Package: MLP

Version: 1.7.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MLP_1.7.3.tar.gz

StartedAt: 2013-03-24 07:53:09 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 08:01:16 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 487.5 seconds

RetCode: 0

Status:  OK

CheckDir: MLP.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MLP.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MLP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MLP' version '1.7.3'
* 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 'MLP' can be installed ... [15s/16s] 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 ... [150s/160s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
MLP         77.524  7.920  87.509
getGeneSets 44.039  4.804  55.653
plot.MLP     5.109  0.416   5.732
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.MLP.R' [153s/172s]
 [154s/173s] 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 'MLP' ...
** R
** inst
** preparing package for lazy loading
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** installing vignettes
   'UsingMLP.Rnw' 
** testing if installed package can be loaded
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
* DONE (MLP)

name	user	system	elapsed
MLP	77.524	7.920	87.509
getGeneSets	44.039	4.804	55.653
mlpBarplot	0.039	0.013	0.052
plot.MLP	5.109	0.416	5.732
plotGOgraph	1.412	0.057	1.472
plotGeneSetSignificance	1.322	0.076	1.405