Package: PrecisionTrialDrawer

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PrecisionTrialDrawer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PrecisionTrialDrawer_1.0.1.tar.gz

StartedAt: 2019-10-16 05:42:43 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:46:41 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 237.9 seconds

RetCode: 0

Status:  OK

CheckDir: PrecisionTrialDrawer.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PrecisionTrialDrawer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PrecisionTrialDrawer_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PrecisionTrialDrawer.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PrecisionTrialDrawer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PrecisionTrialDrawer’ version ‘1.0.1’
* 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 ‘PrecisionTrialDrawer’ 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
newCancerPanel 0.87  0.034   5.572
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PrecisionTrialDrawer
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘PrecisionTrialDrawer’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
** testing if installed package can be loaded from final location
Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
** testing if installed package keeps a record of temporary installation path
* DONE (PrecisionTrialDrawer)

name	user	system	elapsed
CancerPanel-class	0.002	0.001	0.003
PrecisionTrialDrawer-package	0.329	0.021	0.348
appendRepo	1.432	0.063	1.494
coocMutexPlot	2.437	0.133	2.570
coveragePlot	0.333	0.026	0.360
coverageStackPlot	0.367	0.046	0.458
cpArguments	0.047	0.007	0.054
cpData	0.036	0.008	0.044
cpDataSubset	0.015	0.007	0.022
cpDesign	0.038	0.007	0.045
cpFreq	0.400	0.062	0.462
cpObj	0.317	0.016	0.333
cpObj2	0.079	0.011	0.089
dataExtractor	0.604	0.018	0.623
filterFusions	0.589	0.041	0.630
filterMutations	1.634	0.090	1.724
getAlterations	0.332	0.010	0.645
newCancerPanel	0.870	0.034	5.572
panelDesigner	0.469	0.030	4.614
panelOptimizer	0.002	0.001	0.003
panelexample	0.011	0.003	0.014
propPowerSampleSize	1.458	0.038	1.501
saturationPlot	2.851	0.152	3.005
showCancerStudy	0.020	0.000	0.042
showTumorType	0.054	0.001	0.077
subsetAlterations	0.847	0.058	0.904
survPowerSampleSize	1.222	0.019	1.243
survPowerSampleSize1Arm	1.279	0.013	1.293