BioC 3.5: CHECK report for DESeq2 on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DESeq2_1.15.38.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DESeq2.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.15.38’
* 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 ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
* 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 ... 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/DESeq2.Rcheck/00check.log’
for details.

* installing *source* package ‘DESeq2’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c DESeq2.cpp -o DESeq2.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-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	4.753	0.047	4.801
DESeqDataSet	0.424	0.001	0.426
coef	1.831	0.025	1.856
collapseReplicates	0.189	0.001	0.190
counts	0.086	0.001	0.086
design	0.048	0.000	0.049
dispersionFunction	1.338	0.025	1.364
estimateDispersions	0.523	0.001	0.524
estimateDispersionsGeneEst	1.015	0.005	1.020
estimateSizeFactors	0.169	0.000	0.170
estimateSizeFactorsForMatrix	0.067	0.000	0.066
fpkm	0.270	0.014	0.283
fpm	0.136	0.015	0.151
lfcShrink	3.084	0.022	3.106
makeExampleDESeqDataSet	0.068	0.001	0.069
nbinomLRT	1.434	0.023	1.458
nbinomWaldTest	1.154	0.010	1.164
normalizationFactors	1.226	0.017	1.242
plotCounts	0.121	0.003	0.125
plotDispEsts	0.761	0.007	0.769
plotMA	1.456	0.009	1.468
plotPCA	4.455	0.012	4.472
plotSparsity	0.094	0.001	0.095
results	4.850	0.054	4.907
rlog	2.027	0.010	2.054
summary	1.748	0.026	1.774
varianceStabilizingTransformation	1.168	0.003	1.172
vst	1.329	0.075	1.407

BioC 3.5: CHECK report for DESeq2 on oaxaca

Summary

Command output