Package: segmentSeq

Version: 1.12.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch segmentSeq_1.12.1.tar.gz

StartedAt: 2013-05-01 10:48:07 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 10:56:24 -0700 (Wed, 01 May 2013)

EllapsedTime: 496.3 seconds

RetCode: 0

Status:  OK

CheckDir: segmentSeq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/segmentSeq.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '1.12.1'
* 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 'segmentSeq' can be installed ... [24s/26s] 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 ... NOTE
.partheuristicSeg: no visible global function definition for
  '.methFunction'
.partheuristicSeg: no visible global function definition for
  '.constructMethNulls'
.partheuristicSeg: no visible global function definition for
  'getMethylatedCounts'
.squeezeAlign: no visible global function definition for
  'findMethChunks'
.stratifySample: no visible binding for global variable 'sD'
.stratifySample: no visible binding for global variable 'lensameFlag'
.stratifySample: no visible binding for global variable 'seglens'
processAD : partCounts: no visible global function definition for
  'getMethylatedCounts'
* 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 ... [242s/246s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
classifySeg         62.356  0.452  64.403
lociLikelihoods     30.848  0.252  31.836
heuristicSeg        30.567  0.430  31.262
processAD           20.003  0.179  20.297
segmentSeq-package  18.898  0.321  19.485
segData-class       18.311  0.348  18.832
plotGenome          16.585  0.126  17.048
alignmentData-class  6.590  0.083   6.708
getCounts            6.230  0.083   6.355
findChunks           5.994  0.092   6.196
getOverlaps          5.812  0.061   6.239
readMethods          4.909  0.098   5.071
* 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
  '/Users/biocbuild/bbs-2.12-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
** testing if installed package can be loaded
* DONE (segmentSeq)

name	user	system	elapsed
alignmentData-class	6.590	0.083	6.708
classifySeg	62.356	0.452	64.403
findChunks	5.994	0.092	6.196
getCounts	6.230	0.083	6.355
getOverlaps	5.812	0.061	6.239
heuristicSeg	30.567	0.430	31.262
lociLikelihoods	30.848	0.252	31.836
plotGenome	16.585	0.126	17.048
processAD	20.003	0.179	20.297
readMethods	4.909	0.098	5.071
segData-class	18.311	0.348	18.832
segmentSeq-package	18.898	0.321	19.485