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: 2013-03-25 04:01:44 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:09:55 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 490.4 seconds

RetCode: 0

Status:  OK

CheckDir: phenoTest.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/phenoTest.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.7.4'
* 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 ... [40s/40s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [48s/49s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
findCopyNumber      9.751  3.007  12.879
ExpressionPhenoTest 8.466  0.518   8.998
* 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	0.685	0.035	0.723
ExpressionPhenoTest	8.466	0.518	8.998
epheno-class	0.015	0.008	0.022
epheno	0.049	0.010	0.060
epheno2html	0.011	0.008	0.018
eset	0.183	0.017	0.201
eset.genelevel	0.137	0.013	0.150
eset2genelevel	0.007	0.006	0.014
findCopyNumber	9.751	3.007	12.879
genesInArea	0.290	0.028	0.323
getEsPositions	0.300	0.030	0.331
getGo	0.008	0.007	0.016
getKegg	0.009	0.007	0.017
getVars2test	0.050	0.010	0.061
gsea	0.424	0.100	0.526
gsea.kegg.go	0.018	0.013	0.032
gsea2html	1.326	0.125	1.459
gseaData-class	0.004	0.006	0.010
gseaSignatures-class	0.012	0.007	0.019
gseaSignatures	0.056	0.017	0.073
gseaSignaturesSign-class	0.012	0.009	0.022
gseaSignaturesVar-class	0.010	0.007	0.017
gseaSignificance	0.010	0.006	0.017
gseaSignificanceSign-class	0.004	0.006	0.010
gseaSignificanceVar-class	0.014	0.008	0.022
heatmapPhenoTest	0.484	0.040	0.529
pAdjust	0.052	0.012	0.065
plot.gsea	0.009	0.006	0.014
plot.gseaSignatures	0.008	0.005	0.012
plots4epheno	0.112	0.018	0.130
smoothCoxph	0.248	0.021	0.270
summary.gsea	0.007	0.005	0.012
summary.gseaSignificance	0.008	0.005	0.013
write.html	0.009	0.008	0.018