[BioC] Building Rgraphviz w/ Graphviz 2.14

Li.Long at isb-sib.ch Li.Long at isb-sib.ch
Fri Sep 21 14:41:29 CEST 2007


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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