Package: segmentSeq

Version: 1.5.1

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch segmentSeq_1.5.1.tar.gz

StartedAt: 2011-07-07 03:34:15 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 03:43:48 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 572.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: segmentSeq.Rcheck

Warnings: 1

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/segmentSeq.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '1.5.1'
* checking package name space 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 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
plotGenome: no visible binding for global variable 'ss'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'plotGenome':
plotGenome
  Code: function(aD, sD, chr = 1, limits = c(0, 10000), samples = NULL,
                 plotType = "pileup", plotDuplicated = FALSE, density =
                 0, showNumber = TRUE, logScale = FALSE, ...)
  Docs: function(aD, sD, chr = 1, limits = c(0, 10000), samples = NULL,
                 plotType = "chunk", plotDuplicated = FALSE, ...)
  Argument names in code not in docs:
    density showNumber logScale
  Mismatches in argument names:
    Position: 8 Code: density Docs: ...
  Mismatches in argument default values:
    Name: 'plotType' Code: "pileup" Docs: "chunk"

Codoc mismatches from documentation object 'processTags':
processTags
  Code: function(files, dir = ".", replicates, libnames, chrs, chrlens,
                 cols, header = TRUE, gap = 200, verbose = TRUE, strand
                 = NA, ...)
  Docs: function(files, dir = ".", replicates, libnames, chrs, chrlens,
                 cols, header = TRUE, gap = 200, verbose = TRUE, ...)
  Argument names in code not in docs:
    strand
  Mismatches in argument names:
    Position: 11 Code: strand Docs: ...

* 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

WARNING: There was 1 warning, see
  'E:/biocbld/bbs-2.9-bioc/meat/segmentSeq.Rcheck/00check.log'
for details

* installing *source* package 'segmentSeq' ...
** R
** inst
** preparing package for lazy loading

Attaching package: 'baySeq'

The following object(s) are masked from 'package:base':

    rbind

Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:baySeq':

    rbind

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: lattice
Loading required package: Rsamtools
Loading required package: latticeExtra
Loading required package: RColorBrewer
Creating a new generic function for "cbind" in package "segmentSeq"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'segmentSeq.Rnw' 
** testing if installed package can be loaded

* DONE (segmentSeq)

name	user	system	elapsed
alignmentData-class	4.30	0.03	4.38
classifySeg	66.31	0.38	67.59
filterSegments	36.67	0.05	37.13
findChunks	3.52	0.01	3.54
getCounts	4.81	0.02	4.88
getOverlaps	4.31	0.03	4.48
heuristicSeg	49.16	0.06	50.43
lociLikelihoods	45.62	0.06	46.24
mergeSD	75.92	0.07	76.64
plotGenome	6.16	0.00	6.25
processAD	37.41	0.01	37.54
processTags	3.48	0.02	3.52
segData-class	38.17	0.01	38.55
segmentSeq-package	38.94	0.03	39.32