BioC 3.0: CHECK report for DESeq2 on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.6.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/DESeq2.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.6.3’
* 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 ... [31s/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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/33s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [48s/49s]
 [49s/49s] 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
* DONE

* installing *source* package ‘DESeq2’ ...
** libs
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c DESeq2.cpp -o DESeq2.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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	1.768	0.008	1.778
DESeqDataSet	0.052	0.000	0.053
coef	1.236	0.000	1.235
collapseReplicates	0.128	0.000	0.127
counts	0.068	0.004	0.074
design	0.072	0.000	0.074
dispersionFunction	0.816	0.000	0.816
dispersions	0.796	0.004	0.800
estimateDispersions	0.996	0.000	0.995
estimateDispersionsGeneEst	0.848	0.000	0.848
estimateSizeFactors	0.156	0.008	0.164
estimateSizeFactorsForMatrix	0.080	0.000	0.079
fpkm	0.248	0.000	0.247
fpm	0.156	0.000	0.154
makeExampleDESeqDataSet	0.076	0.000	0.078
nbinomLRT	1.317	0.000	1.317
nbinomWaldTest	1.668	0.000	1.696
normalizationFactors	1.712	0.000	1.716
plotCounts	0.164	0.000	0.163
plotDispEsts	0.840	0.000	0.839
plotMA	1.996	0.000	1.999
plotPCA	1.400	0.000	1.404
replaceOutliers	0.648	0.000	0.651
results	3.820	0.004	3.827
rlog	1.544	0.000	1.548
sizeFactors	0.084	0.004	0.091
summary	1.276	0.000	1.286
varianceStabilizingTransformation	1.237	0.004	1.272

BioC 3.0: CHECK report for DESeq2 on zin1

Summary

Command output