[BioC] installing Rgraphviz under CentOS 5.6

[Ou, Jianhong]

Hi Martin,

Thans a lots. You are right. The problem is that a system configuration issue. When I tried

sudo LD_LIBRARY_PATH=/usr/lib:/usr/local/lib R CMD INSTALL Rgraphviz_1.30.1.tar.gz

It works well. However, I should use 

LD_LIBRARY_PATH=/usr/lib:/usr/local/lib R

before I load the Rgraphviz package everytime.

I will fix this latter.

Thank you very much for your help.

Yours sincerely,

Jianhong Ou

jianhong.ou at umassmed.edu


On Sep 28, 2011, at 1:22 PM, Martin Morgan wrote:

> On 09/28/2011 09:35 AM, Ou, Jianhong wrote:
>> Here is the output,
>> 
>> $dot -V
>> dot - graphviz version 2.28.0 (20110621.2140)
>> 
>> $ dot -otestfile
>> graph graphname{
>> 	a -- b -- c;
>> 	b -- d;
>> }
>> graph graphname {
>> 	node [label="\N"];
>> 	graph [bb="0,0,126,180"];
>> 	a [pos="63,162", width="0.75", height="0.5"];
>> 	b [pos="63,90", width="0.75", height="0.5"];
>> 	c [pos="27,18", width="0.75", height="0.5"];
>> 	d [pos="99,18", width="0.75", height="0.5"];
>> 	a -- b [pos="63,143.7 63,132.85 63,118.92 63,108.1"];
>> 	b -- c [pos="54.65,72.765 48.835,61.456 41.11,46.437 35.304,35.147"];
>> 	b -- d [pos="71.35,72.765 77.165,61.456 84.89,46.437 90.696,35.147"];
>> }
>> 
>> 
>> Yours sincerely,
> 
> I'm really just guess at this point; what about
> 
>    sudo R CMD ldd -r
> 
> for Rgraphviz.so and the libraries that are causing problems?
> 
>> 
>> Jianhong Ou
>> 
>> jianhong.ou at umassmed.edu
>> 
>> 
>> On Sep 28, 2011, at 12:14 PM, Martin Morgan wrote:
>> 
>>> On 09/28/2011 06:53 AM, Ou, Jianhong wrote:
>>>> $ R CMD ldd /usr/local/lib/libgvc.so.6
>>>> 	linux-vdso.so.1 =>    (0x00007fff173fc000)
>>>> 	libxdot.so.4 =>   /usr/local/lib/libxdot.so.4 (0x00002b5c100e0000)
>>>> 	libgraph.so.5 =>   /usr/local/lib/libgraph.so.5 (0x00002b5c102e4000)
>>>> 	libcdt.so.5 =>   /usr/local/lib/libcdt.so.5 (0x00002b5c104f0000)
>>>> 	libpathplan.so.4 =>   /usr/local/lib/libpathplan.so.4 (0x00002b5c106f5000)
>>>> 	libdl.so.2 =>   /lib64/libdl.so.2 (0x00002b5c10914000)
>>>> 	libexpat.so.0 =>   /lib64/libexpat.so.0 (0x00002b5c10b18000)
>>>> 	libz.so.1 =>   /usr/lib64/libz.so.1 (0x00002b5c10d3a000)
>>>> 	libm.so.6 =>   /lib64/libm.so.6 (0x00002b5c10f4f000)
>>>> 	libc.so.6 =>   /lib64/libc.so.6 (0x00002b5c111d2000)
>>>> 	/lib64/ld-linux-x86-64.so.2 (0x000000349cc00000)
>>>> $ ls -l /usr/local/lib/libgvc.so.6
>>>> lrwxrwxrwx 1 root root 15 Jun 22 11:55 /usr/local/lib/libgvc.so.6 ->   libgvc.so.6.0.0
>>>> 
>>>> Is that mean I should reinstall the graphiv?
>>> 
>>> too hard to tell; sort of looks like you have 64 bit R, 32 bit graphviz
>>> and you want 64 bit of each. Does graphviz actually work, e.g.,
>>> 
>>>    dot --version
>>> 
>>> ? It does not help to truncate the email; I am intentionally not
>>> replying to the list to avoid confusing any final resolution. Martin
>>> 
>>>> 
>>>> Yours sincerely,
>>>> 
>>>> Jianhong Ou
>>>> 
>>>> jianhong.ou at umassmed.edu
>>>> 
>>>> 
>>>> On Sep 28, 2011, at 9:49 AM, Martin Morgan wrote:
>>>> 
>>>>> ls -l /usr/local/lib/libgvc.so.6
>>>> 
>>>> 
>>> 
>>> 
>>> --
>>> Computational Biology
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>>> 
>>> Location: M1-B861
>>> Telephone: 206 667-2793
>> 
>> 
> 
> 
> -- 
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> 
> Location: M1-B861
> Telephone: 206 667-2793