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Topic: R myDSL effort - dependancy problem

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Doofer

Group: Members
Posts: 12
Joined: Mar. 2005

Posted: Mar. 15 2005,20:16

I'd really like R (GPL stats package - yes, you can google on 'r'... which is cool...) as a myDSL extension. I've tried installing it, but apt-get gives a perl dependancy error, and downloading and dpkg-ing kicks up a long list of unmet dependencies.

However, before I beetle off and bloat my DSL distro with loads of libs, I note that the myDSL extension for Octave seems to work fine, despite needing many of the same libraries as R.

R is to SPSS or SPLUS what Octave is to Matlab. It's about my being able to show my colleagues that DSL is a realistic working environment they can carry with them, rather than a curio for computer freaks. I already have my students learning stats with R... blazing the GPL/non-Gates trail here, even if my linux skills are limited...

mikshaw

Group: Members
Posts: 4856
Joined: July 2004

Posted: Mar. 15 2005,21:05

My guess is that the Octave extension was created by first installing all dependencies, then Octave, and then the deps would have been included in the extension.

--------------
http://www.tldp.org/LDP/intro-linux/html/index.html

clacker

Group: Members
Posts: 570
Joined: June 2004

Posted: Mar. 16 2005,01:10

Doofer, I was able to install R from debian by using apt-get (/etc/apt/sources.list set to unstable) but running from the liveCD I had to remove two links and replace them with copies before I started. I had to run the following as root before I ran apt-get install r-base:

Code Sample

rm /etc/ld.so.conf
rm /etc/ld.so.cache
cp /KNOPPIX/etc/ld.so.conf /etc/ld.so.conf
cp /KNOPPIX/etc/ld.so.cache /etc/ld.so.cache

I was able to make a dsl file (24 megs). perl is newer than the version in GTK2.dsl, and that download is 15 megs where only 5 is perl. The version of tcltk is newer than the version in the repository so I couldn't use those either.

What I need help on, and then I can upload this dsl, is creating a script that runs ldconfig. I don't want to overwrite anyone's files, but I do need to run ldconfig to add the atlas library. Here is what I have so far, but it doesn't work. My first if statement is flawed but I don't know how to write it correctly:

Code Sample

#!/bin/bash
#
# an example of getting around ld.so.cache and ld.so.conf problems
#
# check first to see if your files are already in the ld.so.conf
# this will avoid duplicate entries
#
# test for atlas being installed already
#
if true
###### if grep /usr/lib/atlas /etc/ld.so.conf > /dev/null ### failed, why???
then
echo it's already loaded # assume it went well before and exit
else
echo it wasn't there
if [ -L /etc/ld.so.cache ] # if it's a symbolic link, we need to replace it with a real file
then
echo it was a symbolic link
sudo rm -f /etc/ld.so.cache
sudo cp /KNOPPIX/etc/ld.so.cache /etc/ld.so.cache
fi
cat /etc/ld.so.conf > /home/dsl/tmpconfig
echo /usr/lib/atlas >> /home/dsl/tmpconfig
sudo ldconfig -f /home/dsl/tmpconfig
rm tmpconfig
fi
exit

I thought

if grep word file
then
echo true
else
echo false
fi

was a valid statement. Can some one show me the way? All I want to do is get a writable ld.so.cache and the use ldconfig to write to it. I can't believe I'm so close and then getting closelined by an if statement.

cbagger01

Group: Members
Posts: 4264
Joined: Oct. 2003

Posted: Mar. 16 2005,04:56

Try this:

Code Sample

if test `grep word file -c` -ge 1
then
echo true
else
echo false
fi

aesenadorjr Offline

Group: Members
Posts: 11
Joined: Feb. 2005

Posted: Mar. 16 2005,05:01

I was able to make a R.uci file, but the process I used made it impossible to share the file because I had to remaster DSL to include gcc, g77, g++, make, binutils, libncurses-dev, and libreadline-dev (following meo's procedures, see posts). I downloaded the R source tarball from the R-CRAN site and compiled it afterwards. Note that I did not need to have Perl as this was used only for compiling the man/info/html docs. Unfortunately, the libraries I obtained by apt-get install was from the testing branch and is newer than the ones in the original DSL liveCD. I tested my R.uci to confirm that it works with my remastered DSL and not work on the original.

One other thing. So, clacker, how did you do the Octave.tar.gz? Using apt-get? I was not successful in this, so I had to remaster DSL. I originally thought you compiled it from source because you also made that very nice gcc dsl.

32 replies since Mar. 15 2005,20:16

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Damn Small Linux Board » MyDSL Extensions » myDSL Extensions (deprecated) » R myDSL effort - dependancy problem