BioC 3.2: CHECK report for DESeq 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 DESeq_1.22.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/DESeq.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESeq/DESCRIPTION’ ... OK
* this is package ‘DESeq’ version ‘1.22.1’
* 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 ‘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 ... [66s/66s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
nbinomTestForMatrices 21.846  0.207  22.072
nbinomTest            12.028  0.155  12.195
* 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
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c pval.c -o pval.o
pval.c:26:11: warning: unused variable 'esttotalperlength' [-Wunused-variable]
   double esttotalperlength = total/2;
          ^
1 warning generated.
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 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	0.590	0.029	0.619
conditions	1.414	0.023	1.437
counts	1.300	0.014	1.315
dispTable	1.906	0.057	1.966
estimateDispersions	1.764	0.016	1.783
estimateSizeFactors	1.240	0.023	1.264
estimateSizeFactorsForMatrix	1.222	0.017	1.239
fitInfo	1.706	0.046	1.752
fitNbinomGLMs	0.001	0.000	0.001
fitNbinomGLMsForMatrix	0	0	0
getBaseMeansAndVariances	1.338	0.013	1.352
getVarianceStabilizedData	2.114	0.045	2.159
makeExampleCountDataSet	1.294	0.009	1.304
nbinomGLMTest	1.934	0.028	1.962
nbinomTest	12.028	0.155	12.195
nbinomTestForMatrices	21.846	0.207	22.072
newCountDataSet	1.309	0.011	1.321
plotDispEsts	1.782	0.033	1.817
plotMA	0.001	0.000	0.000
plotPCA	2.085	0.053	2.143
sizeFactors	1.421	0.020	1.441

BioC 3.2: CHECK report for DESeq on oaxaca

Summary

Command output