BioC 3.1: CHECK report for DESeq2 on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.8.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/DESeq2.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.8.2’
* 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 ... [25s/39s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [29s/45s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
results 4.826  0.019   6.997
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [43s/60s]
 [43s/60s] 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

Status: OK

* installing *source* package ‘DESeq2’ ...
** libs
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c DESeq2.cpp -o DESeq2.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.1-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/DESeq2.Rcheck/DESeq2/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (DESeq2)

name	user	system	elapsed
DESeq	1.377	0.010	2.414
DESeqDataSet	0.037	0.000	0.065
coef	1.922	0.009	3.366
collapseReplicates	0.097	0.000	0.149
counts	0.072	0.000	0.088
design	0.054	0.000	0.066
dispersionFunction	1.539	0.001	2.462
estimateDispersions	0.724	0.000	1.316
estimateDispersionsGeneEst	0.780	0.000	1.392
estimateSizeFactors	0.125	0.000	0.242
estimateSizeFactorsForMatrix	0.068	0.000	0.147
fpkm	0.213	0.000	0.449
fpm	0.121	0.000	0.241
makeExampleDESeqDataSet	0.062	0.000	0.125
nbinomLRT	1.139	0.001	1.826
nbinomWaldTest	1.527	0.000	2.419
normalizationFactors	1.492	0.008	2.228
plotCounts	0.128	0.000	0.169
plotDispEsts	0.753	0.000	0.968
plotMA	1.510	0.001	2.209
plotPCA	1.283	0.000	2.158
plotSparsity	0.071	0.000	0.072
results	4.826	0.019	6.997
rlog	1.358	0.000	2.070
summary	2.010	0.001	2.443
varianceStabilizingTransformation	0.905	0.004	1.298

BioC 3.1: CHECK report for DESeq2 on zin2

Summary

Command output