Package: PrecisionTrialDrawer

Version: 1.0.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PrecisionTrialDrawer.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PrecisionTrialDrawer_1.0.1.tar.gz

StartedAt: 2019-10-16 04:03:17 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:06:09 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 172.1 seconds

RetCode: 0

Status:  OK

CheckDir: PrecisionTrialDrawer.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PrecisionTrialDrawer.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PrecisionTrialDrawer_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/PrecisionTrialDrawer.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.0.1’
* 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 0.531  0.004   9.545
panelDesigner  0.509  0.004   7.076
* 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-3.9-bioc/R/bin/R CMD INSTALL PrecisionTrialDrawer
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* installing to library ‘/home/biocbuild/bbs-3.9-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	0.001	0.000	0.001
PrecisionTrialDrawer-package	0.171	0.003	0.176
appendRepo	1.299	0.024	1.323
coocMutexPlot	2.022	0.009	2.031
coveragePlot	0.267	0.012	0.279
coverageStackPlot	0.319	0.012	0.331
cpArguments	0.019	0.004	0.022
cpData	0.037	0.003	0.041
cpDataSubset	0.014	0.001	0.014
cpDesign	0.031	0.000	0.032
cpFreq	0.346	0.011	0.374
cpObj	0.311	0.004	0.315
cpObj2	0.058	0.000	0.059
dataExtractor	0.400	0.004	0.403
filterFusions	0.578	0.016	0.595
filterMutations	1.617	0.008	1.625
getAlterations	0.304	0.004	0.605
newCancerPanel	0.531	0.004	9.545
panelDesigner	0.509	0.004	7.076
panelOptimizer	0.000	0.001	0.001
panelexample	0.005	0.005	0.009
propPowerSampleSize	0.986	0.024	1.010
saturationPlot	2.156	0.024	2.180
showCancerStudy	0.018	0.004	0.044
showTumorType	0.050	0.000	0.072
subsetAlterations	0.711	0.004	0.715
survPowerSampleSize	1.038	0.000	1.038
survPowerSampleSize1Arm	1.104	0.008	1.112