Package: segmentSeq

Version: 1.8.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings segmentSeq_1.8.0.tar.gz

StartedAt: 2012-09-24 03:36:39 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 03:43:16 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 396.5 seconds

RetCode: 0

Status:  OK

CheckDir: segmentSeq.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/segmentSeq.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.8.0’
* 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 ‘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 ... NOTE
.stratifySample: no visible binding for global variable ‘sD’
.stratifySample: no visible binding for global variable ‘lensameFlag’
.stratifySample: no visible binding for global variable ‘seglens’
* 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 installed files from ‘inst/doc’ ... 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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘segmentSeq’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘segmentSeq.Rnw’ 
** testing if installed package can be loaded

* DONE (segmentSeq)

name	user	system	elapsed
alignmentData-class	5.612	0.016	5.632
classifySeg	50.320	0.072	50.472
findChunks	5.284	0.000	5.303
getCounts	5.432	0.004	5.434
getOverlaps	4.929	0.004	4.934
heuristicSeg	26.913	0.008	27.712
lociLikelihoods	28.366	0.008	28.842
plotGenome	13.705	0.004	14.043
processAD	20.033	0.008	20.510
readMethods	5.524	0.000	5.523
segData-class	17.754	0.012	17.788
segmentSeq-package	17.929	0.008	17.938