Nabble - debian-med

Re: debian imagej

2008-10-06T13:34:46Z

On Mon, 6 Oct 2008, Johan Henriksson wrote:

> it seems you adopted the package before I did.

I actually did NOT adopt the package but putted it under Debian Med team maintenance.
The main work on this package was done by Paolo Ariano <paolo.ariano@...>
and I just sponsored the package to the Debian mirror, because Paolo is no official
Debian maintainer and thus has no permission to upload. In case you
would like to package medicine related plugins you should seriosely
consider Debian Med group maintenance as well - please see the Debian Med
policy:

http://debian-med.alioth.debian.org/docs/policy.html

> I am making a package
> that depends on IJ (a plugin) that uses JNI. how shall I install these
> files such that imagej puts them in the java.library.path?

I have no ideas about imagej in special nor about Java pathes
in general, sorry. I just foreward your question to the Debian Med
mailing list.

> some of the .SOs belong to another package and are in
> /usr/lib/micro-manager/, some are IJ-specific and can be put anywhere.
>
> if you don't have a strategy yet I would propose having every plugin add
> one or more new one-line files in a standard location containing the
> path to the so-files. the IJ script then assembles java.library.path.

I hope somebody more educated is able to answer this question.

> I'm lost when it comes to pending packages. how can I obtain the new
> imagej .deb?

You can either obtain the packaging stuff from SVN and build
the package yourself from source (inspecting the source for
packaging seems to be a good idea for your own plans!) or
you might have a look into the incoming queue of the Debian mirror.

Kind regards

Andreas.

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Re: Name poll (Was: New name: Call for opinions)

2008-10-06T05:32:38Z

On Fri, 26 Sep 2008, Andreas Tille wrote:

> Once the poll is restarted from scratch no additional name suggestions
> will be accepted. The new name will be in the set specified inside
> the poll.
>
> People several times criticised that this type of poll is inferior
> to a condorset voting method. In the case of an unclear result
> with 2 or 3 competing names I would suggest to take all names
> which at least reach a number of 70% of the maximum votes (so
> if the "winner" get 10 votes take all the names that at least get
> 7 votes) and put them into a condorset ballot (including the
> "non of the above" option). This sounds like a lot of effort
> for just finding a name (I never thought that I would do this
> just to find a name) but I was convinced that it needs some effort
> to find general acceptance and I would really like to make sure
> that people accept the change.

Here is the set those naming suggestions that reached the limit I have
set above:

Debian Pure Blends 16 votes
Debian Spins 14 votes
Integrated Debian Projects 12 votes
Debian Slice 12 votes

70% of 16 is 11.2 so every other suggestion like

Debian Remix 11 votes
Debian Integrated Solutions 9 votes
Debian subproject 9 votes
Integrated Debian Distribution 8 votes
...

are below in the doodle poll for a new name.

> http://doodle.ch/ggey86bvqnmcnuyb

Looking further that
9 of 14 voters for Debian Spins voted for Debian Pure Blends as well,
7 of 12 voters for Integrated Debian Projects voted for Debian Pure
Blends as well,
5 of 12 voters for Debian Slice voted for Debian Pure Blends as well,
seems to give a hint that we might have some kind of raw consensus for the
suggestion that at least won the Doodle poll.

My personal opinion: I liked it from the beginning when I heard the suggestion
the first time at Extremadura meeting.

To come to a final conclusion for a new name I would like to know whether
a considerable number of people insist on a condorset voting and if these
people would volunteer to support this voting by spending some time on the
technical details. My problem is that I'll be offline next week and as
I told you I would like to see a consensus until OSWC (actually I will
have ma talk at 22. October). So there is not much time left. So in
case you have honest concerns about Debian Pure Blends or you feel the
way we found this name is really inacceptable speak up now and ask for a
condorcet voting about the four suggestions above. It would be nice if
you would add to this request your involvement into the stuff we are
talking about - I just have read a few names on the poll I do not remember
from one of the mailing list.

Kind regards and thanks for joining the poll

Andreas.
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[VAC] 10.-17. October Sardinia / Italy

2008-10-06T00:04:10Z

Hi,

I'll be completely offline (no laptop, no internet) for one week for
holiday with my family in North of Sardinia. Swapping keys and some
nice Italian wine would be nice if somebody is in this area (in a
traveling distance that is accepted by the rest of my family ;-)).

My packages are mostly team maintained. The remaining ones do not
have bugs with severity higher than "normal". Feel free to NMU any
package featuring a problem you see urgend need to fix.

