BioC 2.12: CHECK report for DriverNet on george2

Package: DriverNet

Version: 1.0.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings DriverNet_1.0.0.tar.gz

StartedAt: 2013-10-09 01:24:51 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:27:47 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 176.1 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 3.0.1 (2013-05-16)
* 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 ‘1.0.0’
* 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 ... [145s/150s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
DriverNet-package       69.564  0.204  69.797
computeDrivers          42.627  0.108  47.880
computeRandomizedResult 29.637  0.016  29.709
* 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
** testing if installed package can be loaded
* DONE (DriverNet)

name	user	system	elapsed
DriverNet-package	69.564	0.204	69.797
DriverNetResult-class	0.020	0.008	0.029
actualEvents	0.076	0.036	0.113
computeDrivers	42.627	0.108	47.880
computeRandomizedResult	29.637	0.016	29.709
drivers	0.064	0.040	0.103
getPatientOutlierMatrix	0.316	0.000	0.318
preprocessMatrices	0.388	0.008	0.396
resultSummary	0.456	0.032	0.488
sampleDriversList	0.024	0.008	0.031
sampleGeneNames	0.044	0.000	0.043
sampleInfluenceGraph	0.293	0.008	0.299
samplePatientExpressionMatrix	0.100	0.004	0.107
samplePatientMutationMatrix	0.016	0.000	0.018
samplePatientOutlierMatrix	0.020	0.000	0.021
sampleRandomDriversResult	0.008	0.004	0.013
totalEvents	0.016	0.012	0.025