Error when installing Rgraphviz on Centos
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jmh5ad ▴ 20
@jmh5ad-15716
Last seen 24 months ago

I am running R/3.6.0 on a multi-user Centos 7.6 system and have not been able to install Rgraphviz in my account.

I have downloaded the tarball, Rgraphviz2.28.0.tar.gz, and am using the command: R CMD INSTALL Rgraphviz2.28.0.tar.gz

The error message that I am getting is this:

In file included from LL_funcs.c:1:0:
common.h:22:8: error: unknown type name ‘Agdict_t’
 extern Agdict_t *agdictof(void *);

I also have tried expanding the tarball and running configure manually. I get the following message:

In file included from LL_funcs.c:1:0:
common.h:22:8: error: unknown type name ‘Agdict_t’
 extern Agdict_t *agdictof(void *);
        ^~~~~~~~
LL_funcs.c: In function ‘getClusterPtr’:
LL_funcs.c:24:20: warning: implicit declaration of function ‘agfindsubg’; did you mean  agidsubg’? [-Wimplicit-function-declaration]
     Agraph_t *sg = agfindsubg(g, subGName);
                    ^~~~~~~~~~
                    agidsubg
LL_funcs.c:24:20: warning: initialization makes pointer from integer without a cast [-Wint-conversion]
LL_funcs.c: In function ‘getDefAttrs’:
LL_funcs.c:31:5: error: unknown type name ‘Agdict_t’; did you mean ‘Agdisc_t’?
     Agdict_t *dict = agdictof(obj);

Any suggestions on how to fix this are greatly appreciated.

Rgraphviz Installation Error • 417 views
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The tag you used (software error) is too general and the Rgraphviz maintainers won't necessarily pay attention to a post with such a general tag. Since this is about an installation error with the Rgraphviz package, I'd suggest you tag your post with Rgraphviz.

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Thank you -- I've updated the tags.

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Thank you -- I've updated the tags.

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Thank you -- I've updated the tags.

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Do you have graphviz installed on your system? (e.g. https://centos.pkgs.org/7/centos-x86_64/graphviz-devel-2.30.1-21.el7.x86_64.rpm.html )

It's listed as an 'optional requirement' on the Rgraphviz homepage, but maybe it's not so optional on CentOS?

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Yes, we have graphviz and graphviz-devel installed on our system. In the newer versions of Rgraphviz, one has the option of using the graphviz code that comes bundled with Rgraphviz or of using the system version. I have tried both options and get the same error message either way.

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We are using gcc/7.1.0 to build the package. We suspect that the error is with using a header file in that version of the compiler. My colleague was able to install the package on a stand-alone machine using gcc/4.8.5 and intel/18.0.

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