Kind regards

Andreas.

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Re: Debian-Med images for Amazon Compute Cloud?!?

2008-10-05T02:00:11Z

> Le Tue, Feb 26, 2008 at 03:51:57PM +0100, Steffen Moeller a écrit :
> > Hello,
> >
> > you may have heard of the compute cluster of Amazon that everyone can
> > use on a per-cpu-minute-basis. It is pretty amazing. 1000 CPU hours is
> > 100$ or in other words if you exchange your 100% busy 500$ zero-energy
> > machine every 7 months then you are better of with Amazon.
> >
> > I found a Debian Etch image
> > http://developer.amazonwebservices.com/connect/entry.jspa?externalID=639
> >
> > and some Ubuntu with minimal Bioinformatics
> > http://developer.amazonwebservices.com/connect/entry.jspa?externalID=1259&categoryID=101

Hi all,

you may be interested by the recent blog entry of Russel Cocker, who
made a draft package for the Amazon ec2 tools:

http://etbe.coker.com.au/2008/10/04/getting-started-with-amazon-ec2/

Have a nice day,

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Re: Improvement of the QA pages.

2008-10-02T02:36:15Z

[Debian-Custom in CC because this effort of Debian Med is of general
interest regarding QA work inside our projects.]

Hi,

if you now look at

http://qa.debian.org/developer.php?login=debian-med-packaging@...&ordering=3

you see (nearly - see below) the information which I would like to be viewed.
The script I used

alioth:/srv/alioth.debian.org/chroot/home/groups/cdd/webtools/ddpo_register

does now regard the source packages over the binary packages which makes
much more sense on ddpo.

Here are some constraints:

1. bio-dev beats bio:
Even if bio is listed first the fact that emboss is subscribed to
both bio and bio-dev leads to the effect that emboss is listed under
bio-dev. This is not nice esthetically. I see 3 chances to handle
this:

1) Ignore it. People who are interested in the biological part
will parse both sections anyway.
2) Saying this I wonder whether we should combine bio and bio-dev
as well as imaging and imaging-dev because QA-wise it is the
same target audience.
3) Try to fix it - but I have neigher an idea how nor the effort
this might cost.

2. Implicite dependencies:
There are some packages that are not mentioned explicitely in the
tasks files becuase they depend from other packages mentioned in
the task file and thus on installation time they are installed
nicely - but on the QA pages they are not displayed in the right
category. I see also chances to handle this:

1) Ignoring is not prefered here - it just looks ugly.
2) Mentioning them in the tasks file with an extra field for
instance "DDPO-Depends" and parse this field only for the
ddpo issue, or rather find a more generic field name because
we might need it later for other things as well.
3) Try to parse the dependencies of the packages mentioned in
the tasks files and mention them as well. This would lead
to the effect that some more packages will be listed in our
sections which are not related to our work at all (for
instance apache, postgresql, etc.) because several of our
packages might need general dependencies. What do you
think about this. Please think twice! Somehow it is not
really uninteresting to make sure that the dependencies are
in good shape as well. We might add a section
<task>-dependencies
for such kind of stuff. But I'm really undecided about
this and would like to hear your opinion.

3. Sloppy maintainers ;-)
Well, finally this is no constraint but an advantage: We see if
maintainers did not care for including their packages in tasks
file dependencies. I blame for instance mafft uploaders and others
for not keeping me informed that this is missing in the depends ...
But now I'll catch you all if I see something mentioned in no
specific section ... ;-))

Any comment is welcome

Andreas.
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Re: plink package in NEW

2008-10-02T00:00:38Z

Le Thu, Oct 02, 2008 at 08:21:50AM +0200, Andreas Tille a écrit :
> On Thu, 2 Oct 2008, Charles Plessy wrote:
>
>> I also would prefer links to packages. It sometimes happen that the svn
>> version is not buildable because it is under work.
>
> You mean links from which page?

I meant to suggest Upstream to add a link to packages.debian.org/plink
when it will be ready.

Sorry for the unclearness,

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Re: Zotero - a reference manager software. (Re: [Cdd-commits] r1113 - projects/science/trunk/debian-science/tasks)

2008-10-01T23:29:39Z

On Wed, 1 Oct 2008, Will Hill wrote:

> KBibtex

Will be in Suggests of med-typesetting.

Thanks for the hint

Andreas.

