Please consider free license for segemehl

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Please consider free license for segemehl

Andreas Tille-5
Hello,

I'm writing you on behalf of the Debian Med team which is a group inside
Debian with the objective to package free software in the field of
medicine and biology for official Debian.  We have assembled several
known tools which you can see on our so called biology task page[1].
Also Segemehl will show up on this page in the "Packaging has started
and developers might try the packaging code in VCS" section after about
24 hours.

Since I've got a request from my colleagues to install segemehl I also
intend to package this for Debian.  Unfortunately the licensing
information at the website and inside the code is quite sparse.  The
only hint I've found is if I call the executables it prints:

  SEGEMEHL is free software for non-commercial use
  (C) 2008 Bioinformatik Leipzig

>From a Debian point of view this is non-free since it puts a restriction
on the usage of the software.  I wonder whether you might consider some
free license like GPL, BSD or similar.

Since I had a look onto the source archive I'd like to give some
additional hints:

   1. The archive contains a file
        segemehl_0_2_0/segemehl/cscope.out
      which most probably is not intended to be distributed.
   2. It would be also great if you could strip backup files
      (*~) from the source tarball.
   3. There is an object file
        segemehl_0_2_0/segemehl/libs/remapping.o
      which also made it probably unintended into the tarball

Finally it looks unusual that you are distributing all files under
segemehl_0_2_0/segemehl instead of simply putting everything into just
segemehl_0_2_0.

If you are interested I could provide manpages for the three executables
created by the default build process.  These will be part of the Debian
package (provided you will consider a free license and we can distribute
the package inside Debian).

As a hint for a naming convention:  All three executables are ending
with ".x" which is quite unusual.  While it might be help against name
space pollution specifically for such generic names as "lack" you might
consider droping this extension in a next version.

Kind regards

       Andreas.

[1] https://blends.debian.org/med/tasks/bio

--
http://fam-tille.de

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Re: Please consider free license for segemehl

Andreas Tille-5
Hi again,

I have not yet received any response since three weeks.  I wonder
whether I was using a proper address.  It would be great if you could
comment on the license issue and I wonder whether the technical hints
I have given were helpful.

Kind regards

       Andreas.

On Mon, Jun 20, 2016 at 02:21:38PM +0200, Andreas Tille wrote:

> Hello,
>
> I'm writing you on behalf of the Debian Med team which is a group inside
> Debian with the objective to package free software in the field of
> medicine and biology for official Debian.  We have assembled several
> known tools which you can see on our so called biology task page[1].
> Also Segemehl will show up on this page in the "Packaging has started
> and developers might try the packaging code in VCS" section after about
> 24 hours.
>
> Since I've got a request from my colleagues to install segemehl I also
> intend to package this for Debian.  Unfortunately the licensing
> information at the website and inside the code is quite sparse.  The
> only hint I've found is if I call the executables it prints:
>
>   SEGEMEHL is free software for non-commercial use
>   (C) 2008 Bioinformatik Leipzig
>
> >From a Debian point of view this is non-free since it puts a restriction
> on the usage of the software.  I wonder whether you might consider some
> free license like GPL, BSD or similar.
>
> Since I had a look onto the source archive I'd like to give some
> additional hints:
>
>    1. The archive contains a file
>         segemehl_0_2_0/segemehl/cscope.out
>       which most probably is not intended to be distributed.
>    2. It would be also great if you could strip backup files
>       (*~) from the source tarball.
>    3. There is an object file
>         segemehl_0_2_0/segemehl/libs/remapping.o
>       which also made it probably unintended into the tarball
>
> Finally it looks unusual that you are distributing all files under
> segemehl_0_2_0/segemehl instead of simply putting everything into just
> segemehl_0_2_0.
>
> If you are interested I could provide manpages for the three executables
> created by the default build process.  These will be part of the Debian
> package (provided you will consider a free license and we can distribute
> the package inside Debian).
>
> As a hint for a naming convention:  All three executables are ending
> with ".x" which is quite unusual.  While it might be help against name
> space pollution specifically for such generic names as "lack" you might
> consider droping this extension in a next version.
>
> Kind regards
>
>        Andreas.
>
> [1] https://blends.debian.org/med/tasks/bio
>
> --
> http://fam-tille.de
>
>

--
http://fam-tille.de

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Re: Please consider free license for segemehl

Andreas Tille-5
Hi,

my mail might have been lost over holidays.  It would be nice to get at
least some response.

Thanks

      Andreas.

