BioC 3.1: 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 DESeq_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/DESeq.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.20.0’
* 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 ... [14s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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.
* 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’
prepareScvBiasCorrectionFits : <anonymous>: no visible global function
  definition for ‘locfit’
* 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 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 ... [100s/100s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
nbinomTestForMatrices 36.503  0.057  36.581
nbinomTest            19.809  0.038  19.860
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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/Library/Frameworks/R.framework/Resources/lib -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-3.1-bioc/meat/DESeq.Rcheck/DESeq/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 (DESeq)

name	user	system	elapsed
CountDataSet-class	0.001	0.000	0.001
adjustScvForBias	0.881	0.019	0.900
conditions	1.624	0.013	1.636
counts	1.664	0.003	1.667
dispTable	3.137	0.015	3.157
estimateDispersions	2.343	0.009	2.352
estimateSizeFactors	1.766	0.004	1.770
estimateSizeFactorsForMatrix	1.938	0.003	1.944
fitInfo	2.907	0.009	2.919
fitNbinomGLMs	0.001	0.000	0.000
fitNbinomGLMsForMatrix	0.001	0.000	0.001
getBaseMeansAndVariances	2.267	0.009	2.277
getVarianceStabilizedData	3.404	0.012	3.421
makeExampleCountDataSet	2.041	0.004	2.047
nbinomGLMTest	2.990	0.023	3.021
nbinomTest	19.809	0.038	19.860
nbinomTestForMatrices	36.503	0.057	36.581
newCountDataSet	1.690	0.006	1.696
plotDispEsts	2.736	0.014	2.758
plotMA	0.001	0.001	0.001
plotPCA	3.233	0.014	3.622
sizeFactors	1.942	0.003	1.948

BioC 3.1: CHECK report for DESeq on petty

Summary

Command output