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Re: plink package in NEW

2008-10-01T23:21:50Z

On Thu, 2 Oct 2008, Charles Plessy wrote:

> I also would prefer links to packages. It sometimes happen that the svn
> version is not buildable because it is under work.

You mean links from which page? From the auto generated tasks pages?
I tried to do so in case I was aware that a prebuilded binary package
exists. For the specific plink package I did not really felt the
presure to change the information in the tasks files because I expect
it to be available from the mirror quite soon. If you think this is
not the case please either add the link to the tasks file as Pkg-URL
or just ask me: Andreas, please add the inoffical package URL ...
to the tasks file.

Kind regards

Andreas.

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Re: Zotero - a reference manager software. (Re: [Cdd-commits] r1113 - projects/science/trunk/debian-science/tasks)

2008-10-01T20:27:13Z

KBibtex

http://packages.debian.org/lenny/kbibtex

On Wednesday 01 October 2008, Andreas Tille wrote:
> BTW, if you know some killer applications like this just post it here!!!

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Re: Improvement of the QA pages.

2008-10-01T17:52:58Z

Le Wed, Oct 01, 2008 at 02:46:19PM +0200, David Paleino a écrit :
>
> You should thank Andreas for subscribing those packages via DDPO bot.
> You should thank me if you're using "ordering=3" [1], which puts the sections
> on top, and main/contrib/non-free at the end.
> And, you should thank me if my second patch to qa.d.o will ever be accepted [2]

Wow, thanks to both of you, then !

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Re: Zotero - a reference manager software. (Re: [Cdd-commits] r1113 - projects/science/trunk/debian-science/tasks)

2008-10-01T17:39:14Z

Le Wed, Oct 01, 2008 at 12:33:34PM -0400, Gabriel Grant a écrit :
>
> If we do decide to just package this one extension individually, I
> wouldn't mind giving it a try, although I have no mozilla packaging
> experience.

Hi,

It seems that the project of Ubuntu is fairly ambitious, so since
Zotero is of a particular interest for our communauty, I would advise to
not wait before the automatic packaging is available in Ubuntu; it can
take time... This said, it is of course a good idea to consult the
Ubuntu developpers and the Debian Iceweasel maintainers if necessary.

To say things frankly, I fear that cooperation will be difficult on this
project as the very idea of having Debian packages downstream of Ubuntu
will probably provoke at least a very heated debate. But maybe I am
pessimistic... As least for me it would be no problem.

Another good reason for having an independant pakage is that if I
understand correctly, Zotero also has a component that interacts with
OpenOffice, so I do not know if its packaging can easily be part of an
automated scheme that will give its best for extensions that only depend
on Mozilla and not other applications.

By the way, would you like to develop the package within our Subversion
repository? If yes, you can ask to join our Gforge project on the
following address:

http://alioth.debian.org/project/request.php?group_id=30063

Have a nice day,

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

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Re: plink package in NEW

2008-10-01T17:04:07Z

Le Wed, Oct 01, 2008 at 12:23:00PM -0400, Faheem Mitha a écrit :
>
> Ok. Well, I was just thinking of putting links to the svn repos as given
> above. It is easy to build Debian packages from the source, if one has
> the packaging (which you provide). This also has the advantage that it
> does not require a user to wait for updates, but maybe you guys would be
> fast on updates. However, maybe links to actual packages would be easier
> regardless.

Hi all,

I also would prefer links to packages. It sometimes happen that the svn
version is not buildable because it is under work.

Have a nice day,

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Re: Zotero - a reference manager software. (Re: [Cdd-commits] r1113 - projects/science/trunk/debian-science/tasks)

2008-10-01T13:32:16Z

On Wed, 1 Oct 2008, Gabriel Grant wrote:

> I can second the recommendation of this software: I find this
> extension absolutely essential when conducting research. The
> integration with both Firefox and OpenOffice has made it a key point
> in convincing fellow researchers to give Linux a try, as one of the
> most common barriers they've presented is that they can't live without
> EndNote.

Cool.

> As a side note, packing the OOo extension that gives this
> integration should also be considered.

Good int.

> The other issue they discussed are the extension's frequent releases,
> and how Ubuntu is instituting a standardized method for maintaining
> Firefox extensions (automatically import new updates into the current
> development release then push them into backports shortly thereafter.
> Does anyone know if there are any such plans for Debian? Is there a
> standardized method of packaging Mozilla extensions? If not (a quick
> search doesn't reveal anything), it might be worth collaborating with
> the Ubuntu folks to have avoid needless duplication of work, as they
> seem to have put quite a bit of thought into the issue.

