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Old 05-21-2010, 07:00 AM
Charles Plessy
 
Default Packaging Gzstream?

Dear all,

I am interested in a set of programs, the ‘BEDtools’, whose source includes a
convenience copy of the gzstream library.

http://bedtools.googlecode.com
http://www.cs.unc.edu/Research/compgeom/gzstream/

A quick apt-file search indicates that at least two other packages (CCed) may
be using the gzstream library, k3d and freecad. So it seems that it would
make sense to package the gzstream library separately.

But I notice that this library has not been updated since 2003, and obviously,
if only two programs in Debian are using it, there may be a more suitable
alternative, that would be worth suggesting to the authors of BEDtools.

Does anybody has a good recommendation to replace gzstream by something more
“mainstream” without too much work? If not, are there volunteers to co-maintain
gzstream in Debian (it looks simple, but since I am not a C programmer, I am
not comfortable with library packaging).

Have a nice day,

--
Charles Plessy
Debian Med packaging team
Tsurumi, Kanagawa, Japan


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Old 05-21-2010, 08:37 AM
RoboTux
 
Default Packaging Gzstream?

Le vendredi 21 mai 2010 09:00:56, Charles Plessy a écrit :
> Dear all,
>
> I am interested in a set of programs, the ‘BEDtools’, whose source includes
> a convenience copy of the gzstream library.
>
> http://bedtools.googlecode.com
> http://www.cs.unc.edu/Research/compgeom/gzstream/
>
> A quick apt-file search indicates that at least two other packages (CCed)
> may be using the gzstream library, k3d and freecad. So it seems that it
> would make sense to package the gzstream library separately.
>
> But I notice that this library has not been updated since 2003, and
> obviously, if only two programs in Debian are using it, there may be a
> more suitable alternative, that would be worth suggesting to the authors
> of BEDtools.

I found this http://www.codeproject.com/KB/stl/zipstream.aspx and there are
other alternatives listed here http://www.zlib.net/apps.gz.html but I don't
know if they are as convenient as gzstream for C++.
>
> Does anybody has a good recommendation to replace gzstream by something
> more “mainstream” without too much work? If not, are there volunteers to
> co-maintain gzstream in Debian (it looks simple, but since I am not a C
> programmer, I am not comfortable with library packaging).
I'm up to co-maintain it with you but I'm not DD so you would be my sponsor
for that particular package. Let me know if this is ok for you.
>
> Have a nice day,

Best regards.
 
Old 05-21-2010, 08:58 AM
Adam Borowski
 
Default Packaging Gzstream?

On Fri, May 21, 2010 at 04:00:56PM +0900, Charles Plessy wrote:
> Dear all,
>
> I am interested in a set of programs, the ‘BEDtools’, whose source includes a
> convenience copy of the gzstream library.
>
> http://bedtools.googlecode.com
> http://www.cs.unc.edu/Research/compgeom/gzstream/
>
> A quick apt-file search indicates that at least two other packages (CCed) may
> be using the gzstream library, k3d and freecad. So it seems that it would
> make sense to package the gzstream library separately.

It appears to be just a single file less than four pages long. It does
nothing but translate zlib's API to C++ iostream API. While generally
avoiding duplicated code is a very good idea, it doesn't have to be done
with any small snippet. Heck, I've written three zlib wrappers myself (two
of them had bzip2 support as well), and it never came to me that it's a task
big enough to be worth a whole library.

But then, many other simple bindings like this one have packages of their own.

> But I notice that this library has not been updated since 2003, and obviously,
> if only two programs in Debian are using it, there may be a more suitable
> alternative, that would be worth suggesting to the authors of BEDtools.

Uhm, what for? zlib's API doesn't change, iostream is set in stone by the
language standard. This tiny library isn't stagnant, it's finished. You
don't need to update code unless either of the APIs change, some new
features are needed or a bug is found.

--
1KB // Microsoft corollary to Hanlon's razor:
// Never attribute to stupidity what can be
// adequately explained by malice.


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Old 05-21-2010, 09:48 AM
Mathieu Malaterre
 
Default Packaging Gzstream?

On Fri, May 21, 2010 at 9:00 AM, Charles Plessy <plessy@debian.org> wrote:
> Dear all,
>
> I am interested in a set of programs, the ‘BEDtools’, whose source includes a
> convenience copy of the gzstream library.
>
> http://bedtools.googlecode.com
> http://www.cs.unc.edu/Research/compgeom/gzstream/
>
> A quick apt-file search indicates that at least two other packages (CCed) may
> be using the gzstream library, k3d and freecad. So it seems that it would
> make sense to package the gzstream library separately.
>
> But I notice that this library has not been updated since 2003, and obviously,
> if only two programs in Debian are using it, there may be a more suitable
> alternative, that would be worth suggesting to the authors of BEDtools.
>
> Does anybody has a good recommendation to replace gzstream by something more
> “mainstream” without too much work? If not, are there volunteers to co-maintain
> gzstream in Debian (it looks simple, but since I am not a C programmer, I am
> not comfortable with library packaging).

