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This page was generated on 2021-10-15 15:06:46 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the peakPantheR package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1366/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
peakPantheR 1.6.1 (landing page) Arnaud Wolfer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: peakPantheR |
Version: 1.6.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings peakPantheR_1.6.1.tar.gz |
StartedAt: 2021-10-14 22:11:36 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:28:17 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 1000.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: peakPantheR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings peakPantheR_1.6.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/peakPantheR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘peakPantheR/DESCRIPTION’ ... OK * this is package ‘peakPantheR’ version ‘1.6.1’ * 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 R 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 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 16.601 0.222 16.839 peakPantheR_parallelAnnotation 12.185 0.075 12.266 outputAnnotationDiagnostic-peakPantheRAnnotation-method 11.478 0.088 11.575 outputAnnotationResult-peakPantheRAnnotation-method 11.266 0.075 11.356 EICs-peakPantheRAnnotation-method 10.288 0.393 10.696 retentionTimeCorrection-peakPantheRAnnotation-method 7.840 0.048 7.896 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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/Versions/Current/Resources/bin/R CMD INSTALL peakPantheR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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 1.6.1 > > test_check("peakPantheR") [ FAIL 0 | WARN 6 | SKIP 0 | PASS 1434 ] Warning messages: 1: In .Internal(gc(verbose, reset, full)) : closing unused connection 8 (/private/tmp/RtmpONrbco/notValidXML.mzML) 2: In .Internal(gc(verbose, reset, full)) : closing unused connection 7 (/private/tmp/RtmpONrbco/notValidXML.mzML) 3: In .Internal(gc(verbose, reset, full)) : closing unused connection 6 (/Library/Frameworks/R.framework/Versions/4.1/Resources/library/peakPantheR/extdata/test_fakemzML.mzML) 4: In .Internal(gc(verbose, reset, full)) : closing unused connection 5 (/Library/Frameworks/R.framework/Versions/4.1/Resources/library/peakPantheR/extdata/test_fakemzML.mzML) > > proc.time() user system elapsed 633.086 3.984 829.134
peakPantheR.Rcheck/peakPantheR-Ex.timings
name | user | system | elapsed | |
EICs-peakPantheRAnnotation-method | 10.288 | 0.393 | 10.696 | |
FIR-peakPantheRAnnotation-method | 0.329 | 0.022 | 0.351 | |
ROI-peakPantheRAnnotation-method | 0.211 | 0.010 | 0.220 | |
TIC-peakPantheRAnnotation-method | 0.212 | 0.010 | 0.222 | |
acquisitionTime-peakPantheRAnnotation-method | 0.193 | 0.011 | 0.203 | |
annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.187 | 0.011 | 0.197 | |
annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.235 | 0.012 | 0.247 | |
annotationTable-peakPantheRAnnotation-method | 0.363 | 0.013 | 0.376 | |
annotation_diagnostic_multiplot_UI_helper | 0.108 | 0.001 | 0.109 | |
annotation_fit_summary_UI_helper | 0.009 | 0.000 | 0.010 | |
annotation_showMethod_UI_helper | 0.007 | 0.001 | 0.008 | |
annotation_showText_UI_helper | 0.001 | 0.001 | 0.001 | |
cpdID-peakPantheRAnnotation-method | 0.247 | 0.011 | 0.258 | |
cpdMetadata-peakPantheRAnnotation-method | 0.230 | 0.011 | 0.242 | |
cpdName-peakPantheRAnnotation-method | 0.274 | 0.012 | 0.286 | |
dataPoints-peakPantheRAnnotation-method | 0.224 | 0.010 | 0.235 | |
filename-peakPantheRAnnotation-method | 0.911 | 0.013 | 0.924 | |
filepath-peakPantheRAnnotation-method | 0.218 | 0.010 | 0.228 | |
initialise_annotation_from_files_UI_helper | 0.022 | 0.002 | 0.024 | |
isAnnotated-peakPantheRAnnotation-method | 0.280 | 0.012 | 0.292 | |
load_annotation_from_file_UI_helper | 0.010 | 0.001 | 0.011 | |
nbCompounds-peakPantheRAnnotation-method | 0.188 | 0.008 | 0.196 | |
nbSamples-peakPantheRAnnotation-method | 0.270 | 0.013 | 0.283 | |
outputAnnotationDiagnostic-peakPantheRAnnotation-method | 11.478 | 0.088 | 11.575 | |
outputAnnotationFeatureMetadata_UI_helper | 0.010 | 0.001 | 0.011 | |
outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.037 | 0.001 | 0.039 | |
outputAnnotationResult-peakPantheRAnnotation-method | 11.266 | 0.075 | 11.356 | |
outputAnnotationSpectraMetadata_UI_helper | 0.011 | 0.001 | 0.013 | |
peakFit-peakPantheRAnnotation-method | 0.276 | 0.013 | 0.290 | |
peakPantheRAnnotation | 0.301 | 0.016 | 0.316 | |
peakPantheR_ROIStatistics | 16.601 | 0.222 | 16.839 | |
peakPantheR_loadAnnotationParamsCSV | 0.010 | 0.002 | 0.011 | |
peakPantheR_parallelAnnotation | 12.185 | 0.075 | 12.266 | |
peakPantheR_plotEICFit | 0.406 | 0.003 | 0.411 | |
peakPantheR_plotPeakwidth | 0.594 | 0.014 | 0.609 | |
peakPantheR_singleFileSearch | 4.205 | 0.046 | 4.253 | |
peakPantheR_start_GUI | 0 | 0 | 0 | |
peakTables-peakPantheRAnnotation-method | 0.303 | 0.013 | 0.315 | |
resetAnnotation-peakPantheRAnnotation-method | 0.283 | 0.012 | 0.295 | |
resetFIR-peakPantheRAnnotation-method | 0.009 | 0.001 | 0.009 | |
retentionTimeCorrection-peakPantheRAnnotation-method | 7.840 | 0.048 | 7.896 | |
spectraMetadata-peakPantheRAnnotation-method | 0.291 | 0.013 | 0.303 | |
spectraPaths_and_metadata_UI_helper | 0.005 | 0.002 | 0.007 | |
spectra_metadata_colourScheme_UI_helper | 0.006 | 0.001 | 0.007 | |
uROI-peakPantheRAnnotation-method | 0.301 | 0.014 | 0.314 | |
uROIExist-peakPantheRAnnotation-method | 0.266 | 0.011 | 0.278 | |
useFIR-peakPantheRAnnotation-method | 0.271 | 0.012 | 0.283 | |
useUROI-peakPantheRAnnotation-method | 0.270 | 0.012 | 0.282 | |