It sounds very reasonable to learn from Ububtu. To not forget this
hint I would like to link to an existing Ububtu package of Zotero
on the Debian Science tasks pages (BTW, do you think we shoudl list
it in Debian Med as well?) - but I have no idea where I can find the
package you are mentioning.

> This may be something that should be discussed on a broader list, but
> I'm not sure which one (med is the only Debian list I'm on),

BTW, if you know some killer applications like this just post it here!!!
There is no need to wait until some of us by chance stumbles upon this
stuff - just make some noise if you know something we do obviosely no
know yet. (The things we know are on the tasks pages ...)

> If we do decide to just package this one extension individually, I
> wouldn't mind giving it a try, although I have no mozilla packaging
> experience.

The only thing I know is biofox ...

Kind regards

Andreas.

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Re: Zotero - a reference manager software. (Re: [Cdd-commits] r1113 - projects/science/trunk/debian-science/tasks)

2008-10-01T09:33:34Z

I can second the recommendation of this software: I find this
extension absolutely essential when conducting research. The
integration with both Firefox and OpenOffice has made it a key point
in convincing fellow researchers to give Linux a try, as one of the
most common barriers they've presented is that they can't live without
EndNote. As a side note, packing the OOo extension that gives this
integration should also be considered.

There are, however, a couple issues, raised by Ubuntu packagers[1],
that need to be addressed. First, is the ECL license that Zotero
uses[2], although considered open source[3], is not one we
traditionally deal with. The Ubuntu folks have essentially decided
that it is "probably good enough," which also probably applies to
Debian, but it is certainly a question worth investigating.

The other issue they discussed are the extension's frequent releases,
and how Ubuntu is instituting a standardized method for maintaining
Firefox extensions (automatically import new updates into the current
development release then push them into backports shortly thereafter.
Does anyone know if there are any such plans for Debian? Is there a
standardized method of packaging Mozilla extensions? If not (a quick
search doesn't reveal anything), it might be worth collaborating with
the Ubuntu folks to have avoid needless duplication of work, as they
seem to have put quite a bit of thought into the issue.

This may be something that should be discussed on a broader list, but
I'm not sure which one (med is the only Debian list I'm on), so please
post wherever you feel is appropriate (but if you could keep me in the
CC list, I would appreciate it)

If we do decide to just package this one extension individually, I
wouldn't mind giving it a try, although I have no mozilla packaging
experience.

Cheers,
-Gabriel

[1]: https://bugs.launchpad.net/ubuntu/+bug/239575
[2]: http://www.zotero.org/documentation/#small_print_stuff
[3]: http://www.opensource.org/licenses/ecl1.php

On Wed, Oct 1, 2008 at 7:59 AM, Andreas Tille <tillea@...> wrote:

> On Wed, 1 Oct 2008, Charles Plessy wrote:
>
>> this looks very interesting. Any volunteer with some mozilla
>> background ?
>
> BTW, I've taken the hint from mentioning the lawsuite in a German
> newsticker - so this
>
> http://dltj.org/article/zotero-lawsuit-extracts/
>
> seems to be a really good advertising for zotero ...
>
> Kind regards
>
> Andreas.
>
> --
> http://fam-tille.de
>

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Re: plink package in NEW

2008-10-01T09:23:00Z

On Wed, 1 Oct 2008, Steffen Moeller wrote:

> Faheem Mitha wrote:
>> On Wed, 1 Oct 2008, Dominique Belhachemi wrote:
>>
>>> On Tue, 2008-09-30 at 13:12 -0400, Faheem Mitha wrote:
>>>> Dear Debian Med Developers,
>>>>
>>>> Can you point me to the Debian sources for the plink Debian package that
>>>> is currently sitting in NEW?
>>>
>>> Sure. ;-)
>>>
>>> Vcs-Browser:
>>> http://svn.debian.org/wsvn/debian-med/trunk/packages/plink/trunk/?rev=0&sc=0
>>>
>>> Vcs-Svn:
>>> svn://svn.debian.org/svn/debian-med/trunk/packages/plink/trunk/
>>
>> Suggestion: mention the existence of this packaging to the plink people.
>> Maybe they'll put a link at
>> http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml or somewhere.
>
> Hello, go ahead, but until the package hits in incoming, there is not
> much to talk about, really. Updates to later versions, like the 1.0.4
> you are mentioning, are then going quickly. I presume the delay of plink
> is because of all the hard work going into Lenny these days. I put
> our ftpmaster on the CC line for that case that there are insights to
> spread, but probably this email only took more time of our masters.

Ok. Well, I was just thinking of putting links to the svn repos as given
above. It is easy to build Debian packages from the source, if one has the
packaging (which you provide). This also has the advantage that it does
not require a user to wait for updates, but maybe you guys would be fast
on updates. However, maybe links to actual packages would be easier
regardless.

Regards, Faheem.

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Re: Improvement of the QA pages.

2008-10-01T07:13:54Z

On Wed, 1 Oct 2008, David Paleino wrote:

>> http://qa.debian.org/developer.php?login=debian-med-packaging@...
>
> You should thank Andreas for subscribing those packages via DDPO bot.

For subscribing you can also "thank" to

alioth:/srv/alioth.debian.org/chroot/home/groups/cdd/webtools/ddpo_register

script. It is just in the testing phase and I did not yet announced it.
I would like to find out first whether it might cause any problems in ddtp
if I blindly add subscriptions or whether I should check first if a package
is just subscribed. Currently all packages that exist in unstable and
are mentioned in a task file in SVN are blindly subscribed.

> You should thank me if you're using "ordering=3" [1], which puts the sections
> on top, and main/contrib/non-free at the end.

Looking at main/nonf-free it is easy to detect which packages are missing in
the tasks files (or are not subscribed for reasons I have to check ...)

> And, you should thank me if my second patch to qa.d.o will ever be accepted [2]

I consider linking to these pages from the tasks pages once this will work.

Kind regards

Andreas.

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Re: Improvement of the QA pages.

2008-10-01T05:46:19Z

On Wed, 1 Oct 2008 21:36:17 +0900, Charles Plessy wrote:

> Hi all,

Hi Charles,

> who can we thank for having the info about our meta-packages on the QA
> pages of the Debian Med packaging team? It is really great !
>
> http://qa.debian.org/developer.php?login=debian-med-packaging@...

You should thank Andreas for subscribing those packages via DDPO bot.
You should thank me if you're using "ordering=3" [1], which puts the sections
on top, and main/contrib/non-free at the end.
And, you should thank me if my second patch to qa.d.o will ever be accepted [2]

Enjoy :)
David

[1]
<http://qa.debian.org/developer.php?login=debian-med-packaging%40lists.alioth.debian.org&ordering=3>
[2] See #500546 and [3], for example.
[3]
http://alioth.debian.org/~hanska-guest/wml/developer.php?login=debian-med-packaging%40lists.alioth.debian.org&ddpo_section=bio

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Improvement of the QA pages.

2008-10-01T05:36:17Z

Hi all,

who can we thank for having the info about our meta-packages on the QA
pages of the Debian Med packaging team? It is really great !

http://qa.debian.org/developer.php?login=debian-med-packaging@...

Have a nice day,

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Re: Zotero - a reference manager software. (Re: [Cdd-commits] r1113 - projects/science/trunk/debian-science/tasks)

2008-10-01T04:59:43Z

On Wed, 1 Oct 2008, Charles Plessy wrote:

> this looks very interesting. Any volunteer with some mozilla
> background ?

BTW, I've taken the hint from mentioning the lawsuite in a German
newsticker - so this

http://dltj.org/article/zotero-lawsuit-extracts/

seems to be a really good advertising for zotero ...

Kind regards

Andreas.

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Re: plink package in NEW

2008-10-01T03:04:28Z

Faheem Mitha wrote:

>
>
> On Wed, 1 Oct 2008, Dominique Belhachemi wrote:
>
>> On Tue, 2008-09-30 at 13:12 -0400, Faheem Mitha wrote:
>>> Dear Debian Med Developers,
>>>
>>> Can you point me to the Debian sources for the plink Debian package that
>>> is currently sitting in NEW?
>>
>> Sure. ;-)
>>
>> Vcs-Browser:
>> http://svn.debian.org/wsvn/debian-med/trunk/packages/plink/trunk/?rev=0&sc=0
>>
>>
>> Vcs-Svn:
>> svn://svn.debian.org/svn/debian-med/trunk/packages/plink/trunk/
>
> Suggestion: mention the existence of this packaging to the plink people.
> Maybe they'll put a link at
> http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml or somewhere.

