Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:48 -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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings peakPantheR_1.6.1.tar.gz |
StartedAt: 2021-10-14 10:58:41 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:14:07 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 926.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: peakPantheR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings peakPantheR_1.6.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/peakPantheR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (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 17.095 0.176 17.272 peakPantheR_parallelAnnotation 13.280 0.092 13.373 outputAnnotationResult-peakPantheRAnnotation-method 12.746 0.071 12.820 outputAnnotationDiagnostic-peakPantheRAnnotation-method 12.118 0.048 12.178 retentionTimeCorrection-peakPantheRAnnotation-method 8.985 0.028 9.013 EICs-peakPantheRAnnotation-method 7.806 0.281 8.095 * 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: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL peakPantheR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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-pc-linux-gnu (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 (/tmp/RtmpkadPpT/notValidXML.mzML) 2: In .Internal(gc(verbose, reset, full)) : closing unused connection 7 (/tmp/RtmpkadPpT/notValidXML.mzML) 3: In .Internal(gc(verbose, reset, full)) : closing unused connection 6 (/home/biocbuild/bbs-3.13-bioc/R/library/peakPantheR/extdata/test_fakemzML.mzML) 4: In .Internal(gc(verbose, reset, full)) : closing unused connection 5 (/home/biocbuild/bbs-3.13-bioc/R/library/peakPantheR/extdata/test_fakemzML.mzML) > > proc.time() user system elapsed 623.061 7.867 765.720
peakPantheR.Rcheck/peakPantheR-Ex.timings
name | user | system | elapsed | |
EICs-peakPantheRAnnotation-method | 7.806 | 0.281 | 8.095 | |
FIR-peakPantheRAnnotation-method | 0.143 | 0.019 | 0.163 | |
ROI-peakPantheRAnnotation-method | 0.158 | 0.007 | 0.167 | |
TIC-peakPantheRAnnotation-method | 0.178 | 0.005 | 0.182 | |
acquisitionTime-peakPantheRAnnotation-method | 0.142 | 0.000 | 0.142 | |
annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.138 | 0.000 | 0.139 | |
annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.131 | 0.007 | 0.138 | |
annotationTable-peakPantheRAnnotation-method | 0.128 | 0.000 | 0.128 | |
annotation_diagnostic_multiplot_UI_helper | 0.071 | 0.000 | 0.071 | |
annotation_fit_summary_UI_helper | 0.007 | 0.000 | 0.007 | |
annotation_showMethod_UI_helper | 0.003 | 0.000 | 0.003 | |
annotation_showText_UI_helper | 0.001 | 0.000 | 0.001 | |
cpdID-peakPantheRAnnotation-method | 0.139 | 0.011 | 0.150 | |
cpdMetadata-peakPantheRAnnotation-method | 0.141 | 0.000 | 0.140 | |
cpdName-peakPantheRAnnotation-method | 0.144 | 0.000 | 0.144 | |
dataPoints-peakPantheRAnnotation-method | 0.149 | 0.008 | 0.157 | |
filename-peakPantheRAnnotation-method | 0.170 | 0.013 | 0.182 | |
filepath-peakPantheRAnnotation-method | 0.169 | 0.012 | 0.181 | |
initialise_annotation_from_files_UI_helper | 0.015 | 0.000 | 0.015 | |
isAnnotated-peakPantheRAnnotation-method | 0.174 | 0.000 | 0.173 | |
load_annotation_from_file_UI_helper | 0.006 | 0.000 | 0.006 | |
nbCompounds-peakPantheRAnnotation-method | 0.167 | 0.000 | 0.167 | |
nbSamples-peakPantheRAnnotation-method | 0.148 | 0.007 | 0.157 | |
outputAnnotationDiagnostic-peakPantheRAnnotation-method | 12.118 | 0.048 | 12.178 | |
outputAnnotationFeatureMetadata_UI_helper | 0.004 | 0.000 | 0.005 | |
outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.021 | 0.000 | 0.021 | |
outputAnnotationResult-peakPantheRAnnotation-method | 12.746 | 0.071 | 12.820 | |
outputAnnotationSpectraMetadata_UI_helper | 0.003 | 0.004 | 0.006 | |
peakFit-peakPantheRAnnotation-method | 0.149 | 0.008 | 0.156 | |
peakPantheRAnnotation | 0.147 | 0.005 | 0.153 | |
peakPantheR_ROIStatistics | 17.095 | 0.176 | 17.272 | |
peakPantheR_loadAnnotationParamsCSV | 0.007 | 0.000 | 0.007 | |
peakPantheR_parallelAnnotation | 13.280 | 0.092 | 13.373 | |
peakPantheR_plotEICFit | 0.266 | 0.020 | 0.286 | |
peakPantheR_plotPeakwidth | 0.346 | 0.004 | 0.350 | |
peakPantheR_singleFileSearch | 4.394 | 0.044 | 4.438 | |
peakPantheR_start_GUI | 0 | 0 | 0 | |
peakTables-peakPantheRAnnotation-method | 0.191 | 0.000 | 0.191 | |
resetAnnotation-peakPantheRAnnotation-method | 0.175 | 0.000 | 0.175 | |
resetFIR-peakPantheRAnnotation-method | 0.005 | 0.000 | 0.005 | |
retentionTimeCorrection-peakPantheRAnnotation-method | 8.985 | 0.028 | 9.013 | |
spectraMetadata-peakPantheRAnnotation-method | 0.192 | 0.008 | 0.200 | |
spectraPaths_and_metadata_UI_helper | 0.000 | 0.003 | 0.003 | |
spectra_metadata_colourScheme_UI_helper | 0.004 | 0.000 | 0.004 | |
uROI-peakPantheRAnnotation-method | 0.179 | 0.004 | 0.183 | |
uROIExist-peakPantheRAnnotation-method | 0.166 | 0.008 | 0.173 | |
useFIR-peakPantheRAnnotation-method | 0.185 | 0.000 | 0.184 | |
useUROI-peakPantheRAnnotation-method | 0.180 | 0.004 | 0.184 | |