BioC 3.2: CHECK report for RTCGAToolbox on zin1

Package: RTCGAToolbox

Version: 1.99.4

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RTCGAToolbox_1.99.4.tar.gz

StartedAt: 2015-08-24 03:30:35 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:31:30 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 54.8 seconds

RetCode: 0

Status:  OK

CheckDir: RTCGAToolbox.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RTCGAToolbox_1.99.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/RTCGAToolbox.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.99.4’
* 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 ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 loading without being on the library search path ... 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
getFirehoseData: possible error in .makeExprMat(export.file, "",
  "miRNAArray", 100, TRUE, runDate): unused argument (runDate)
getReport: no visible binding for global variable
  ‘UCSC.HG19.Human.CytoBandIdeogram’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/20s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
getReport 13.455  0.183  13.642
* 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/RTCGAToolbox.Rcheck/00check.log’
for details.

* installing *source* package ‘RTCGAToolbox’ ...
** R
** data
** inst
** preparing 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
getCNGECorrelation	1.040	0.004	1.043
getData-methods	0.079	0.012	0.092
getData	0.085	0.008	0.094
getDiffExpressedGenes	0.384	0.004	0.389
getFirehoseAnalyzeDates	0.005	0.000	0.340
getFirehoseData	0.093	0.000	0.093
getFirehoseDatasets	0.002	0.000	0.159
getFirehoseRunningDates	0.003	0.000	0.328
getMutationRate	0.105	0.000	0.105
getReport	13.455	0.183	13.642
getSurvival	0.204	0.000	0.204
showResults-CorResult	0.957	0.031	0.991
showResults-DGEResult	0.681	0.004	0.700
showResults	0.318	0.000	0.321