Rgraphviz install issues
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Byron Ellis ▴ 280
@byron-ellis-11
Last seen 7.2 years ago
That reminds me, right about the time CVS went away, I needed to reinstall Ruuid and whipped up a quick patch to get it to build under OS X without installing glib (because I'm too lazy to install glib). Basically, do the same thing as Win32. Seems to work swimmingly. Sorry about the bad diff, but, you know, CVS. :-) uuidP.h: 10a11 > 21,22d21 < < 25,31d23 < < #if defined(__APPLE_CC__) < typedef unsigned long guint32; < typedef unsigned short guint16; < typedef unsigned char guint8; < typedef unsigned char guchar; < #else 33,34d24 < #endif < On Sep 30, 2004, at 10:54 AM, Jeff Gentry wrote: >> I have installed, via darwinports, graphviz (v1.16) running in x11 (I >> dyn092203:~ apb$ sudo R CMD INSTALL /Users/apb/Rgraphviz_1.4.0.tar.gz >> Rgraphviz.c:244: warning: implicit declaration of function `GD_gvc' >> Rgraphviz.c:244: error: invalid lvalue in assignment > >> Clearly, something else is missing in my effort..... Any advice would >> be appreciated. > > If you're using that new of a version of Graphviz, you need to use the > devel version of Rgraphviz. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > --- Byron Ellis (bellis@hsph.harvard.edu) "Oook" -- The Librarian
Ruuid Rgraphviz Ruuid Rgraphviz • 652 views
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@andrew-beckerman-935
Last seen 7.2 years ago
Jeff - thanks for the advice, but unfortunately, no dice.... I download the development Rgraphviz pacakge, and using the same routine with exporting my library location for graphviz, get the same error.... any more ideas? the offending line seems to be this: ld: can't locate file for: -ldotneato cheers andrew dyn092203:~ apb$ export LD_LIBRARY_PATH=/opt/local/lib/graphviz dyn092203:~ apb$ sudo R CMD INSTALL /Users/apb/Rgraphviz_1-1.4.23.tar.gz Password: * Installing *source* package 'Rgraphviz' ... checking for graphviz... checking for dotneato-config... /opt/local/bin//dotneato-config /opt/local/bin//dotneato-config configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/opt/local/include/graphviz -I/usr/local/include -Wall -fno-common -g -O2 -c Rgraphviz.c -o Rgraphviz.o In file included from /opt/local/include/graphviz/render.h:45, from common.h:22, from Rgraphviz.c:1: /opt/local/include/graphviz/macros.h:34:1: warning: "NEW" redefined In file included from common.h:13, from Rgraphviz.c:1: /Library/Frameworks/R.framework/Resources/include/Rdefines.h:129:1: warning: this is the location of the previous definition gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/opt/local/include/graphviz -I/usr/local/include -Wall -fno-common -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o In file included from /opt/local/include/graphviz/render.h:45, from common.h:22, from RgraphvizInit.c:1: /opt/local/include/graphviz/macros.h:34:1: warning: "NEW" redefined In file included from common.h:13, from RgraphvizInit.c:1: /Library/Frameworks/R.framework/Resources/include/Rdefines.h:129:1: warning: this is the location of the previous definition gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o Rgraphviz.so Rgraphviz.o RgraphvizInit.o -Wl -ldotneato -lm -lcc_dynamic -framework R ld: can't locate file for: -ldotneato make: *** [Rgraphviz.so] Error 1 ERROR: compilation failed for package 'Rgraphviz' ** Removing '/Library/Frameworks/R.framework/Versions/1.9.1/Resources/library/ Rgraphviz' On 30 Sep 2004, at 18:54, Jeff Gentry wrote: >> I have installed, via darwinports, graphviz (v1.16) running in x11 (I >> dyn092203:~ apb$ sudo R CMD INSTALL /Users/apb/Rgraphviz_1.4.0.tar.gz >> Rgraphviz.c:244: warning: implicit declaration of function `GD_gvc' >> Rgraphviz.c:244: error: invalid lvalue in assignment > >> Clearly, something else is missing in my effort..... Any advice would >> be appreciated. > > If you're using that new of a version of Graphviz, you need to use the > devel version of Rgraphviz. > > ---------------------------------------------------------------------- -- --------- Dr. Andrew Beckerman Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK ph +44 (0)114 222 0026; fx +44 (0)114 222 0002 http://www.shef.ac.uk/beckslab ---------------------------------------------------------------------- -- ----------
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> Jeff - thanks for the advice, but unfortunately, no dice.... I download > the development Rgraphviz pacakge, and using the same routine with > exporting my library location for graphviz, get the same error.... any > more ideas? the offending line seems to be this: ld: can't locate file > for: -ldotneato That doesn't appear to be the same error at all, unless I'm missing something. That error means that you haven't pointed your LD_LIBRARY_PATH to where the graphviz libraries are sitting.
