Package: DESeq

Version: 1.6.1

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings DESeq_1.6.1.tar.gz

StartedAt: 2012-03-24 00:03:48 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 00:07:03 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 194.4 seconds

RetCode: 0

Status:  OK

CheckDir: DESeq.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/DESeq.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESeq/DESCRIPTION’ ... OK
* this is package ‘DESeq’ version ‘1.6.1’
* 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 ‘DESeq’ 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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 compiled code ... 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

* installing *source* package ‘DESeq’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c pval.c -o pval.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o DESeq.so pval.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/DESeq.Rcheck/DESeq/libs
** R
** inst
** preparing package for lazy loading
locfit 1.5-6 	 2010-01-20 
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘DESeq.Rnw’ 
** testing if installed package can be loaded
locfit 1.5-6 	 2010-01-20 

* DONE (DESeq)

name	user	system	elapsed
CountDataSet-class	0	0	0
adjustScvForBias	0.748	0.004	0.755
conditions	2.012	0.008	2.073
counts	2.212	0.000	2.220
dispTable	3.704	0.004	3.748
estimateDispersions	2.992	0.008	3.005
estimateSizeFactors	2.077	0.000	2.075
estimateSizeFactorsForMatrix	1.832	0.000	1.882
fitInfo	2.904	0.000	2.926
fitNbinomGLMs	0	0	0
fitNbinomGLMsForMatrix	0	0	0
getBaseMeansAndVariances	2.116	0.004	2.118
getVarianceStabilizedData	4.248	0.000	4.248
makeExampleCountDataSet	1.828	0.000	1.856
nbinomGLMTest	2.257	0.000	2.262
nbinomTest	21.161	0.020	21.584
nbinomTestForMatrices	38.250	0.012	38.526
newCountDataSet	2.280	0.004	2.284
sizeFactors	2.013	0.000	2.018