[GenABEL-dev] ProbABEL autotools integration branch in SVN

[Yurii Aulchenko]

Hi Lennart,

These are great news! I will study new ProbABEL with considerable interest :)

Latex - I think you are right that we should not force users to have
Latex installed. So maybe we should keep PDF as part of source; this
may be not that elegant, but is user friendly.

Best,
Yurii

On 27 Jul 2011, at 00:29, "L.C. Karssen" <l.karssen at erasmusmc.nl> wrote:

> 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
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