BioC 2.11: CHECK report for DESeq on perceval

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/DESeq.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.10.1'
* 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 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' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
nbinomTestForMatrices 38.075  2.420  41.404
nbinomTest            20.813  1.288  22.777
* 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.11-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-2.11-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	0	0
adjustScvForBias	0.757	0.023	0.813
conditions	2.181	0.038	2.267
counts	2.465	0.037	2.557
dispTable	3.552	0.332	4.096
estimateDispersions	3.198	0.278	3.511
estimateSizeFactors	2.243	0.054	2.316
estimateSizeFactorsForMatrix	2.115	0.038	2.167
fitInfo	3.025	0.282	3.346
fitNbinomGLMs	0.000	0.000	0.001
fitNbinomGLMsForMatrix	0.000	0.000	0.001
getBaseMeansAndVariances	2.356	0.051	2.426
getVarianceStabilizedData	3.812	0.562	4.426
makeExampleCountDataSet	2.174	0.028	2.211
nbinomGLMTest	2.694	0.033	2.751
nbinomTest	20.813	1.288	22.777
nbinomTestForMatrices	38.075	2.420	41.404
newCountDataSet	2.222	0.036	2.281
plotDispEsts	3.092	0.320	3.608
plotMA	0.001	0.000	0.000
plotPCA	3.616	0.496	4.260
sizeFactors	2.165	0.042	2.210

Summary

Command output