R SIG Debian - Feb 2010 - A newbee problem compiling R in ubuntu.

Dear R users:

Maybe it is a silly question, but I'm don't understand what am I doing
wrong (I make the same steps, and it works).

In a new karmik koala ubuntu installation I compile the last patched
2.10.1 version of R (r51070).

Every thing was right (I install all the dev libraries I need).

First I type:

./configure  --enable-R-shlib

And I obtain:

R is now configured for i686-pc-linux-gnu  Source directory:          .
Installation directory:    /usr/local
C compiler:                gcc -std=gnu99  -g -O2
Fortran 77 compiler:       gfortran  -g -O2
C++ compiler:              g++  -g -O2
Fortran 90/95 compiler:    gfortran -g -O2
Obj-C compiler:         gcc -g -O2
Interfaces supported:      X11, tcltk
External libraries:        readline, ICU
Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo
Options enabled:           shared R library, shared BLAS, R profiling,
Java
  Recommended packages:      yes


Then I type "make", 
following with:
sudo make install.

Then when I try to call R it shows me this message:

Fatal error: unable to open the base package

But if I work as superuser, like "sudo R", everything works fine.

I understand that it is a privileges issue, but where and how can I fix
the problem?

Thank you for your help.

Sorry for the newbee question.

Kenneth

On 31 January 2010 at 23:02, Kenneth Roy Cabrera Torres wrote:
| Dear R users:
| 
| Maybe it is a silly question, but I'm don't understand what am I doing
| wrong (I make the same steps, and it works).

Here is a simple suggestion:  go to 

     http://cran.r-project.org/bin/linux/ubuntu/

and read how to obtain pre-built current binaries for your Ubuntu system.

| In a new karmik koala ubuntu installation I compile the last patched
| 2.10.1 version of R (r51070).
| 
| Every thing was right (I install all the dev libraries I need).
| 
| First I type:
| 
| ./configure  --enable-R-shlib

We use more configuration that that so our packages are more complete.
 
| And I obtain:
| 
| R is now configured for i686-pc-linux-gnu  Source directory:          .
| Installation directory:    /usr/local
| C compiler:                gcc -std=gnu99  -g -O2
| Fortran 77 compiler:       gfortran  -g -O2
| C++ compiler:              g++  -g -O2
| Fortran 90/95 compiler:    gfortran -g -O2
| Obj-C compiler:         gcc -g -O2
| Interfaces supported:      X11, tcltk
| External libraries:        readline, ICU
| Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo
| Options enabled:           shared R library, shared BLAS, R profiling,
| Java
|   Recommended packages:      yes

Looks fine, though we end with better BLAS support, profiling support, ...

  Source directory:          .
  Installation directory:    /usr

  C compiler:                gcc -std=gnu99  -g -O2
  Fortran 77 compiler:       gfortran  -g -O2

  C++ compiler:              g++  -g -O2
  Fortran 90/95 compiler:    gfortran -g -O2
  Obj-C compiler:	      

  Interfaces supported:      X11, tcltk
  External libraries:        readline, BLAS(generic), LAPACK(generic)
  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo
  Options enabled:           shared R library, R profiling, memory profiling,
Java

  Recommended packages:      no

| Then I type "make", 
| following with:
| sudo make install.
| 
| Then when I try to call R it shows me this message:
| 
| Fatal error: unable to open the base package
| 
| But if I work as superuser, like "sudo R", everything works fine.
| 
| I understand that it is a privileges issue, but where and how can I fix
| the problem?

That is close to impossible to say based on the information you provided.
Some files must have gotten root access when you meant to have only user
access.  You could use a tool like strace to see exactly where the access
fails.

Or you can simply take advantage of the fact that others have volunteered to
provide you with timely updates of proper packages you could use.  Your pick.

Dirk
 
| Thank you for your help.
| 
| Sorry for the newbee question.
| 
| Kenneth
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
Three out of two people have difficulties with fractions.

Thank you Mr. Dirk Eddelbuettel:
> Here is a simple suggestion:  go to 
> 
>      http://cran.r-project.org/bin/linux/ubuntu/
> 
> and read how to obtain pre-built current binaries for your Ubuntu system.
I got the ubuntu repositorie and I "sudo aptitude install" all the R
related files...

But still the problem.
> | 
> | Then when I try to call R it shows me this message:
> | 
> | Fatal error: unable to open the base package
> | 
> | But if I work as superuser, like "sudo R", everything works
fine.
> | 
> | I understand that it is a privileges issue, but where and how can I fix
> | the problem?
> 
> That is close to impossible to say based on the information you provided.
> Some files must have gotten root access when you meant to have only user
> access.  You could use a tool like strace to see exactly where the access
> fails.
I try the precompiled version, but I still have the problem...

With "strace" I got a very large output... where do I look for to see
the problem?

Thank you for your help

On Sun, Jan 31, 2010 at 10:02 PM, Kenneth Roy Cabrera Torres
<krcabrer at une.net.co> wrote:
> Dear R users:
>
> Maybe it is a silly question, but I'm don't understand what am I
doing
> wrong (I make the same steps, and it works).
>
> In a new karmik koala ubuntu installation I compile the last patched
> 2.10.1 version of R (r51070).
>
> Every thing was right (I install all the dev libraries I need).
>
> First I type:
>
> ./configure ?--enable-R-shlib
>
> And I obtain:
>

Dear Kenneth:

Let me share you a handy thing I learned. You can get the commands
that the R packages are built with, along with the source code.  Make
a directory (this will download a bunch of stuff)

apt-get source r-base-core

that should download a tarball of original R source code, a diff file
that is applied to build R deb, and it will open the code and apply
the diff.  You can look inside the directory, in a subdirectory
"debian", where the configure files that control package building are
kept.

If you type "dpkg-buildpackage -rfakeroot"  in the directory where all
that stuff got opened up (the one "above" the debian subdirectory), it
will build the debian packages.  It would not be an incredibly
difficult thing to replace that R source package with the new one you
want to use.  But I don't think you need to.  Just look in the rules
file under debian subdirectory, you will see the configure statement
they use.  I think in there you'll also find information about what
devel packages they assume you have.

I find it to be a little difficult to revise debian builds, so I don't
really mean you ought to do that. But you could.  And I often have!


-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas