[BioC] Building Rgraphviz w/ Graphviz 2.14

[Robert Gentleman]

Hi,
  Since graphviz 2.14.x came out after BioC 2.0, it is not compatible, 
and since we are less than one month from a release, we probably will 
not back port anything.
   Everything works well on the devel arm (R 2.6.0 alpha/beta and BioC 2.1)

   best wishes
     Robert

Emil Lundberg wrote:
> Hi all,
> 
> I have trouble installing/compiling Rgraphviz 1.14.1 for BioC 2.0.  
> I'm on Mac OS X 10.4.1 server (Intel). This thread started on the  
> MacPorts mailing list (providers of the Graphviz package for OS X),  
> then took a side tour to the Graphviz developers, but I now believe  
> it belongs here.
> 
> Response from macports-users: http://lists.macosforge.org/pipermail/ 
> macports-users/2007-September/005630.html
> Response from graphviz-devel: https://mailman.research.att.com/ 
> pipermail/graphviz-devel/2007/000450.html
> 
> The root of the problem is that graphviz >=2.14 is missing some  
> header files as compared to older versions. I assume this is due to  
> the cleanup of the code rather than missing functionality, but in any  
> case, a revision of the Rgraphviz package is probably in order.
> 
> Until an Rgraphviz update hits the trunk, do you have any tips on how  
> I can get the current Rgraphviz to compile manually? Or dare I try  
> the OS X binary? Se below for compilation specifics.
> 
> TIA,
> 
> Emil Lundberg
> MicroArray Datawarehouse Resource (MADR)
> Linnaeus Centre for Bioinformatics (LCB)
> Biomedical Centre (BMC)
> Uppsala University
> 
> 
> **********
> (manually in the Rgraphviz directory, or through bioclite("Rgraphviz"))
> % R CMD INSTALL .
> * Installing to library '/opt/local/lib/R/library'
> * Installing *source* package 'Rgraphviz' ...
> configure: No --with-graphviz option was specified. Trying to find  
> graphviz using other methods.
> checking for pkg-config... /opt/local/bin/pkg-config
> configure: Found graphviz 2.14.1
> configure: We have inferred the following flags for graphviz
> configure: ..PKG_CPPFLAGS=-I/opt/local/include/graphviz
> configure: ..PKG_LIBS=-L/opt/local/lib -lgvc
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> /opt/local/bin/gcc-mp-4.2 -std=gnu99 -I/opt/local/lib/R/include -I/ 
> opt/local/lib/R/include -I/opt/local/include/graphviz    - 
> DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=14 -I/opt/local/include  - 
> D__NO_MATH_INLINES  -fPIC  -O2 -c LL_funcs.c -o LL_funcs.o
> In file included from /opt/local/include/graphviz/gvc.h:20,
>                   from common.h:30,
>                   from LL_funcs.c:1:
> /opt/local/include/graphviz/types.h:27:1: warning: "TRUE" redefined
> In file included from common.h:5,
>                   from LL_funcs.c:1:
> /opt/local/lib/R/include/Rdefines.h:148:1: warning: this is the  
> location of the previous definition
> In file included from LL_funcs.c:1:
> common.h:41:20: error: gvcint.h: No such file or directory
> common.h:42:21: error: globals.h: No such file or directory
> make: *** [LL_funcs.o] Error 1
> chmod: /opt/local/lib/R/library/Rgraphviz/libs/*: No such file or  
> directory
> ERROR: compilation failed for package 'Rgraphviz'
> ** Removing '/opt/local/lib/R/library/Rgraphviz'
> 
> I've already tried removing the gvcint.h and globals.h includes from  
> common.h, but I then get:
> 
> [...]
> graphvizVersion.c: In function 'Rgraphviz_graphvizVersion':
> graphvizVersion.c:24: error: dereferencing pointer to incomplete type
> 
> 
> **********
> 
> Thanks guys for adressing this. My graphviz (2.14-1 from MacPorts) is  
> missing the following headers compared to Ryan's 2.12:
> 
> aghdr.h
> agxbuf.h
> arith.h		(back as of 2.14-3)
> ast_common.h
> dthdr.h
> exgram.h
> exlib.h
> expr.h
> globals.h	(requested by Rgraphviz)
> grammar.h
> gvcint.h	(requested by Rgraphviz)
> libgraph.h
> logic.h
> malloc.h
> parser.h
> pathplan.h
> pathutil.h
> solvers.h
> tri.h
> triefa.h
> vis.h
> vispath.h
> vmstub.h
> 
> To clarify matters, the Rgraphviz is an external R package that  
> depends on the Bioconductor package, so the R developers might not  
> know about it. R builds fine using the current MacPorts version  
> (don't know about the devel), and so does Bioconductor, but neither  
> depend on graphviz as such.
> 
> The maintainers of Rgraphviz have already made a good effort in that  
> package's header files to accomodate different versions of graphviz  
> (up to 2.10 at least), so this is hopefully what they need to know to  
> update the Rgraphviz package. I'm forwarding this to the bioconductor  
> mailing list.
> 
> 
> best,
> 
> /Emil
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org