Package: RBGL

Version: 1.11.1

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check RBGL_1.11.1.tar.gz

RetCode: 1

Time: 156.7 seconds

Status: ERROR

CheckDir: RBGL.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/Users/biocbuild/2.0d/Rpacks/RBGL.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-10-21 r39702)
* checking for file 'RBGL/DESCRIPTION' ... OK
* this is package 'RBGL' version '1.11.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'RBGL' 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 whether the name space 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
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating RBGL-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'RBGL-Ex.R' failed.
The error most likely occurred in:

> ### * FileDep
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: FileDep
> ### Title: FileDep: a graphNEL object representing a file dependency
> ###   dataset example in boost graph library
> ### Aliases: FileDep
> ### Keywords: graphs
> 
> ### ** Examples
> 
> # this is how the graph of data(FileDep) was obtained
> library(graph)
> fd <- file(system.file("XML/FileDep.gxl",package="RBGL"), open="r")
> show(fromGXL(fd))
Loading required package: XML

Attaching package: 'XML'


	The following object(s) are masked from package:graph :

	 addNode 

A graphNEL graph with directed edges
Number of Nodes = 15 
Number of Edges = 19 
> if (require(Rgraphviz))
+  {
+  data(FileDep)
+  plot(FileDep)
+  }
Loading required package: Rgraphviz
Loading required package: geneplotter
Loading required package: annotate
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997

 *** 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(FileDep)
 6: plot(FileDep)
aborting ...

* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
** arch - i386
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IboostIncl  -fPIC  -g -O2 -march=pentium-m -mtune=prescott -c bbc.cpp -o bbc.o
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g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IboostIncl  -fPIC  -g -O2 -march=pentium-m -mtune=prescott -c cliques.cpp -o cliques.o
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g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IboostIncl  -fPIC  -g -O2 -march=pentium-m -mtune=prescott -c clusteringCoef.cpp -o clusteringCoef.o
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g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IboostIncl  -fPIC  -g -O2 -march=pentium-m -mtune=prescott -c hcs.cpp -o hcs.o
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g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IboostIncl  -fPIC  -g -O2 -march=pentium-m -mtune=prescott -c incrConnComp.cpp -o incrConnComp.o
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g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IboostIncl  -fPIC  -g -O2 -march=pentium-m -mtune=prescott -c interfaces.cpp -o interfaces.o
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g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IboostIncl  -fPIC  -g -O2 -march=pentium-m -mtune=prescott -c layout.cpp -o layout.o
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g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IboostIncl  -fPIC  -g -O2 -march=pentium-m -mtune=prescott -c minST.cpp -o minST.o
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g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IboostIncl  -fPIC  -g -O2 -march=pentium-m -mtune=prescott -c mincut.cpp -o mincut.o
/var/tmp//ccjTCq2D.s:55080:indirect jmp without `*'
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g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IboostIncl  -fPIC  -g -O2 -march=pentium-m -mtune=prescott -c ordering.cpp -o ordering.o
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/var/tmp//ccciGMUJ.s:105384:indirect jmp without `*'
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IboostIncl  -fPIC  -g -O2 -march=pentium-m -mtune=prescott -c shortestPath.cpp -o shortestPath.o
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g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IboostIncl  -fPIC  -g -O2 -march=pentium-m -mtune=prescott -c sna.cpp -o sna.o
/var/tmp//cchtGD3w.s:71411:indirect jmp without `*'
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g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IboostIncl  -fPIC  -g -O2 -march=pentium-m -mtune=prescott -c transitive_closure.cpp -o transitive_closure.o
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g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3   -IboostIncl  -fPIC  -g -O2 -march=pentium-m -mtune=prescott -c wavefront.cpp -o wavefront.o
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g++-4.0 -arch i386 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o RBGL.so bbc.o cliques.o clusteringCoef.o hcs.o incrConnComp.o interfaces.o layout.o minST.o mincut.o ordering.o shortestPath.o sna.o transitive_closure.o wavefront.o   -F/Library/Frameworks/R.framework/.. -framework R
** R
** data
** inst
** save image
Loading required package: graph
** help
 >>> Building/Updating help pages for package 'RBGL'
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  FileDep                           text    html    latex   example
  RBGL.overview                     text    html    latex
  astarSearch                       text    html    latex   example
  bandwidth                         text    html    latex   example
  bccluster                         text    html    latex   example
  bellman.ford.sp                   text    html    latex   example
  betweenness                       text    html    latex   example
  bfs                               text    html    latex   example
  biConnComp                        text    html    latex   example
  clusteringCoef                    text    html    latex   example
  clusteringCoefAppr                text    html    latex   example
  coloring                          text    html    latex   example
  connectedComp                     text    html    latex   example
  dag.sp                            text    html    latex   example
  dijkstra.sp                       text    html    latex   example
  edgeConn                          text    html    latex   example
  extractPath                       text    html    latex   example
  floyd.warshall.all.pairs.sp       text    html    latex   example
  gprofile                          text    html    latex   example
  graphGenerator                    text    html    latex   example
  highlyConnSG                      text    html    latex   example
  incrConnComp                      text    html    latex   example
  is.triangulated                   text    html    latex   example
  isomorphism                       text    html    latex   example
  johnson.all.pairs.sp              text    html    latex   example
  kCliques                          text    html    latex   example
  kCores                            text    html    latex   example
  lambdaSets                        text    html    latex   example
  layout                            text    html    latex   example
  maxClique                         text    html    latex   example
  maxFlow                           text    html    latex   example
  minCut                            text    html    latex   example
  mstree.kruskal                    text    html    latex   example
  ordering                          text    html    latex   example
  prim.minST                        text    html    latex   example
  separates                         text    html    latex   example
  sp.between                        text    html    latex   example
  strongComp                        text    html    latex   example
  transClosure                      text    html    latex   example
  transitivity                      text    html    latex   example
  tsort                             text    html    latex   example
  wavefront                         text    html    latex   example
** building package indices ...
* DONE (RBGL)