[BioC] Building Rgraphviz w/ Graphviz 2.14

[Emil Lundberg]

Thanks Li and Robert for quick replies. I applied the version- 
specific fixes to common.h and graphvizVersion.c from 1.15.9 to the  
1.14.1 distro, and it compiles/installs nicely against graphviz  
2.14-1. I'll let you know if it doesn't work out somehow.


/Emil


> A correction:  the nightly build is based on graphviz 2.12.  From  
> what I
> could see in testing with graphviz 2.14, I don't expect major  
> portability
> issues on Mac OS.
>
> If you encounter additional problem with graphviz-2.14 in Rgraphviz
> 1.15.9, please don't hesitate to let me know.
>
> Thanks,
>
> Li
>
>>
>> This is done already for Rgraphviz.  If you get latest codes,  
>> either from
>> svn, source code download (1.15.9) or the upcoming official  
>> release in the
>> beginning of Oct, you should be able to get it run with graphviz  
>> 2.14.
>> The nightly build on Mac OS X (10.4.10) is all OK.
>>
>> Li
>>
>>> 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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>>
>>
>