Package: Category

Version: 2.19.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Category_2.19.0.tar.gz

StartedAt: 2011-05-05 13:37:34 -0700 (Thu, 05 May 2011)

EndedAt: 2011-05-05 13:41:19 -0700 (Thu, 05 May 2011)

EllapsedTime: 224.4 seconds

RetCode: 0

Status:  OK

CheckDir: Category.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/Category.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Category/DESCRIPTION’ ... OK
* this is package ‘Category’ version ‘2.19.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘Category’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘Category.pdf’ from 782Kb to 228Kb
     compacted ‘ChromBand.pdf’ from 507Kb to 174Kb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* 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

* installing *source* package ‘Category’ ...
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘Category.Rnw’ 
   ‘ChromBand.Rnw’ 
** testing if installed package can be loaded

* DONE (Category)

name	user	system	elapsed
ChrBandTree-class	22.306	0.643	28.385
ChrMapHyperGParams-class	0.003	0.000	0.003
ChrMapHyperGResult-class	0.002	0.000	0.003
ChrMapLinearMParams-class	0.002	0.001	0.002
ChrMapLinearMResult-class	0.002	0.000	0.003
DatPkg-class	0.110	0.007	0.195
HyperGResult-accessors	1.316	0.094	1.592
LinearMParams-class	0.002	0.000	0.003
LinearMResult-class	0.002	0.001	0.002
LinearMResultBase-class	0.002	0.001	0.002
MAPAmat	16.622	0.683	21.927
applyByCategory	0.005	0.001	0.006
cateGOryMatrix	0.776	0.076	1.206
cb_parse_band_Hs	0.000	0.000	0.001
cb_parse_band_Mm	0.001	0.001	0.001
findAMstats	0.002	0.000	0.003
getPathNames	0.227	0.016	0.393
gseattperm	6.584	0.189	8.679
makeChrBandGraph	14.744	0.265	18.922
makeEBcontr	0.561	0.014	0.583
probes2MAP	0.384	0.016	0.466
probes2Path	0.115	0.007	0.257
ttperm	0.037	0.002	0.039