Thanks guys for adressing this. In essence, the missing headers were intentional, so this now an issue for the Rgraphviz developers. I'm forwarding this to the Bioconductor mailing list. FYI, 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 the information below is hopefully what they need to know to update the Rgraphviz package. Thanks again, Emil Lundberg MicroArray Datawarehouse Resource (MADR) Linnaeus Centre for Bioinformatics (LCB) Biomedical Centre (BMC) Uppsala University 21 sep 2007 kl. 03.15 skrev John Ellson:
In the Fedora graphviz-2.14.1-3 version (also in 2.15 upstream), arith.h was added back in.
Dropping the rest of those headers was intentional.
I believe the issue of gvcint.h has already been discussed with the R developers. Emden added some functions in lib/gvc/gvc.c to access username, version, builddate info. I suspect this is only in graphviz-2.15 at this time.
The code is stable enough this week that perhaps I should push out another release (there is also a significant fix for irregular character spacing in bitmap outputs). Does anybody know for sure if R builds OK with the latest development snapshots?
John
Ryan Schmidt wrote:
Emil Lundberg reported [1] on the MacPorts mailing list that his Graphviz 2.14 installation doesn't have some headers that Rgraphviz requires. I checked on my system and see that Graphviz 2.12 has these headers in $(prefix)/include/graphviz:
aghdr.h agraph.h agxbuf.h arith.h ast_common.h cdt.h color.h demand_loading.c dot_builtins.c dthdr.h exgram.h exlib.h expr.h geom.h globals.h grammar.h graph.h gv.cpp gv.i gvc.h gvcext.h gvcint.h gvcjob.h gvcommon.h gvplugin.h gvplugin_device.h gvplugin_layout.h gvplugin_loadimage.h gvplugin_render.h gvplugin_textlayout.h libgraph.h logic.h malloc.h no_demand_loading.c pack.h parser.h pathgeom.h pathplan.h pathutil.h solvers.h textpara.h tri.h triefa.h types.h usershape.h vis.h vispath.h vmstub.h
But graphviz 2.15.20070920.0439 only installs these headers:
agraph.h arith.h cdt.h color.h demand_loading.c dot_builtins.c geom.h graph.h gv.cpp gv.i gvc.h gvcext.h gvcjob.h gvcommon.h gvplugin.h gvplugin_device.h gvplugin_layout.h gvplugin_loadimage.h gvplugin_render.h gvplugin_textlayout.h no_demand_loading.c pack.h pathgeom.h pathplan.h textpara.h types.h usershape.h
Several fewer, as you see. Of those missing, apparently Rgraphviz requires globals.h and gvcint.h to build. Is it intentional that Graphviz now installs fewer headers? If so, I guess the Rgraphviz developers have to make some changes?
[1] http://lists.macosforge.org/pipermail/macports-users/2007- September/005610.html
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