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

xinan yang xnyang at seu.edu.cn
Tue Nov 22 16:21:56 CET 2005

Hi Robert,

You are right, the package GDD is not necessary.
But the package Rgraphviz stilol doesn"t work, even after I reinstalling 

I have download the graphviz-2.6.tar.gz
after typing:
$ tar -xvfz graphviz......
$ cd graphviz-2.6
$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 
  libdotneato.so.0: cannot open shared object file: No such file or 
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?


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

More information about the Bioc-devel mailing list