| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:40 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1477/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| peakPantheR 1.13.2 (landing page) Arnaud Wolfer
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: peakPantheR |
| Version: 1.13.2 |
| 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/site-library --timings peakPantheR_1.13.2.tar.gz |
| StartedAt: 2023-04-12 08:16:22 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 08:39:24 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 1382.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: peakPantheR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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/site-library --timings peakPantheR_1.13.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/peakPantheR.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.13.2’
* 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 loading without being on the library search path ... 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
outputAnnotationDiagnostic-peakPantheRAnnotation-method 23.176 0.524 26.527
peakPantheR_ROIStatistics 21.560 0.368 21.936
outputAnnotationResult-peakPantheRAnnotation-method 20.240 0.312 24.372
retentionTimeCorrection-peakPantheRAnnotation-method 17.078 0.108 19.440
peakPantheR_parallelAnnotation 15.797 0.172 15.969
EICs-peakPantheRAnnotation-method 10.488 0.604 11.726
peakPantheR_singleFileSearch 6.099 0.040 6.217
* 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 ...
‘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: OK
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/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 Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 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 1.13.2
>
> test_check("peakPantheR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1438 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
closing unused connection 10 (/tmp/Rtmp7Uuqc6/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 9 (/tmp/Rtmp7Uuqc6/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (/tmp/Rtmp7Uuqc6/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (/tmp/Rtmp7Uuqc6/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (/home/biocbuild/bbs-3.17-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (/home/biocbuild/bbs-3.17-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
>
> proc.time()
user system elapsed
774.023 11.011 963.947
peakPantheR.Rcheck/peakPantheR-Ex.timings
| name | user | system | elapsed | |
| EICs-peakPantheRAnnotation-method | 10.488 | 0.604 | 11.726 | |
| FIR-peakPantheRAnnotation-method | 1.213 | 0.040 | 1.253 | |
| ROI-peakPantheRAnnotation-method | 0.314 | 0.004 | 0.317 | |
| TIC-peakPantheRAnnotation-method | 0.352 | 0.000 | 0.352 | |
| acquisitionTime-peakPantheRAnnotation-method | 0.369 | 0.004 | 0.373 | |
| annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.331 | 0.004 | 0.336 | |
| annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.343 | 0.016 | 0.359 | |
| annotationTable-peakPantheRAnnotation-method | 0.345 | 0.004 | 0.349 | |
| annotation_diagnostic_multiplot_UI_helper | 0.186 | 0.016 | 0.203 | |
| annotation_fit_summary_UI_helper | 0.014 | 0.000 | 0.014 | |
| annotation_showMethod_UI_helper | 0.003 | 0.004 | 0.007 | |
| annotation_showText_UI_helper | 0.001 | 0.000 | 0.001 | |
| cpdID-peakPantheRAnnotation-method | 0.417 | 0.016 | 0.486 | |
| cpdMetadata-peakPantheRAnnotation-method | 0.457 | 0.012 | 0.470 | |
| cpdName-peakPantheRAnnotation-method | 0.441 | 0.020 | 0.604 | |
| dataPoints-peakPantheRAnnotation-method | 0.380 | 0.004 | 0.557 | |
| filename-peakPantheRAnnotation-method | 0.426 | 0.004 | 0.672 | |
| filepath-peakPantheRAnnotation-method | 0.395 | 0.008 | 0.603 | |
| initialise_annotation_from_files_UI_helper | 0.024 | 0.000 | 0.040 | |
| isAnnotated-peakPantheRAnnotation-method | 0.393 | 0.004 | 0.802 | |
| load_annotation_from_file_UI_helper | 0.007 | 0.004 | 0.011 | |
| nbCompounds-peakPantheRAnnotation-method | 0.417 | 0.004 | 0.841 | |
| nbSamples-peakPantheRAnnotation-method | 0.374 | 0.012 | 0.762 | |
| outputAnnotationDiagnostic-peakPantheRAnnotation-method | 23.176 | 0.524 | 26.527 | |
| outputAnnotationFeatureMetadata_UI_helper | 0.008 | 0.000 | 0.008 | |
| outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.037 | 0.000 | 0.038 | |
| outputAnnotationResult-peakPantheRAnnotation-method | 20.240 | 0.312 | 24.372 | |
| outputAnnotationSpectraMetadata_UI_helper | 0.009 | 0.000 | 0.009 | |
| peakFit-peakPantheRAnnotation-method | 0.27 | 0.00 | 0.27 | |
| peakPantheRAnnotation | 0.178 | 0.000 | 0.178 | |
| peakPantheR_ROIStatistics | 21.560 | 0.368 | 21.936 | |
| peakPantheR_loadAnnotationParamsCSV | 0.006 | 0.000 | 0.007 | |
| peakPantheR_parallelAnnotation | 15.797 | 0.172 | 15.969 | |
| peakPantheR_plotEICFit | 0.293 | 0.004 | 0.298 | |
| peakPantheR_plotPeakwidth | 0.512 | 0.000 | 0.512 | |
| peakPantheR_singleFileSearch | 6.099 | 0.040 | 6.217 | |
| peakPantheR_start_GUI | 0 | 0 | 0 | |
| peakTables-peakPantheRAnnotation-method | 0.427 | 0.000 | 0.426 | |
| resetAnnotation-peakPantheRAnnotation-method | 0.408 | 0.012 | 0.420 | |
| resetFIR-peakPantheRAnnotation-method | 0.009 | 0.000 | 0.008 | |
| retentionTimeCorrection-peakPantheRAnnotation-method | 17.078 | 0.108 | 19.440 | |
| spectraMetadata-peakPantheRAnnotation-method | 0.175 | 0.004 | 0.178 | |
| 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 | 0.181 | 0.000 | 0.180 | |
| uROIExist-peakPantheRAnnotation-method | 0.196 | 0.000 | 0.197 | |
| useFIR-peakPantheRAnnotation-method | 0.176 | 0.004 | 0.180 | |
| useUROI-peakPantheRAnnotation-method | 0.221 | 0.004 | 0.225 | |