Package: segmentSeq

Version: 1.9.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch segmentSeq_1.9.1.tar.gz

StartedAt: 2012-06-21 03:32:58 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 03:41:32 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 514.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: segmentSeq.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/segmentSeq.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '1.9.1'
* 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 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
.partheuristicSeg : methFunction: warning in pbeta(prop, combCs,
  combTs, log = FALSE, lower.tail = FALSE): partial argument match of
  'log' to 'log.p'
.partheuristicSeg : densityFunction: no visible binding for global
  variable 'locCutoff'
.partheuristicSeg: no visible binding for global variable 'locCutoff'
.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 ... WARNING
Undocumented code objects:
  'coord2gff3'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'heuristicSeg':
heuristicSeg
  Code: function(sD, aD, RKPM = 1000, gap = 100, prop = 0.2, subRegion
                 = NULL, largeness = 1e+08, getLikes = TRUE, verbose =
                 TRUE, cl = NULL)
  Docs: function(sD, aD, RKPM = 1000, gap = 100, subRegion = NULL,
                 largeness = 1e+08, getLikes = TRUE, verbose = TRUE,
                 cl)
  Argument names in code not in docs:
    prop
  Mismatches in argument names (first 3):
    Position: 5 Code: prop Docs: subRegion
    Position: 6 Code: subRegion Docs: largeness
    Position: 7 Code: largeness Docs: getLikes
  Mismatches in argument default values:
    Name: 'cl' Code: NULL Docs: 

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under 'inst/doc' ... 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

WARNING: There were 2 warnings.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-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	7.621	0.559	8.284
classifySeg	63.973	2.302	67.967
findChunks	6.723	0.575	7.365
getCounts	6.470	0.550	7.153
getOverlaps	6.585	0.533	7.250
heuristicSeg	34.010	2.404	37.410
lociLikelihoods	35.213	2.467	38.597
plotGenome	16.618	0.632	17.560
processAD	25.132	2.431	28.241
readMethods	6.365	0.583	7.199
segData-class	24.869	2.433	27.793
segmentSeq-package	24.911	2.398	27.667