BioC 2.12: CHECK report for DESeq on petty

Package: DESeq

Version: 1.12.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DESeq_1.12.1.tar.gz

StartedAt: 2013-10-08 22:09:51 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:15:29 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 338.4 seconds

RetCode: 0

Status:  OK

CheckDir: DESeq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/DESeq.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [19s/19s] 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 sizes of PDF files under 'inst/doc' ... 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 ... [147s/149s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
nbinomTestForMatrices     45.270  0.248  45.869
nbinomTest                24.867  0.144  25.418
plotPCA                    5.988  0.052   6.161
dispTable                  5.602  0.080   5.723
getVarianceStabilizedData  5.463  0.113   5.637
estimateDispersions        5.109  0.036   5.207
fitInfo                    4.934  0.049   5.039
* 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
  '/Users/biocbuild/bbs-2.12-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  -c pval.c -o pval.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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-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	0.223	0.002	0.226
adjustScvForBias	0.750	0.018	0.782
conditions	3.974	0.072	4.103
counts	3.559	0.027	3.621
dispTable	5.602	0.080	5.723
estimateDispersions	5.109	0.036	5.207
estimateSizeFactors	3.808	0.021	3.902
estimateSizeFactorsForMatrix	3.508	0.047	3.602
fitInfo	4.934	0.049	5.039
fitNbinomGLMs	0.007	0.002	0.010
fitNbinomGLMsForMatrix	0.008	0.002	0.009
getBaseMeansAndVariances	3.599	0.029	3.699
getVarianceStabilizedData	5.463	0.113	5.637
makeExampleCountDataSet	3.488	0.025	3.528
nbinomGLMTest	4.195	0.021	4.242
nbinomTest	24.867	0.144	25.418
nbinomTestForMatrices	45.270	0.248	45.869
newCountDataSet	3.599	0.013	3.782
plotDispEsts	4.822	0.047	4.993
plotMA	0.006	0.001	0.008
plotPCA	5.988	0.052	6.161
sizeFactors	3.875	0.015	4.014