BioC 3.4: CHECK report for DESeq2 on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DESeq2_1.14.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DESeq2.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.14.1’
* 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 ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c DESeq2.cpp -o DESeq2.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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	1.120	0.008	1.128
DESeqDataSet	0.036	0.000	0.036
coef	1.832	0.008	1.844
collapseReplicates	0.104	0.000	0.107
counts	0.068	0.000	0.068
design	0.048	0.008	0.055
dispersionFunction	1.048	0.012	1.061
estimateDispersions	0.452	0.000	0.450
estimateDispersionsGeneEst	0.476	0.000	0.475
estimateSizeFactors	0.104	0.000	0.107
estimateSizeFactorsForMatrix	0.056	0.000	0.059
fpkm	0.148	0.000	0.148
fpm	0.104	0.000	0.102
makeExampleDESeqDataSet	0.060	0.000	0.061
nbinomLRT	0.760	0.000	0.759
nbinomWaldTest	0.936	0.000	0.937
normalizationFactors	1.092	0.000	1.092
plotCounts	0.072	0.000	0.071
plotDispEsts	0.472	0.000	0.472
plotMA	1.080	0.000	1.084
plotPCA	1.672	0.004	1.679
plotSparsity	0.076	0.000	0.075
results	3.792	0.000	3.798
rlog	1.280	0.004	1.284
summary	1.780	0.000	1.779
varianceStabilizingTransformation	0.648	0.000	0.647
vst	1.436	0.016	1.453

BioC 3.4: CHECK report for DESeq2 on malbec1

Summary

Command output