BioC 2.13: CHECK report for DESeq on zin1

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/DESeq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESeq/DESCRIPTION’ ... OK
* this is package ‘DESeq’ version ‘1.14.0’
* 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 ... [8s/8s] 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 installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘whbiocvignette.sty’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘DESeq.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [88s/88s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
nbinomTestForMatrices 31.954  0.016  32.033
nbinomTest            16.857  0.012  16.897
* 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 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/DESeq.Rcheck/00check.log’
for details.

* installing *source* package ‘DESeq’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c pval.c -o pval.o
pval.c: In function ‘add_from_both_sides’:
pval.c:26:11: warning: unused variable ‘esttotalperlength’ [-Wunused-variable]
gcc -std=gnu99 -shared -L/usr/local/lib -o DESeq.so pval.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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	0.004	0.000	0.004
adjustScvForBias	0.600	0.004	0.604
conditions	1.996	0.004	2.004
counts	1.976	0.000	1.978
dispTable	2.764	0.012	2.781
estimateDispersions	2.512	0.008	2.524
estimateSizeFactors	1.960	0.000	1.964
estimateSizeFactorsForMatrix	1.825	0.000	1.829
fitInfo	2.508	0.012	2.524
fitNbinomGLMs	0.000	0.000	0.003
fitNbinomGLMsForMatrix	0.004	0.000	0.001
getBaseMeansAndVariances	1.860	0.000	1.862
getVarianceStabilizedData	2.852	0.004	2.856
makeExampleCountDataSet	1.924	0.004	1.928
nbinomGLMTest	2.664	0.008	2.675
nbinomTest	16.857	0.012	16.897
nbinomTestForMatrices	31.954	0.016	32.033
newCountDataSet	1.873	0.000	1.875
plotDispEsts	2.436	0.004	2.445
plotMA	0.000	0.000	0.001
plotPCA	3.080	0.000	3.085
sizeFactors	1.936	0.000	1.940

BioC 2.13: CHECK report for DESeq on zin1

Summary

Command output