Arnaud Wolfer
| Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/peakPantheR |
| git_branch: devel |
| git_last_commit: 4d6e977 |
| git_last_commit_date: 2024-10-29 10:40:22 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-23 11:40 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
| 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 1514/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| peakPantheR 1.21.0 (landing page) Arnaud Wolfer
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| 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: 1.21.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings peakPantheR_1.21.0.tar.gz |
| StartedAt: 2024-12-23 00:52:12 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 01:15:23 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 1391.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: peakPantheR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings peakPantheR_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/peakPantheR.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.21.0’
* 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 21.839 0.257 22.104
peakPantheR_parallelAnnotation 15.736 0.154 15.891
outputAnnotationResult-peakPantheRAnnotation-method 15.536 0.152 15.689
outputAnnotationDiagnostic-peakPantheRAnnotation-method 15.283 0.304 15.621
EICs-peakPantheRAnnotation-method 10.410 0.612 11.029
retentionTimeCorrection-peakPantheRAnnotation-method 9.418 0.064 9.482
peakPantheR_singleFileSearch 5.167 0.036 5.203
* 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-3.21-bioc/R/bin/R CMD INSTALL peakPantheR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-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) (2024-10-21 r87258) -- "Unsuffered Consequences"
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 1.21.0
>
> 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/Rtmpw0QG0o/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 9 (/tmp/Rtmpw0QG0o/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (/tmp/Rtmpw0QG0o/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (/tmp/Rtmpw0QG0o/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (/home/biocbuild/bbs-3.21-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (/home/biocbuild/bbs-3.21-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
>
> proc.time()
user system elapsed
797.282 20.852 1085.373
peakPantheR.Rcheck/peakPantheR-Ex.timings
| name | user | system | elapsed | |
| EICs-peakPantheRAnnotation-method | 10.410 | 0.612 | 11.029 | |
| FIR-peakPantheRAnnotation-method | 0.053 | 0.002 | 0.055 | |
| ROI-peakPantheRAnnotation-method | 0.016 | 0.001 | 0.016 | |
| TIC-peakPantheRAnnotation-method | 0.015 | 0.000 | 0.015 | |
| acquisitionTime-peakPantheRAnnotation-method | 0.015 | 0.000 | 0.015 | |
| annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.013 | 0.002 | 0.015 | |
| annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.015 | 0.000 | 0.015 | |
| annotationTable-peakPantheRAnnotation-method | 0.013 | 0.002 | 0.015 | |
| annotation_diagnostic_multiplot_UI_helper | 0.101 | 0.001 | 0.102 | |
| annotation_fit_summary_UI_helper | 0.007 | 0.000 | 0.007 | |
| annotation_showMethod_UI_helper | 0.003 | 0.000 | 0.004 | |
| annotation_showText_UI_helper | 0.001 | 0.001 | 0.001 | |
| cpdID-peakPantheRAnnotation-method | 0.014 | 0.002 | 0.016 | |
| cpdMetadata-peakPantheRAnnotation-method | 0.015 | 0.001 | 0.016 | |
| cpdName-peakPantheRAnnotation-method | 0.015 | 0.000 | 0.015 | |
| dataPoints-peakPantheRAnnotation-method | 0.015 | 0.002 | 0.017 | |
| filename-peakPantheRAnnotation-method | 0.018 | 0.000 | 0.018 | |
| filepath-peakPantheRAnnotation-method | 0.012 | 0.002 | 0.015 | |
| initialise_annotation_from_files_UI_helper | 0.012 | 0.000 | 0.012 | |
| isAnnotated-peakPantheRAnnotation-method | 0.018 | 0.000 | 0.018 | |
| load_annotation_from_file_UI_helper | 0.006 | 0.000 | 0.006 | |
| nbCompounds-peakPantheRAnnotation-method | 0.017 | 0.001 | 0.018 | |
| nbSamples-peakPantheRAnnotation-method | 0.018 | 0.000 | 0.018 | |
| outputAnnotationDiagnostic-peakPantheRAnnotation-method | 15.283 | 0.304 | 15.621 | |
| outputAnnotationFeatureMetadata_UI_helper | 0.005 | 0.000 | 0.005 | |
| outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.021 | 0.001 | 0.022 | |
| outputAnnotationResult-peakPantheRAnnotation-method | 15.536 | 0.152 | 15.689 | |
| outputAnnotationSpectraMetadata_UI_helper | 0.006 | 0.000 | 0.006 | |
| peakFit-peakPantheRAnnotation-method | 0.017 | 0.000 | 0.016 | |
| peakPantheRAnnotation | 0.025 | 0.000 | 0.025 | |
| peakPantheR_ROIStatistics | 21.839 | 0.257 | 22.104 | |
| peakPantheR_loadAnnotationParamsCSV | 0.003 | 0.002 | 0.006 | |
| peakPantheR_parallelAnnotation | 15.736 | 0.154 | 15.891 | |
| peakPantheR_plotEICFit | 0.309 | 0.002 | 0.310 | |
| peakPantheR_plotPeakwidth | 0.526 | 0.001 | 0.527 | |
| peakPantheR_quickEIC | 4.469 | 0.041 | 4.521 | |
| peakPantheR_singleFileSearch | 5.167 | 0.036 | 5.203 | |
| peakPantheR_start_GUI | 0.000 | 0.000 | 0.001 | |
| peakTables-peakPantheRAnnotation-method | 0.017 | 0.000 | 0.018 | |
| resetAnnotation-peakPantheRAnnotation-method | 0.020 | 0.003 | 0.023 | |
| resetFIR-peakPantheRAnnotation-method | 0.005 | 0.001 | 0.005 | |
| retentionTimeCorrection-peakPantheRAnnotation-method | 9.418 | 0.064 | 9.482 | |
| spectraMetadata-peakPantheRAnnotation-method | 0.017 | 0.000 | 0.017 | |
| spectraPaths_and_metadata_UI_helper | 0.001 | 0.001 | 0.002 | |
| spectra_metadata_colourScheme_UI_helper | 0.004 | 0.000 | 0.004 | |
| uROI-peakPantheRAnnotation-method | 0.017 | 0.000 | 0.017 | |
| uROIExist-peakPantheRAnnotation-method | 0.014 | 0.002 | 0.015 | |
| useFIR-peakPantheRAnnotation-method | 0.016 | 0.000 | 0.016 | |
| useUROI-peakPantheRAnnotation-method | 0.015 | 0.002 | 0.017 | |