BioC 2.12: CHECK report for HiTC on george2

Package: HiTC

Version: 1.4.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings HiTC_1.4.0.tar.gz

StartedAt: 2013-10-09 02:33:05 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:40:16 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 431.0 seconds

RetCode: 0

Status:  OK

CheckDir: HiTC.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/HiTC.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.4.0’
* 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 ... [29s/29s] 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 ... [127s/128s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
mapC              22.314  1.696  24.210
HTCexp-class      22.837  0.168  23.089
CQC               22.750  0.188  23.127
getExpectedCounts 16.521  0.168  16.833
intervalsDist      7.912  0.236   8.253
binningC           5.081  0.012   5.095
* 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	22.750	0.188	23.127
HTCexp-class	22.837	0.168	23.089
HTClist-class	0.024	0.000	0.024
Nora_5C	0.696	0.004	0.700
binningC	5.081	0.012	5.095
discretize	0.000	0.012	0.011
export.my5C	0.004	0.008	0.010
exportC	0.020	0.004	0.023
extractRegion	0.772	0.004	0.775
getExpectedCounts	16.521	0.168	16.833
import.my5C	1.136	0.000	1.283
importC	0.008	0.000	0.009
intervalsDist	7.912	0.236	8.253
mapC	22.314	1.696	24.210
pca.hic	4.76	0.00	4.79
removeIntervals	0.420	0.004	0.424
setIntervalScale	3.404	0.012	3.423