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

[xinan yang]

Hi Robert and Byron,

Thanks for your prompt reply.  It seems work  using "sudo make install" !
because, in the shell, it "R CMD INSTALL" works, which did not work before:

%whereis graphviz
graphviz: /usr/local/lib/graphviz

%export LD_LIBRARY_PATH=/usr/local/lib/graphviz
%R CMD REMOVE Rgraphviz
% R CMD INSTALL Rgraphviz

Then I can load the package.


But , after open a new shell, it still doesn"t work!
%R
 > 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'
 > 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"

other attached packages:
   graph    Ruuid  cluster
 "1.8.0"  "1.5.3" "1.10.2"


I must re-type "export LD_LIBRARY_PATH=/usr/local/lib/graphviz" to let 
it works!


BTW,
What should I do if I want to update the graphviz-2.2 to graphviz 2.6?
Simply download the graphviz-2.2.0, then "./configure","make","sudo make 
install" in the directory of graphviz-2.6?
Should I uninstall the previous one?

The same question for R, How to install R-2.2.0 while keep the old version?


Thanks!

Xinan



Byron Ellis wrote:

> You probably didn't properly install graphviz since it clearly can't  
> find libneato (which is part of graphviz). If you really did 'make  
> install' you probably want to 'sudo make install' to put them in /usr/ 
> local/lib (unless you did something weird to your prefix, which can  
> also happen).
>
> On Nov 22, 2005, at 7:21 AM, 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
>>>
>>
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> ---
> Byron Ellis (ellis at stat.harvard.edu)
> "Oook" -- The Librarian
>
>
>