[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
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