Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-25 11:39 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4690 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4404 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4353 |
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 1493/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
peakPantheR 1.19.0 (landing page) Arnaud Wolfer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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: 1.19.0 |
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_1.19.0.tar.gz |
StartedAt: 2024-06-24 22:05:33 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 22:28:03 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 1349.8 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_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/peakPantheR.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘peakPantheR/DESCRIPTION’ ... OK * this is package ‘peakPantheR’ version ‘1.19.0’ * 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 22.093 0.470 23.022 peakPantheR_parallelAnnotation 16.605 0.159 16.899 outputAnnotationDiagnostic-peakPantheRAnnotation-method 15.810 0.155 16.077 outputAnnotationResult-peakPantheRAnnotation-method 15.225 0.139 15.446 EICs-peakPantheRAnnotation-method 12.619 0.706 13.443 retentionTimeCorrection-peakPantheRAnnotation-method 10.897 0.085 11.056 peakPantheR_singleFileSearch 5.296 0.063 5.398 * 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/4.4-x86_64/Resources/library’ * installing *source* package ‘peakPantheR’ ... ** 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 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" Copyright (C) 2024 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 1.19.0 > > test_check("peakPantheR") 2024-06-24 22:14:23.851 R[67226:169610924] XType: com.apple.fonts is not accessible. 2024-06-24 22:14:23.851 R[67226:169610924] XType: XTFontStaticRegistry is enabled. 2024-06-24 22:14:39.965 R[97086:169786645] XType: com.apple.fonts is not accessible. 2024-06-24 22:14:39.965 R[97086:169786645] XType: XTFontStaticRegistry is enabled. 2024-06-24 22:14:50.205 R[97717:169788085] XType: com.apple.fonts is not accessible. 2024-06-24 22:14:50.205 R[97717:169788085] XType: XTFontStaticRegistry is enabled. 2024-06-24 22:19:09.223 R[19230:169832874] XType: com.apple.fonts is not accessible. 2024-06-24 22:19:09.223 R[19230:169832874] XType: XTFontStaticRegistry is enabled. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1478 ] Warning messages: 1: In .Internal(gc(verbose, reset, full)) : closing unused connection 10 (/private/tmp/RtmpaB2lki/notValidXML.mzML) 2: In .Internal(gc(verbose, reset, full)) : closing unused connection 9 (/private/tmp/RtmpaB2lki/notValidXML.mzML) 3: In .Internal(gc(verbose, reset, full)) : closing unused connection 8 (/private/tmp/RtmpaB2lki/notValidXML.mzML) 4: In .Internal(gc(verbose, reset, full)) : closing unused connection 7 (/private/tmp/RtmpaB2lki/notValidXML.mzML) 5: In .Internal(gc(verbose, reset, full)) : closing unused connection 6 (/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/peakPantheR/extdata/test_fakemzML.mzML) > > proc.time() user system elapsed 829.337 9.309 1146.251
peakPantheR.Rcheck/peakPantheR-Ex.timings
name | user | system | elapsed | |
EICs-peakPantheRAnnotation-method | 12.619 | 0.706 | 13.443 | |
FIR-peakPantheRAnnotation-method | 0.074 | 0.005 | 0.078 | |
ROI-peakPantheRAnnotation-method | 0.069 | 0.004 | 0.074 | |
TIC-peakPantheRAnnotation-method | 0.076 | 0.005 | 0.082 | |
acquisitionTime-peakPantheRAnnotation-method | 0.069 | 0.006 | 0.076 | |
annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.062 | 0.004 | 0.067 | |
annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.063 | 0.005 | 0.068 | |
annotationTable-peakPantheRAnnotation-method | 0.066 | 0.005 | 0.072 | |
annotation_diagnostic_multiplot_UI_helper | 0.120 | 0.017 | 0.137 | |
annotation_fit_summary_UI_helper | 0.007 | 0.001 | 0.008 | |
annotation_showMethod_UI_helper | 0.003 | 0.001 | 0.004 | |
annotation_showText_UI_helper | 0.001 | 0.001 | 0.001 | |
cpdID-peakPantheRAnnotation-method | 0.069 | 0.005 | 0.075 | |
cpdMetadata-peakPantheRAnnotation-method | 0.073 | 0.006 | 0.080 | |
cpdName-peakPantheRAnnotation-method | 0.068 | 0.006 | 0.073 | |
dataPoints-peakPantheRAnnotation-method | 0.065 | 0.006 | 0.071 | |
filename-peakPantheRAnnotation-method | 0.067 | 0.005 | 0.073 | |
filepath-peakPantheRAnnotation-method | 0.099 | 0.006 | 0.106 | |
initialise_annotation_from_files_UI_helper | 0.014 | 0.001 | 0.015 | |
isAnnotated-peakPantheRAnnotation-method | 0.064 | 0.004 | 0.067 | |
load_annotation_from_file_UI_helper | 0.008 | 0.001 | 0.010 | |
nbCompounds-peakPantheRAnnotation-method | 0.069 | 0.004 | 0.074 | |
nbSamples-peakPantheRAnnotation-method | 0.070 | 0.004 | 0.075 | |
outputAnnotationDiagnostic-peakPantheRAnnotation-method | 15.810 | 0.155 | 16.077 | |
outputAnnotationFeatureMetadata_UI_helper | 0.006 | 0.000 | 0.007 | |
outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.030 | 0.001 | 0.031 | |
outputAnnotationResult-peakPantheRAnnotation-method | 15.225 | 0.139 | 15.446 | |
outputAnnotationSpectraMetadata_UI_helper | 0.006 | 0.000 | 0.008 | |
peakFit-peakPantheRAnnotation-method | 0.075 | 0.004 | 0.079 | |
peakPantheRAnnotation | 0.082 | 0.005 | 0.087 | |
peakPantheR_ROIStatistics | 22.093 | 0.470 | 23.022 | |
peakPantheR_loadAnnotationParamsCSV | 0.006 | 0.002 | 0.008 | |
peakPantheR_parallelAnnotation | 16.605 | 0.159 | 16.899 | |
peakPantheR_plotEICFit | 0.393 | 0.004 | 0.398 | |
peakPantheR_plotPeakwidth | 0.662 | 0.016 | 0.685 | |
peakPantheR_quickEIC | 4.860 | 0.061 | 4.969 | |
peakPantheR_singleFileSearch | 5.296 | 0.063 | 5.398 | |
peakPantheR_start_GUI | 0 | 0 | 0 | |
peakTables-peakPantheRAnnotation-method | 0.076 | 0.005 | 0.080 | |
resetAnnotation-peakPantheRAnnotation-method | 0.080 | 0.006 | 0.086 | |
resetFIR-peakPantheRAnnotation-method | 0.006 | 0.001 | 0.006 | |
retentionTimeCorrection-peakPantheRAnnotation-method | 10.897 | 0.085 | 11.056 | |
spectraMetadata-peakPantheRAnnotation-method | 0.076 | 0.005 | 0.080 | |
spectraPaths_and_metadata_UI_helper | 0.003 | 0.002 | 0.004 | |
spectra_metadata_colourScheme_UI_helper | 0.004 | 0.001 | 0.005 | |
uROI-peakPantheRAnnotation-method | 0.079 | 0.005 | 0.083 | |
uROIExist-peakPantheRAnnotation-method | 0.073 | 0.004 | 0.078 | |
useFIR-peakPantheRAnnotation-method | 0.066 | 0.005 | 0.071 | |
useUROI-peakPantheRAnnotation-method | 0.076 | 0.005 | 0.081 | |