Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-12 11:40 -0400 (Thu, 12 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4713 |
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4450 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4430 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4428 |
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 1504/2258 | 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 | |||||||||
teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.19.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings peakPantheR_1.19.0.tar.gz |
StartedAt: 2024-09-12 01:39:29 -0400 (Thu, 12 Sep 2024) |
EndedAt: 2024-09-12 02:01:05 -0400 (Thu, 12 Sep 2024) |
EllapsedTime: 1296.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: peakPantheR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings peakPantheR_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/peakPantheR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.5 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 19.980 0.380 20.360 outputAnnotationDiagnostic-peakPantheRAnnotation-method 15.387 0.268 15.655 peakPantheR_parallelAnnotation 14.008 0.140 14.149 outputAnnotationResult-peakPantheRAnnotation-method 13.923 0.220 14.143 EICs-peakPantheRAnnotation-method 11.097 0.592 11.689 retentionTimeCorrection-peakPantheRAnnotation-method 9.040 0.092 9.132 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
peakPantheR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL peakPantheR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1478 ] Warning messages: 1: In .Internal(gc(verbose, reset, full)) : closing unused connection 10 (/tmp/RtmpfOFJvu/notValidXML.mzML) 2: In .Internal(gc(verbose, reset, full)) : closing unused connection 9 (/tmp/RtmpfOFJvu/notValidXML.mzML) 3: In .Internal(gc(verbose, reset, full)) : closing unused connection 8 (/tmp/RtmpfOFJvu/notValidXML.mzML) 4: In .Internal(gc(verbose, reset, full)) : closing unused connection 7 (/tmp/RtmpfOFJvu/notValidXML.mzML) 5: In .Internal(gc(verbose, reset, full)) : closing unused connection 6 (/home/biocbuild/bbs-3.20-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML) 6: In .Internal(gc(verbose, reset, full)) : closing unused connection 5 (/home/biocbuild/bbs-3.20-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML) > > proc.time() user system elapsed 723.011 21.086 1002.772
peakPantheR.Rcheck/peakPantheR-Ex.timings
name | user | system | elapsed | |
EICs-peakPantheRAnnotation-method | 11.097 | 0.592 | 11.689 | |
FIR-peakPantheRAnnotation-method | 0.048 | 0.000 | 0.048 | |
ROI-peakPantheRAnnotation-method | 0.040 | 0.003 | 0.044 | |
TIC-peakPantheRAnnotation-method | 0.035 | 0.007 | 0.043 | |
acquisitionTime-peakPantheRAnnotation-method | 0.051 | 0.000 | 0.051 | |
annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.04 | 0.00 | 0.04 | |
annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.053 | 0.000 | 0.053 | |
annotationTable-peakPantheRAnnotation-method | 0.048 | 0.000 | 0.047 | |
annotation_diagnostic_multiplot_UI_helper | 0.108 | 0.004 | 0.112 | |
annotation_fit_summary_UI_helper | 0.008 | 0.000 | 0.007 | |
annotation_showMethod_UI_helper | 0.003 | 0.000 | 0.003 | |
annotation_showText_UI_helper | 0.000 | 0.000 | 0.001 | |
cpdID-peakPantheRAnnotation-method | 0.033 | 0.003 | 0.037 | |
cpdMetadata-peakPantheRAnnotation-method | 0.043 | 0.000 | 0.042 | |
cpdName-peakPantheRAnnotation-method | 0.038 | 0.000 | 0.038 | |
dataPoints-peakPantheRAnnotation-method | 0.037 | 0.004 | 0.041 | |
filename-peakPantheRAnnotation-method | 0.045 | 0.000 | 0.045 | |
filepath-peakPantheRAnnotation-method | 0.040 | 0.000 | 0.039 | |
initialise_annotation_from_files_UI_helper | 0.013 | 0.000 | 0.013 | |
isAnnotated-peakPantheRAnnotation-method | 0.047 | 0.000 | 0.047 | |
load_annotation_from_file_UI_helper | 0.006 | 0.000 | 0.005 | |
nbCompounds-peakPantheRAnnotation-method | 0.045 | 0.000 | 0.045 | |
nbSamples-peakPantheRAnnotation-method | 0.043 | 0.000 | 0.043 | |
outputAnnotationDiagnostic-peakPantheRAnnotation-method | 15.387 | 0.268 | 15.655 | |
outputAnnotationFeatureMetadata_UI_helper | 0.004 | 0.000 | 0.005 | |
outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.021 | 0.000 | 0.021 | |
outputAnnotationResult-peakPantheRAnnotation-method | 13.923 | 0.220 | 14.143 | |
outputAnnotationSpectraMetadata_UI_helper | 0.005 | 0.000 | 0.006 | |
peakFit-peakPantheRAnnotation-method | 0.040 | 0.000 | 0.041 | |
peakPantheRAnnotation | 0.048 | 0.003 | 0.052 | |
peakPantheR_ROIStatistics | 19.98 | 0.38 | 20.36 | |
peakPantheR_loadAnnotationParamsCSV | 0.005 | 0.000 | 0.006 | |
peakPantheR_parallelAnnotation | 14.008 | 0.140 | 14.149 | |
peakPantheR_plotEICFit | 0.291 | 0.000 | 0.291 | |
peakPantheR_plotPeakwidth | 0.485 | 0.024 | 0.509 | |
peakPantheR_quickEIC | 4.154 | 0.052 | 4.206 | |
peakPantheR_singleFileSearch | 4.730 | 0.027 | 4.758 | |
peakPantheR_start_GUI | 0 | 0 | 0 | |
peakTables-peakPantheRAnnotation-method | 0.040 | 0.004 | 0.043 | |
resetAnnotation-peakPantheRAnnotation-method | 0.049 | 0.000 | 0.049 | |
resetFIR-peakPantheRAnnotation-method | 0.004 | 0.000 | 0.004 | |
retentionTimeCorrection-peakPantheRAnnotation-method | 9.040 | 0.092 | 9.132 | |
spectraMetadata-peakPantheRAnnotation-method | 0.047 | 0.000 | 0.047 | |
spectraPaths_and_metadata_UI_helper | 0.002 | 0.000 | 0.002 | |
spectra_metadata_colourScheme_UI_helper | 0.004 | 0.000 | 0.004 | |
uROI-peakPantheRAnnotation-method | 0.041 | 0.000 | 0.041 | |
uROIExist-peakPantheRAnnotation-method | 0.044 | 0.000 | 0.043 | |
useFIR-peakPantheRAnnotation-method | 0.039 | 0.000 | 0.039 | |
useUROI-peakPantheRAnnotation-method | 0.036 | 0.003 | 0.040 | |