Rgraphviz build problems
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@sean-davis-490
Last seen 6 weeks ago
United States
I am having some problems building Rgraphviz. I have installed graphviz from source on MacOS 10.2.8 without too much difficulty. However, when I try to install Rgraphviz, I get: [holmes:~/R-1.8.0/library] sdavis% R INSTALL Rgraphviz_1.0.tar.gz * Installing *source* package 'Rgraphviz' ... ** libs gcc -no-cpp-precomp -I/Users/sdavis/R-1.8.0/include `dotneato-config --cflags` -I/sw/include -I/usr/local/include -Wall -fno-common -g -O2 -c Rgraphviz.c -o Rgraphviz.o cc1: warning: changing search order for system directory "/usr/local/include" cc1: warning: as it has already been specified as a non-system directory In file included from /usr/local/include/graphviz/render.h:26, from common.h:19, from Rgraphviz.c:1: /usr/local/include/graphviz/macros.h:28:1: warning: "NEW" redefined In file included from common.h:11, from Rgraphviz.c:1: /Users/sdavis/R-1.8.0/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:28, from common.h:19, 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:28, from common.h:19, 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:29, from common.h:19, from Rgraphviz.c:1: /usr/local/include/graphviz/graph.h:11: warning: ignoring #pragma prototyped In file included from common.h:20, from Rgraphviz.c:1: /usr/local/include/graphviz/graph.h:11: warning: ignoring #pragma prototyped In file included from common.h:23, from Rgraphviz.c:1: /usr/local/include/graphviz/adjust.h:11: warning: ignoring #pragma prototyped gcc -bundle -flat_namespace -undefined suppress -L/sw/lib -L/usr/local/lib -o Rg raphviz.so Rgraphviz.o -Wl,`dotneato-config --libs` -lm -lcc_dynamic ld: can't locate file for: -ldotneato make: *** [Rgraphviz.so] Error 1 ERROR: compilation failed for package 'Rgraphviz' ** Removing '/Users/sdavis/R-1.8.0/library/Rgraphviz' [holmes:~] sdavis% dotneato-config --libs -L/usr/local/lib/graphviz -ldotneato Any ideas? Thanks, Sean [[alternative HTML version deleted]]
Rgraphviz Rgraphviz • 584 views
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@kasper-daniel-hansen-459
Last seen 7.1 years ago
On Wed, Nov 12, 2003 at 10:55:03AM -0500, Sean Davis wrote: > I am having some problems building Rgraphviz. I have installed graphviz > from source on MacOS 10.2.8 without too much difficulty. However, when I > try to install Rgraphviz, I get: <snip> Without looking to closely at the output I guess it is because it doesn't find the Graphviz libraries. On my machine they are installed to a subdirectory of the standard library directory, eg. something like /usr/lib/graphviz instead of /usr/lib. You need to tell gcc to look in this place when searching for libraries. On Linux, this may be set by using the environmnet variable LD_LIBRARY_PATH. To be specific, I do # export LD_LIBRARY_PATH=/usr/lib/graphviz # R CMD INSTALL Rgraphviz_1.0.tar.gz (both commands executed from the same shell). -- Kasper Daniel Hansen, Research Assistent Department of Biostatistics, University of Copenhagen
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On 11/12/03 11:25 AM, "Kasper Daniel Hansen" <k.hansen@biostat.ku.dk> wrote: > On Wed, Nov 12, 2003 at 10:55:03AM -0500, Sean Davis wrote: >> I am having some problems building Rgraphviz. I have installed graphviz >> from source on MacOS 10.2.8 without too much difficulty. However, when I >> try to install Rgraphviz, I get: > <snip> > > Without looking to closely at the output I guess it is because it doesn't find > the Graphviz libraries. On my machine > they are installed to a subdirectory of the standard library directory, eg. > something like /usr/lib/graphviz instead of > /usr/lib. You need to tell gcc to look in this place when searching for > libraries. On Linux, this may be set by using > the environmnet variable LD_LIBRARY_PATH. To be specific, I do > # export LD_LIBRARY_PATH=/usr/lib/graphviz > # R CMD INSTALL Rgraphviz_1.0.tar.gz > (both commands executed from the same shell). Thanks for the quick response. Actually, the compile command includes dotneato-config --libs which does point to the right directory for the graphviz libraries on my machine: Prompt> dotneato-config --libs -L /usr/local/lib/graphviz -ldotneato What file is associated with -ldotneato that I should look for? Thanks again, Sean
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A.J. Rossini ▴ 810
@aj-rossini-209
Last seen 7.1 years ago
Sean Davis <sdavis2@mail.nih.gov> writes: > On 11/12/03 11:25 AM, "Kasper Daniel Hansen" <k.hansen@biostat.ku.dk> wrote: > >> On Wed, Nov 12, 2003 at 10:55:03AM -0500, Sean Davis wrote: >>> I am having some problems building Rgraphviz. I have installed graphviz >>> from source on MacOS 10.2.8 without too much difficulty. However, when I >>> try to install Rgraphviz, I get: >> <snip> >> >> Without looking to closely at the output I guess it is because it doesn't find >> the Graphviz libraries. On my machine >> they are installed to a subdirectory of the standard library directory, eg. >> something like /usr/lib/graphviz instead of >> /usr/lib. You need to tell gcc to look in this place when searching for >> libraries. On Linux, this may be set by using >> the environmnet variable LD_LIBRARY_PATH. To be specific, I do >> # export LD_LIBRARY_PATH=/usr/lib/graphviz >> # R CMD INSTALL Rgraphviz_1.0.tar.gz >> (both commands executed from the same shell). > > Thanks for the quick response. > > Actually, the compile command includes dotneato-config --libs which does > point to the right directory for the graphviz libraries on my machine: > > Prompt> dotneato-config --libs > -L /usr/local/lib/graphviz -ldotneato > > What file is associated with -ldotneato that I should look for? libdotneato.so (or libdotneato.so.X.Y X,Y integers, possibly missing). -- rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
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