Package: RTCGAToolbox

Version: 2.12.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RTCGAToolbox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RTCGAToolbox_2.12.1.tar.gz

StartedAt: 2019-04-16 02:31:47 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:34:46 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 178.8 seconds

RetCode: 0

Status:  OK

CheckDir: RTCGAToolbox.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:RTCGAToolbox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RTCGAToolbox_2.12.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/RTCGAToolbox.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTCGAToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTCGAToolbox’ version ‘2.12.1’
* 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 ‘RTCGAToolbox’ 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 ... NOTE
.getGISTIC: no visible global function definition for ‘mcols<-’
Undefined global functions or variables:
  mcols<-
* 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
getReport 7.877  0.261   8.209
* 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-3.8-bioc/meat/RTCGAToolbox.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RTCGAToolbox
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RTCGAToolbox’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RTCGAToolbox)

name	user	system	elapsed
biocExtract	0.000	0.000	0.001
getBroadSubtypes	0.012	0.002	0.228
getCNGECorrelation	1.533	0.060	1.609
getData	0.441	0.295	0.741
getDiffExpressedGenes	0.288	0.025	0.316
getFirehoseAnalyzeDates	0.002	0.001	0.162
getFirehoseData	0.051	0.012	0.063
getFirehoseDatasets	0.002	0.001	0.164
getFirehoseRunningDates	0.005	0.002	0.322
getGISTICPeaks	1.880	0.581	3.175
getMutationRate	0.047	0.006	0.053
getReport	7.877	0.261	8.209
getSurvival	0.161	0.009	0.171
showResults-CorResult	1.171	0.094	1.271
showResults-DGEResult	0.244	0.011	0.256
showResults	0.234	0.020	0.257