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Old 01-19-2010, 11:29 PM
Charles Plessy
 
Default Is tabular data in binary format acceptable for Debian ?

Dear all,

I would like to ask on this list a question I asked to the FTP team last
December, and for which I have not received answer yet.

Is tabular data in a binary format that can be read, written, modified and
exported using free software acceptable for Debian, or shall we contact the
upstream author to check if he used an intermediate format (be it text, or
binary like .odt or .xls) and require the addition of this file to the source,
or shall we provide a text export?

I ask because it was one of the reasons for rejecting the r-cran-epir
package.

> * Also the data/*.Rdata files appear to be binary. I don't know enough about
> them to make an iformed decision on if those can be built from source or if
> they are in their native format.

These files are tables stored as binary R objects. Using the GNU R program, one
can load, modify, display and save them, and export them to common formats such
as CSV. I tried to clarify the situation with the FTP team, but no answer seems
to come since my last email, on the 8th of January. http://bugs.debian.org/557199
I therefore submit the question to everybody's sagacity on Debian's main discussion
place.

An important part of the problem is that other r-cran-* packages have similar
files, since they play a role in the documentation, as example data, and also
in regression tests.

I am currently holding my work on the r-cran-* packages on which I am uploader.
My personnal policy is to not upload anything if I am not sure it would not be
accepted as a new package.

Have a nice day,

--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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Old 01-19-2010, 11:56 PM
Ben Finney
 
Default Is tabular data in binary format acceptable for Debian ?

Charles Plessy <plessy@debian.org> writes:

> Is tabular data in a binary format that can be read, written, modified
> and exported using free software acceptable for Debian, or shall we
> contact the upstream author to check if he used an intermediate format
> (be it text, or binary like .odt or .xls) and require the addition of
> this file to the source, or shall we provide a text export?

I can't speak for the Debian ftpmaster team, but I would think the usual
guideline applies: We should seek “the preferred form of the work for
making modifications to it”[0] as the source form of the work.

So, if upstream uses some canonical form of the tabular data for making
modifications to it, that should be in the source package.


[0] Licensing wonks will recognise this as a definition from the GPL.
Regardless of the license for a given work, that definition is a
useful one that, IMO, makes the right distinction on what is and is
not the source of a work.

--
“I do not believe in immortality of the individual, and I |
` consider ethics to be an exclusively human concern with no |
_o__) superhuman authority behind it.” —Albert Einstein, letter, 1953 |
Ben Finney


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Old 01-20-2010, 07:54 AM
Andreas Tille
 
Default Is tabular data in binary format acceptable for Debian ?

On Wed, Jan 20, 2010 at 11:56:00AM +1100, Ben Finney wrote:
> > an intermediate format
> > (be it text, or binary like .odt or .xls) and require the addition of
>
> I can't speak for the Debian ftpmaster team, but I would think the usual
> guideline applies: We should seek "the preferred form of the work for
> making modifications to it" as the source form of the work.
>
> So, if upstream uses some canonical form of the tabular data for making
> modifications to it, that should be in the source package.

I perfectly agree here. The idea that there should be a conversion to
any other binary format like .odt (I know it is compressed XML, but it
is presented in binary form) or .xls would be contraproductive at best
because you would need to install just another package to read this
while R which just can read the data is installed via dependencies.

Perhaps it would be a reasonable compromise if README.Source would
mention a short command line which converts the data into text form?

Kind regards

Andreas.

--
http://fam-tille.de


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Old 01-20-2010, 08:30 AM
Jean-Christophe Dubacq
 
Default Is tabular data in binary format acceptable for Debian ?

Charles Plessy a crit :
> Dear all,
>
> I would like to ask on this list a question I asked to the FTP team last
> December, and for which I have not received answer yet.
>
> Is tabular data in a binary format that can be read, written, modified and
> exported using free software acceptable for Debian, or shall we contact the
> upstream author to check if he used an intermediate format (be it text, or
> binary like .odt or .xls) and require the addition of this file to the source,
> or shall we provide a text export?

I had a question similar to that for a program which comes bounded with
a trained neural network. There are files with raw weights. It is
possible to retrain on build the program, but it would take a very long
time, and the resulting network wouldn't even be the same. What is the
"source" in this case? I do not see what "editing" means in this context.


--
Jean-Christophe Dubacq


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Old 01-20-2010, 08:58 AM
Dmitrijs Ledkovs
 
Default Is tabular data in binary format acceptable for Debian ?

2010/1/20 Jean-Christophe Dubacq <jcdubacq1@free.fr>:
> Charles Plessy a écrit :
>> Dear all,
>>
>> I would like to ask on this list a question I asked to the FTP team last
>> December, and for which I have not received answer yet.
>>
>> Is tabular data in a binary format that can be read, written, modified and
>> exported using free software acceptable for Debian, or shall we contact the
>> upstream author to check if he used an intermediate format (be it text, or
>> binary like .odt or .xls) and require the addition of this file to the source,
>> or shall we provide a text export?
>
> I had a question similar to that for a program which comes bounded with
> a trained neural network. There are files with raw weights. It is
> possible to retrain on build the program, but it would take a very long
> time, and the resulting network wouldn't even be the same. What is the
> "source" in this case? I do not see what "editing" means in this context.
>

Oh yeah, I remember that thread =) was quite interesting.

If you are not sure do not make assumptions...... and that's what
ftpmasters did.

As for that neural network stuff do it in post-install scripts =) make
the users happy as for why dpkg is using all cpu cores forever on that
package. *just kidding*

--
With best regards


Dmitrijs Ledkovs (for short Dima),
Ледков Дмитрий Юрьевич

() ascii ribbon campaign - against html e-mail
/ www.asciiribbon.org - against proprietary attachments


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Old 01-20-2010, 09:07 AM
Charles Plessy
 
Default Is tabular data in binary format acceptable for Debian ?

Le Wed, Jan 20, 2010 at 09:54:44AM +0100, Andreas Tille a écrit :
> On Wed, Jan 20, 2010 at 11:56:00AM +1100, Ben Finney wrote:
> > > an intermediate format
> > > (be it text, or binary like .odt or .xls) and require the addition of
> >
> > I can't speak for the Debian ftpmaster team, but I would think the usual
> > guideline applies: We should seek "the preferred form of the work for
> > making modifications to it" as the source form of the work.
> >
> > So, if upstream uses some canonical form of the tabular data for making
> > modifications to it, that should be in the source package.
>
> I perfectly agree here. The idea that there should be a conversion to
> any other binary format like .odt (I know it is compressed XML, but it
> is presented in binary form) or .xls would be contraproductive at best
> because you would need to install just another package to read this
> while R which just can read the data is installed via dependencies.
>
> Perhaps it would be a reasonable compromise if README.Source would
> mention a short command line which converts the data into text form?

Hi Andreas,

this time, I disagree with you: all the above is a lot of work that I am not
willing to do. A user of the R software is able to do this conversion by
himself, so I do not see what is the added value here.

And I think that the “the preferred form of the work” is a very unfortunate
wording. Some people prefer bananas, and others apples. As long as there is no
information loss, why not simply accept the R binary format, which can be read,
written, modified and converted with R? The method that the current upstream
developer prefers is not necessarly the same as the one others would prefer.
What matters is that the material in the sources provides the essential
freedoms to use, study, modify and distribute, and I argue that the R binary
objects do, as much as a txt.gz, a .xls or a .ods file would.

The r-cran-* packages are a large collection of small, interdependant R
libraries. If the ones that contain R binary tables are RC-buggy (which is what
is suggested by the rejection email and the absence of answer from the FTP
team), or if packaging them is time-consuming, then I am not willing to work on
R packages in Debian anymore and will remove myself from the Uploader fields
where I am currently, because I think that there are much more useful tasks in
Debian than providing text exports of R tables that nobody ever asked for until
now.

(And of course, I do not want to prevent anybody to add these text dumps if
they want, as long as it does not become a requirement).

Have a nice day,

--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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Old 01-20-2010, 09:22 AM
Andreas Tille
 
Default Is tabular data in binary format acceptable for Debian ?

On Wed, Jan 20, 2010 at 07:07:38PM +0900, Charles Plessy wrote:
> > Perhaps it would be a reasonable compromise if README.Source would
> > mention a short command line which converts the data into text form?
>
> this time, I disagree with you: all the above is a lot of work that I am not
> willing to do. A user of the R software is able to do this conversion by
> himself, so I do not see what is the added value here.

Well, my compromise suggestion was intended to be a fallback if
ftpmaster insists on the rejection. Perhaps just nobody cared about the
issue and that's the reason for the silence. The conversion to text
has no added value than the proof that the data are simply to get -
much simpler than any .odt or .xls form which would *really* make a
lot of work.

> And I think that the ???the preferred form of the work??? is a very unfortunate
> wording. Some people prefer bananas, and others apples. As long as there is no
> information loss, why not simply accept the R binary format,

I understood Ben's wording exactly this way that the R format actually
*is* the prefered format for an R related package - so Ben (and me) are
agreeinig with you that the source format is fine.

> which can be read,
> written, modified and converted with R? The method that the current upstream
> developer prefers is not necessarly the same as the one others would prefer.

IMHO the format which is used by the tool which handles the format is
quite natural and thus any reasonable person would assume that it is
prefered by most users, right?

> What matters is that the material in the sources provides the essential
> freedoms to use, study, modify and distribute, and I argue that the R binary
> objects do, as much as a txt.gz, a .xls or a .ods file would.

At least I was objecting .xls or .ods (strongly) and agree with the
binary R format inside the source while making a suggestion how to
obtain a text form easily *in* *case* ftpmaster disagrees.

Kind regards

Andreas.

--
http://fam-tille.de


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Old 01-20-2010, 12:02 PM
Manuel Prinz
 
Default Is tabular data in binary format acceptable for Debian ?

Am Mittwoch, den 20.01.2010, 11:22 +0100 schrieb Andreas Tille:
> On Wed, Jan 20, 2010 at 07:07:38PM +0900, Charles Plessy wrote:
> > this time, I disagree with you: all the above is a lot of work that I am not
> > willing to do. A user of the R software is able to do this conversion by
> > himself, so I do not see what is the added value here.
>
> Well, my compromise suggestion was intended to be a fallback if
> ftpmaster insists on the rejection.

I do not expect them to, as they have been very open to reasonable
arguments in the past. (At least that is my experience.) Adding HOWTOs
to README.Source is IMHO not worth the overhead it produces on the
maintainer's side. Every R user knows (well, should know) how to deal
with those files. If that's not the case, this is documented elsewhere
already.

> I understood Ben's wording exactly this way that the R format actually
> *is* the prefered format for an R related package - so Ben (and me) are
> agreeinig with you that the source format is fine.

I understood it this way as well. Speaking as an R user, Rdata is
definitely the "preferred form of modification". You load it into R,
edit it, save it, done.

So +1 for "preferred form of modification".

Best regards
Manuel


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Old 01-20-2010, 01:42 PM
Andreas Tille
 
Default Is tabular data in binary format acceptable for Debian ?

On Wed, Jan 20, 2010 at 02:02:48PM +0100, Manuel Prinz wrote:
> > Well, my compromise suggestion was intended to be a fallback if
> > ftpmaster insists on the rejection.
>
> I do not expect them to, as they have been very open to reasonable
> arguments in the past. (At least that is my experience.)

I think & hope so. I just tried to avoid even worse formats just in
case.

> Adding HOWTOs
> to README.Source is IMHO not worth the overhead it produces on the
> maintainer's side. Every R user knows (well, should know) how to deal
> with those files.

Yes, but you can not assume that ftpmaster is an R *user* nor is
README.Source a document which is targeting at an end user.

Kind regards

Andreas.

--
http://fam-tille.de


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Old 01-20-2010, 01:57 PM
Martin Langhoff
 
Default Is tabular data in binary format acceptable for Debian ?

On Wed, Jan 20, 2010 at 3:42 PM, Andreas Tille <andreas@an3as.eu> wrote:
>> Adding HOWTOs
>> to README.Source is IMHO not worth the overhead it produces on the
>> maintainer's side. Every R user knows (well, should know) how to deal
>> with those files.
>
> Yes, but you can not assume that ftpmaster is an R *user* nor is
> README.Source a document which is targeting at an end user.

Exactly. Someone who is not an R user may want to get the data. It is
relevant to have a "how to extract this data in case you need it"
section in README.Debian or README.Source.

cheers,


m
--
martin.langhoff@gmail.com
martin@laptop.org -- School Server Architect
- ask interesting questions
- don't get distracted with shiny stuff - working code first
- http://wiki.laptop.org/go/User:Martinlanghoff


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