On Wed, Jul 13, 2016 at 08:47:44AM +0200, Andreas Tille wrote:

> Hi again,
>
> I have not yet received any response since three weeks.  I wonder
> whether I was using a proper address.  It would be great if you could
> comment on the license issue and I wonder whether the technical hints
> I have given were helpful.
>
> Kind regards
>
>        Andreas.
>
> On Mon, Jun 20, 2016 at 02:21:38PM +0200, Andreas Tille wrote:
> > Hello,
> >
> > I'm writing you on behalf of the Debian Med team which is a group inside
> > Debian with the objective to package free software in the field of
> > medicine and biology for official Debian.  We have assembled several
> > known tools which you can see on our so called biology task page[1].
> > Also Segemehl will show up on this page in the "Packaging has started
> > and developers might try the packaging code in VCS" section after about
> > 24 hours.
> >
> > Since I've got a request from my colleagues to install segemehl I also
> > intend to package this for Debian.  Unfortunately the licensing
> > information at the website and inside the code is quite sparse.  The
> > only hint I've found is if I call the executables it prints:
> >
> >   SEGEMEHL is free software for non-commercial use
> >   (C) 2008 Bioinformatik Leipzig
> >
> > >From a Debian point of view this is non-free since it puts a restriction
> > on the usage of the software.  I wonder whether you might consider some
> > free license like GPL, BSD or similar.
> >
> > Since I had a look onto the source archive I'd like to give some
> > additional hints:
> >
> >    1. The archive contains a file
> >         segemehl_0_2_0/segemehl/cscope.out
> >       which most probably is not intended to be distributed.
> >    2. It would be also great if you could strip backup files
> >       (*~) from the source tarball.
> >    3. There is an object file
> >         segemehl_0_2_0/segemehl/libs/remapping.o
> >       which also made it probably unintended into the tarball
> >
> > Finally it looks unusual that you are distributing all files under
> > segemehl_0_2_0/segemehl instead of simply putting everything into just
> > segemehl_0_2_0.
> >
> > If you are interested I could provide manpages for the three executables
> > created by the default build process.  These will be part of the Debian
> > package (provided you will consider a free license and we can distribute
> > the package inside Debian).
> >
> > As a hint for a naming convention:  All three executables are ending
> > with ".x" which is quite unusual.  While it might be help against name
> > space pollution specifically for such generic names as "lack" you might
> > consider droping this extension in a next version.
> >
> > Kind regards
> >
> >        Andreas.
> >
> > [1] https://blends.debian.org/med/tasks/bio
> >
> > --
> > http://fam-tille.de
> >
> >
>
> --
> http://fam-tille.de
>
>

--
http://fam-tille.de

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Re: Please consider free license for segemehl

Andreas Tille-5
Hi again,

I'd like to refresh my question about a free license for segemehl.
While the current release cycle for Debian 9 Stretch is closed it might
be interesting to integrate segemehl into the next stable Debian
release.  I guess you remember the well thought arguments from other
scientists for free source code but if you want I could assemble these
again for your kind reconsidering.

Kind regards

       Andreas.


On Wed, Aug 10, 2016 at 05:24:19PM +0200, Andreas Tille wrote:

> Hi,
>
> my mail might have been lost over holidays.  It would be nice to get at
> least some response.
>
> Thanks
>
>       Andreas.
>
> On Wed, Jul 13, 2016 at 08:47:44AM +0200, Andreas Tille wrote:
> > Hi again,
> >
> > I have not yet received any response since three weeks.  I wonder
> > whether I was using a proper address.  It would be great if you could
> > comment on the license issue and I wonder whether the technical hints
> > I have given were helpful.
> >
> > Kind regards
> >
> >        Andreas.
> >
> > On Mon, Jun 20, 2016 at 02:21:38PM +0200, Andreas Tille wrote:
> > > Hello,
> > >
> > > I'm writing you on behalf of the Debian Med team which is a group inside
> > > Debian with the objective to package free software in the field of
> > > medicine and biology for official Debian.  We have assembled several
> > > known tools which you can see on our so called biology task page[1].
> > > Also Segemehl will show up on this page in the "Packaging has started
> > > and developers might try the packaging code in VCS" section after about
> > > 24 hours.
> > >
> > > Since I've got a request from my colleagues to install segemehl I also
> > > intend to package this for Debian.  Unfortunately the licensing
> > > information at the website and inside the code is quite sparse.  The
> > > only hint I've found is if I call the executables it prints:
> > >
> > >   SEGEMEHL is free software for non-commercial use
> > >   (C) 2008 Bioinformatik Leipzig
> > >
> > > >From a Debian point of view this is non-free since it puts a restriction
> > > on the usage of the software.  I wonder whether you might consider some
> > > free license like GPL, BSD or similar.
> > >
> > > Since I had a look onto the source archive I'd like to give some
> > > additional hints:
> > >
> > >    1. The archive contains a file
> > >         segemehl_0_2_0/segemehl/cscope.out
> > >       which most probably is not intended to be distributed.
> > >    2. It would be also great if you could strip backup files
> > >       (*~) from the source tarball.
> > >    3. There is an object file
> > >         segemehl_0_2_0/segemehl/libs/remapping.o
> > >       which also made it probably unintended into the tarball
> > >
> > > Finally it looks unusual that you are distributing all files under
> > > segemehl_0_2_0/segemehl instead of simply putting everything into just
> > > segemehl_0_2_0.
> > >
> > > If you are interested I could provide manpages for the three executables
> > > created by the default build process.  These will be part of the Debian
> > > package (provided you will consider a free license and we can distribute
> > > the package inside Debian).
> > >
> > > As a hint for a naming convention:  All three executables are ending
> > > with ".x" which is quite unusual.  While it might be help against name
> > > space pollution specifically for such generic names as "lack" you might
> > > consider droping this extension in a next version.
> > >
> > > Kind regards
> > >
> > >        Andreas.
> > >
> > > [1] https://blends.debian.org/med/tasks/bio
> > >
> > > --
> > > http://fam-tille.de
> > >
> > >
> >
> > --
> > http://fam-tille.de
> >
> >
>
> --
> http://fam-tille.de
>
>

