Package: PatientGeneSets

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PatientGeneSets_1.0.0.tar.gz

StartedAt: 2011-03-31 07:07:39 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 07:11:21 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 222.7 seconds

RetCode: 0

Status:  OK

CheckDir: PatientGeneSets.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/PatientGeneSets.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PatientGeneSets/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PatientGeneSets’ version ‘1.0.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘PatientGeneSets’ 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) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘PatientGeneSets’ ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c get.cdf.het.berns.c -o get.cdf.het.berns.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o PatientGeneSets.so get.cdf.het.berns.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.7-bioc/meat/PatientGeneSets.Rcheck/PatientGeneSets/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Loading Tcl/Tk interface ... done
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (PatientGeneSets)

name	user	system	elapsed
cma.scores	0.000	0.001	0.001
combine.sims	0.000	0.000	0.001
do.gene.set.analysis	6.629	0.656	7.515
extract.sims.method	0.000	0.000	0.001
sim.data.p.values	87.070	53.109	144.672