Arnaud Wolfer
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/peakPantheR |
| git_branch: RELEASE_3_18 |
| git_last_commit: 8a9ba02 |
| git_last_commit_date: 2024-02-26 17:51:10 -0400 (Mon, 26 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:37:06 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 1520/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| peakPantheR 1.16.1 (landing page) Arnaud Wolfer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.16.1 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:peakPantheR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings peakPantheR_1.16.1.tar.gz |
| StartedAt: 2024-03-28 03:42:55 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 04:01:50 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 1134.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: peakPantheR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:peakPantheR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings peakPantheR_1.16.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/peakPantheR.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'peakPantheR/DESCRIPTION' ... OK
* this is package 'peakPantheR' version '1.16.1'
* 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 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 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 22.55 0.20 22.89
peakPantheR_parallelAnnotation 16.48 0.11 16.59
outputAnnotationDiagnostic-peakPantheRAnnotation-method 16.30 0.25 16.61
outputAnnotationResult-peakPantheRAnnotation-method 15.21 0.25 15.47
EICs-peakPantheRAnnotation-method 14.33 0.51 15.45
retentionTimeCorrection-peakPantheRAnnotation-method 11.05 0.10 11.14
peakPantheR_singleFileSearch 5.33 0.06 5.39
* 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: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL peakPantheR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 1.16.1
>
> test_check("peakPantheR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1458 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
closing unused connection 10 (F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpsfmaeT\notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 9 (F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpsfmaeT\notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpsfmaeT\notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpsfmaeT\notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (F:\biocbuild\bbs-3.18-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (F:\biocbuild\bbs-3.18-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
>
> proc.time()
user system elapsed
756.09 8.60 935.64
peakPantheR.Rcheck/peakPantheR-Ex.timings
| name | user | system | elapsed | |
| EICs-peakPantheRAnnotation-method | 14.33 | 0.51 | 15.45 | |
| FIR-peakPantheRAnnotation-method | 0.20 | 0.05 | 0.25 | |
| ROI-peakPantheRAnnotation-method | 0.28 | 0.02 | 0.30 | |
| TIC-peakPantheRAnnotation-method | 0.17 | 0.05 | 0.22 | |
| acquisitionTime-peakPantheRAnnotation-method | 0.25 | 0.01 | 0.26 | |
| annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.27 | 0.03 | 0.30 | |
| annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.25 | 0.03 | 0.29 | |
| annotationTable-peakPantheRAnnotation-method | 0.17 | 0.08 | 0.25 | |
| annotation_diagnostic_multiplot_UI_helper | 0.14 | 0.01 | 0.15 | |
| annotation_fit_summary_UI_helper | 0 | 0 | 0 | |
| annotation_showMethod_UI_helper | 0 | 0 | 0 | |
| annotation_showText_UI_helper | 0 | 0 | 0 | |
| cpdID-peakPantheRAnnotation-method | 0.19 | 0.04 | 0.22 | |
| cpdMetadata-peakPantheRAnnotation-method | 0.21 | 0.04 | 0.25 | |
| cpdName-peakPantheRAnnotation-method | 0.25 | 0.05 | 0.29 | |
| dataPoints-peakPantheRAnnotation-method | 0.28 | 0.02 | 0.30 | |
| filename-peakPantheRAnnotation-method | 0.32 | 0.01 | 0.32 | |
| filepath-peakPantheRAnnotation-method | 0.29 | 0.02 | 0.32 | |
| initialise_annotation_from_files_UI_helper | 0.01 | 0.00 | 0.03 | |
| isAnnotated-peakPantheRAnnotation-method | 0.27 | 0.01 | 0.29 | |
| load_annotation_from_file_UI_helper | 0.00 | 0.02 | 0.01 | |
| nbCompounds-peakPantheRAnnotation-method | 0.27 | 0.04 | 0.31 | |
| nbSamples-peakPantheRAnnotation-method | 0.25 | 0.07 | 0.31 | |
| outputAnnotationDiagnostic-peakPantheRAnnotation-method | 16.30 | 0.25 | 16.61 | |
| outputAnnotationFeatureMetadata_UI_helper | 0 | 0 | 0 | |
| outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.01 | 0.00 | 0.02 | |
| outputAnnotationResult-peakPantheRAnnotation-method | 15.21 | 0.25 | 15.47 | |
| outputAnnotationSpectraMetadata_UI_helper | 0 | 0 | 0 | |
| peakFit-peakPantheRAnnotation-method | 0.28 | 0.03 | 0.31 | |
| peakPantheRAnnotation | 0.30 | 0.02 | 0.31 | |
| peakPantheR_ROIStatistics | 22.55 | 0.20 | 22.89 | |
| peakPantheR_loadAnnotationParamsCSV | 0.00 | 0.00 | 0.02 | |
| peakPantheR_parallelAnnotation | 16.48 | 0.11 | 16.59 | |
| peakPantheR_plotEICFit | 0.36 | 0.00 | 0.36 | |
| peakPantheR_plotPeakwidth | 0.5 | 0.0 | 0.5 | |
| peakPantheR_singleFileSearch | 5.33 | 0.06 | 5.39 | |
| peakPantheR_start_GUI | 0 | 0 | 0 | |
| peakTables-peakPantheRAnnotation-method | 0.30 | 0.04 | 0.33 | |
| resetAnnotation-peakPantheRAnnotation-method | 0.31 | 0.03 | 0.34 | |
| resetFIR-peakPantheRAnnotation-method | 0.00 | 0.01 | 0.02 | |
| retentionTimeCorrection-peakPantheRAnnotation-method | 11.05 | 0.10 | 11.14 | |
| spectraMetadata-peakPantheRAnnotation-method | 0.28 | 0.03 | 0.31 | |
| spectraPaths_and_metadata_UI_helper | 0.01 | 0.02 | 0.03 | |
| spectra_metadata_colourScheme_UI_helper | 0 | 0 | 0 | |
| uROI-peakPantheRAnnotation-method | 0.24 | 0.05 | 0.28 | |
| uROIExist-peakPantheRAnnotation-method | 0.23 | 0.03 | 0.27 | |
| useFIR-peakPantheRAnnotation-method | 0.28 | 0.00 | 0.28 | |
| useUROI-peakPantheRAnnotation-method | 0.24 | 0.00 | 0.23 | |