Package: phenoTest

Version: 0.99.3

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings phenoTest_0.99.3.tar.gz

StartedAt: 2011-02-24 21:50:42 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 21:52:23 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 100.6 seconds

RetCode: 0

Status:  OK

CheckDir: phenoTest.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/phenoTest.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘0.99.3’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘phenoTest’ can be installed ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘phenoTest’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c getEs.c -o getEs.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o phenoTest.so getEs.o -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/phenoTest.Rcheck/phenoTest/libs
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: AnnotationDbi
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (phenoTest)

name	user	system	elapsed
ClusterPhenoTest	0.264	0.004	0.267
ExpressionPhenoTest	5.724	0.016	5.741
epheno-class	0.004	0.000	0.002
epheno	0.004	0.000	0.005
epheno2html	0	0	0
eset	0.024	0.000	0.023
getVars2test	0.008	0.000	0.009
gseaSignatures-class	0.000	0.000	0.001
gseaSignatures	0.008	0.000	0.009
gseaSignaturesSign-class	0.000	0.000	0.001
gseaSignaturesVar-class	0.000	0.000	0.001
gseaSignificance	0	0	0
gseaSignificanceSign-class	0	0	0
gseaSignificanceVar-class	0.000	0.000	0.001
heatmapPhenoTest	0.26	0.00	0.26
pAdjust	0.012	0.000	0.012
plot.gseaSignatures	0	0	0
plots4epheno	0.040	0.000	0.042
smoothCoxph	0.052	0.000	0.054
summary.gseaSignificance	0	0	0