Package: HiTC

Version: 1.3.2

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings HiTC_1.3.2.tar.gz

StartedAt: 2013-01-16 03:31:00 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 03:35:45 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 284.7 seconds

RetCode: 0

Status:  OK

CheckDir: HiTC.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/HiTC.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 ‘HiTC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiTC’ version ‘1.3.2’
* 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 ‘HiTC’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mapC              16.517  0.088  16.639
CQC               15.193  0.108  15.305
HTCexp-class      14.469  0.076  14.561
getExpectedCounts 11.437  0.140  11.602
intervalsDist      6.004  0.196   6.202
* 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 ‘HiTC’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘HiTC’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘HiTC.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded

* DONE (HiTC)

name	user	system	elapsed
CQC	15.193	0.108	15.305
HTCexp-class	14.469	0.076	14.561
HTClist-class	0.004	0.000	0.004
Nora_5C	0.564	0.008	0.571
binningC	4.124	0.004	4.131
discretize	0.004	0.004	0.008
export.my5C	0.016	0.000	0.015
exportC	0.004	0.004	0.007
extractRegion	0.568	0.012	0.582
getExpectedCounts	11.437	0.140	11.602
import.my5C	0.844	0.008	0.853
importC	0.008	0.000	0.005
intervalsDist	6.004	0.196	6.202
mapC	16.517	0.088	16.639
removeIntervals	0.252	0.004	0.254
setIntervalScale	1.997	0.000	1.995