BioC 2.14: CHECK report for DESeq on petty

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DESeq_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/DESeq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESeq/DESCRIPTION’ ... OK
* this is package ‘DESeq’ version ‘1.16.0’
* 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 ‘DESeq’ can be installed ... [18s/18s] 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 ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘locfit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotMA: no visible binding for global variable ‘baseMean’
* 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 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 ... [132s/134s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
nbinomTestForMatrices 42.604  0.075  42.834
nbinomTest            22.928  0.050  23.065
* 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 were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/DESeq.Rcheck/00check.log’
for details.

* installing *source* package ‘DESeq’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c pval.c -o pval.o
pval.c: In function ‘add_from_both_sides’:
pval.c:26: warning: unused variable ‘esttotalperlength’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o DESeq.so pval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/DESeq.Rcheck/DESeq/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 (DESeq)

name	user	system	elapsed
CountDataSet-class	0.001	0.000	0.001
adjustScvForBias	1.583	0.017	1.607
conditions	3.118	0.016	3.143
counts	3.133	0.008	3.151
dispTable	4.725	0.019	4.779
estimateDispersions	4.030	0.018	4.116
estimateSizeFactors	3.254	0.026	3.430
estimateSizeFactorsForMatrix	3.043	0.007	3.065
fitInfo	4.076	0.010	4.132
fitNbinomGLMs	0.001	0.000	0.001
fitNbinomGLMsForMatrix	0.001	0.000	0.001
getBaseMeansAndVariances	3.068	0.007	3.081
getVarianceStabilizedData	4.501	0.014	4.522
makeExampleCountDataSet	2.953	0.007	2.966
nbinomGLMTest	4.653	0.010	4.672
nbinomTest	22.928	0.050	23.065
nbinomTestForMatrices	42.604	0.075	42.834
newCountDataSet	3.065	0.007	3.077
plotDispEsts	4.311	0.039	4.419
plotMA	0.000	0.000	0.001
plotPCA	4.903	0.018	4.937
sizeFactors	3.155	0.006	3.180

BioC 2.14: CHECK report for DESeq on petty

Summary

Command output