Package: peakPantheR

Version: 1.0.0

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_1.0.0.tar.gz

StartedAt: 2020-04-15 04:32:09 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:44:36 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 746.6 seconds

RetCode: 0

Status:  OK

CheckDir: peakPantheR.Rcheck

Warnings: 0

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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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/peakPantheR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.0.0’
* 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 or elapsed time > 5s
                                                          user system elapsed
peakPantheR_ROIStatistics                               13.376  0.207  13.781
peakPantheR_parallelAnnotation                           9.484  0.060   9.641
outputAnnotationDiagnostic-peakPantheRAnnotation-method  8.380  0.057   8.495
outputAnnotationResult-peakPantheRAnnotation-method      8.250  0.038   8.364
EICs-peakPantheRAnnotation-method                        7.141  0.326   7.534
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL peakPantheR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 1.0.0 

> 
> test_check("peakPantheR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1245 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
438.384   3.793 617.290 

name	user	system	elapsed
EICs-peakPantheRAnnotation-method	7.141	0.326	7.534
FIR-peakPantheRAnnotation-method	0.215	0.008	0.224
ROI-peakPantheRAnnotation-method	0.177	0.009	0.189
TIC-peakPantheRAnnotation-method	0.164	0.008	0.173
acquisitionTime-peakPantheRAnnotation-method	0.173	0.008	0.187
annotationDiagnosticPlots-peakPantheRAnnotation-method	0.188	0.009	0.198
annotationParamsDiagnostic-peakPantheRAnnotation-method	0.187	0.008	0.197
annotationTable-peakPantheRAnnotation-method	0.195	0.008	0.203
cpdID-peakPantheRAnnotation-method	0.201	0.009	0.211
cpdMetadata-peakPantheRAnnotation-method	0.198	0.008	0.208
cpdName-peakPantheRAnnotation-method	0.226	0.008	0.235
dataPoints-peakPantheRAnnotation-method	0.208	0.008	0.218
filename-peakPantheRAnnotation-method	0.222	0.009	0.235
filepath-peakPantheRAnnotation-method	0.210	0.008	0.220
isAnnotated-peakPantheRAnnotation-method	0.207	0.008	0.215
nbCompounds-peakPantheRAnnotation-method	0.207	0.009	0.219
nbSamples-peakPantheRAnnotation-method	0.211	0.007	0.220
outputAnnotationDiagnostic-peakPantheRAnnotation-method	8.380	0.057	8.495
outputAnnotationResult-peakPantheRAnnotation-method	8.250	0.038	8.364
peakFit-peakPantheRAnnotation-method	0.165	0.006	0.171
peakPantheRAnnotation	0.245	0.008	0.256
peakPantheR_ROIStatistics	13.376	0.207	13.781
peakPantheR_loadAnnotationParamsCSV	0.015	0.002	0.018
peakPantheR_parallelAnnotation	9.484	0.060	9.641
peakPantheR_plotEICFit	0.535	0.003	0.549
peakPantheR_plotPeakwidth	0.826	0.037	0.878
peakPantheR_singleFileSearch	3.072	0.029	3.161
peakTables-peakPantheRAnnotation-method	0.196	0.007	0.206
resetAnnotation-peakPantheRAnnotation-method	0.239	0.008	0.248
resetFIR-peakPantheRAnnotation-method	0.008	0.000	0.007
spectraMetadata-peakPantheRAnnotation-method	0.226	0.008	0.236
uROI-peakPantheRAnnotation-method	0.247	0.008	0.255
uROIExist-peakPantheRAnnotation-method	0.209	0.008	0.218
useFIR-peakPantheRAnnotation-method	0.191	0.006	0.199
useUROI-peakPantheRAnnotation-method	0.206	0.009	0.216