Package: DESeq

Version: 1.11.6

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings DESeq_1.11.6.tar.gz

StartedAt: 2013-03-25 01:10:32 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:16:23 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 350.5 seconds

RetCode: 0

Status:  OK

CheckDir: DESeq.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/DESeq.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.11.6’
* 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 ... [21s/23s] 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 ... [150s/159s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
nbinomTestForMatrices     49.843  0.024  52.676
nbinomTest                26.530  0.040  27.099
getVarianceStabilizedData  6.781  0.004   6.855
plotPCA                    6.669  0.004   7.430
dispTable                  6.420  0.044   6.954
fitInfo                    5.072  0.064   5.522
estimateDispersions        4.804  0.072   5.399
plotDispEsts               4.760  0.008   5.554
* 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
   ‘DESeq.Rnw’ 
** testing if installed package can be loaded
* DONE (DESeq)

name	user	system	elapsed
CountDataSet-class	0.012	0.000	0.013
adjustScvForBias	0.732	0.000	0.745
conditions	3.620	0.008	3.627
counts	3.545	0.016	3.813
dispTable	6.420	0.044	6.954
estimateDispersions	4.804	0.072	5.399
estimateSizeFactors	3.224	0.016	3.260
estimateSizeFactorsForMatrix	2.805	0.052	3.199
fitInfo	5.072	0.064	5.522
fitNbinomGLMs	0.012	0.000	0.014
fitNbinomGLMsForMatrix	0.012	0.000	0.014
getBaseMeansAndVariances	2.808	0.048	3.186
getVarianceStabilizedData	6.781	0.004	6.855
makeExampleCountDataSet	2.636	0.000	2.637
nbinomGLMTest	3.588	0.012	3.615
nbinomTest	26.530	0.040	27.099
nbinomTestForMatrices	49.843	0.024	52.676
newCountDataSet	2.716	0.000	2.902
plotDispEsts	4.760	0.008	5.554
plotMA	0.016	0.000	0.013
plotPCA	6.669	0.004	7.430
sizeFactors	2.908	0.000	3.203