BioC 3.2: CHECK report for DESeq on perceval

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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_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/DESeq.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.22.0’
* 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 ... [10s/10s] 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 ... [78s/78s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
nbinomTestForMatrices 30.969  0.023  30.993
nbinomTest            16.512  0.015  16.527
* 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-3.2-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-3.2-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	0.523	0.003	0.526
conditions	1.456	0.006	1.462
counts	1.513	0.006	1.520
dispTable	2.328	0.009	2.337
estimateDispersions	1.971	0.007	1.979
estimateSizeFactors	1.336	0.006	1.342
estimateSizeFactorsForMatrix	1.354	0.003	1.356
fitInfo	1.825	0.007	1.832
fitNbinomGLMs	0	0	0
fitNbinomGLMsForMatrix	0.001	0.001	0.000
getBaseMeansAndVariances	1.372	0.004	1.376
getVarianceStabilizedData	2.129	0.020	2.149
makeExampleCountDataSet	1.330	0.002	1.332
nbinomGLMTest	2.050	0.002	2.052
nbinomTest	16.512	0.015	16.527
nbinomTestForMatrices	30.969	0.023	30.993
newCountDataSet	1.381	0.005	1.386
plotDispEsts	1.883	0.009	1.891
plotMA	0.000	0.000	0.001
plotPCA	2.271	0.014	2.287
sizeFactors	1.365	0.002	1.367

BioC 3.2: CHECK report for DESeq on perceval

Summary

Command output