Package: phenoTest

Version: 1.4.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings phenoTest_1.4.0.tar.gz

StartedAt: 2012-04-01 02:40:56 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 02:45:53 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 297.0 seconds

RetCode: 0

Status:  OK

CheckDir: phenoTest.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/phenoTest.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* 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 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
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/phenoTest.Rcheck/00check.log'
for details.

* installing *source* package 'phenoTest' ...
** R
** data
** inst
** preparing package for lazy loading
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
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
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning: replacing previous import 'coerce' when loading 'cellHTS2'
Warning: replacing previous import 'initialize' when loading 'cellHTS2'

* DONE (phenoTest)

name	user	system	elapsed
ClusterPhenoTest	0.168	0.012	0.189
ExpressionPhenoTest	5.369	0.012	5.396
epheno-class	0.004	0.000	0.001
epheno	0.020	0.000	0.032
epheno2html	0	0	0
eset	0.100	0.004	0.119
eset.genelevel	0.072	0.004	0.088
eset2genelevel	0	0	0
findCopyNumber	5.980	0.020	6.071
genesInArea	0.188	0.004	0.226
getEsPositions	0.184	0.012	0.230
getGo	0	0	0
getKegg	0	0	0
getVars2test	0.020	0.004	0.037
gsea	0.292	0.004	0.304
gsea.kegg.go	0	0	0
gsea2html	0.668	0.016	0.719
gseaData-class	0.004	0.000	0.000
gseaSignatures-class	0.000	0.000	0.001
gseaSignatures	0.032	0.000	0.040
gseaSignaturesSign-class	0	0	0
gseaSignaturesVar-class	0.000	0.000	0.001
gseaSignificance	0.004	0.000	0.000
gseaSignificanceSign-class	0	0	0
gseaSignificanceVar-class	0.000	0.000	0.001
heatmapPhenoTest	0.264	0.004	0.279
pAdjust	0.024	0.004	0.045
plot.gsea	0.000	0.000	0.001
plot.gseaSignatures	0.004	0.000	0.000
plots4epheno	0.064	0.000	0.083
smoothCoxph	0.140	0.000	0.154
summary.gsea	0	0	0
summary.gseaSignificance	0	0	0
write.html	0	0	0