Package: Category

Version: 2.24.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings Category_2.24.0.tar.gz

StartedAt: 2013-03-24 23:53:54 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:59:27 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 333.3 seconds

RetCode: 0

Status:  OK

CheckDir: Category.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Category.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘2.24.0’
* 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 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 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 26.558  0.144  27.223
MAPAmat           15.953  0.060  16.189
makeChrBandGraph  14.173  0.080  14.456
* 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	26.558	0.144	27.223
ChrMapHyperGParams-class	0.000	0.000	0.002
ChrMapHyperGResult-class	0.000	0.000	0.001
ChrMapLinearMParams-class	0	0	0
ChrMapLinearMResult-class	0.000	0.000	0.001
DatPkg-class	0.072	0.000	0.073
HyperGResult-accessors	0.856	0.008	0.961
LinearMResult-class	0.004	0.000	0.001
MAPAmat	15.953	0.060	16.189
applyByCategory	0.008	0.000	0.007
cateGOryMatrix	0.436	0.040	0.653
cb_parse_band_Hs	0	0	0
cb_parse_band_Mm	0.000	0.000	0.001
findAMstats	0.000	0.000	0.001
getPathNames	0.144	0.008	0.172
gseattperm	3.936	0.096	4.146
makeChrBandGraph	14.173	0.080	14.456
makeEBcontr	0.360	0.016	0.395
probes2MAP	0.260	0.004	0.287
probes2Path	0.104	0.000	0.135
ttperm	0.016	0.004	0.022