Package: segmentSeq

Version: 1.4.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings segmentSeq_1.4.0.tar.gz

StartedAt: 2011-10-20 14:28:18 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:38:33 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 614.8 seconds

RetCode: 0

Status:  OK

CheckDir: segmentSeq.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/segmentSeq.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘segmentSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘segmentSeq’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘segmentSeq’ 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 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 ‘segmentSeq’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic for ‘cbind’ in package ‘segmentSeq’
    (the supplied definition differs from and overrides the implicit generic
    in package ‘base’: Signatures differ:  (...), (deparse.level))
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (segmentSeq)

name	user	system	elapsed
alignmentData-class	6.184	0.032	6.223
classifySeg	72.373	0.220	74.242
filterSegments	40.778	0.128	43.181
findChunks	5.749	0.004	5.994
getCounts	5.356	0.044	5.462
getOverlaps	4.300	0.008	4.466
heuristicSeg	51.564	0.096	52.801
lociLikelihoods	50.463	0.104	51.463
mergeSD	83.149	0.224	84.407
plotGenome	5.096	0.000	5.105
processAD	41.331	0.056	41.461
processTags	7.080	0.004	7.098
segData-class	43.199	0.072	43.459
segmentSeq-package	41.587	0.056	42.739