Package: RTCGAToolbox

Version: 2.17.3

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_2.17.3.tar.gz

StartedAt: 2020-01-16 08:28:06 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 08:32:56 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 289.7 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_2.17.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/RTCGAToolbox.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.17.3’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘IRanges’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.setAnnoRows: no visible binding for global variable ‘hugos’
Undefined global functions or variables:
  hugos
* 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 (user + system) or elapsed time > 5s
            user system elapsed
getReport 12.602  0.744  13.385
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-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/4.0/Resources/library’
* installing *source* package ‘RTCGAToolbox’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RTCGAToolbox)

name	user	system	elapsed
biocExtract	0.000	0.000	0.001
getBroadSubtypes	0.014	0.005	0.197
getCNGECorrelation	2.274	0.113	2.387
getData	0.609	0.582	1.192
getDiffExpressedGenes	0.456	0.053	0.511
getFirehoseAnalyzeDates	0.042	0.013	0.398
getFirehoseData	0.059	0.013	0.073
getFirehoseDatasets	0.008	0.003	0.425
getFirehoseRunningDates	0.014	0.004	0.505
getGISTICPeaks	1.746	0.413	3.625
getMutationRate	0.090	0.012	0.102
getReport	12.602	0.744	13.385
getSurvival	0.158	0.015	0.174
showResults-CorResult	1.735	0.194	1.928
showResults-DGEResult	0.297	0.030	0.328
showResults	1.283	0.040	1.369