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: 2013-03-25 03:04:05 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:09:16 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 311.0 seconds

RetCode: 0

Status:  OK

CheckDir: HiTC.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/HiTC.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 ... [22s/22s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [100s/100s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mapC              17.390  4.202  21.708
HTCexp-class      16.582  1.778  18.435
getExpectedCounts 12.264  1.612  13.962
CQC               12.491  0.378  12.933
intervalsDist      7.293  0.401   7.738
binningC           5.343  0.095   5.440
* 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	12.491	0.378	12.933
HTCexp-class	16.582	1.778	18.435
HTClist-class	0.008	0.007	0.015
Nora_5C	0.616	0.037	0.654
binningC	5.343	0.095	5.440
discretize	0.003	0.006	0.010
export.my5C	0.003	0.005	0.009
exportC	0.008	0.008	0.017
extractRegion	0.597	0.024	0.622
getExpectedCounts	12.264	1.612	13.962
import.my5C	0.600	0.021	0.621
importC	0.018	0.010	0.027
intervalsDist	7.293	0.401	7.738
mapC	17.390	4.202	21.708
pca.hic	3.766	0.047	3.816
removeIntervals	0.415	0.020	0.437
setIntervalScale	2.487	0.081	2.570