[BioC] installing Rgraphviz under CentOS 5.6

[Kasper Daniel Hansen]

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
>
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