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

7 messages · Byron Ellis, Robert Gentleman, Jeff Gentry +1 more

Original

1

7

Byron Ellis

Mon, Nov 21, 2005 6:35 PM #

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

Robert Gentleman

Mon, Nov 21, 2005 6:46 PM #

Hi,
  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,
   Robert

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
206-667-7700
rgentlem at fhcrc.org

Byron Ellis

Mon, Nov 21, 2005 7:23 PM #

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

Xinan Yang

Tue, Nov 22, 2005 7:21 AM #

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:

Jeff Gentry

Tue, Nov 22, 2005 7:38 AM #

Why do you think that setting environment vars in one shell will carry
over to another automagically?  You need to include them in your shell's
init scripts (e.g. .bashrc/.bash_profile, etc) for them to be universal
like that.

Xinan Yang

Tue, Nov 22, 2005 8:13 AM #

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

Xinan Yang

Tue, Nov 22, 2005 9:13 AM #

Hi Ellis,

I tried the graphviz-2.6.0, the default installed path is still 
"/usr/local/lib/graphviz". and the worse is Rgraphviz-1.8.0 "unable to 
load shared library '/usr/local/lib/R/library/ 
Rgraphviz/libs/Rgraphviz.so': " again.

Then I re-tried graphviz-2.2 as mentioned in last email, it works, but 
need to type the path for R.
Where is the deault path for graphviz as Rgraphviz looks for?

need more help to simplify that.


xinan

Byron Ellis wrote: