Package: HiTC

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HiTC_1.4.0.tar.gz

StartedAt: 2013-05-01 06:50:34 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 06:56:34 -0700 (Wed, 01 May 2013)

EllapsedTime: 360.2 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 Patched (2013-04-08 r62531)
* 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 '1.4.0'
* 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 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 ... [23s/24s] 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 ... [108s/109s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mapC              18.556  2.202  21.029
HTCexp-class      16.939  0.893  18.069
CQC               17.410  0.377  18.156
getExpectedCounts 13.456  0.946  14.649
intervalsDist      7.354  0.530   8.111
binningC           4.904  0.212   5.231
pca.hic            4.954  0.056   5.046
* 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
** testing if installed package can be loaded
* DONE (HiTC)

name	user	system	elapsed
CQC	17.410	0.377	18.156
HTCexp-class	16.939	0.893	18.069
HTClist-class	0.003	0.005	0.009
Nora_5C	0.587	0.030	0.637
binningC	4.904	0.212	5.231
discretize	0.003	0.007	0.011
export.my5C	0.004	0.007	0.010
exportC	0.012	0.010	0.022
extractRegion	0.690	0.026	0.724
getExpectedCounts	13.456	0.946	14.649
import.my5C	1.007	0.050	1.082
importC	0.005	0.009	0.014
intervalsDist	7.354	0.530	8.111
mapC	18.556	2.202	21.029
pca.hic	4.954	0.056	5.046
removeIntervals	0.514	0.015	0.537
setIntervalScale	2.877	0.087	3.013