Package: DEDS

Version: 1.25.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings DEDS_1.25.0.tar.gz

StartedAt: 2011-02-24 19:09:40 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:10:15 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 35.0 seconds

RetCode: 0

Status:  OK

CheckDir: DEDS.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/DEDS.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 ‘DEDS/DESCRIPTION’ ... OK
* this is package ‘DEDS’ version ‘1.25.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘DEDS’ 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 ... NOTE
prepare_Rd: comp.fdr.Rd:52-54: Dropping empty section \details
prepare_Rd: deds.pval.Rd:65-68: Dropping empty section \examples
prepare_Rd: hist.DEDS.Rd:47-50: Dropping empty section \examples
* 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 ‘DEDS’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c deds.c -o deds.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c distance.c -o distance.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c input.c -o input.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c manip.c -o manip.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c random.c -o random.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c sampling.c -o sampling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c stat_fun.c -o stat_fun.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o DEDS.so deds.o distance.o input.o manip.o random.o sampling.o stat_fun.o -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/DEDS.Rcheck/DEDS/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (DEDS)

name	user	system	elapsed
aggregateFun	0.008	0.000	0.008
comp.B	0.004	0.000	0.003
comp.F	0.364	0.000	0.362
comp.FC	0.008	0.000	0.006
comp.SAM	1.516	0.000	1.520
comp.adjp	0.008	0.000	0.009
comp.ebayes	0.000	0.000	0.004
comp.fdr	0.012	0.004	0.017
comp.modF	0.004	0.000	0.003
comp.modt	0.004	0.000	0.003
comp.stat	0.008	0.004	0.010
comp.t	0.028	0.000	0.026
comp.unadjp	0.008	0.000	0.009
deds.chooseTest	6.860	0.016	6.909
deds.genExtra	0	0	0
deds.stat	5.368	0.004	5.379
deds.stat.linkC	0.024	0.000	0.023
pairs.DEDS	0.132	0.000	0.131
qqnorm.DEDS	0.048	0.000	0.047
topgenes	0.032	0.000	0.031