Package: Rgraphviz

Version: 1.14.0

Command: /loc/biocbuild/bbs-2.0-bioc/R/bin/R CMD check Rgraphviz_1.14.0.tar.gz

RetCode: 1

Time: 248.3 seconds

Status: ERROR

CheckDir: Rgraphviz.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/loc/biocbuild/bbs-2.0-bioc/meat/Rgraphviz.Rcheck'
* using R version 2.5.0 (2007-04-23)
* checking for file 'Rgraphviz/DESCRIPTION' ... OK
* this is package 'Rgraphviz' version '1.14.0'
* checking package dependencies ... OK
* 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 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 name space can be loaded with stated dependencies ... 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 ... 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:

> ### * clusterData-methods
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: clusterData-methods
> ### Title: Get and set attributes for a cluster of an Ragraph object
> ### Aliases: clusterData-methods clusterData<--methods clusterData
> ###   clusterData<-
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> library(graph)
> library(Rgraphviz)
> 
> g1_gz <- gzfile(system.file("GXL/graphExample-01.gxl.gz",package="graph"), open="rb")
> g11_gz <- gzfile(system.file("GXL/graphExample-11.gxl.gz",package="graph"), open="rb")
> g1 <- fromGXL(g1_gz)
Loading required package: XML
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical = TRUE,  : 
	 there is no package called 'XML'
Error in fromGXL(g1_gz) : XML package needed
Execution halted

* Installing *source* package 'Rgraphviz' ...
configure: No --with-graphviz option was specified. Trying to find graphviz using other methods.
checking for pkg-config... /usr/local/bin/pkg-config
sh: gnome-config: not found
Package libgvc was not found in the pkg-config search path.
Perhaps you should add the directory containing `libgvc.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libgvc' found
configure: pkg-config was not able to find the graphviz library libgvc. This either indicates that graphviz is old or that something is wrong. Verify graphviz is installed and that PKG_CONFIG_PATH is correct.
configure: Using dotneato-config to find graphviz
checking for dotneato-config... /usr/local/bin/dotneato-config
configure: Found graphviz 2.2.1
configure: We have inferred the following flags for graphviz
configure: ..PKG_CPPFLAGS=-I/usr/local/include/graphviz
configure: ..PKG_LIBS=-L/usr/local/lib/graphviz -ldotneato -lm
checking for whether compiler has bool... checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... no
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=2 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include    -fPIC  -g -O2 -Wall -c LL_funcs.c -o LL_funcs.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:19,
                 from LL_funcs.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from LL_funcs.c:1:
/loc/biocbuild/bbs-2.0-bioc/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=2 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include    -fPIC  -g -O2 -Wall -c Rgraphviz.c -o Rgraphviz.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:19,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from Rgraphviz.c:1:
/loc/biocbuild/bbs-2.0-bioc/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=2 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include    -fPIC  -g -O2 -Wall -c RgraphvizInit.c -o RgraphvizInit.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:19,
                 from RgraphvizInit.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from RgraphvizInit.c:1:
/loc/biocbuild/bbs-2.0-bioc/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=2 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include    -fPIC  -g -O2 -Wall -c agopen.c -o agopen.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:19,
                 from agopen.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from agopen.c:1:
/loc/biocbuild/bbs-2.0-bioc/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=2 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include    -fPIC  -g -O2 -Wall -c agread.c -o agread.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:19,
                 from agread.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from agread.c:1:
/loc/biocbuild/bbs-2.0-bioc/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=2 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include    -fPIC  -g -O2 -Wall -c agwrite.c -o agwrite.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:19,
                 from agwrite.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from agwrite.c:1:
/loc/biocbuild/bbs-2.0-bioc/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=2 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include    -fPIC  -g -O2 -Wall -c bezier.c -o bezier.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:19,
                 from bezier.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from bezier.c:1:
/loc/biocbuild/bbs-2.0-bioc/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=2 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include    -fPIC  -g -O2 -Wall -c buildEdgeList.c -o buildEdgeList.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:19,
                 from buildEdgeList.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from buildEdgeList.c:1:
/loc/biocbuild/bbs-2.0-bioc/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=2 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include    -fPIC  -g -O2 -Wall -c buildNodeList.c -o buildNodeList.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:19,
                 from buildNodeList.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from buildNodeList.c:1:
/loc/biocbuild/bbs-2.0-bioc/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=2 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include    -fPIC  -g -O2 -Wall -c doLayout.c -o doLayout.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:19,
                 from doLayout.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from doLayout.c:1:
/loc/biocbuild/bbs-2.0-bioc/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
doLayout.c: In function 'getEdgeLocs':
doLayout.c:34: warning: unused variable 'tmp_ed'
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=2 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include    -fPIC  -g -O2 -Wall -c graphvizVersion.c -o graphvizVersion.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:19,
                 from graphvizVersion.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from graphvizVersion.c:1:
/loc/biocbuild/bbs-2.0-bioc/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/usr/local/include/graphviz  -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=2 -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -I/usr/local/include    -fPIC  -g -O2 -Wall -c init.c -o init.o
In file included from /usr/local/include/graphviz/render.h:53,
                 from common.h:19,
                 from init.c:1:
/usr/local/include/graphviz/macros.h:41:1: warning: "NEW" redefined
In file included from common.h:5,
                 from init.c:1:
/loc/biocbuild/bbs-2.0-bioc/R/include/Rdefines.h:143:1: warning: this is the location of the previous definition
gcc -std=gnu99 -G -L/usr/local/lib -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o -L/usr/local/lib/graphviz -ldotneato -lm  -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lR
** R
** inst
** save image
Loading required package: graph
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()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: lattice
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
  agopenSimple                      text    html    latex   example
  agwrite                           text    html    latex   example
  boundingBox-class                 text    html    latex   example
  buildNodeList                     text    html    latex   example
  clusterData-methods               text    html    latex   example
  getDefaultAttrs                   text    html    latex   example
  graphData-methods                 text    html    latex
  graphDataDefaults-methods         text    html    latex
  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
  toFile                            text    html    latex   example
  xyPoint-class                     text    html    latex   example
** building package indices ...
* DONE (Rgraphviz)