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: 2013-03-25 01:14:52 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:17:53 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 181.4 seconds

RetCode: 0

Status:  OK

CheckDir: DriverNet.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/DriverNet.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ... [2s/2s] 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 ... [147s/152s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
DriverNet-package       69.892  0.332  74.209
computeDrivers          44.791  0.088  45.877
computeRandomizedResult 28.878  0.028  29.234
* 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	69.892	0.332	74.209
DriverNetResult-class	0.020	0.008	0.028
actualEvents	0.080	0.032	0.116
computeDrivers	44.791	0.088	45.877
computeRandomizedResult	28.878	0.028	29.234
drivers	0.092	0.016	0.108
getPatientOutlierMatrix	0.324	0.000	0.339
preprocessMatrices	0.396	0.008	0.407
resultSummary	0.324	0.004	0.328
sampleDriversList	0.040	0.004	0.047
sampleGeneNames	0.036	0.004	0.039
sampleInfluenceGraph	0.232	0.000	0.232
samplePatientExpressionMatrix	0.100	0.004	0.103
samplePatientMutationMatrix	0.016	0.004	0.023
samplePatientOutlierMatrix	0.024	0.000	0.021
sampleRandomDriversResult	0.012	0.000	0.011
totalEvents	0.024	0.008	0.029