Package: phenoTest

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phenoTest_1.4.0.tar.gz

StartedAt: 2012-09-24 01:15:58 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 01:22:17 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 379.8 seconds

RetCode: 0

Status:  OK

CheckDir: phenoTest.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/phenoTest.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.4.0'
* 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 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-2.10-bioc/meat/phenoTest.Rcheck/00check.log'
for details.

* installing *source* package 'phenoTest' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'coerce' when loading 'cellHTS2'
Warning: replacing previous import 'initialize' when loading 'cellHTS2'
** help
*** installing help indices
** building package indices
** installing vignettes
   'phenoTest.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'coerce' when loading 'cellHTS2'
Warning: replacing previous import 'initialize' when loading 'cellHTS2'

* DONE (phenoTest)

name	user	system	elapsed
ClusterPhenoTest	0.348	0.026	0.376
ExpressionPhenoTest	10.058	0.042	10.103
epheno-class	0.002	0.000	0.003
epheno	0.037	0.003	0.041
epheno2html	0.001	0.000	0.000
eset	0.213	0.015	0.229
eset.genelevel	0.142	0.010	0.152
eset2genelevel	0.000	0.001	0.000
findCopyNumber	11.125	3.183	14.363
genesInArea	0.262	0.016	0.278
getEsPositions	0.249	0.014	0.266
getGo	0	0	0
getKegg	0	0	0
getVars2test	0.029	0.003	0.032
gsea	0.414	0.097	0.514
gsea.kegg.go	0.000	0.000	0.001
gsea2html	0.892	0.102	0.996
gseaData-class	0.001	0.000	0.001
gseaSignatures-class	0.000	0.000	0.001
gseaSignatures	0.030	0.003	0.032
gseaSignaturesSign-class	0.000	0.001	0.001
gseaSignaturesVar-class	0.001	0.000	0.001
gseaSignificance	0	0	0
gseaSignificanceSign-class	0.001	0.000	0.001
gseaSignificanceVar-class	0.000	0.000	0.001
heatmapPhenoTest	0.333	0.016	0.356
pAdjust	0.036	0.004	0.039
plot.gsea	0.001	0.000	0.000
plot.gseaSignatures	0	0	0
plots4epheno	0.077	0.005	0.082
smoothCoxph	0.204	0.013	0.218
summary.gsea	0.000	0.000	0.001
summary.gseaSignificance	0	0	0
write.html	0	0	0