--
http://fam-tille.de

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Re: Please consider free license for segemehl

Carnë Draug
On 25 April 2017 at 12:52, Andreas Tille <[hidden email]> wrote:

> Hi again,
>
> I'd like to refresh my question about a free license for segemehl.
> While the current release cycle for Debian 9 Stretch is closed it might
> be interesting to integrate segemehl into the next stable Debian
> release.  I guess you remember the well thought arguments from other
> scientists for free source code but if you want I could assemble these
> again for your kind reconsidering.
>
> Kind regards
>
>        Andreas.

But segemehl is linked to the GNU Scientific Library which is GPL.
Can it even be non-free software?

Carnë

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Re: Please consider free license for segemehl

Steve Hoffmann
Dear Carnë,

we will soon release a new, officially GPLed version.

I will keep you updated!

Thank you very much
Steve

> Am 25.04.2017 um 14:03 schrieb Carnë Draug <[hidden email]>:
>
> On 25 April 2017 at 12:52, Andreas Tille <[hidden email]> wrote:
>> Hi again,
>>
>> I'd like to refresh my question about a free license for segemehl.
>> While the current release cycle for Debian 9 Stretch is closed it might
>> be interesting to integrate segemehl into the next stable Debian
>> release.  I guess you remember the well thought arguments from other
>> scientists for free source code but if you want I could assemble these
>> again for your kind reconsidering.
>>
>> Kind regards
>>
>>       Andreas.
>
> But segemehl is linked to the GNU Scientific Library which is GPL.
> Can it even be non-free software?
>
> Carnë

--
Dr. Steve Hoffmann

Transcriptome Bioinformatics
LIFE Research Complex
University Leipzig

Haertelstrasse 16-18
04107 Leipzig

Phone: +49 341 97 16 711
Fax:   +49 341 97 16 679
skype: steve_hoffmann

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Re: Please consider free license for segemehl

Andreas Tille-5
In reply to this post by Carnë Draug
Hi Carnë,

On Tue, Apr 25, 2017 at 01:03:34PM +0100, Carnë Draug wrote:

> On 25 April 2017 at 12:52, Andreas Tille <[hidden email]> wrote:
> > Hi again,
> >
> > I'd like to refresh my question about a free license for segemehl.
> > While the current release cycle for Debian 9 Stretch is closed it might
> > be interesting to integrate segemehl into the next stable Debian
> > release.  I guess you remember the well thought arguments from other
> > scientists for free source code but if you want I could assemble these
> > again for your kind reconsidering.
>
> But segemehl is linked to the GNU Scientific Library which is GPL.
> Can it even be non-free software?

