Package: HiTC

Version: 1.3.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HiTC_1.3.3.tar.gz

StartedAt: 2013-03-24 06:31:45 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 06:37:48 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 362.3 seconds

RetCode: 0

Status:  OK

CheckDir: HiTC.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/HiTC.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 'HiTC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HiTC' version '1.3.3'
* 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 ... [24s/25s] 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 ... [112s/113s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mapC              20.094  1.947  22.403
HTCexp-class      17.648  0.844  18.829
CQC               17.281  0.349  17.944
getExpectedCounts 15.487  0.910  16.453
intervalsDist      8.331  0.494   8.858
binningC           5.050  0.187   5.354
pca.hic            5.144  0.065   5.256
* 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	17.281	0.349	17.944
HTCexp-class	17.648	0.844	18.829
HTClist-class	0.004	0.006	0.010
Nora_5C	0.650	0.036	0.723
binningC	5.050	0.187	5.354
discretize	0.015	0.013	0.027
export.my5C	0.004	0.007	0.011
exportC	0.004	0.007	0.011
extractRegion	0.672	0.022	0.696
getExpectedCounts	15.487	0.910	16.453
import.my5C	0.920	0.033	0.953
importC	0.004	0.008	0.011
intervalsDist	8.331	0.494	8.858
mapC	20.094	1.947	22.403
pca.hic	5.144	0.065	5.256
removeIntervals	0.488	0.017	0.510
setIntervalScale	2.922	0.053	3.000