Package: phenoTest

Version: 1.7.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phenoTest_1.7.4.tar.gz

StartedAt: 2013-03-24 08:44:05 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 08:53:36 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 570.9 seconds

RetCode: 0

Status:  OK

CheckDir: phenoTest.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/phenoTest.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 'phenoTest/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phenoTest' version '1.7.4'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* 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 'phenoTest' can be installed ... [52s/55s] 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.gseaData':
  'plot.gseaData'

S3 methods shown with full name in documentation object 'plot.gseaSignatures':
  'plot.gseaSignaturesSign'

S3 methods shown with full name in documentation object 'summary.gseaData':
  'summary.gseaData'

S3 methods shown with full name in documentation object 'summary.gseaSignificance':
  'summary.gseaSignificanceSign'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... [52s/53s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
findCopyNumber      10.069  0.739  11.132
ExpressionPhenoTest  9.619  0.338  10.039
* 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/phenoTest.Rcheck/00check.log'
for details.

* installing *source* package 'phenoTest' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'phenoTest.Rnw' 
** testing if installed package can be loaded
* DONE (phenoTest)

name	user	system	elapsed
ClusterPhenoTest	1.079	0.025	1.120
ExpressionPhenoTest	9.619	0.338	10.039
epheno-class	0.005	0.007	0.012
epheno	0.043	0.009	0.053
epheno2html	0.012	0.006	0.019
eset	0.192	0.011	0.206
eset.genelevel	0.132	0.011	0.144
eset2genelevel	0.003	0.004	0.008
findCopyNumber	10.069	0.739	11.132
genesInArea	0.332	0.020	0.356
getEsPositions	0.323	0.017	0.341
getGo	0.012	0.005	0.017
getKegg	0.014	0.006	0.020
getVars2test	0.049	0.008	0.058
gsea	0.472	0.044	0.521
gsea.kegg.go	0.019	0.010	0.028
gsea2html	1.126	0.076	1.207
gseaData-class	0.015	0.004	0.018
gseaSignatures-class	0.015	0.003	0.019
gseaSignatures	0.066	0.012	0.078
gseaSignaturesSign-class	0.015	0.005	0.021
gseaSignaturesVar-class	0.006	0.005	0.011
gseaSignificance	0.002	0.004	0.007
gseaSignificanceSign-class	0.014	0.006	0.021
gseaSignificanceVar-class	0.017	0.006	0.023
heatmapPhenoTest	0.524	0.029	0.581
pAdjust	0.056	0.009	0.065
plot.gsea	0.014	0.003	0.017
plot.gseaSignatures	0.003	0.003	0.005
plots4epheno	0.099	0.011	0.113
smoothCoxph	0.252	0.017	0.271
summary.gsea	0.002	0.003	0.006
summary.gseaSignificance	0.014	0.005	0.020
write.html	0.016	0.006	0.021