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Hi, I have fixed my Rgraphviz issuse...sicne I was dealing with it recently..this might help because I have done it on my linux fedora core 2 OS don't do RPM thing..plz..since you have linux.... 1. download Graphviz 2. tar -xvzf 3. go to Graphviz directory ./configure --prefix=/usr --exec-prefix=/usr 4. make 5. make install 6. download Rgraphviz (from same shell) 7. just do: R CMD INSTALL Rgraphviz*.gz 8. type $ whereis graphviz graphviz: /usr/lib/graphviz /usr/local/lib/graphviz /usr/include/graphviz /usr/share/graphviz you can see above couple of path to graphviz and you will take first one(whatever is on your system): /usr/lib/graphviz 9. now, whenever you want to load Rgraphviz in to your R first from linux prompt: $ export LD_LIBRARY_PATH=/usr/lib/graphviz and $ R you can set this path in to your login script. please let me know, if you have any trouble with installing R graphviz. thanks Saurin --- Andrew Beckerman <a.beckerman@sheffield.ac.uk> wrote: > Jeff - thanks for the advice, but unfortunately, no > dice.... I download > the development Rgraphviz pacakge, and using the > same routine with > exporting my library location for graphviz, get the > same error.... any > more ideas? the offending line seems to be this: > ld: can't locate file > for: -ldotneato > > cheers > andrew > > dyn092203:~ apb$ export > LD_LIBRARY_PATH=/opt/local/lib/graphviz > dyn092203:~ apb$ sudo R CMD INSTALL > /Users/apb/Rgraphviz_1-1.4.23.tar.gz > Password: > * Installing *source* package 'Rgraphviz' ... > checking for graphviz... checking for > dotneato-config... > /opt/local/bin//dotneato-config > /opt/local/bin//dotneato-config > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -no-cpp-precomp > -I/Library/Frameworks/R.framework/Resources/include > > -I/opt/local/include/graphviz -I/usr/local/include > -Wall -fno-common > -g -O2 -c Rgraphviz.c -o Rgraphviz.o > In file included from > /opt/local/include/graphviz/render.h:45, > from common.h:22, > from Rgraphviz.c:1: > /opt/local/include/graphviz/macros.h:34:1: warning: > "NEW" redefined > In file included from common.h:13, > from Rgraphviz.c:1: > /Library/Frameworks/R.framework/Resources/include/Rdefines.h:129:1: > > warning: this is the location of the previous > definition > gcc -no-cpp-precomp > -I/Library/Frameworks/R.framework/Resources/include > > -I/opt/local/include/graphviz -I/usr/local/include > -Wall -fno-common > -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o > In file included from > /opt/local/include/graphviz/render.h:45, > from common.h:22, > from RgraphvizInit.c:1: > /opt/local/include/graphviz/macros.h:34:1: warning: > "NEW" redefined > In file included from common.h:13, > from RgraphvizInit.c:1: > /Library/Frameworks/R.framework/Resources/include/Rdefines.h:129:1: > > warning: this is the location of the previous > definition > gcc -bundle -flat_namespace -undefined suppress > -L/usr/local/lib -o > Rgraphviz.so Rgraphviz.o RgraphvizInit.o -Wl > -ldotneato -lm > -lcc_dynamic -framework R > ld: can't locate file for: -ldotneato > make: *** [Rgraphviz.so] Error 1 > ERROR: compilation failed for package 'Rgraphviz' > ** Removing > '/Library/Frameworks/R.framework/Versions/1.9.1/Resources/library/ > > Rgraphviz' > On 30 Sep 2004, at 18:54, Jeff Gentry wrote: > > >> I have installed, via darwinports, graphviz > (v1.16) running in x11 (I > >> dyn092203:~ apb$ sudo R CMD INSTALL > /Users/apb/Rgraphviz_1.4.0.tar.gz > >> Rgraphviz.c:244: warning: implicit declaration of > function `GD_gvc' > >> Rgraphviz.c:244: error: invalid lvalue in > assignment > > > >> Clearly, something else is missing in my > effort..... Any advice would > >> be appreciated. > > > > If you're using that new of a version of Graphviz, > you need to use the > > devel version of Rgraphviz. > > > > > ---------------------------------------------------------------------- -- > > --------- > Dr. Andrew Beckerman > Department of Animal and Plant Sciences, University > of Sheffield, > Alfred Denny Building, Western Bank, Sheffield S10 > 2TN, UK > ph +44 (0)114 222 0026; fx +44 (0)114 222 0002 > http://www.shef.ac.uk/beckslab > ---------------------------------------------------------------------- -- > > ---------- > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > _______________________________ Declare Yourself - Register online to vote today!
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