Package: affycoretools

Version: 1.31.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affycoretools_1.31.5.tar.gz

StartedAt: 2013-03-25 01:00:13 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:07:42 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 449.4 seconds

RetCode: 0

Status:  OK

CheckDir: affycoretools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/affycoretools.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 'affycoretools/DESCRIPTION' ... OK
* this is package 'affycoretools' version '1.31.5'
* 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 'affycoretools' can be installed ... [37s/38s] OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [36s/36s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
plotDeg 13.893  0.355   14.26
* 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/affycoretools.Rcheck/00check.log'
for details.

* installing *source* package 'affycoretools' ...
** R
** inst
** preparing package for lazy loading
No methods found in "GenomicRanges" for requests: summary
** help
*** installing help indices
** building package indices
** installing vignettes
   'affycoretools.Rnw' 
   'affycoretools_biomaRt.Rnw' 
** testing if installed package can be loaded
No methods found in "GenomicRanges" for requests: summary
* DONE (affycoretools)

name	user	system	elapsed
annBM	0.007	0.006	0.013
makeVenn	0.012	0.012	0.026
plotDeg	13.893	0.355	14.260
plotPCA	0.111	0.017	0.128
vennCounts2	0.128	0.018	0.147
vennPage	0.033	0.011	0.045