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Package 421/479HostnameOS / ArchBUILDCHECKBUILD BIN
segmentSeq 1.5.1
Thomas J. Hardcastle
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/segmentSeq
Last Changed Rev: 55431 / Revision: 56603
Last Changed Date: 2011-05-11 08:17:57 -0700 (Wed, 11 May 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

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

Command output

* 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

segmentSeq.Rcheck/00install.out:

* 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)

segmentSeq.Rcheck/segmentSeq-Ex.timings:

nameusersystemelapsed
alignmentData-class4.300.034.38
classifySeg66.31 0.3867.59
filterSegments36.67 0.0537.13
findChunks3.520.013.54
getCounts4.810.024.88
getOverlaps4.310.034.48
heuristicSeg49.16 0.0650.43
lociLikelihoods45.62 0.0646.24
mergeSD75.92 0.0776.64
plotGenome6.160.006.25
processAD37.41 0.0137.54
processTags3.480.023.52
segData-class38.17 0.0138.55
segmentSeq-package38.94 0.0339.32