Arnaud Wolfer
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/peakPantheR |
| git_branch: RELEASE_3_13 |
| git_last_commit: 3308eac |
| git_last_commit_date: 2021-06-23 16:02:41 -0400 (Wed, 23 Jun 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:15 -0400 (Fri, 15 Oct 2021).
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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 1366/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| peakPantheR 1.6.1 (landing page) Arnaud Wolfer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: peakPantheR |
| Version: 1.6.1 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:peakPantheR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings peakPantheR_1.6.1.tar.gz |
| StartedAt: 2021-10-15 03:15:31 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 03:42:26 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 1614.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: peakPantheR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:peakPantheR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings peakPantheR_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/peakPantheR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.6.1'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
peakPantheR_ROIStatistics 13.35 0.42 13.76
peakPantheR_parallelAnnotation 10.36 0.11 10.47
outputAnnotationResult-peakPantheRAnnotation-method 9.67 0.05 9.72
outputAnnotationDiagnostic-peakPantheRAnnotation-method 8.75 0.04 8.80
EICs-peakPantheRAnnotation-method 6.77 0.47 7.23
retentionTimeCorrection-peakPantheRAnnotation-method 6.85 0.03 6.89
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
peakPantheR_ROIStatistics 15.28 0.12 15.40
peakPantheR_parallelAnnotation 12.37 0.08 12.45
outputAnnotationDiagnostic-peakPantheRAnnotation-method 11.70 0.05 11.75
outputAnnotationResult-peakPantheRAnnotation-method 10.70 0.03 10.73
retentionTimeCorrection-peakPantheRAnnotation-method 7.94 0.01 7.95
EICs-peakPantheRAnnotation-method 7.62 0.29 7.91
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/peakPantheR_1.6.1.tar.gz && rm -rf peakPantheR.buildbin-libdir && mkdir peakPantheR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=peakPantheR.buildbin-libdir peakPantheR_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL peakPantheR_1.6.1.zip && rm peakPantheR_1.6.1.tar.gz peakPantheR_1.6.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
82 1763k 82 1452k 0 0 1448k 0 0:00:01 0:00:01 --:--:-- 1449k
100 1763k 100 1763k 0 0 1534k 0 0:00:01 0:00:01 --:--:-- 1535k
install for i386
* 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
install for x64
* installing *source* package 'peakPantheR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'peakPantheR' as peakPantheR_1.6.1.zip
* DONE (peakPantheR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'peakPantheR' successfully unpacked and MD5 sums checked
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peakPantheR.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 1.6.1
>
> test_check("peakPantheR")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 1417 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQb1jfz\notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpQb1jfz\notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (C:\Users\biocbuild\bbs-3.13-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (C:\Users\biocbuild\bbs-3.13-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
>
> proc.time()
user system elapsed
479.39 4.21 627.31
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peakPantheR.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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 1.6.1
>
> test_check("peakPantheR")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 1434 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpy2DTXh\notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\Rtmpy2DTXh\notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (C:\Users\biocbuild\bbs-3.13-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (C:\Users\biocbuild\bbs-3.13-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
>
> proc.time()
user system elapsed
590.20 3.29 745.46
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peakPantheR.Rcheck/examples_i386/peakPantheR-Ex.timings
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peakPantheR.Rcheck/examples_x64/peakPantheR-Ex.timings
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