Package: clipper

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clipper_1.0.0.tar.gz

StartedAt: 2013-05-01 03:51:13 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 03:57:26 -0700 (Wed, 01 May 2013)

EllapsedTime: 373.5 seconds

RetCode: 0

Status:  OK

CheckDir: clipper.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/clipper.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'clipper/DESCRIPTION' ... OK
* this is package 'clipper' 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 'clipper' can be installed ... [31s/33s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [62s/64s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
pathwayTest    21.569  0.281  22.127
clipper         9.383  0.320  10.227
easyClip        5.157  0.123   5.391
cliqueMeanTest  4.558  0.231   5.004
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [20s/21s]
 [21s/21s] OK
* 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 'clipper' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (clipper)

name	user	system	elapsed
clipper	9.383	0.320	10.227
cliqueMeanTest	4.558	0.231	5.004
cliqueVarianceTest	4.328	0.196	4.582
deleteEdge	0.328	0.008	0.337
easyClip	5.157	0.123	5.391
getGraphEntryGenes	0.512	0.017	0.544
getJunctionTreePaths	0.505	0.006	0.520
nameCliques	0.016	0.006	0.023
pathwayTest	21.569	0.281	22.127
plotInCytoscape	0.004	0.007	0.011
prunePaths	0.024	0.014	0.039