[BioC] Building Rgraphviz w/ Graphviz 2.14

[Li.Long at isb-sib.ch]

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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>>
>
>