Problem installing Rgraphviz
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@nicholas-lewin-koh-63
Last seen 7.1 years ago
Hi, I get the following error installing Rgraphviz: R CMD INSTALL Rgraphviz * Installing *source* package 'Rgraphviz' ... ** libs gcc -I/usr/local/lib/R/include dotneato-config --cflags -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c Rgraphviz.c -o Rgraphviz.o In file included from Rgraphviz.c:1: common.h:21:22: gvconfig.h: No such file or directory In file included from /usr/local/include/graphviz/render.h:49, from common.h:22, from Rgraphviz.c:1: /usr/local/include/graphviz/macros.h:28:1: warning: "NEW" redefined In file included from common.h:13, from Rgraphviz.c:1: /usr/local/lib/R/include/Rdefines.h:129:1: warning: this is the location of the previous definition In file included from /usr/local/include/graphviz/types.h:11, from /usr/local/include/graphviz/render.h:51, from common.h:22, from Rgraphviz.c:1: /usr/local/include/graphviz/pathplan.h:11: warning: ignoring #pragma prototyped In file included from /usr/local/include/graphviz/pathplan.h:16, from /usr/local/include/graphviz/types.h:11, from /usr/local/include/graphviz/render.h:51, from common.h:22, from Rgraphviz.c:1: /usr/local/include/graphviz/pathgeom.h:11: warning: ignoring #pragma prototyped In file included from /usr/local/include/graphviz/render.h:52, from common.h:22, from Rgraphviz.c:1: /usr/local/include/graphviz/graph.h:11: warning: ignoring #pragma prototyped In file included from /usr/local/include/graphviz/render.h:55, from common.h:22, from Rgraphviz.c:1: /usr/local/include/graphviz/gvrender.h:12: warning: ignoring #pragma prototyped In file included from /usr/local/include/graphviz/gvrender.h:19, from /usr/local/include/graphviz/render.h:55, from common.h:22, from Rgraphviz.c:1: /usr/local/include/graphviz/gvrenderint.h:12: warning: ignoring #pragma prototyped In file included from common.h:23, from Rgraphviz.c:1: /usr/local/include/graphviz/graph.h:11: warning: ignoring #pragma prototyped In file included from common.h:26, from Rgraphviz.c:1: /usr/local/include/graphviz/adjust.h:11: warning: ignoring #pragma prototyped In file included from common.h:28, from Rgraphviz.c:1: /usr/local/include/graphviz/gvrender.h:12: warning: ignoring #pragma prototyped Rgraphviz.c: In function Rgraphviz_init': Rgraphviz.c:80: Info' undeclared (first use in this function) Rgraphviz.c:80: (Each undeclared identifier is reported only once Rgraphviz.c:80: for each function it appears in.) Rgraphviz.c: In function Rgraphviz_graphvizVersion': Rgraphviz.c:567: Info' undeclared (first use in this function) make: *** [Rgraphviz.o] Error 1 ERROR: compilation failed for package 'Rgraphviz' ** Removing '/usr/local/lib/R/library/Rgraphviz' I looked at the source code and I couldn't find Info declared anywhere including the graphviz or R headers, I thought it might be a global variable. Is this an oversight in the development version or something I forgot to configure on my system. I am using a fresh install of R-1.9.0 on RH linux 9.0 and I have graphviz-1.12 and Rgraphviz_1.3.22 Thanks Nicholas
Rgraphviz Rgraphviz • 679 views
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@kasper-daniel-hansen-459
Last seen 7.1 years ago
On Wed, Apr 14, 2004 at 10:09:45AM +0800, Nicholas Lewin-Koh wrote: > I looked at the source code and I couldn't find Info declared anywhere > including the graphviz or R headers, I > thought it might be a global variable. Is this an oversight in the > development version or something > I forgot to configure on my system. I am using a fresh install of R-1.9.0 > on RH linux 9.0 and I have graphviz-1.12 > and Rgraphviz_1.3.22 It seems there are problems finding the graphviz headers. This will depend on how you installed the graphviz package and how your system looks through libraries. A quick fix is to use the environment variable LD_LIBRARY_PATH to set the library path. Try something like # export LD_LIBRARY_PATH=/usr/lib/graphviz with the exact path depending on your graphviz install. This is followed by installing Rgraphviz from the same shell. -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen
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On Wed, Apr 14, 2004 at 05:05:25PM +0200, Kasper Daniel Hansen wrote: > On Wed, Apr 14, 2004 at 10:09:45AM +0800, Nicholas Lewin-Koh wrote: > > I looked at the source code and I couldn't find Info declared anywhere > > including the graphviz or R headers, I > > thought it might be a global variable. Is this an oversight in the > > development version or something > > I forgot to configure on my system. I am using a fresh install of R-1.9.0 > > on RH linux 9.0 and I have graphviz-1.12 > > and Rgraphviz_1.3.22 > > It seems there are problems finding the graphviz headers. This will > depend on how you installed the graphviz package and how your system > looks through libraries. > > A quick fix is to use the environment variable LD_LIBRARY_PATH to set > the library path. Try something like > # export LD_LIBRARY_PATH=/usr/lib/graphviz > with the exact path depending on your graphviz install. This is followed > by installing Rgraphviz from the same shell. Sorry, was a bit quick on the trigger - look at Jeff's answer. -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen
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Jeff Gentry ★ 3.9k
@jeff-gentry-12
Last seen 7.1 years ago
> I looked at the source code and I couldn't find Info declared anywhere > including the graphviz or R headers, I > thought it might be a global variable. Is this an oversight in the > development version or something > I forgot to configure on my system. I am using a fresh install of R-1.9.0 > on RH linux 9.0 and I have graphviz-1.12 > and Rgraphviz_1.3.22 There was a slight change between Graphviz 1.12 and 1.11, and I'll be committing a change in the next few minutes so that Rgraphviz works against 1.12. At the same time, I'm going to modify the language of the SystemsRequirements field to say that it requires "Graphviz version 1.12" and not use the ">=" as that often turns out to not be true. Graphviz version 1.12 will be the version that the BioC 1.4 Rgraphviz will be using. When 1.4 is released, the Rgraphviz in the devel branch at that point will be working against Graphviz 1.13. -J