Package: Category

Version: 2.25.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Category_2.25.1.tar.gz

StartedAt: 2013-03-24 03:14:40 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 03:21:17 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 396.6 seconds

RetCode: 0

Status:  OK

CheckDir: Category.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Category.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Category/DESCRIPTION' ... OK
* this is package 'Category' version '2.25.1'
* 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 'Category' can be installed ... [22s/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 ... 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 installed files from 'inst/doc' ... OK
* checking examples ... [78s/79s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ChrBandTree-class 25.886  0.533  26.560
MAPAmat           17.362  0.702  18.111
makeChrBandGraph  14.312  0.520  15.014
gseattperm         5.080  0.222   5.380
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [94s/98s]
 [95s/99s] 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
** help
*** installing help indices
** building package indices
** installing vignettes
   'Category.Rnw' 
   'ChromBand.Rnw' 
** testing if installed package can be loaded
* DONE (Category)

name	user	system	elapsed
ChrBandTree-class	25.886	0.533	26.560
ChrMapHyperGParams-class	0.005	0.005	0.010
ChrMapHyperGResult-class	0.004	0.004	0.008
ChrMapLinearMParams-class	0.013	0.005	0.019
ChrMapLinearMResult-class	0.004	0.005	0.009
DatPkg-class	0.123	0.020	0.143
HyperGResult-accessors	1.181	0.094	1.500
LinearMResult-class	0.003	0.005	0.009
MAPAmat	17.362	0.702	18.111
applyByCategory	0.021	0.007	0.027
cateGOryMatrix	0.674	0.091	0.778
cb_parse_band_Hs	0.018	0.003	0.021
cb_parse_band_Mm	0.003	0.002	0.005
findAMstats	0.015	0.006	0.022
getPathNames	0.218	0.016	0.235
gseattperm	5.080	0.222	5.380
makeChrBandGraph	14.312	0.520	15.014
makeEBcontr	0.429	0.022	0.482
probes2MAP	0.422	0.025	0.520
probes2Path	0.146	0.016	0.182
ttperm	0.052	0.014	0.074