Good catch.  At least the haarz.x target needs GSL.  While haarz.x is not
build in the default target I tried this and it has shown that it does
not even build with recent libgsl-dev 2.3:

segemehl/segemehl(master) $ make haarz.x
gcc -Wall -pedantic -std=c99 -g -O3 -DFIXINSMALL -DFIXINBACKSPLICE -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Isrc -Ilibs -Ilibs/sufarray -Lsrc   -c -o libs/splines.o libs/splines.c
gcc -Wall -pedantic -std=c99 -g -O3 -DFIXINSMALL -DFIXINBACKSPLICE -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Isrc -Ilibs -Ilibs/sufarray -Lsrc   -c -o libs/snvsplines.o libs/snvsplines.c
libs/snvsplines.c: In function ‘getcutoff’:
libs/snvsplines.c:196:5: error: too many arguments to function ‘gsl_bspline_deriv_eval’
     gsl_bspline_deriv_eval(xi, 0, dB, fit.bw, dbw);
     ^~~~~~~~~~~~~~~~~~~~~~
In file included from libs/splines.h:18:0,
                 from libs/snvsplines.c:37:
/usr/include/gsl/gsl_bspline.h:107:1: note: declared here
 gsl_bspline_deriv_eval(const double x,
 ^~~~~~~~~~~~~~~~~~~~~~
libs/snvsplines.c:213:5: error: too many arguments to function ‘gsl_bspline_deriv_eval’
     gsl_bspline_deriv_eval(xi, 2, dB, fit.bw, dbw);
     ^~~~~~~~~~~~~~~~~~~~~~
...


I'm not sure in how far it is legal to ship code depending from GPL
software if this is not part of the default build.

Its an interesting argument to free the code to enable people making it
compatible to latest GSL anyway.

Kind regards

      Andreas.

Carnë, you can find some preliminary packaging here:

[1] https://anonscm.debian.org/git/debian-med/segemehl.git

--
http://fam-tille.de

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Re: Please consider free license for segemehl

Andreas Tille-5
In reply to this post by Steve Hoffmann
Dear Steve,

cool, thanks a lot

      Andreas.

On Tue, Apr 25, 2017 at 02:17:34PM +0200, Steve Hoffmann wrote:

> Dear Carnë,
>
> we will soon release a new, officially GPLed version.
>
> I will keep you updated!
>
> Thank you very much
> Steve
>
> > Am 25.04.2017 um 14:03 schrieb Carnë Draug <[hidden email]>:
> >
> > On 25 April 2017 at 12:52, Andreas Tille <[hidden email]> wrote:
> >> Hi again,
> >>
> >> I'd like to refresh my question about a free license for segemehl.
> >> While the current release cycle for Debian 9 Stretch is closed it might
> >> be interesting to integrate segemehl into the next stable Debian
> >> release.  I guess you remember the well thought arguments from other
> >> scientists for free source code but if you want I could assemble these
> >> again for your kind reconsidering.
> >>
> >> Kind regards
> >>
> >>       Andreas.
> >
> > But segemehl is linked to the GNU Scientific Library which is GPL.
> > Can it even be non-free software?
> >
> > Carnë
>
> --
> Dr. Steve Hoffmann
>
> Transcriptome Bioinformatics
> LIFE Research Complex
> University Leipzig
>
> Haertelstrasse 16-18
> 04107 Leipzig
>
> Phone: +49 341 97 16 711
> Fax:   +49 341 97 16 679
> skype: steve_hoffmann
>
>

--
http://fam-tille.de

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Re: Please consider free license for segemehl

Andreas Tille-5
In reply to this post by Steve Hoffmann
Hi Steve,

any news about the new release?

Kind regards

       Andreas.

On Tue, Apr 25, 2017 at 02:17:34PM +0200, Steve Hoffmann wrote:

> Dear Carnë,
>
> we will soon release a new, officially GPLed version.
>
> I will keep you updated!
>
> Thank you very much
> Steve
>
> > Am 25.04.2017 um 14:03 schrieb Carnë Draug <[hidden email]>:
> >
> > On 25 April 2017 at 12:52, Andreas Tille <[hidden email]> wrote:
> >> Hi again,
> >>
> >> I'd like to refresh my question about a free license for segemehl.
> >> While the current release cycle for Debian 9 Stretch is closed it might
> >> be interesting to integrate segemehl into the next stable Debian
> >> release.  I guess you remember the well thought arguments from other
> >> scientists for free source code but if you want I could assemble these
> >> again for your kind reconsidering.
> >>
> >> Kind regards
> >>
> >>       Andreas.
> >
> > But segemehl is linked to the GNU Scientific Library which is GPL.
> > Can it even be non-free software?
> >
> > Carnë
>
> --
> Dr. Steve Hoffmann
>
> Transcriptome Bioinformatics
> LIFE Research Complex
> University Leipzig
>
> Haertelstrasse 16-18
> 04107 Leipzig
>
> Phone: +49 341 97 16 711
> Fax:   +49 341 97 16 679
> skype: steve_hoffmann
>
>

--
http://fam-tille.de