BioC 2.12: CHECK report for DESeq2 on petty

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/DESeq2.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'DESeq2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DESeq2' version '1.0.19'
* 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 'DESeq2' can be installed ... [37s/37s] 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 ... 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 compilation flags in Makevars ... 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 ... [48s/48s] 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 'DESeq2' ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include"   -fPIC  -mtune=core2 -g -O2  -c DESeq2.cpp -o DESeq2.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o DESeq2.so DESeq2.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/DESeq2.Rcheck/DESeq2/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DESeq2)

name	user	system	elapsed
DESeq	3.611	0.067	3.752
DESeqDataSet	0.166	0.002	0.172
counts	0.184	0.002	0.187
design	0.197	0.001	0.200
dispersionFunction	1.909	0.034	1.960
dispersions	1.584	0.017	1.635
estimateDispersions	1.897	0.012	1.954
estimateDispersionsGeneEst	1.445	0.009	1.465
estimateSizeFactors	0.232	0.003	0.237
estimateSizeFactorsForMatrix	0.191	0.003	0.195
makeExampleDESeqDataSet	0.198	0.003	0.201
nbinomLRT	2.651	0.012	2.686
nbinomWaldTest	2.802	0.032	2.850
normalizationFactors	3.045	0.017	3.112
plotDispEsts	2.068	0.018	2.101
plotMA	2.484	0.015	2.517
plotPCA	3.217	0.020	3.268
results	3.015	0.019	3.067
rlogTransformation	3.341	0.011	3.384
sizeFactors	0.230	0.005	0.235
varianceStabilizingTransformation	1.463	0.017	1.490

BioC 2.12: CHECK report for DESeq2 on petty

Summary

Command output