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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