.003 | 0.036 | |
annotation_diagnostic_multiplot_UI_helper | 0.133 | 0.018 | 0.151 | |
annotation_fit_summary_UI_helper | 0.010 | 0.002 | 0.011 | |
annotation_showMethod_UI_helper | 0.005 | 0.002 | 0.006 | |
annotation_showText_UI_helper | 0.000 | 0.001 | 0.002 | |
cpdID-peakPantheRAnnotation-method | 0.028 | 0.003 | 0.031 | |
cpdMetadata-peakPantheRAnnotation-method | 0.028 | 0.003 | 0.031 | |
cpdName-peakPantheRAnnotation-method | 0.027 | 0.003 | 0.030 | |
dataPoints-peakPantheRAnnotation-method | 0.028 | 0.003 | 0.030 | |
filename-peakPantheRAnnotation-method | 0.028 | 0.003 | 0.030 | |
filepath-peakPantheRAnnotation-method | 0.029 | 0.003 | 0.032 | |
initialise_annotation_from_files_UI_helper | 0.015 | 0.003 | 0.018 | |
isAnnotated-peakPantheRAnnotation-method | 0.027 | 0.003 | 0.030 | |
load_annotation_from_file_UI_helper | 0.008 | 0.002 | 0.011 | |
nbCompounds-peakPantheRAnnotation-method | 0.026 | 0.003 | 0.029 | |
nbSamples-peakPantheRAnnotation-method | 0.027 | 0.003 | 0.030 | |
outputAnnotationDiagnostic-peakPantheRAnnotation-method | 16.609 | 0.146 | 16.830 | |
outputAnnotationFeatureMetadata_UI_helper | 0.006 | 0.000 | 0.007 | |
outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.028 | 0.001 | 0.029 | |
outputAnnotationResult-peakPantheRAnnotation-method | 15.406 | 0.118 | 15.589 | |
outputAnnotationSpectraMetadata_UI_helper | 0.005 | 0.001 | 0.005 | |
peakFit-peakPantheRAnnotation-method | 0.026 | 0.002 | 0.028 | |
peakPantheRAnnotation | 0.034 | 0.002 | 0.037 | |
peakPantheR_ROIStatistics | 21.063 | 0.256 | 21.416 | |
peakPantheR_loadAnnotationParamsCSV | 0.007 | 0.001 | 0.008 | |
peakPantheR_parallelAnnotation | 16.222 | 0.135 | 16.431 | |
peakPantheR_plotEICFit | 0.387 | 0.004 | 0.392 | |
peakPantheR_plotPeakwidth | 0.613 | 0.013 | 0.629 | |
peakPantheR_quickEIC | 4.670 | 0.053 | 4.747 | |
peakPantheR_singleFileSearch | 5.513 | 0.064 | 5.614 | |
peakPantheR_start_GUI | 0.000 | 0.000 | 0.001 | |
peakTables-peakPantheRAnnotation-method | 0.025 | 0.002 | 0.028 | |
resetAnnotation-peakPantheRAnnotation-method | 0.031 | 0.003 | 0.034 | |
resetFIR-peakPantheRAnnotation-method | 0.007 | 0.001 | 0.008 | |
retentionTimeCorrection-peakPantheRAnnotation-method | 10.431 | 0.089 | 10.632 | |
spectraMetadata-peakPantheRAnnotation-method | 0.027 | 0.002 | 0.029 | |
spectraPaths_and_metadata_UI_helper | 0.002 | 0.002 | 0.003 | |
spectra_metadata_colourScheme_UI_helper | 0.005 | 0.001 | 0.006 | |
uROI-peakPantheRAnnotation-method | 0.022 | 0.001 | 0.024 | |
uROIExist-peakPantheRAnnotation-method | 0.025 | 0.002 | 0.026 | |
useFIR-peakPantheRAnnotation-method | 0.023 | 0.002 | 0.025 | |
useUROI-peakPantheRAnnotation-method | 0.025 | 0.002 | 0.028 | |