Package: r3Cseq

Version: 1.0.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings r3Cseq_1.0.0.tar.gz

StartedAt: 2012-03-24 02:09:49 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:13:41 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 232.9 seconds

RetCode: 0

Status:  OK

CheckDir: r3Cseq.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/r3Cseq.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘r3Cseq/DESCRIPTION’ ... OK
* this is package ‘r3Cseq’ version ‘1.0.0’
* 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 whether package ‘r3Cseq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 examples ... OK
* 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 ‘r3Cseq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘r3Cseq.Rnw’ 
** testing if installed package can be loaded

* DONE (r3Cseq)

name	user	system	elapsed
calculateRPM	0.572	0.004	0.579
contrCoverage	0.024	0.008	0.035
contrInteractionRegions	0.184	0.000	0.183
contrRPM	0.088	0.008	0.095
expCoverage	0.024	0.008	0.034
expInteractionRegions	0.180	0.004	0.183
expRPM	0.092	0.008	0.102
export3Cseq2bedGraph	0.616	0.008	0.630
exportInteractions2text	0.292	0.000	0.293
generate3CseqReport	4.105	0.048	4.280
getCoverage	6.284	0.044	6.334
getInteractions	0.188	0.000	0.187
getReadCountPerRestrictionFragment	14.833	0.724	15.862
getViewpoint	0.660	0.028	0.714
plot3Cecdf	0.484	0.008	0.491
plotInteractionsNearViewpoint	1.220	0.008	1.307
plotInteractionsPerChromosome	0.540	0.008	0.642
plotOverviewInteractions	1.492	0.008	1.585
r3Cseq-class	0.044	0.004	0.051