[Bioc-devel] [BioC] Bioconductor1.6(Rgraphviz etc.) install problem with red hat9.0

Robert Gentleman rgentlem at fhcrc.org
Tue Nov 22 03:46:46 CET 2005

  I think Byron is essentially right, and his advice will almost surely 
fix your problem. You might also try and set your LD_LIBRARY path (there 
seems to be some sort of disconnect between your building of Rgraphviz 
and your running of R, possibly these are done from different accounts 
and the right libraries are not being found?)

  And, also Rgraphviz has a configure script and you should be able to 
use the --with-graphviz flag. Please see the R Extensions manual for 
more details on how that works.

  Best wishes,

xinan yang wrote:
> Hi Robert,
> You are right, the package GDD is not necessary.
> But the package Rgraphviz stilol doesn"t work, even after I reinstalling 
> everything.
> I have download the graphviz-2.6.tar.gz
> after typing:
> $ tar -xvfz graphviz......
> $ cd graphviz-2.6
> $./configure
> $make
> $make check
> $make install
> Now, in R:
>  > sessionInfo()
> R version 2.2.0, 2005-10-06, i686-pc-linux-gnu
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "base"
>  > library(Rgraphviz)
> Loading required package: graph
> Loading required package: cluster
> Loading required package: Ruuid
> Creating a new generic function for 'print' in 'Ruuid'
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>        unable to load shared library 
> '/usr/local/lib/R/library/Rgraphviz/libs/Rgraphviz.so':
>  libdotneato.so.0: cannot open shared object file: No such file or 
> directory
> Error: .onLoad failed in 'loadNamespace' for 'Rgraphviz'
> Error: package/namespace load failed for 'Rgraphviz'
> But it is there:
> $ cd /usr/local/lib/R/library/Rgraphviz/libs/
> $ ls -al
> total 108
> drwxr-xr-x    2 root     root         4096 Nov 21 16:24 .
> drwxr-xr-x   12 root     root         4096 Nov 21 16:24 ..
> -rwxr-xr-x    1 root     root        94257 Nov 21 16:24 Rgraphviz.so
> What was wrong?
> xinan
> Robert Gentleman wrote:
>> Hi,
>>  Your problems are with missing redhat libraries, and those are the 
>> folks who are going to have to help you. This does not really have 
>> much to do with Bioconductor, except in  the fact that it uses these 
>> libraries and you do not have them installed.
>> xnyang at seu.edu.cn wrote:
>>> Hello all,
>>> I want to install the R-2.1.1 and bioconductor 1.6 in Redhat 9.0,
>>> The problems are:
>>> 1) after downloaded the R-2.1.1 packages, and % tar -xvfz, and % cd 
>>> R-2.1.1
>>>    I did % ./configure
>>   I don't know what packages you downloaded, for BioC, please read the 
>> manual page as we describe pretty clearly the recommended way to 
>> install Bioconductor. But many (and certainly all the ones you have 
>> had problems with, require other libraries to be installed).
>>   The errors below have to do with a package named GDD, I am not sure 
>> why you are attempting to install it. But it relies on the gd library, 
>> so that is the place to start. Google can often be of some help, as 
>> can the R mailing list archive.
>>  If you want Rgraphviz, then you will need to install graphviz from 
>> ATT, and make sure that you install a "developer version" as you will 
>> need header files (that is the case with almost all RedHat packages, 
>> you need to make sure the header files are installed, and in the 
>> RedHat world, that often means installing a developer version - but I 
>> have not used RedHat in years).
>>  best wishes
>>    Robert

Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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