BioC 2.8: CHECK report for DESeq on lamb2

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/DESeq.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 ‘DESeq/DESCRIPTION’ ... OK
* this is package ‘DESeq’ version ‘1.3.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘DESeq’ 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 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 ‘DESeq’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-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-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/DESeq.Rcheck/DESeq/libs
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: akima
Loading required package: lattice
locfit 1.5-6 	 2010-01-20 
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (DESeq)

name	user	system	elapsed
CountDataSet-class	0.004	0.000	0.000
adjustScvForBias	0.596	0.004	0.602
conditions	2.736	0.004	2.742
counts	2.648	0.004	2.650
estimateSizeFactors	2.688	0.000	2.691
estimateSizeFactorsForMatrix	2.600	0.008	2.608
estimateVarianceFunctionForMatrix	2.924	0.000	2.931
estimateVarianceFunctions	3.237	0.004	3.255
getBaseMeansAndVariances	2.704	0.000	2.708
getRawScvDistanceMatrix	5.732	0.000	5.795
getRawScvForSamplePair	2.800	0.000	2.806
getVarianceStabilizedData	3.457	0.004	3.503
makeExampleCountDataSet	2.608	0.004	2.647
nbinomFitGLM	0	0	0
nbinomGLMTest	3.972	0.000	4.042
nbinomGLMsForMatrix	0	0	0
nbinomTest	12.169	0.016	12.268
nbinomTestForMatrices	12.317	0.004	12.415
newCountDataSet	2.796	0.004	2.802
rawVarFunc	0	0	0
rawVarFuncTable	3.072	0.004	3.083
residualsEcdfPlot	3.260	0.004	3.272
residualsEcdfPlotFromDiagnostics	3.236	0.004	3.243
scvPlot	3.157	0.004	3.164
sizeFactors	2.584	0.004	2.588
varianceFitDiagnostics	3.220	0.004	3.241
varianceFitDiagnosticsForMatrix	3.136	0.000	3.143

Summary

Command output