Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:19 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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 |
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1446/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
peakPantheR 1.13.1 (landing page) Arnaud Wolfer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: peakPantheR |
Version: 1.13.1 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings peakPantheR_1.13.1.tar.gz |
StartedAt: 2023-02-07 11:00:49 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 11:12:40 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 710.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: peakPantheR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings peakPantheR_1.13.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/peakPantheR.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘peakPantheR/DESCRIPTION’ ... OK * this is package ‘peakPantheR’ version ‘1.13.1’ * 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 19.866 0.135 20.972 peakPantheR_parallelAnnotation 14.707 0.044 15.853 outputAnnotationDiagnostic-peakPantheRAnnotation-method 14.488 0.060 16.297 outputAnnotationResult-peakPantheRAnnotation-method 14.147 0.044 14.948 EICs-peakPantheRAnnotation-method 11.187 0.324 11.973 retentionTimeCorrection-peakPantheRAnnotation-method 9.532 0.020 9.918 peakPantheR_singleFileSearch 4.991 0.007 5.458 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(peakPantheR) This is peakPantheR version 1.13.1 > > test_check("peakPantheR") Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘getting-started.Rmd’ using ‘UTF-8’... OK ‘parallel-annotation.Rmd’ using ‘UTF-8’... OK ‘peakPantheR-GUI.Rmd’ using ‘UTF-8’... OK ‘real-time-annotation.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.17-bioc/meat/peakPantheR.Rcheck/00check.log’ for details.
peakPantheR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL peakPantheR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 1.13.1 > > test_check("peakPantheR") Killed
peakPantheR.Rcheck/peakPantheR-Ex.timings
name | user | system | elapsed | |
EICs-peakPantheRAnnotation-method | 11.187 | 0.324 | 11.973 | |
FIR-peakPantheRAnnotation-method | 0.202 | 0.012 | 0.214 | |
ROI-peakPantheRAnnotation-method | 0.191 | 0.016 | 0.209 | |
TIC-peakPantheRAnnotation-method | 0.202 | 0.008 | 0.210 | |
acquisitionTime-peakPantheRAnnotation-method | 0.207 | 0.008 | 0.309 | |
annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.184 | 0.016 | 0.201 | |
annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.181 | 0.028 | 0.225 | |
annotationTable-peakPantheRAnnotation-method | 0.207 | 0.004 | 0.223 | |
annotation_diagnostic_multiplot_UI_helper | 0.145 | 0.004 | 0.149 | |
annotation_fit_summary_UI_helper | 0.010 | 0.000 | 0.009 | |
annotation_showMethod_UI_helper | 0.005 | 0.000 | 0.004 | |
annotation_showText_UI_helper | 0 | 0 | 0 | |
cpdID-peakPantheRAnnotation-method | 0.195 | 0.008 | 0.220 | |
cpdMetadata-peakPantheRAnnotation-method | 0.202 | 0.004 | 0.206 | |
cpdName-peakPantheRAnnotation-method | 0.199 | 0.008 | 0.214 | |
dataPoints-peakPantheRAnnotation-method | 0.206 | 0.000 | 0.211 | |
filename-peakPantheRAnnotation-method | 0.199 | 0.004 | 0.203 | |
filepath-peakPantheRAnnotation-method | 0.206 | 0.000 | 0.206 | |
initialise_annotation_from_files_UI_helper | 0.017 | 0.000 | 0.017 | |
isAnnotated-peakPantheRAnnotation-method | 0.206 | 0.000 | 0.206 | |
load_annotation_from_file_UI_helper | 0.008 | 0.000 | 0.008 | |
nbCompounds-peakPantheRAnnotation-method | 0.211 | 0.000 | 0.267 | |
nbSamples-peakPantheRAnnotation-method | 0.203 | 0.004 | 0.207 | |
outputAnnotationDiagnostic-peakPantheRAnnotation-method | 14.488 | 0.060 | 16.297 | |
outputAnnotationFeatureMetadata_UI_helper | 0.007 | 0.000 | 0.007 | |
outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.033 | 0.000 | 0.034 | |
outputAnnotationResult-peakPantheRAnnotation-method | 14.147 | 0.044 | 14.948 | |
outputAnnotationSpectraMetadata_UI_helper | 0.007 | 0.000 | 0.007 | |
peakFit-peakPantheRAnnotation-method | 0.186 | 0.000 | 0.188 | |
peakPantheRAnnotation | 0.182 | 0.012 | 0.196 | |
peakPantheR_ROIStatistics | 19.866 | 0.135 | 20.972 | |
peakPantheR_loadAnnotationParamsCSV | 0.009 | 0.000 | 0.009 | |
peakPantheR_parallelAnnotation | 14.707 | 0.044 | 15.853 | |
peakPantheR_plotEICFit | 0.463 | 0.000 | 0.469 | |
peakPantheR_plotPeakwidth | 0.704 | 0.000 | 0.752 | |
peakPantheR_singleFileSearch | 4.991 | 0.007 | 5.458 | |
peakPantheR_start_GUI | 0 | 0 | 0 | |
peakTables-peakPantheRAnnotation-method | 0.219 | 0.012 | 0.232 | |
resetAnnotation-peakPantheRAnnotation-method | 0.243 | 0.000 | 0.243 | |
resetFIR-peakPantheRAnnotation-method | 0.003 | 0.004 | 0.008 | |
retentionTimeCorrection-peakPantheRAnnotation-method | 9.532 | 0.020 | 9.918 | |
spectraMetadata-peakPantheRAnnotation-method | 0.204 | 0.000 | 0.204 | |
spectraPaths_and_metadata_UI_helper | 0.003 | 0.000 | 0.003 | |
spectra_metadata_colourScheme_UI_helper | 0.007 | 0.000 | 0.007 | |
uROI-peakPantheRAnnotation-method | 0.211 | 0.004 | 0.215 | |
uROIExist-peakPantheRAnnotation-method | 0.218 | 0.000 | 0.218 | |
useFIR-peakPantheRAnnotation-method | 0.212 | 0.000 | 0.212 | |
useUROI-peakPantheRAnnotation-method | 0.188 | 0.012 | 0.200 | |