Compiling ggobi fails (error in graphviz.c)

[Alex]

Hi there,

I'm trying to use R and rggobi, but compilation of ggobi on my 64-bit Arch Linux fails.

I downloaded this file: http://www.ggobi.org/downloads/ggobi-2.1.9.tar.bz2

Now, this command works, and I can start ggobi from console:
./configure && make && sudo make install

When I try to install rggobi, though, R throws me an error that "No package 'ggobi' found".

If I go (as the manual suggests) ./configure --with-all-plugins && make , it (i.e. make) fails with the errors attached below.

Does anyone know how I can fix this?

graphviz.c: In function 'dot_neato_layout_cb':
graphviz.c:215:3: error: too few arguments to function 'aginit'
   aginit();
   ^
In file included from /usr/include/graphviz/types.h:49:0,
                 from /usr/include/graphviz/gvc.h:17,
                 from graphviz.c:16:
/usr/include/graphviz/cgraph.h:359:13: note: declared here
 extern void aginit(Agraph_t * g, int kind, char *rec_name, int rec_size,
             ^
graphviz.c:220:3: error: incompatible type for argument 2 of 'agopen'
   graph = agopen("graph", kind);
   ^
In file included from /usr/include/graphviz/types.h:49:0,
                 from /usr/include/graphviz/gvc.h:17,
                 from graphviz.c:16:
/usr/include/graphviz/cgraph.h:266:18: note: expected 'Agdesc_t' but argument is of type 'gint'
 extern Agraph_t *agopen(char *name, Agdesc_t desc, Agdisc_t * disc);
                  ^
graphviz.c:220:3: error: too few arguments to function 'agopen'
   graph = agopen("graph", kind);
   ^
In file included from /usr/include/graphviz/types.h:49:0,
                 from /usr/include/graphviz/gvc.h:17,
                 from graphviz.c:16:
/usr/include/graphviz/cgraph.h:266:18: note: declared here
 extern Agraph_t *agopen(char *name, Agdesc_t desc, Agdisc_t * disc);
                  ^
graphviz.c:226:5: error: too few arguments to function 'agnode'
     agnode(graph, name);
     ^
In file included from /usr/include/graphviz/types.h:49:0,
                 from /usr/include/graphviz/gvc.h:17,
                 from graphviz.c:16:
/usr/include/graphviz/cgraph.h:280:18: note: declared here
 extern Agnode_t *agnode(Agraph_t * g, char *name, int createflag);
                  ^
graphviz.c:248:7: error: too few arguments to function 'agedge'
       edge = agedge(graph, tail, head);
       ^
In file included from /usr/include/graphviz/types.h:49:0,
                 from /usr/include/graphviz/gvc.h:17,
                 from graphviz.c:16:
/usr/include/graphviz/cgraph.h:291:18: note: declared here
 extern Agedge_t *agedge(Agraph_t * g, Agnode_t * t, Agnode_t * h,
                  ^
graphviz.c:270:35: error: request for member 'x' in something not a structure or union
       pos[i][0] = ND_coord_i(node).x;
                                   ^
graphviz.c:271:35: error: request for member 'y' in something not a structure or union
       pos[i][1] = ND_coord_i(node).y;
                                   ^
graphviz.c:285:36: error: 'Agnode_t' has no member named 'name'
       agsafeset (graph, "root", ctr->name, NULL);
                                    ^
graphviz.c:315:13: warning: assignment makes pointer from integer without a cast [enabled by default]
         sym = agfindattr(graph,"dim");  
             ^
graphviz.c:317:15: warning: assignment makes pointer from integer without a cast [enabled by default]
           sym = agraphattr(graph,"dim","");
               ^
graphviz.c:319:26: error: 'attrsym_t' has no member named 'index'
         agxset(graph, sym->index, buf);
                          ^
graphviz.c:354:11: error: 'Agnode_t' has no member named 'u'
       node->u.width = node->u.height = .001;
           ^
graphviz.c:354:27: error: 'Agnode_t' has no member named 'u'
       node->u.width = node->u.height = .001;
                           ^
Makefile:393: recipe for target 'plugin_la-graphviz.lo' failed

[Michael Lawrence]

On Fri, Jan 10, 2014 at 1:17 AM, Alex <alexander.w...@gmail.com> wrote:

Hi there,

I'm trying to use R and rggobi, but compilation of ggobi on my 64-bit Arch Linux fails.

I downloaded this file: http://www.ggobi.org/downloads/ggobi-2.1.9.tar.bz2

Now, this command works, and I can start ggobi from console:
./configure && make && sudo make install

When I try to install rggobi, though, R throws me an error that "No package 'ggobi' found".

Probably need to ensure that your PKG_CONFIG_PATH is set to according to your prefix. So if you installed to /usr/local, run
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig

 

If I go (as the manual suggests) ./configure --with-all-plugins && make , it (i.e. make) fails with the errors attached below.

Does anyone know how I can fix this?

Downgrade to graphviz 2.28 if possible. I think 2.30 has some major API breakage. Will address this eventually....

If you don't need the graph layout plugin, you could just enable the plugins you want, see configure --help.
 

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