Hi, I'm having trouble running Rgraphviz 1.8. The installation appears to go OK, but calling Rgraphviz in a session invokes the following error: > library(Rgraphviz) Loading required package: graph Loading required package: cluster Loading required package: Ruuid Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/usr/local/lib/R/site-library/Rgraphviz/libs/Rgraphviz.so': libdotneato.so.0: cannot open shared object file: No such file or directory Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz' Error: package/namespace load failed for 'Rgraphviz' ########### As far as I can tell I have all the dependencies installed above the minimum required version. The install looks like the following: ######## # R CMD INSTALL Rgraphviz_1.8.0.tar.gz * Installing *source* package 'Rgraphviz' ... checking for graphviz... checking for dotneato-config... /usr/bin/dotneato-config /usr/bin/dotneato-config configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -I/usr/lib/R/include -I/usr/include/graphviz -DGRAPHVIZGT_1_16 -fPIC -g -O2 -c Rgraphviz.c -o Rgraphviz.o In file included from /usr/include/graphviz/render.h:53, from common.h:32, from Rgraphviz.c:1: /usr/include/graphviz/macros.h:41:1: warning: "NEW" redefined In file included from common.h:15, from Rgraphviz.c:1: /usr/lib/R/include/Rdefines.h:134:1: warning: this is the location of the previous definition gcc -I/usr/lib/R/include -I/usr/include/graphviz -DGRAPHVIZGT_1_16 -fPIC -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o In file included from /usr/include/graphviz/render.h:53, from common.h:32, from RgraphvizInit.c:1: /usr/include/graphviz/macros.h:41:1: warning: "NEW" redefined In file included from common.h:15, from RgraphvizInit.c:1: /usr/lib/R/include/Rdefines.h:134:1: warning: this is the location of the previous definition gcc -shared -o Rgraphviz.so Rgraphviz.o RgraphvizInit.o -L/usr/lib/graphviz -ldotneato -lm -L/usr/lib/R/lib -lR ** R ** inst ** save image Loading required package: graph Loading required package: cluster Loading required package: Ruuid Creating a new generic function for 'lines' in 'Rgraphviz' Creating a new generic function for 'plot' in 'Rgraphviz' .... the rest as per normal. Any ideas would be appreciated.

Shamit Soneji <shamit.soneji at="" imm.ox.ac.uk=""> writes: > I'm having trouble running Rgraphviz 1.8. The installation appears to go > OK, but calling Rgraphviz in a session invokes the following error: > >> library(Rgraphviz) > Loading required package: graph > Loading required package: cluster > Loading required package: Ruuid > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library > '/usr/local/lib/R/site-library/Rgraphviz/libs/Rgraphviz.so': > libdotneato.so.0: cannot open shared object file: No such file or > directory > Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz' > Error: package/namespace load failed for 'Rgraphviz' > > ########### > > As far as I can tell I have all the dependencies installed above the > minimum required version. The install looks like the following: Where are the graphviz shared libraries (the .so files) installed? Most likely, you need to add them to your linker path. On Linux, try: export LD_LIBRARY_PATH=/path/to/graphviz/libs + seth

Hi Shamit, You seem to have the libdotneato.so.0 library under /usr/lib/graphviz on your system but the dynamic loader doesn't "know" it... If you are on a Linux system and if you have root access to it, you can add this line /usr/lib/graphviz to the /etc/ld.so.conf file and then run /sbin/ldconfig (you will need root access for both: editing /etc/ld.so.conf and running /sbin/ldconfig). This will add all the shared objects (the lib*.so.x.y.z files) found in /usr/lib/graphviz to the list of registered shared objects. Then try 'library(Rgraphviz)' again (you should not need to re-install Rgraphviz). Let me know if this doesn't work. H. Shamit Soneji wrote: > Hi, > > I'm having trouble running Rgraphviz 1.8. The installation appears to go > OK, but calling Rgraphviz in a session invokes the following error: > >> library(Rgraphviz) > > Loading required package: graph > Loading required package: cluster > Loading required package: Ruuid > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library > '/usr/local/lib/R/site-library/Rgraphviz/libs/Rgraphviz.so': > libdotneato.so.0: cannot open shared object file: No such file or > directory > Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz' > Error: package/namespace load failed for 'Rgraphviz' > > ########### > > As far as I can tell I have all the dependencies installed above the > minimum required version. The install looks like the following: > > ######## > > # R CMD INSTALL Rgraphviz_1.8.0.tar.gz > * Installing *source* package 'Rgraphviz' ... > checking for graphviz... checking for > dotneato-config... /usr/bin/dotneato-config > /usr/bin/dotneato-config > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -I/usr/lib/R/include -I/usr/include/graphviz -DGRAPHVIZGT_1_16 > -fPIC -g -O2 -c Rgraphviz.c -o Rgraphviz.o > In file included from /usr/include/graphviz/render.h:53, > from common.h:32, > from Rgraphviz.c:1: > /usr/include/graphviz/macros.h:41:1: warning: "NEW" redefined > In file included from common.h:15, > from Rgraphviz.c:1: > /usr/lib/R/include/Rdefines.h:134:1: warning: this is the location of > the previous definition > gcc -I/usr/lib/R/include -I/usr/include/graphviz -DGRAPHVIZGT_1_16 > -fPIC -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o > In file included from /usr/include/graphviz/render.h:53, > from common.h:32, > from RgraphvizInit.c:1: > /usr/include/graphviz/macros.h:41:1: warning: "NEW" redefined > In file included from common.h:15, > from RgraphvizInit.c:1: > /usr/lib/R/include/Rdefines.h:134:1: warning: this is the location of > the previous definition > gcc -shared -o Rgraphviz.so Rgraphviz.o RgraphvizInit.o > -L/usr/lib/graphviz -ldotneato -lm -L/usr/lib/R/lib -lR > ** R > ** inst > ** save image > Loading required package: graph > Loading required package: cluster > Loading required package: Ruuid > Creating a new generic function for 'lines' in 'Rgraphviz' > Creating a new generic function for 'plot' in 'Rgraphviz' > .... the rest as per normal. > > > Any ideas would be appreciated. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- ------------------------ Hervé Pagès E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319