GDCM is using zipstream.

http://www.codeproject.com/KB/stl/zipstream.aspx

I do not remember why I gave up on gzstream (license issue ?). I
cannot volunteer -at the moment-, but I can help with C programming
issues.

HTH
--
Mathieu


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Old 05-21-2010, 09:54 AM
roucaries bastien
 
Default Packaging Gzstream?

On Fri, May 21, 2010 at 11:48 AM, Mathieu Malaterre
<mathieu.malaterre@gmail.com> wrote:
> On Fri, May 21, 2010 at 9:00 AM, Charles Plessy <plessy@debian.org> wrote:
>> Dear all,
>>
>> I am interested in a set of programs, the ‘BEDtools’, whose source includes a
>> convenience copy of the gzstream library.
>>
>> http://bedtools.googlecode.com
>> http://www.cs.unc.edu/Research/compgeom/gzstream/
>>
>> A quick apt-file search indicates that at least two other packages (CCed) may
>> be using the gzstream library, k3d and freecad. So it seems that it would
>> make sense to package the gzstream library separately.
>>
>> But I notice that this library has not been updated since 2003, and obviously,
>> if only two programs in Debian are using it, there may be a more suitable
>> alternative, that would be worth suggesting to the authors of BEDtools.
>>
>> Does anybody has a good recommendation to replace gzstream by something more
>> “mainstream” without too much work? If not, are there volunteers to co-maintain
>> gzstream in Debian (it looks simple, but since I am not a C programmer, I am
>> not comfortable with library packaging).
>
> GDCM is using zipstream.
>
> http://www.codeproject.com/KB/stl/zipstream.aspx
>
> I do not remember why I gave up on gzstream (license issue ?). I
> cannot volunteer -at the moment-, but I can help with C programming
> issues.

boostiostream is better and does not need to to call zflush

http://www.boost.org/doc/libs/1_35_0/libs/iostreams/doc/classes/gzip.html

> HTH
> --
> Mathieu
>
> --
> debian-science-maintainers mailing list
> debian-science-maintainers@lists.alioth.debian.org
> http://lists.alioth.debian.org/mailman/listinfo/debian-science-maintainers
>


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Old 05-21-2010, 10:31 AM
Teemu Ikonen
 
Default Packaging Gzstream?

On Fri, May 21, 2010 at 11:48 AM, Mathieu Malaterre
<mathieu.malaterre@gmail.com> wrote:
> On Fri, May 21, 2010 at 9:00 AM, Charles Plessy <plessy@debian.org> wrote:
[...]
>> A quick apt-file search indicates that at least two other packages (CCed) may
>> be using the gzstream library, k3d and freecad. So it seems that it would
>> make sense to package the gzstream library separately.
>>
>> But I notice that this library has not been updated since 2003, and obviously,
>> if only two programs in Debian are using it, there may be a more suitable
>> alternative, that would be worth suggesting to the authors of BEDtools.
>>
>> Does anybody has a good recommendation to replace gzstream by something more
>> “mainstream” without too much work? If not, are there volunteers to co-maintain
>> gzstream in Debian (it looks simple, but since I am not a C programmer, I am
>> not comfortable with library packaging).
>
> GDCM is using zipstream.
>
> http://www.codeproject.com/KB/stl/zipstream.aspx
>
> I do not remember why I gave up on gzstream (license issue ?). I
> cannot volunteer -at the moment-, but I can help with C programming
> issues.

Hi all,

I would not mind getting rid of the internal copy of gzstream in
freecad, but the copy in freecad is patched, so this will not be easy
even if it is packaged to Debian.

Teemu


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Old 05-26-2010, 02:17 PM
Charles Plessy
 
Default Packaging Gzstream?

Le Fri, May 21, 2010 at 10:58:05AM +0200, Adam Borowski a crit :
> On Fri, May 21, 2010 at 04:00:56PM +0900, Charles Plessy wrote:
> >
> > A quick apt-file search indicates that at least two other packages (CCed) may
> > be using the gzstream library, k3d and freecad. So it seems that it would
> > make sense to package the gzstream library separately.
>
> It appears to be just a single file less than four pages long. It does
> nothing but translate zlib's API to C++ iostream API. While generally
> avoiding duplicated code is a very good idea, it doesn't have to be done
> with any small snippet. Heck, I've written three zlib wrappers myself (two
> of them had bzip2 support as well), and it never came to me that it's a task
> big enough to be worth a whole library.

Since nobody contradicted Adam, I will go for the simplest way and package the
software with its convenience copy of gzstream. When contacting upstream, I will
nevertheless recommed them the boostiostream library.

Thanks everybody for your answers, and have a nice day,

--
Charles Plessy
Debian Med packaging team
Tsurumi, Kanagawa, Japan


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