Package: phenoTest

Version: 1.7.4

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings phenoTest_1.7.4.tar.gz

StartedAt: 2013-01-16 05:12:24 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 05:20:12 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 468.2 seconds

RetCode: 0

Status:  OK

CheckDir: phenoTest.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/phenoTest.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
findCopyNumber      10.137  0.024  10.205
ExpressionPhenoTest  8.100  0.024   8.132
* 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
  ‘/loc/home/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	0.988	0.008	1.001
ExpressionPhenoTest	8.100	0.024	8.132
epheno-class	0.016	0.000	0.015
epheno	0.036	0.004	0.039
epheno2html	0.008	0.004	0.013
eset	0.156	0.004	0.162
eset.genelevel	0.076	0.004	0.081
eset2genelevel	0.012	0.000	0.010
findCopyNumber	10.137	0.024	10.205
genesInArea	0.272	0.004	0.277
getEsPositions	0.268	0.012	0.283
getGo	0.016	0.000	0.015
getKegg	0.016	0.000	0.015
getVars2test	0.040	0.004	0.042
gsea	0.440	0.008	0.448
gsea.kegg.go	0.032	0.000	0.034
gsea2html	1.680	0.000	1.682
gseaData-class	0.020	0.000	0.017
gseaSignatures-class	0.004	0.000	0.005
gseaSignatures	0.052	0.004	0.057
gseaSignaturesSign-class	0.016	0.000	0.017
gseaSignaturesVar-class	0.004	0.000	0.004
gseaSignificance	0.016	0.000	0.016
gseaSignificanceSign-class	0.016	0.000	0.016
gseaSignificanceVar-class	0.004	0.000	0.004
heatmapPhenoTest	0.400	0.000	0.411
pAdjust	0.056	0.004	0.061
plot.gsea	0.004	0.000	0.003
plot.gseaSignatures	0.016	0.000	0.016
plots4epheno	0.080	0.000	0.078
smoothCoxph	0.200	0.004	0.202
summary.gsea	0.016	0.000	0.015
summary.gseaSignificance	0.004	0.000	0.003
write.html	0.032	0.000	0.032