[BioC] installing Rgraphviz under CentOS 5.6

Ou, Jianhong Jianhong.Ou at umassmed.edu
Wed Sep 28 15:32:37 CEST 2011


Hi Martin,

Is everything resolved?

$R CMD ldd Rgraphviz/src/Rgraphviz.so
	linux-vdso.so.1 =>  (0x00007fffd7f0b000)
	libgvc.so.6 => /usr/local/lib/libgvc.so.6 (0x00002afd60706000)
	libc.so.6 => /lib64/libc.so.6 (0x00002afd609a5000)
	libxdot.so.4 => /usr/local/lib/libxdot.so.4 (0x00002afd60cfd000)
	libgraph.so.5 => /usr/local/lib/libgraph.so.5 (0x00002afd60f00000)
	libcdt.so.5 => /usr/local/lib/libcdt.so.5 (0x00002afd6110d000)
	libpathplan.so.4 => /usr/local/lib/libpathplan.so.4 (0x00002afd61312000)
	libdl.so.2 => /lib64/libdl.so.2 (0x00002afd6151a000)
	libexpat.so.0 => /lib64/libexpat.so.0 (0x00002afd6171f000)
	libz.so.1 => /usr/lib64/libz.so.1 (0x00002afd61941000)
	libm.so.6 => /lib64/libm.so.6 (0x00002afd61b55000)
	/lib64/ld-linux-x86-64.so.2 (0x000000349cc00000)

Thank you for your time.

Yours sincerely,

Jianhong Ou

jianhong.ou at umassmed.edu


On Sep 27, 2011, at 6:09 PM, Martin Morgan wrote:

> On 09/27/2011 12:48 PM, Ou, Jianhong wrote:
>> 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
> 
> I guess at this point you have the Rgraphviz.so in Rgraphviz/src. Try
> 
>  R CMD ldd Rgraphviz/src/Rgraphviz.so
> 
> to see the libraries Rgraphviz will try to link to. Everything should 
> resolve. If not it's a system configuration issue, maybe ldconfig 
> instead of LD_LIBRARY_PATH, maybe permissions on the graphviz libraries, 
> maybe full path to graphviz directory in LD_LIBRARY_PATH?
> 
> Martin
> 
>>>> 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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>>>> 
>> 
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> 
> 
> -- 
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> 
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