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This page was generated on 2021-09-17 15:06:47 -0400 (Fri, 17 Sep 2021).

CHECK results for peakPantheR on machv2

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- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/peakPantheR.git to
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raw results

Package 1366/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.6.1  (landing page)
Arnaud Wolfer
Snapshot Date: 2021-09-16 04:50:11 -0400 (Thu, 16 Sep 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)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: peakPantheR
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings peakPantheR_1.6.1.tar.gz
StartedAt: 2021-09-16 22:17:33 -0400 (Thu, 16 Sep 2021)
EndedAt: 2021-09-16 22:34:09 -0400 (Thu, 16 Sep 2021)
EllapsedTime: 996.3 seconds
RetCode: 0
Status:   OK  
CheckDir: peakPantheR.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings peakPantheR_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/peakPantheR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 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 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                               17.028  0.235  17.278
peakPantheR_parallelAnnotation                          12.431  0.107  12.543
EICs-peakPantheRAnnotation-method                       11.361  0.426  11.796
outputAnnotationResult-peakPantheRAnnotation-method     11.282  0.076  11.368
outputAnnotationDiagnostic-peakPantheRAnnotation-method 11.215  0.093  11.326
retentionTimeCorrection-peakPantheRAnnotation-method     7.713  0.053   7.775
* 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


Installation output

peakPantheR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL peakPantheR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)

Tests output

peakPantheR.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 (/private/tmp/RtmppPaMpo/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/private/tmp/RtmppPaMpo/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (/Library/Frameworks/R.framework/Versions/4.1/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (/Library/Frameworks/R.framework/Versions/4.1/Resources/library/peakPantheR/extdata/test_fakemzML.mzML)
> 
> proc.time()
   user  system elapsed 
631.439   3.814 822.561 

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method11.361 0.42611.796
FIR-peakPantheRAnnotation-method0.2840.0220.306
ROI-peakPantheRAnnotation-method0.2530.0120.265
TIC-peakPantheRAnnotation-method0.2830.0130.296
acquisitionTime-peakPantheRAnnotation-method0.2640.0130.278
annotationDiagnosticPlots-peakPantheRAnnotation-method0.2930.0140.307
annotationParamsDiagnostic-peakPantheRAnnotation-method0.2590.0120.271
annotationTable-peakPantheRAnnotation-method0.3610.0110.371
annotation_diagnostic_multiplot_UI_helper0.1180.0020.119
annotation_fit_summary_UI_helper0.0110.0010.011
annotation_showMethod_UI_helper0.0070.0010.008
annotation_showText_UI_helper0.0010.0010.002
cpdID-peakPantheRAnnotation-method0.2520.0110.264
cpdMetadata-peakPantheRAnnotation-method0.2830.0130.295
cpdName-peakPantheRAnnotation-method0.2300.0110.241
dataPoints-peakPantheRAnnotation-method0.2120.0110.223
filename-peakPantheRAnnotation-method0.8770.0160.924
filepath-peakPantheRAnnotation-method0.2050.0100.216
initialise_annotation_from_files_UI_helper0.0150.0010.017
isAnnotated-peakPantheRAnnotation-method0.2230.0100.233
load_annotation_from_file_UI_helper0.0080.0010.009
nbCompounds-peakPantheRAnnotation-method0.2650.0110.276
nbSamples-peakPantheRAnnotation-method0.2620.0120.274
outputAnnotationDiagnostic-peakPantheRAnnotation-method11.215 0.09311.326
outputAnnotationFeatureMetadata_UI_helper0.0080.0010.008
outputAnnotationParamsCSV-peakPantheRAnnotation-method0.0330.0010.034
outputAnnotationResult-peakPantheRAnnotation-method11.282 0.07611.368
outputAnnotationSpectraMetadata_UI_helper0.0090.0010.010
peakFit-peakPantheRAnnotation-method0.2760.0120.288
peakPantheRAnnotation0.2820.0120.294
peakPantheR_ROIStatistics17.028 0.23517.278
peakPantheR_loadAnnotationParamsCSV0.0130.0020.015
peakPantheR_parallelAnnotation12.431 0.10712.543
peakPantheR_plotEICFit0.4640.0040.502
peakPantheR_plotPeakwidth0.6430.0160.660
peakPantheR_singleFileSearch3.9800.0484.030
peakPantheR_start_GUI0.0000.0000.001
peakTables-peakPantheRAnnotation-method0.2140.0090.223
resetAnnotation-peakPantheRAnnotation-method0.2850.0200.373
resetFIR-peakPantheRAnnotation-method0.0090.0010.010
retentionTimeCorrection-peakPantheRAnnotation-method7.7130.0537.775
spectraMetadata-peakPantheRAnnotation-method0.2850.0130.299
spectraPaths_and_metadata_UI_helper0.0040.0020.006
spectra_metadata_colourScheme_UI_helper0.0090.0010.009
uROI-peakPantheRAnnotation-method0.2920.0130.305
uROIExist-peakPantheRAnnotation-method0.2340.0110.245
useFIR-peakPantheRAnnotation-method0.2590.0130.272
useUROI-peakPantheRAnnotation-method0.2460.0110.257