[BioC] Rgraphviz warnings in R-2.0

[Saurin Jani]

Hi,

I am using R-2.0 and trying to do:

> install.packages2("Rgraphviz",develOK = TRUE);

I have graphviz version 1.12 installed from  AT&T
website. 


I get below output:

> install.packages2("Rgraphviz",develOK = TRUE);
Note: You did not specify a download type.  Using a
default value of: Source
This will be fine for almost all users

[1] "Attempting to download Rgraphviz from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing Rgraphviz"
* Installing *source* package 'Rgraphviz' ...
checking for graphviz... checking for
dotneato-config... /usr/local/bin/dotneato-config
/usr/local/bin/dotneato-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/usr/local/lib/R/include
-I/usr/local/include/graphviz -DGRAPHVIZ_1_12
-I/usr/local/include -D__NO_MATH_INLINES -mieee-fp
-Wall -fPIC  -g -O2 -c Rgraphviz.c -o Rgraphviz.o
In file included from
/usr/local/include/graphviz/render.h:49,
                 from common.h:22,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/macros.h:28:1: warning:
"NEW" redefined
In file included from common.h:13,
                 from Rgraphviz.c:1:
/usr/local/lib/R/include/Rdefines.h:129:1: warning:
this is the location of the previous definition
In file included from
/usr/local/include/graphviz/types.h:11,
                 from
/usr/local/include/graphviz/render.h:51,
                 from common.h:22,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/pathplan.h:11: warning:
ignoring #pragma prototyped
In file included from
/usr/local/include/graphviz/pathplan.h:16,
                 from
/usr/local/include/graphviz/types.h:11,
                 from
/usr/local/include/graphviz/render.h:51,
                 from common.h:22,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/pathgeom.h:11: warning:
ignoring #pragma prototyped
In file included from
/usr/local/include/graphviz/render.h:52,
                 from common.h:22,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/graph.h:11: warning:
ignoring #pragma prototyped
In file included from
/usr/local/include/graphviz/render.h:55,
                 from common.h:22,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/gvrender.h:12: warning:
ignoring #pragma prototyped
In file included from
/usr/local/include/graphviz/gvrender.h:19,
                 from
/usr/local/include/graphviz/render.h:55,
                 from common.h:22,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/gvrenderint.h:12: warning:
ignoring #pragma prototyped
In file included from common.h:23,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/graph.h:11: warning:
ignoring #pragma prototyped
In file included from common.h:26,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/adjust.h:11: warning:
ignoring #pragma prototyped
In file included from common.h:28,
                 from Rgraphviz.c:1:
/usr/local/include/graphviz/gvrender.h:12: warning:
ignoring #pragma prototyped
gcc -I/usr/local/lib/R/include
-I/usr/local/include/graphviz -DGRAPHVIZ_1_12
-I/usr/local/include -D__NO_MATH_INLINES -mieee-fp
-Wall -fPIC  -g -O2 -c RgraphvizInit.c -o
RgraphvizInit.o
In file included from
/usr/local/include/graphviz/render.h:49,
                 from common.h:22,
                 from RgraphvizInit.c:1:
/usr/local/include/graphviz/macros.h:28:1: warning:
"NEW" redefined
In file included from common.h:13,
                 from RgraphvizInit.c:1:
/usr/local/lib/R/include/Rdefines.h:129:1: warning:
this is the location of the previous definition
In file included from
/usr/local/include/graphviz/types.h:11,
                 from
/usr/local/include/graphviz/render.h:51,
                 from common.h:22,
                 from RgraphvizInit.c:1:
/usr/local/include/graphviz/pathplan.h:11: warning:
ignoring #pragma prototyped
In file included from
/usr/local/include/graphviz/pathplan.h:16,
                 from
/usr/local/include/graphviz/types.h:11,
                 from
/usr/local/include/graphviz/render.h:51,
                 from common.h:22,
                 from RgraphvizInit.c:1:
/usr/local/include/graphviz/pathgeom.h:11: warning:
ignoring #pragma prototyped
In file included from
/usr/local/include/graphviz/render.h:52,
                 from common.h:22,
                 from RgraphvizInit.c:1:
/usr/local/include/graphviz/graph.h:11: warning:
ignoring #pragma prototyped
In file included from
/usr/local/include/graphviz/render.h:55,
                 from common.h:22,
                 from RgraphvizInit.c:1:
/usr/local/include/graphviz/gvrender.h:12: warning:
ignoring #pragma prototyped
In file included from
/usr/local/include/graphviz/gvrender.h:19,
                 from
/usr/local/include/graphviz/render.h:55,
                 from common.h:22,
                 from RgraphvizInit.c:1:
/usr/local/include/graphviz/gvrenderint.h:12: warning:
ignoring #pragma prototyped
In file included from common.h:23,
                 from RgraphvizInit.c:1:
/usr/local/include/graphviz/graph.h:11: warning:
ignoring #pragma prototyped
In file included from common.h:26,
                 from RgraphvizInit.c:1:
/usr/local/include/graphviz/adjust.h:11: warning:
ignoring #pragma prototyped
In file included from common.h:28,
                 from RgraphvizInit.c:1:
/usr/local/include/graphviz/gvrender.h:12: warning:
ignoring #pragma prototyped
common.h:33: warning: `gvc' defined but not used
gcc -shared -L/usr/local/lib -o Rgraphviz.so
Rgraphviz.o RgraphvizInit.o -Wl
-L/usr/local/lib/graphviz -ldotneato -lm
** R
** inst
** save image
Loading required package: cluster
Loading required package: Ruuid
Creating a new generic function for "print" in "Ruuid"
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
         Vignettes contain introductory material.  To
view,
         simply type: openVignette()
         For details on reading vignettes, see
         the openVignette help page.
Creating a new generic function for "lines" in
"Rgraphviz"
Creating a new generic function for "plot" in
"Rgraphviz"


Warning messages:
1: Undefined slot classes in definition of "Ragraph":
boundBox (class " boundingBox ") in:
.completeClassSlots(ClassDef, where)
2: Undefined slot classes in definition of
"boundingBox": botLeft (class " xyPoint "), upRight
(class " xyPoint ") in: .completeClassSlots(ClassDef,
where)
3: Undefined slot classes in definition of "AgNode":
center (class " xyPoint "), txtLabel (class "
AgTextLabel ") in: .completeClassSlots(ClassDef,
where)
4: Undefined slot classes in definition of "AgEdge":
sp (class " xyPoint "), ep (class " xyPoint "),
txtLabel (class " AgTextLabel ") in:
.completeClassSlots(ClassDef, where)







** 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
  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
* DONE (Rgraphviz)
[1] "Installation complete"
>From URL: 
http://www.bioconductor.org/repository/devel/package/Source
        Rgraphviz version 1.4.23



Thank you,
Saurin