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CHECK report for peakPantheR on celaya2

This page was generated on 2020-01-16 13:55:25 -0500 (Thu, 16 Jan 2020).

Package 1241/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
peakPantheR 1.1.0
Arnaud Wolfer
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/peakPantheR
Branch: master
Last Commit: 35708e9
Last Changed Date: 2019-10-29 13:43:42 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: peakPantheR
Version: 1.1.0
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_1.1.0.tar.gz
StartedAt: 2020-01-16 07:21:57 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 07:40:44 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 1127.3 seconds
RetCode: 0
Status:  OK 
CheckDir: peakPantheR.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /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_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/peakPantheR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.1.0’
* 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 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                               21.590  0.521  22.175
EICs-peakPantheRAnnotation-method                       14.866  1.184  16.058
peakPantheR_parallelAnnotation                          14.760  0.128  14.884
outputAnnotationDiagnostic-peakPantheRAnnotation-method 14.446  0.125  14.595
outputAnnotationResult-peakPantheRAnnotation-method     14.392  0.067  14.458
peakPantheR_singleFileSearch                             5.405  0.084   5.489
* 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
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 1.1.0 

> 
> test_check("peakPantheR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1245 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
687.573   7.303 930.504 

Example timings

peakPantheR.Rcheck/peakPantheR-Ex.timings

nameusersystemelapsed
EICs-peakPantheRAnnotation-method14.866 1.18416.058
FIR-peakPantheRAnnotation-method0.4680.0450.512
ROI-peakPantheRAnnotation-method0.3420.0130.355
TIC-peakPantheRAnnotation-method0.3810.0170.398
acquisitionTime-peakPantheRAnnotation-method0.3210.0120.332
annotationDiagnosticPlots-peakPantheRAnnotation-method0.3480.0120.360
annotationParamsDiagnostic-peakPantheRAnnotation-method0.3340.0130.348
annotationTable-peakPantheRAnnotation-method0.4730.0170.489
cpdID-peakPantheRAnnotation-method0.3930.0140.408
cpdMetadata-peakPantheRAnnotation-method0.3750.0140.389
cpdName-peakPantheRAnnotation-method0.3670.0150.383
dataPoints-peakPantheRAnnotation-method0.3630.0130.377
filename-peakPantheRAnnotation-method0.3820.0120.395
filepath-peakPantheRAnnotation-method1.2150.0171.232
isAnnotated-peakPantheRAnnotation-method0.3990.0150.414
nbCompounds-peakPantheRAnnotation-method0.3300.0180.347
nbSamples-peakPantheRAnnotation-method0.2940.0140.308
outputAnnotationDiagnostic-peakPantheRAnnotation-method14.446 0.12514.595
outputAnnotationResult-peakPantheRAnnotation-method14.392 0.06714.458
peakFit-peakPantheRAnnotation-method0.3980.0150.413
peakPantheRAnnotation0.4110.0140.424
peakPantheR_ROIStatistics21.590 0.52122.175
peakPantheR_loadAnnotationParamsCSV0.0180.0010.020
peakPantheR_parallelAnnotation14.760 0.12814.884
peakPantheR_plotEICFit0.7710.0030.775
peakPantheR_plotPeakwidth1.0200.0421.064
peakPantheR_singleFileSearch5.4050.0845.489
peakTables-peakPantheRAnnotation-method0.3990.0130.412
resetAnnotation-peakPantheRAnnotation-method0.4290.0140.443
resetFIR-peakPantheRAnnotation-method0.0090.0010.010
spectraMetadata-peakPantheRAnnotation-method0.4320.0190.450
uROI-peakPantheRAnnotation-method0.3890.0140.403
uROIExist-peakPantheRAnnotation-method0.4110.0120.423
useFIR-peakPantheRAnnotation-method0.4070.0140.420
useUROI-peakPantheRAnnotation-method0.3850.0130.397