[GenABEL-dev] ProbABEL autotools integration branch in SVN

[L.C. Karssen]

Dear list,

I've just committed rev. 755 to SVN in which I merged the ProbABEL
autotools branch back into trunk. So as of now the directory
pkg/ProbABEL contains the changes that were made in the
autotools-integration branch. 

The main work on autoconf and automake integration for ProbABEL is now
done. From now on we can almost (see note below) simply run
./configure
make
make install 
from the ProbABEL directory. In order to make a tar.gz file for
distribution use:
./configure
make distcheck 
and for windows I guess we should run 
make dist-zip

The 'almost' I referred to earlier relates to the doc directory. At this
moment there is no automake Makefile.am yet for that directory. There
are two reasons for that:
1) I'm not yet sure how to go about this. As far as I know there is no
automake support for LaTeX to PDF yet. However, I think I could put the
old Makefile rules in there with a little tweaking to make it work
2) If we follow 1) and don't store the pdf in SVN, we force all users
who want to install ProbABEL to have a functioning LaTeX install
(./configure doesn't check for this AFAIK). I don't think we want to add
LaTeX to the ProbABEL dependencies.
Any suggestions on this issue is much appreciated. 

In the mean time, to generate the documentation simply run the following
before running ./configure:
cd doc
make
make clean-doc
cd ..
This will result in the PDF, which will then be incorporated in the
tar.gz file when running 
make distcheck. 

If you're testing ./configure etc. in the ProbABEL SVN dir and make some
changes, don't forget to run 
make distclean 
before committing the changes. This removes any leftover intermediate
files (that should not end up in the repo). Also, to remove the PDF from
the doc directory run
cd doc
make clean
cd ..


Don't hesitate to contact me in case you have questions. And for those
who want to try to make .deb, .rpm or .tgz packages: go ahead and let me
know if it works!

Lennart.


On ma, 2011-06-27 at 19:28 +0200, L.C. Karssen wrote:
> Dear list,
> 
> Those of you that keep an eye on the SVN repo have noticed that I've
> added a branch called ProbABEL/autotools-integration. In that branch I'm
> trying to convert the ProbABEL package to use autoconf and automake. The
> reasons for this change are:
> - most (dare I say 'advanced' here?) Linux/Unix users are used to the
> sequence of ./configure; make; make install when compiling and
> installing software.
> - it makes ProbABEL conform (more) to the GNU coding standards, and as a
> result
> - it is easier to package ProbABEL for various distributions
> (e.g. .deb, .rpm, .tgz)
> - I've been wanting to lean how to use autoconf and automake for some
> time, and ProbABEL seems to be a nice (although slightly complex)
> project to started with. 
> 
> At the moment I've got most of it working: 
> - palinear and palogist are compiled and installed in PREFIX/bin
> - the examples are copied to PREFIX/usr/share/ProbABEL/examples/
> - documentation is copied to PREFIX/usr/share/doc/
> - the probabel_config.cfg file is copied to PREFIX/etc/
> 
> What isn't working yet is:
> - the PDF is not automatically generated from the .tex file. I still use
> the old Makefile in the doc/ directory for that. 
> - I didn't test how this all works for the Windows build
> - pacoxph doesn't compile. It gives this error:
> pacoxph-main.o: In function `coxph_reg::estimate(coxph_data&, int, int,
> double, double, int, int, int, bool, int)':
> /home/lennart/ErasmusMC/R-dev/ABEL-total/branches/ProbABEL/autotools-integration/ProbABEL/src/reg1.h:884: undefined reference to `coxfit2(int*, int*, int*, double*, int*, double*, double*, double*, int*, double*, double*, double*, double*, double*, int*, double*, double*, double*, double*)'
> collect2: ld returned 1 exit status
> 
> even though the function definition seems to be available in reg1.h
> itself... I'll have to look into that. 
> 
> Any help is appreciated! Also if you've got more experience with
> autoconf/automake I'd like to hear your comments.
> 
> 
> 
> Regards,
> 
> Lennart.
> 
> 
> _______________________________________________
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-- 
-----------------------------------------------
L.C. Karssen
Erasmus MC
Department of Epidemiology
Room Ee 2224

Postbus 2040
3000 CA Rotterdam
The Netherlands

phone: +31-10-7044217
fax: +31-10-7044657
e-mail: l.karssen at erasmusmc.nl
GPG key ID: 0E1D39E3
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