Package: PrecisionTrialDrawer

Version: 1.2.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:PrecisionTrialDrawer.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings PrecisionTrialDrawer_1.2.1.tar.gz

StartedAt: 2020-04-15 06:12:17 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:15:35 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 197.8 seconds

RetCode: 0

Status:  OK

CheckDir: PrecisionTrialDrawer.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:PrecisionTrialDrawer.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings PrecisionTrialDrawer_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/PrecisionTrialDrawer.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 ‘PrecisionTrialDrawer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PrecisionTrialDrawer’ version ‘1.2.1’
* 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 1.544  0.016   5.226
panelDesigner  1.344  0.024  14.762
* 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:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL PrecisionTrialDrawer
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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	0.000	0.000	0.002
PrecisionTrialDrawer-package	0.300	0.016	0.316
appendRepo	0.740	0.024	0.779
coocMutexPlot	2.644	0.016	2.704
coveragePlot	0.264	0.004	0.268
coverageStackPlot	0.320	0.004	0.323
cpArguments	0.016	0.000	0.014
cpData	0.016	0.000	0.017
cpDataSubset	0.012	0.000	0.009
cpDesign	0.02	0.00	0.02
cpFreq	0.256	0.012	0.271
cpObj	0.240	0.000	0.242
cpObj2	0.072	0.000	0.072
dataExtractor	0.564	0.000	0.565
filterFusions	1.060	0.000	1.068
filterMutations	1.232	0.008	1.252
getAlterations	0.252	0.004	0.563
newCancerPanel	1.544	0.016	5.226
panelDesigner	1.344	0.024	14.762
panelOptimizer	0.000	0.000	0.001
panelexample	0.008	0.000	0.009
propPowerSampleSize	1.356	0.004	1.363
saturationPlot	2.208	0.020	2.233
showCancerStudy	0.020	0.000	0.064
showTumorType	0.052	0.000	0.094
subsetAlterations	0.732	0.000	0.733
survPowerSampleSize	1.100	0.004	1.112
survPowerSampleSize1Arm	1.136	0.004	1.145