Package: DriverNet

Version: 0.99.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings DriverNet_0.99.0.tar.gz

StartedAt: 2013-01-16 02:08:07 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 02:10:06 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 118.7 seconds

RetCode: 0

Status:  OK

CheckDir: DriverNet.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/DriverNet.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DriverNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DriverNet’ version ‘0.99.0’
* 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 ‘DriverNet’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 for unstated 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
DriverNet-package       47.026  0.160  47.393
computeDrivers          29.450  0.072  29.627
computeRandomizedResult 17.069  0.016  17.103
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘DriverNet’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘DriverNet-Overview.Rnw’ 
** testing if installed package can be loaded

* DONE (DriverNet)

name	user	system	elapsed
DriverNet-package	47.026	0.160	47.393
DriverNetResult-class	0.004	0.016	0.023
actualEvents	0.068	0.020	0.088
computeDrivers	29.450	0.072	29.627
computeRandomizedResult	17.069	0.016	17.103
drivers	0.048	0.040	0.085
getPatientOutlierMatrix	0.244	0.008	0.254
preprocessMatrices	0.232	0.004	0.234
resultSummary	0.316	0.012	0.327
sampleDriversList	0.012	0.012	0.026
sampleGeneNames	0.032	0.000	0.032
sampleInfluenceGraph	0.172	0.008	0.178
samplePatientExpressionMatrix	0.080	0.000	0.082
samplePatientMutationMatrix	0.016	0.000	0.015
samplePatientOutlierMatrix	0.02	0.00	0.02
sampleRandomDriversResult	0.012	0.000	0.009
totalEvents	0.020	0.004	0.026