Package: phenoTest

Version: 1.5.2

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phenoTest_1.5.2.tar.gz

StartedAt: 2012-06-21 02:33:13 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 02:41:18 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 485.6 seconds

RetCode: 0

Status:  OK

CheckDir: phenoTest.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/phenoTest.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'phenoTest/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phenoTest' version '1.5.2'
* 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 whether package 'phenoTest' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-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	0.307	0.027	0.348
ExpressionPhenoTest	8.923	0.067	9.152
epheno-class	0.002	0.001	0.002
epheno	0.031	0.003	0.034
epheno2html	0.000	0.000	0.001
eset	0.206	0.015	0.227
eset.genelevel	0.144	0.011	0.157
eset2genelevel	0.000	0.000	0.001
findCopyNumber	12.898	3.932	18.267
genesInArea	0.357	0.021	0.389
getEsPositions	0.336	0.015	0.357
getGo	0.000	0.000	0.001
getKegg	0	0	0
getVars2test	0.036	0.003	0.039
gsea	0.914	0.122	1.049
gsea.kegg.go	0	0	0
gsea2html	1.174	0.146	1.372
gseaData-class	0.002	0.000	0.001
gseaSignatures-class	0.001	0.000	0.001
gseaSignatures	0.035	0.003	0.039
gseaSignaturesSign-class	0.001	0.000	0.002
gseaSignaturesVar-class	0.001	0.000	0.001
gseaSignificance	0	0	0
gseaSignificanceSign-class	0.001	0.001	0.002
gseaSignificanceVar-class	0.001	0.000	0.002
heatmapPhenoTest	0.504	0.025	0.568
pAdjust	0.042	0.004	0.046
plot.gsea	0.000	0.000	0.001
plot.gseaSignatures	0	0	0
plots4epheno	0.089	0.005	0.094
smoothCoxph	0.242	0.016	0.259
summary.gsea	0	0	0
summary.gseaSignificance	0.001	0.000	0.000
write.html	0	0	0