Package: Category

Version: 2.25.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Category_2.25.1.tar.gz

StartedAt: 2013-01-16 01:14:33 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 01:19:51 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 318.3 seconds

RetCode: 0

Status:  OK

CheckDir: Category.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Category.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ChrBandTree-class 28.718  0.112  28.852
MAPAmat           16.561  0.068  16.637
makeChrBandGraph  14.585  0.052  14.639
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’
 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	28.718	0.112	28.852
ChrMapHyperGParams-class	0.004	0.000	0.006
ChrMapHyperGResult-class	0.004	0.000	0.004
ChrMapLinearMParams-class	0.012	0.000	0.014
ChrMapLinearMResult-class	0.004	0.000	0.004
DatPkg-class	0.072	0.012	0.085
HyperGResult-accessors	0.876	0.012	0.892
LinearMResult-class	0.004	0.004	0.005
MAPAmat	16.561	0.068	16.637
applyByCategory	0.016	0.000	0.019
cateGOryMatrix	0.376	0.020	0.396
cb_parse_band_Hs	0.000	0.000	0.003
cb_parse_band_Mm	0.012	0.000	0.013
findAMstats	0.012	0.000	0.015
getPathNames	0.136	0.008	0.151
gseattperm	3.880	0.056	3.935
makeChrBandGraph	14.585	0.052	14.639
makeEBcontr	0.340	0.008	0.350
probes2MAP	0.288	0.020	0.308
probes2Path	0.092	0.012	0.110
ttperm	0.040	0.004	0.043