[BioC] installing Rgraphviz under CentOS 5.6

Ou, Jianhong Jianhong.Ou at umassmed.edu
Tue Sep 27 21:48:54 CEST 2011


Hi Kasper,

I think it is.

$ echo $LD_LIBRARY_PATH
/usr/local/lib

$ ls /usr/local/lib
graphviz         libcgraph.so        libgraph.so.5.0.0  libgvpr.so        libpathplan.so.4.0.0
libcdt.la        libcgraph.so.6      libgvc.la          libgvpr.so.2      libxdot.la
libcdt.so        libcgraph.so.6.0.0  libgvc.so          libgvpr.so.2.0.0  libxdot.so
libcdt.so.5      libgraph.la         libgvc.so.6        libpathplan.la    libxdot.so.4
libcdt.so.5.0.0  libgraph.so         libgvc.so.6.0.0    libpathplan.so    libxdot.so.4.0.0
libcgraph.la     libgraph.so.5       libgvpr.la         libpathplan.so.4  pkgconfig

$ ls /usr/local/lib/graphviz/
config6                          libgvplugin_gd.la                  libgvplugin_xlib.so
go                               libgvplugin_gd.so                  libgvplugin_xlib.so.6
guile                            libgvplugin_gd.so.6                libgvplugin_xlib.so.6.0.0
io                               libgvplugin_gd.so.6.0.0            lua
java                             libgvplugin_gtk.la                 ocaml
libgvplugin_core.la              libgvplugin_gtk.so                 perl
libgvplugin_core.so              libgvplugin_gtk.so.6               php
libgvplugin_core.so.6            libgvplugin_gtk.so.6.0.0           python
libgvplugin_core.so.6.0.0        libgvplugin_neato_layout.la        python23
libgvplugin_dot_layout.la        libgvplugin_neato_layout.so        python24
libgvplugin_dot_layout.so        libgvplugin_neato_layout.so.6      python25
libgvplugin_dot_layout.so.6      libgvplugin_neato_layout.so.6.0.0  python26
libgvplugin_dot_layout.so.6.0.0  libgvplugin_pango.la               python27
libgvplugin_gdk_pixbuf.la        libgvplugin_pango.so               R
libgvplugin_gdk_pixbuf.so        libgvplugin_pango.so.6             ruby
libgvplugin_gdk_pixbuf.so.6      libgvplugin_pango.so.6.0.0         sharp
libgvplugin_gdk_pixbuf.so.6.0.0  libgvplugin_xlib.la                tcl


Yours sincerely,

Jianhong Ou

jianhong.ou at umassmed.edu


On Sep 27, 2011, at 3:23 PM, Kasper Daniel Hansen wrote:

> Is graphviz in your LD_LIBRARY_PATH?
> 
> Kasper
> 
> On Tue, Sep 27, 2011 at 3:07 PM, Ou, Jianhong <Jianhong.Ou at umassmed.edu> wrote:
>> Dear list,
>> 
>> I met troubles installing Rgraphviz. Could anybody help me to figure this out?
>> 
>> R version 2.13.0 (2011-04-13)
>> Error log,
>> 
>> $ sudo R CMD INSTALL --configure-args='--with-graphviz=/usr/local' Rgraphviz_1.30.1.tar.gz
>> checking for gcc... gcc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ISO C89... none needed
>> checking how to run the C preprocessor... gcc -E
>> checking for grep that handles long lines and -e... /bin/grep
>> checking for egrep... /bin/grep -E
>> checking for ANSI C header files... yes
>> checking for sys/types.h... yes
>> checking for sys/stat.h... yes
>> checking for stdlib.h... yes
>> checking for string.h... yes
>> checking for memory.h... yes
>> checking for strings.h... yes
>> checking for inttypes.h... yes
>> checking for stdint.h... yes
>> checking for unistd.h... yes
>> checking for stdbool.h that conforms to C99... yes
>> checking for _Bool... yes
>> checking for whether compiler has bool... yes
>> configure: Using Graphviz dir '/usr/local'
>> configure: Found Graphviz version '2.28.0'.
>> configure: Graphviz major version is '2' and minor version is '28'.
>> configure: Using the following compilation and linking flags for Rgraphviz
>> configure:    PKG_CPPFLAGS=-I/usr/local/include/graphviz
>> configure:    PKG_LIBS=-L/usr/local/lib/graphviz -L/usr/local/lib -lgvc
>> configure:    GVIZ_DEFS= -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28
>> configure: Setting Graphviz Build version to '2.28.0'.
>> configure: creating ./config.status
>> config.status: creating R/graphviz_build_version.R
>> config.status: creating src/Makevars
>> ** libs
>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz  -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28  -I/usr/local/include    -fpic  -g -O2 -c LL_funcs.c -o LL_funcs.o
>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz  -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28  -I/usr/local/include    -fpic  -g -O2 -c Rgraphviz.c -o Rgraphviz.o
>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz  -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28  -I/usr/local/include    -fpic  -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o
>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz  -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28  -I/usr/local/include    -fpic  -g -O2 -c agopen.c -o agopen.o
>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz  -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28  -I/usr/local/include    -fpic  -g -O2 -c agread.c -o agread.o
>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz  -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28  -I/usr/local/include    -fpic  -g -O2 -c agwrite.c -o agwrite.o
>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz  -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28  -I/usr/local/include    -fpic  -g -O2 -c bezier.c -o bezier.o
>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz  -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28  -I/usr/local/include    -fpic  -g -O2 -c buildEdgeList.c -o buildEdgeList.o
>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz  -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28  -I/usr/local/include    -fpic  -g -O2 -c buildNodeList.c -o buildNodeList.o
>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz  -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28  -I/usr/local/include    -fpic  -g -O2 -c doLayout.c -o doLayout.o
>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz  -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28  -I/usr/local/include    -fpic  -g -O2 -c graphvizVersion.c -o graphvizVersion.o
>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz  -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28  -I/usr/local/include    -fpic  -g -O2 -c init.c -o init.o
>> gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o -L/usr/local/lib/graphviz -L/usr/local/lib -lgvc
>> installing to /usr/local/lib64/R/library/Rgraphviz/libs
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> Creating a new generic function for "head" in "Rgraphviz"
>> Creating a new generic function for "tail" in "Rgraphviz"
>> Creating a new generic function for "lines" in "Rgraphviz"
>> Creating a new generic function for "plot" in "Rgraphviz"
>> ** help
>> *** installing help indices
>> ** building package indices ...
>> ** testing if installed package can be loaded
>> Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
>>  call: value[[3L]](cond)
>>  error: unable to load shared object '/usr/local/lib64/R/library/Rgraphviz/libs/Rgraphviz.so':
>>  libgvc.so.6: cannot open shared object file: No such file or directory
>> 
>>  Check that (1) graphviz is installed on your system; (2) the
>>  installed version of graphviz matches '2.28.0'; 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
>> 
>>  http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
>> 
>>  Ask further questions on the Bioconductor mailing list
>> 
>>  http://bioconductor.org/docs/mailList.html
>> 
>> 
>> Error: loading failed
>> Execution halted
>> ERROR: loading failed
>> 
>> Yours sincerely,
>> 
>> Jianhong Ou
>> 
>> jianhong.ou at umassmed.edu
>> 
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>> 



More information about the Bioconductor mailing list