BioC 2.12: CHECK report for DriverNet on petty

Package: DriverNet

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DriverNet_1.0.0.tar.gz

StartedAt: 2013-10-08 22:12:36 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:14:56 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 140.7 seconds

RetCode: 0

Status:  OK

CheckDir: DriverNet.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/DriverNet.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [107s/108s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
DriverNet-package       50.387  2.708  53.752
computeDrivers          32.957  2.242  35.646
computeRandomizedResult 15.517  0.147  15.817
* 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	50.387	2.708	53.752
DriverNetResult-class	0.027	0.005	0.032
actualEvents	0.056	0.059	0.117
computeDrivers	32.957	2.242	35.646
computeRandomizedResult	15.517	0.147	15.817
drivers	0.052	0.052	0.104
getPatientOutlierMatrix	0.352	0.045	0.396
preprocessMatrices	0.298	0.042	0.342
resultSummary	0.392	0.049	0.447
sampleDriversList	0.030	0.005	0.036
sampleGeneNames	0.051	0.015	0.066
sampleInfluenceGraph	0.234	0.021	0.257
samplePatientExpressionMatrix	0.133	0.017	0.151
samplePatientMutationMatrix	0.019	0.005	0.023
samplePatientOutlierMatrix	0.021	0.005	0.026
sampleRandomDriversResult	0.004	0.003	0.008
totalEvents	0.031	0.005	0.037