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

[Byron Ellis]

Yes, you've chosen to install graphviz in a place not specified in  
the default library path so you need to set an environment variable.  
Why is this a surprise?

On Nov 22, 2005, at 8:13 AM, xinan yang wrote:

> 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
>>
>>
>>
>

---
Byron Ellis (ellis at stat.harvard.edu)
"Oook" -- The Librarian