BioC 2.12: CHECK report for DESeq on george2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/DESeq.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.12.1’
* 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 ... [18s/18s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* 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 examples ... [152s/153s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
nbinomTestForMatrices     51.799  0.020  52.226
nbinomTest                26.906  0.008  26.940
plotPCA                    7.321  0.008   7.345
dispTable                  6.097  0.024   6.136
getVarianceStabilizedData  5.832  0.004   5.904
plotDispEsts               5.356  0.020   5.387
estimateDispersions        5.296  0.012   5.338
fitInfo                    5.136  0.004   5.154
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/DESeq.Rcheck/00check.log’
for details.

* installing *source* package ‘DESeq’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-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-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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	0.400	0.008	0.410
adjustScvForBias	0.632	0.008	0.649
conditions	3.488	0.012	3.561
counts	3.048	0.008	3.058
dispTable	6.097	0.024	6.136
estimateDispersions	5.296	0.012	5.338
estimateSizeFactors	2.996	0.020	3.105
estimateSizeFactorsForMatrix	2.573	0.000	2.627
fitInfo	5.136	0.004	5.154
fitNbinomGLMs	0.016	0.000	0.016
fitNbinomGLMsForMatrix	0.012	0.000	0.015
getBaseMeansAndVariances	3.468	0.004	3.473
getVarianceStabilizedData	5.832	0.004	5.904
makeExampleCountDataSet	3.181	0.000	3.180
nbinomGLMTest	3.108	0.000	3.117
nbinomTest	26.906	0.008	26.940
nbinomTestForMatrices	51.799	0.020	52.226
newCountDataSet	2.928	0.000	2.950
plotDispEsts	5.356	0.020	5.387
plotMA	0.016	0.000	0.015
plotPCA	7.321	0.008	7.345
sizeFactors	2.868	0.000	2.872

BioC 2.12: CHECK report for DESeq on george2

Summary

Command output