Package: Doscheda

Version: 1.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Doscheda.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Doscheda_1.4.1.tar.gz

StartedAt: 2019-04-15 23:36:20 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:40:48 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 267.5 seconds

RetCode: 0

Status:  OK

CheckDir: Doscheda.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:Doscheda.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Doscheda_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Doscheda.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Doscheda/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Doscheda’ version ‘1.4.1’
* 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 ‘Doscheda’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
fitModel-methods         38.970  1.536  44.671
runDoscheda              33.188  0.155  35.496
pcaPlot-methods           5.944  0.110   9.927
runNormalisation-methods  3.704  0.577   6.146
corrPlot-methods          3.804  0.205   6.220
meanSdPlot-methods        2.950  0.087   5.037
* 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 Doscheda
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Doscheda’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
in method for ‘getInput’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘getNorm’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘getFinal’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘getParameters’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘getDatasets’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘boxplot’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘corrPlot’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘densityPlot’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
Creating a new generic function for ‘meanSdPlot’ in package ‘Doscheda’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Doscheda)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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(Doscheda)
> 
> test_check("Doscheda")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  7.689   0.537  10.459 

name	user	system	elapsed
corrPlot-methods	3.804	0.205	6.220
densityPlot-methods	2.490	0.061	4.412
doschedaData	0.068	0.003	0.071
fitModel-methods	38.970	1.536	44.671
getDatasets-methods	0	0	0
getFinal-methods	0	0	0
getInput-methods	0	0	0
getNorm-methods	0	0	0
getParameters-methods	0.000	0.000	0.001
makeReport	0.001	0.000	0.000
meanSdPlot-methods	2.950	0.087	5.037
pcaPlot-methods	5.944	0.110	9.927
processedExample	0.113	0.008	0.122
removePeptides-methods	0.000	0.000	0.001
replicatePlot-methods	2.941	0.051	4.926
runDoscheda	33.188	0.155	35.496
runNormalisation-methods	3.704	0.577	6.146
setData-methods	1.435	0.556	2.006
setParameters-methods	0.003	0.001	0.004
volcanoPlot-methods	2.485	0.038	4.369