Package: PrecisionTrialDrawer

Version: 1.2.1

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_1.2.1.tar.gz

StartedAt: 2020-04-15 04:43:55 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 04:47:17 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 202.5 seconds

RetCode: 0

Status:  OK

CheckDir: PrecisionTrialDrawer.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:PrecisionTrialDrawer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PrecisionTrialDrawer_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/PrecisionTrialDrawer.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.2.1’
* 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 1.569  0.047   8.192
panelDesigner  1.150  0.049   8.073
* 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 PrecisionTrialDrawer
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* 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	0.001	0.001	0.002
PrecisionTrialDrawer-package	0.266	0.021	0.288
appendRepo	0.736	0.046	0.785
coocMutexPlot	2.168	0.055	2.225
coveragePlot	0.263	0.009	0.272
coverageStackPlot	0.30	0.01	0.31
cpArguments	0.021	0.005	0.027
cpData	0.026	0.004	0.031
cpDataSubset	0.011	0.005	0.016
cpDesign	0.035	0.006	0.041
cpFreq	0.339	0.031	0.369
cpObj	0.279	0.009	0.288
cpObj2	0.065	0.005	0.070
dataExtractor	0.594	0.010	0.605
filterFusions	0.882	0.025	0.907
filterMutations	1.170	0.034	1.205
getAlterations	0.213	0.004	0.439
newCancerPanel	1.569	0.047	8.192
panelDesigner	1.150	0.049	8.073
panelOptimizer	0.002	0.000	0.002
panelexample	0.006	0.002	0.008
propPowerSampleSize	1.156	0.020	1.199
saturationPlot	2.236	0.075	2.341
showCancerStudy	0.020	0.001	0.043
showTumorType	0.059	0.000	0.081
subsetAlterations	0.781	0.033	0.852
survPowerSampleSize	1.060	0.015	1.082
survPowerSampleSize1Arm	1.260	0.017	1.343