Package: Rgraphviz

Version: 1.11.10

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check Rgraphviz_1.11.10.tar.gz

RetCode: 1

Time: 78.6 seconds

Status: ERROR

CheckDir: Rgraphviz.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/Users/biocbuild/1.9d/Rpacks/Rgraphviz.Rcheck'
* using R version 2.4.0 alpha (2006-09-07 r39185)
* checking for file 'Rgraphviz/DESCRIPTION' ... OK
* this is package 'Rgraphviz' version '1.11.10'
* checking package dependencies ... WARNING
package 'methods' is used but not declared
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking if this is a source package ... OK
* checking whether package 'Rgraphviz' 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 ... WARNING
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Error in .asEnvironmentPackage(where) : Package 'methods' is not loaded
Error: unable to load R code in package 'Ruuid'
Error: unable to load R code in package 'Rgraphviz'
Execution halted

A namespace must be able to be loaded with just the base namespace loaded:
otherwise if the namespace gets loaded by a saved object, the session will
be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 Rgraphviz-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'Rgraphviz-Ex.R' failed.
The error most likely occurred in:

> ### * AgEdge-class
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: AgEdge-class
> ### Title: Class "AgEdge": A class to describe an edge for a Ragraph object
> ### Aliases: AgEdge-class AgEdge AgEdge<- splines sp ep getSpline
> ###   numSplines head tail arrowsize lines,AgEdge-method show,AgEdge-method
> ###   arrowsize,AgEdge-method color,AgEdge-method ep,AgEdge-method
> ###   getSpline,AgEdge-method head,AgEdge-method numSplines,AgEdge-method
> ###   sp,AgEdge-method splines,AgEdge-method tail,AgEdge-method
> ###   txtLabel,AgEdge-method txtLabel arrowhead,AgEdge-method arrowhead
> ###   arrowtail,AgEdge-method arrowtail
> ### Keywords: classes
> 
> ### ** Examples
> 
> V <- letters[1:10]
> M <- 1:4
> g1 <- randomGraph(V, M, .2)
> z <- agopen(g1,name="foo")

 *** 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(g1, name = "foo")
aborting ...

* Installing *source* package 'Rgraphviz' ...
checking for pkg-config... /opt/local/bin/pkg-config
configure: Found graphviz 2.8
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** arch - i386
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include/graphviz   -DGRAPHVIZGT_1_16 -DGRAPHVIZGT_2_4 -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c Rgraphviz.c -o Rgraphviz.o
Rgraphviz.c: In function 'getListElement':
Rgraphviz.c:56: warning: implicit declaration of function 'Rf_type2char'
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include/graphviz   -DGRAPHVIZGT_1_16 -DGRAPHVIZGT_2_4 -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c RgraphvizInit.c -o RgraphvizInit.o
gcc-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 Rgraphviz.so Rgraphviz.o RgraphvizInit.o -L/opt/local/lib/graphviz -lgvc    -L/Library/Frameworks/R.framework/Resources/lib/i386 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Resources/lib/i386/libRblas.dylib
** R
** inst
** save image
Loading required package: graph
Loading required package: Ruuid
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.

KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Creating a new generic function for 'lines' in 'Rgraphviz'
Creating a new generic function for 'plot' in 'Rgraphviz'
** help
 >>> Building/Updating help pages for package 'Rgraphviz'
     Formats: text html latex example 
  AgEdge-class                      text    html    latex   example
  AgNode-class                      text    html    latex   example
  AgTextLabel-class                 text    html    latex   example
  BezierCurve-class                 text    html    latex   example
  GraphvizAttributes                text    html    latex   example
  GraphvizLayouts                   text    html    latex   example
  Ragraph-class                     text    html    latex   example
  agopen                            text    html    latex   example
  agwrite                           text    html    latex   example
  boundingBox-class                 text    html    latex   example
  buildNodeList                     text    html    latex   example
  getDefaultAttrs                   text    html    latex   example
  graphvizVersion                   text    html    latex   example
  imageMap                          text    html    latex   example
  layoutGraph                       text    html    latex   example
  makeNodeAttrs                     text    html    latex   example
  pEdge-class                       text    html    latex   example
  pNode-class                       text    html    latex   example
  pieGlyph                          text    html    latex   example
  plot-methods                      text    html    latex   example
  removedEdges                      text    html    latex   example
  toDot-methods                     text    html    latex   example
  xyPoint-class                     text    html    latex   example
** building package indices ...
* DONE (Rgraphviz)