Arnaud Wolfer
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/peakPantheR |
| git_branch: master |
| git_last_commit: 19b5404 |
| git_last_commit_date: 2021-10-26 12:54:33 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:16 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1399/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| peakPantheR 1.9.0 (landing page) Arnaud Wolfer
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: peakPantheR |
| Version: 1.9.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:peakPantheR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings peakPantheR_1.9.0.tar.gz |
| StartedAt: 2022-03-17 19:50:19 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:03:38 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 798.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: peakPantheR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:peakPantheR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings peakPantheR_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/peakPantheR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'peakPantheR/DESCRIPTION' ... OK
* this is package 'peakPantheR' version '1.9.0'
* 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 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 14.96 0.31 20.77
outputAnnotationDiagnostic-peakPantheRAnnotation-method 11.72 0.11 11.85
outputAnnotationResult-peakPantheRAnnotation-method 11.39 0.18 12.95
peakPantheR_parallelAnnotation 8.94 0.08 9.01
EICs-peakPantheRAnnotation-method 8.14 0.43 8.56
retentionTimeCorrection-peakPantheRAnnotation-method 6.08 0.05 6.13
* 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:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL peakPantheR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'peakPantheR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'peakPantheR'
finding HTML links ... done
EICs-peakPantheRAnnotation-method html
FIR-peakPantheRAnnotation-method html
ROI-peakPantheRAnnotation-method html
TIC-peakPantheRAnnotation-method html
acquisitionTime-peakPantheRAnnotation-method
html
annotationDiagnosticMultiplot html
annotationDiagnosticPlots-peakPantheRAnnotation-method
html
annotationParamsDiagnostic-peakPantheRAnnotation-method
html
annotationTable-peakPantheRAnnotation-method
html
annotation_diagnostic_multiplot_UI_helper
html
annotation_fit_summary_UI_helper html
annotation_showMethod_UI_helper html
annotation_showText_UI_helper html
cpdID-peakPantheRAnnotation-method html
cpdMetadata-peakPantheRAnnotation-method
html
cpdName-peakPantheRAnnotation-method html
dataPoints-peakPantheRAnnotation-method
html
emgGaussian_guess html
emgGaussian_minpack.lm html
emgGaussian_minpack.lm_objectiveFun html
extractSignalRawData html
filename-peakPantheRAnnotation-method html
filepath-peakPantheRAnnotation-method html
findTargetFeatures html
fitCurve html
gaussian_cerf html
gaussian_erf html
generateIonChromatogram html
getAcquisitionDatemzML html
getTargetFeatureStatistic html
initialise_annotation_from_files_UI_helper
html
integrateFIR html
is.peakPantheR_curveFit html
isAnnotated-peakPantheRAnnotation-method
html
load_annotation_from_file_UI_helper html
nbCompounds-peakPantheRAnnotation-method
html
nbSamples-peakPantheRAnnotation-method
html
outputAnnotationDiagnostic-peakPantheRAnnotation-method
html
outputAnnotationFeatureMetadata_UI_helper
html
outputAnnotationParamsCSV-peakPantheRAnnotation-method
html
outputAnnotationResult-peakPantheRAnnotation-method
html
outputAnnotationSpectraMetadata_UI_helper
html
peakFit-peakPantheRAnnotation-method html
peakPantheR html
peakPantheRAnnotation html
peakPantheR_ROIStatistics html
peakPantheR_applyRTCorrection html
peakPantheR_loadAnnotationParamsCSV html
peakPantheR_parallelAnnotation html
peakPantheR_plotEICFit html
peakPantheR_plotPeakwidth html
peakPantheR_singleFileSearch html
peakPantheR_start_GUI html
peakTables-peakPantheRAnnotation-method
html
plotEICDetectedPeakwidth html
plotHistogram html
predictCurve html
prepare_advanced_target_parameters html
prepare_basic_target_parameters html
resetAnnotation-peakPantheRAnnotation-method
html
resetFIR-peakPantheRAnnotation-method html
retentionTimeCorrection-peakPantheRAnnotation-method
html
saveSingleFileMultiEIC html
skewedGaussian_guess html
