BioC 2.13: CHECK report for DESeq2 on perceval

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/DESeq2.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESeq2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DESeq2’ version ‘1.2.10’
* 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 ... [32s/32s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘DESeq2.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [42s/67s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
results     5.713  0.039   5.761
dispersions 1.480  0.011   6.212
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [29s/30s]
 [30s/30s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/DESeq2.Rcheck/00check.log’
for details.

* 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 -Wall  -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 -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-2.13-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	4.321	0.037	4.358
DESeqDataSet	0.074	0.001	0.076
counts	0.118	0.002	0.119
design	0.120	0.001	0.121
dispersionFunction	1.023	0.012	1.038
dispersions	1.480	0.011	6.212
estimateDispersions	1.064	0.002	1.067
estimateDispersionsGeneEst	1.302	0.008	1.311
estimateSizeFactors	0.179	0.003	0.183
estimateSizeFactorsForMatrix	0.116	0.002	0.118
makeExampleDESeqDataSet	0.135	0.001	0.136
nbinomLRT	2.063	0.022	2.086
nbinomWaldTest	2.017	0.009	2.028
normalizationFactors	1.901	0.010	1.911
plotDispEsts	1.356	0.009	1.388
plotMA	1.747	0.008	3.140
plotPCA	2.168	0.008	2.178
replaceOutliersWithTrimmedMean	0.910	0.009	0.920
results	5.713	0.039	5.761
rlogTransformation	3.041	0.016	3.062
sizeFactors	0.166	0.003	0.168
varianceStabilizingTransformation	2.070	0.007	2.077

BioC 2.13: CHECK report for DESeq2 on perceval

Summary

Command output