Package: DESeq

Version: 1.11.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DESeq_1.11.6.tar.gz

StartedAt: 2013-03-25 02:04:56 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:09:39 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 283.5 seconds

RetCode: 0

Status:  OK

CheckDir: DESeq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/DESeq.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'DESeq/DESCRIPTION' ... OK
* this is package 'DESeq' version '1.11.6'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'DESeq' can be installed ... [16s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... NOTE
plotMA: no visible binding for global variable 'baseMean'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'whbiocvignette.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [138s/139s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
nbinomTestForMatrices     50.012  2.206  52.416
nbinomTest                25.657  1.166  26.946
plotPCA                    4.786  0.456   5.293
getVarianceStabilizedData  4.697  0.362   5.080
* 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/DESeq.Rcheck/00check.log'
for details.

* installing *source* package 'DESeq' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c pval.c -o pval.o
pval.c: In function 'add_from_both_sides':
pval.c:26: warning: unused variable 'esttotalperlength'
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o DESeq.so pval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/DESeq.Rcheck/DESeq/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'DESeq.Rnw' 
** testing if installed package can be loaded
* DONE (DESeq)

name	user	system	elapsed
CountDataSet-class	0.008	0.006	0.013
adjustScvForBias	0.528	0.022	0.551
conditions	2.607	0.029	2.637
counts	2.794	0.023	2.818
dispTable	3.679	0.223	3.907
estimateDispersions	3.577	0.222	3.806
estimateSizeFactors	2.390	0.034	2.425
estimateSizeFactorsForMatrix	2.200	0.031	2.234
fitInfo	4.390	0.284	4.697
fitNbinomGLMs	0.006	0.004	0.010
fitNbinomGLMsForMatrix	0.004	0.004	0.009
getBaseMeansAndVariances	2.606	0.051	2.661
getVarianceStabilizedData	4.697	0.362	5.080
makeExampleCountDataSet	2.357	0.022	2.384
nbinomGLMTest	3.522	0.028	3.551
nbinomTest	25.657	1.166	26.946
nbinomTestForMatrices	50.012	2.206	52.416
newCountDataSet	3.283	0.034	3.316
plotDispEsts	4.602	0.284	4.905
plotMA	0.010	0.005	0.016
plotPCA	4.786	0.456	5.293
sizeFactors	2.433	0.031	2.465