BioC 2.12: CHECK report for HiTC on petty

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: 2013-10-08 22:45:29 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:52:12 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 402.8 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 3.0.1 (2013-05-16)
* 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 ... [27s/28s] 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 ... [121s/123s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mapC              20.963  1.718  23.037
HTCexp-class      18.867  0.608  19.669
CQC               18.625  0.256  19.400
getExpectedCounts 15.742  0.717  16.737
intervalsDist      9.052  0.465   9.607
binningC           6.358  0.193   6.647
pca.hic            6.137  0.032   6.215
* 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	18.625	0.256	19.400
HTCexp-class	18.867	0.608	19.669
HTClist-class	0.002	0.004	0.008
Nora_5C	0.762	0.024	0.793
binningC	6.358	0.193	6.647
discretize	0.003	0.007	0.011
export.my5C	0.003	0.005	0.008
exportC	0.011	0.008	0.018
extractRegion	0.854	0.019	0.894
getExpectedCounts	15.742	0.717	16.737
import.my5C	1.030	0.051	1.106
importC	0.004	0.007	0.011
intervalsDist	9.052	0.465	9.607
mapC	20.963	1.718	23.037
pca.hic	6.137	0.032	6.215
removeIntervals	0.681	0.015	0.703
setIntervalScale	3.693	0.048	3.793