Package: nem

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check nem_1.3.0.tar.gz

RetCode: 1

Time: 67.7 seconds

Status: ERROR

CheckDir: nem.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/Users/biocbuild/2.0d/Rpacks/nem.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-10-21 r39702)
* checking for file 'nem/DESCRIPTION' ... OK
* this is package 'nem' version '1.3.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'nem' can be installed ... 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 syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating nem-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'nem-Ex.R' failed.
The error most likely occurred in:

> ### * SCCgraph
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: SCCgraph
> ### Title: Combines Strongly Connected Components into single nodes
> ### Aliases: SCCgraph
> ### Keywords: graphs
> 
> ### ** Examples
> 
>    data("BoutrosRNAi2002")
>    D   <- BoutrosRNAiDiscrete[,9:16]
>    res <- nem(D,para=c(.13,.05))
4 perturbed genes -> 6 pairwise tests
......
estimating effect positions
>    # 
>    sccg <- SCCgraph(res$graph,name=TRUE)
>    #
>    par(mfrow=c(1,2))
>    plot(res, main="inferred from data")

 *** caught bus error ***
address 0x40, cause 'non-existent physical address'

Traceback:
 1: .Call("Rgraphviz_doLayout", graph, as.integer(type), PACKAGE = "Rgraphviz")
 2: layoutGraph(g)
 3: agopen(x, name = name, layout = TRUE, layoutType = y, attrs = attrs,     nodeAttrs = nodeAttrs, edgeAttrs = edgeAttrs, subGList = subGList,     recipEdges = recipEdges)
 4: .local(x, y, ...)
 5: plot(x = gR, y = "dot", ...)
 6: plot(x = gR, y = "dot", ...)
 7: plot.pairwise(res, main = "inferred from data")
 8: plot(res, main = "inferred from data")
 9: plot(res, main = "inferred from data")
aborting ...

* Installing *source* package 'nem' ...
** R
** data
** inst
** help
 >>> Building/Updating help pages for package 'nem'
     Formats: text html latex example 
  BoutrosRNAi2002                   text    html    latex   example
  FULLmLL                           text    html    latex   example
  SCCgraph                          text    html    latex   example
  enumerate.models                  text    html    latex   example
  local.model.prior                 text    html    latex   example
  mLL                               text    html    latex   example
  nem                               text    html    latex   example
  nem.discretize                    text    html    latex   example
  pairwise.posterior                text    html    latex   example
  plot.effects                      text    html    latex   example
  prune.graph                       text    html    latex   example
  score                             text    html    latex   example
  transitive.closure                text    html    latex   example
  transitive.reduction              text    html    latex   example
** building package indices ...
* DONE (nem)