Package: Doscheda

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Doscheda_1.0.0.tar.gz

StartedAt: 2018-04-12 03:03:04 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:07:19 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 254.4 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 --no-vignettes --timings Doscheda_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Doscheda.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.0’
* 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 ‘Doscheda’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data             2.1Mb
    doc              2.1Mb
    shiny-examples   2.0Mb
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
fitModel-methods         32.002  1.220  37.833
runDoscheda              29.160  0.107  31.467
pcaPlot-methods           6.201  0.093   9.710
runNormalisation-methods  4.096  0.476   6.245
corrPlot-methods          3.918  0.100   5.938
meanSdPlot-methods        3.865  0.046   5.596
densityPlot-methods       3.512  0.054   5.585
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/Doscheda.Rcheck/00check.log’
for details.

* installing *source* package ‘Doscheda’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 
  6.521   0.295   9.054 

name	user	system	elapsed
corrPlot-methods	3.918	0.100	5.938
densityPlot-methods	3.512	0.054	5.585
doschedaData	0.052	0.006	0.058
fitModel-methods	32.002	1.220	37.833
getDatasets-methods	0.000	0.000	0.001
getFinal-methods	0.001	0.001	0.001
getInput-methods	0.001	0.000	0.001
getNorm-methods	0.001	0.000	0.001
getParameters-methods	0.001	0.001	0.001
makeReport	0.001	0.000	0.001
meanSdPlot-methods	3.865	0.046	5.596
pcaPlot-methods	6.201	0.093	9.710
processedExample	0.065	0.006	0.071
removePeptides-methods	0.001	0.001	0.001
replicatePlot-methods	2.306	0.038	4.067
runDoscheda	29.160	0.107	31.467
runNormalisation-methods	4.096	0.476	6.245
setData-methods	1.828	0.386	2.236
setParameters-methods	0.004	0.000	0.004
volcanoPlot-methods	2.381	0.042	4.159