BioC 2.12: CHECK report for vsn on petty

Package: vsn

Version: 3.27.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch vsn_3.27.2.tar.gz

StartedAt: 2013-03-25 05:04:06 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:05:34 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 88.9 seconds

RetCode: 0

Status: OK

CheckDir: vsn.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/vsn.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'vsn/DESCRIPTION' ... OK
* this is package 'vsn' version '3.27.2'
* 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 'vsn' can be installed ... [8s/9s] 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'convergence2.pdf' from 266Kb to 115Kb
  consider running tools::compactPDF() on these files
* checking installed files from 'inst/doc' ... OK
* checking examples ... [14s/14s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
vsnLikelihood 4.198   0.89   5.094
* 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/vsn.Rcheck/00check.log'
for details.

* installing *source* package 'vsn' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c init.c -o init.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c vsn.c -o vsn.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c vsn2.c -o vsn2.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o vsn.so init.o vsn.o vsn2.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/vsn.Rcheck/vsn/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'logLik' from package 'stats' in package 'vsn'
Creating a generic function for 'coef' from package 'stats' in package 'vsn'
Creating a generic function for 'coefficients' from package 'stats' in package 'vsn'
** help
*** installing help indices
** building package indices
** installing vignettes
   'convergence2.Rnw' 
   'likelihoodcomputations.Rnw' 
   'vsn.Rnw' 
** testing if installed package can be loaded
* DONE (vsn)

name	user	system	elapsed
class.vsn	0.661	0.061	0.722
justvsn	1.841	0.181	2.028
kidney	0.046	0.010	0.056
lymphoma	0.054	0.007	0.063
meanSdPlot	0.229	0.042	0.274
normalize.AffyBatch.vsn	0.005	0.004	0.007
sagmbSimulateData	1.152	0.052	1.203
scalingFactorTransformation	0.004	0.005	0.009
vsn	0.923	0.119	1.060
vsn2	0.628	0.076	0.709
vsn2trsf	0.100	0.010	0.111
vsnLikelihood	4.198	0.890	5.094
vsnPlotPar	0.006	0.004	0.010
vsnh	0.034	0.012	0.046

Summary

Command output