CODEWITHSUNDEEP
rosx-liongraphvizmacports
JordanBelf
JordanBelf

Reputation: 3338

Not able to Install R package "Rgraphviz" on Mac OS X Lion

I have spent a lot of time trying to solve this, but still no luck. I am trying to get Rgraphviz to work with R 2.14.1 on a Max OS X Lion

These are the steps I took in order to install and use Rgraphviz on Mac OS X Lion:

  1. Installed graphviz via: sudo port install graphviz

  2. Checked that the installation was successful : pkg-config --modversion libgvc

Result: 2.28.0 <- That means its OK

Under R 2.14.1

source("http://www.bioconductor.org/biocLite.R") biocLite("Rgraphviz")

Whenever I try to use the library I get the following error

Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
call: value[[3L]](cond)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so':
dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so, 6): Library not loaded: /usr/local/lib/libgvc.5.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so

Check that (1) graphviz is installed on your system; (2) the installed version of
graphviz matches '2.26.3'; this is the version used to build this Rgraphviz
package; (3) graphviz is accessible to R, e.g., the path to the graphviz 'bin'
directory is in the system 'PATH' variable.  See additional instructions in the
'README' file of the Rgraphviz 'source' distribution, available at

Some things I notice

Also when I run a locate Rgraphviz.so there are no results.

Any clue towards a solution will be much appreciated, Thanks a lot!

Upvotes: 3

Views: 2569

Answers (2)

user1366998
user1366998

Reputation: 41

One more fail point. If you used Fink to install graphviz, you may still, like me, encounter separate build errors even after you use the configure arguments to point to graphviz, which now look like:

R CMD INSTALL --configure-args='--with-graphviz=/sw' Rgraphviz_1.34.0.tar.gz

The installation will fail during build errors for LL_funcs.c because it is looking for libraries that do not install unless you ALSO install graphviz-dev. You will see this:

In file included from LL_funcs.c:1:
common.h:31:17: error: gvc.h: No such file or directory
common.h:32:22: error: gvplugin.h: No such file or directory
common.h:35:20: error: gvcext.h: No such file or directory
common.h:39:20: error: gvcjob.h: No such file or directory

followed by many more build errors of course. Just be sure to

fink install graphviz-dev

Upvotes: 1

Martino
Martino

Reputation: 11

Thanks for the final answer, the installation seems to work for me! (I still have to check that the package runs properly). Just a quick observation: Graphviz was installed in /usr/local on my machine so that the above command had to be entered as follows:

sudo R CMD INSTALL --configure-args='--with-graphviz=/usr/local' Rgraphviz_1.32.0.tar.gz

Upvotes: 1

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