Package: Doscheda

Version: 1.8.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Doscheda.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Doscheda_1.8.1.tar.gz

StartedAt: 2020-04-15 05:03:36 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:07:59 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 263.7 seconds

RetCode: 0

Status:  OK

CheckDir: Doscheda.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Doscheda.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Doscheda_1.8.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/Doscheda.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.1’
* 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         27.492  0.672  42.789
runDoscheda              23.124  0.004  31.080
pcaPlot-methods           6.044  0.012  19.797
corrPlot-methods          3.552  0.092   6.438
runNormalisation-methods  3.092  0.324  10.612
meanSdPlot-methods        2.864  0.016  10.356
replicatePlot-methods     2.420  0.004  10.462
volcanoPlot-methods       2.248  0.004   8.757
densityPlot-methods       2.132  0.016   8.169
* 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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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL Doscheda
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘Doscheda’ ...
** using staged installation
** 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 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 (Doscheda)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  6.324   0.172  10.745 

name	user	system	elapsed
corrPlot-methods	3.552	0.092	6.438
densityPlot-methods	2.132	0.016	8.169
doschedaData	0.068	0.000	0.069
fitModel-methods	27.492	0.672	42.789
getDatasets-methods	0	0	0
getFinal-methods	0	0	0
getInput-methods	0	0	0
getNorm-methods	0	0	0
getParameters-methods	0.004	0.000	0.000
makeReport	0	0	0
meanSdPlot-methods	2.864	0.016	10.356
pcaPlot-methods	6.044	0.012	19.797
processedExample	0.116	0.000	0.116
removePeptides-methods	0.000	0.000	0.001
replicatePlot-methods	2.420	0.004	10.462
runDoscheda	23.124	0.004	31.080
runNormalisation-methods	3.092	0.324	10.612
setData-methods	0.728	0.188	0.915
setParameters-methods	0.000	0.000	0.002
volcanoPlot-methods	2.248	0.004	8.757