skewedGaussian_minpack.lm html
skewedGaussian_minpack.lm_objectiveFun
html
spectraMetadata-peakPantheRAnnotation-method
html
spectraPaths_and_metadata_UI_helper html
spectra_metadata_colourScheme_UI_helper
html
sub-peakPantheRAnnotation-ANY-ANY-ANY-method
html
uROI-peakPantheRAnnotation-method html
uROIExist-peakPantheRAnnotation-method
html
useFIR-peakPantheRAnnotation-method html
useUROI-peakPantheRAnnotation-method html
*** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'lionessR' is missing or broken
done
peakPantheR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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 1.9.0
>
> test_check("peakPantheR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1434 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpCEJ72h\notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpCEJ72h\notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (D:\biocbuild\bbs-3.15-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (D:\biocbuild\bbs-3.15-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
>
> proc.time()
user system elapsed
499.71 4.26 628.15
peakPantheR.Rcheck/peakPantheR-Ex.timings
| name | user | system | elapsed | |
| EICs-peakPantheRAnnotation-method | 8.14 | 0.43 | 8.56 | |
| FIR-peakPantheRAnnotation-method | 0.20 | 0.04 | 0.25 | |
| ROI-peakPantheRAnnotation-method | 0.19 | 0.05 | 0.23 | |
| TIC-peakPantheRAnnotation-method | 0.27 | 0.00 | 0.26 | |
| acquisitionTime-peakPantheRAnnotation-method | 0.22 | 0.02 | 0.24 | |
| annotationDiagnosticPlots-peakPantheRAnnotation-method | 0.22 | 0.01 | 0.23 | |
| annotationParamsDiagnostic-peakPantheRAnnotation-method | 0.23 | 0.02 | 0.25 | |
| annotationTable-peakPantheRAnnotation-method | 0.25 | 0.00 | 0.25 | |
| annotation_diagnostic_multiplot_UI_helper | 0.11 | 0.00 | 0.11 | |
| annotation_fit_summary_UI_helper | 0.02 | 0.00 | 0.02 | |
| annotation_showMethod_UI_helper | 0 | 0 | 0 | |
| annotation_showText_UI_helper | 0 | 0 | 0 | |
| cpdID-peakPantheRAnnotation-method | 0.25 | 0.03 | 0.28 | |
| cpdMetadata-peakPantheRAnnotation-method | 0.23 | 0.00 | 0.23 | |
| cpdName-peakPantheRAnnotation-method | 0.17 | 0.01 | 0.18 | |
| dataPoints-peakPantheRAnnotation-method | 0.18 | 0.00 | 0.19 | |
| filename-peakPantheRAnnotation-method | 0.22 | 0.02 | 0.24 | |
| filepath-peakPantheRAnnotation-method | 0.14 | 0.05 | 0.18 | |
| initialise_annotation_from_files_UI_helper | 0.04 | 0.00 | 0.03 | |
| isAnnotated-peakPantheRAnnotation-method | 0.21 | 0.01 | 0.24 | |
| load_annotation_from_file_UI_helper | 0.02 | 0.00 | 0.03 | |
| nbCompounds-peakPantheRAnnotation-method | 0.20 | 0.03 | 0.23 | |
| nbSamples-peakPantheRAnnotation-method | 0.22 | 0.02 | 0.23 | |
| outputAnnotationDiagnostic-peakPantheRAnnotation-method | 11.72 | 0.11 | 11.85 | |
| outputAnnotationFeatureMetadata_UI_helper | 0 | 0 | 0 | |
| outputAnnotationParamsCSV-peakPantheRAnnotation-method | 0.02 | 0.01 | 0.04 | |
| outputAnnotationResult-peakPantheRAnnotation-method | 11.39 | 0.18 | 12.95 | |
| outputAnnotationSpectraMetadata_UI_helper | 0.00 | 0.00 | 0.03 | |
| peakFit-peakPantheRAnnotation-method | 0.22 | 0.01 | 0.36 | |
| peakPantheRAnnotation | 0.22 | 0.02 | 0.37 | |
| peakPantheR_ROIStatistics | 14.96 | 0.31 | 20.77 | |
| peakPantheR_loadAnnotationParamsCSV | 0.00 | 0.00 | 0.02 | |
| peakPantheR_parallelAnnotation | 8.94 | 0.08 | 9.01 | |
| peakPantheR_plotEICFit | 0.22 | 0.00 | 0.39 | |
| peakPantheR_plotPeakwidth | 0.31 | 0.00 | 0.31 | |
| peakPantheR_singleFileSearch | 3.11 | 0.04 | 3.16 | |
| peakPantheR_start_GUI | 0 | 0 | 0 | |
| peakTables-peakPantheRAnnotation-method | 0.11 | 0.02 | 0.12 | |
| resetAnnotation-peakPantheRAnnotation-method | 0.12 | 0.00 | 0.13 | |
| resetFIR-peakPantheRAnnotation-method | 0.02 | 0.00 | 0.01 | |
| retentionTimeCorrection-peakPantheRAnnotation-method | 6.08 | 0.05 | 6.13 | |
| spectraMetadata-peakPantheRAnnotation-method | 0.11 | 0.01 | 0.12 | |
| spectraPaths_and_metadata_UI_helper | 0.00 | 0.00 | 0.02 | |
| spectra_metadata_colourScheme_UI_helper | 0 | 0 | 0 | |
| uROI-peakPantheRAnnotation-method | 0.14 | 0.00 | 0.14 | |
| uROIExist-peakPantheRAnnotation-method | 0.07 | 0.05 | 0.12 | |
| useFIR-peakPantheRAnnotation-method | 0.12 | 0.00 | 0.12 | |
| useUROI-peakPantheRAnnotation-method | 0.13 | 0.01 | 0.14 | |