Hello, go ahead, but until the package hits in incoming, there is not
much to talk about, really. Updates to later versions, like the 1.0.4
you are mentioning, are then going quickly. I presume the delay of plink
is because of all the hard work going into Lenny these days. I put
our ftpmaster on the CC line for that case that there are insights to
spread, but probably this email only took more time of our masters.

Best,

Steffen

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Zotero - a reference manager software. (Re: [Cdd-commits] r1113 - projects/science/trunk/debian-science/tasks)

2008-10-01T02:28:37Z

Hi all,

this looks very interesting. Any volunteer with some mozilla
background ?

Have a nice day,

-- Charles

Le Wed, Oct 01, 2008 at 08:54:07AM +0000, CDD Subversion Commit a écrit :

>
> Modified: projects/science/trunk/debian-science/tasks/typesetting
> ==============================================================================
> --- projects/science/trunk/debian-science/tasks/typesetting (original)
> +++ projects/science/trunk/debian-science/tasks/typesetting Wed Oct 1 08:54:07 2008
> +
> +Depends: zotero
> +Homepage: http://www.zotero.org/
> +License: BSD
> +Pkg-Description: reference manager software
> + Zotero is an easy-to-use yet powerful research tool that helps you
> + gather, organize, and analyze sources (citations, full texts, web
> + pages, images, and other objects), and lets you share the results of
> + your research in a variety of ways. An extension to the popular
> + open-source web browser Firefox, Zotero includes the best parts of
> + older reference manager software (like EndNote)—the ability to store
> + author, title, and publication fields and to export that information
> + as formatted references—and the best parts of modern software and web
> + applications (like iTunes and del.icio.us), such as the ability to
> + interact, tag, and search in advanced ways. Zotero integrates tightly
> + with online resources; it can sense when users are viewing a book,
> + article, or other object on the web, and—on many major research and
> + library sites—find and automatically save the full reference
> + information for the item in the correct fields. Since it lives in the
> + web browser, it can effortlessly transmit information to, and receive
> + information from, other web services and applications; since it runs
> + on one’s personal computer, it can also communicate with software
> + running there (such as Microsoft Word). And it can be used offline as
> + well (e.g., on a plane, in an archive without WiFi).
> + .
> + * Automatic capture of citation information from web pages
> + * Storage of PDFs, files, images, links, and whole web pages
> + * Flexible notetaking with autosave
> + * Fast, as-you-type search through your materials
> + * Playlist-like library organization, including saved searches
> + (smart collections) and tags
> + * Platform for new forms of digital research that can be extended
> + with other web tools and services
> + * Formatted citation export (over 1100 styles and growing)
> + * Integration with Microsoft Word and OpenOffice
> + * Saves records and notes in several languages
> + * Integration with WordPress and other blogging software
> + * Remote library backup
> + * Advanced search and data mining tools
> + * Wide variety of import/export options

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Re: plink package in NEW

2008-09-30T17:25:17Z

On Wed, 1 Oct 2008, Dominique Belhachemi wrote:

> On Tue, 2008-09-30 at 13:12 -0400, Faheem Mitha wrote:
>> Dear Debian Med Developers,
>>
>> Can you point me to the Debian sources for the plink Debian package that
>> is currently sitting in NEW?
>
> Sure. ;-)
>
> Vcs-Browser:
> http://svn.debian.org/wsvn/debian-med/trunk/packages/plink/trunk/?rev=0&sc=0
>
> Vcs-Svn:
> svn://svn.debian.org/svn/debian-med/trunk/packages/plink/trunk/

Suggestion: mention the existence of this packaging to the plink people.
Maybe they'll put a link at
http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml or somewhere.

Or I can, if you want.
Regards, Faheem.

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Re: plink package in NEW

2008-09-30T17:19:44Z

On Wed, 1 Oct 2008, Dominique Belhachemi wrote:

Thanks. Looks like it builds fine with 1.0.4. Any idea when plink will hit
incoming?
Take care, Faheem.

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Re: plink package in NEW

2008-09-30T16:28:14Z

On Tue, 2008-09-30 at 13:12 -0400, Faheem Mitha wrote:
> Dear Debian Med Developers,
>
> Can you point me to the Debian sources for the plink Debian package that
> is currently sitting in NEW?

Sure. ;-)

Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/plink/trunk/?rev=0&sc=0

Vcs-Svn:
svn://svn.debian.org/svn/debian-med/trunk/packages/plink/trunk/

Best Regards

Dominique

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plink package in NEW

2008-09-30T10:12:40Z

Dear Debian Med Developers,

Can you point me to the Debian sources for the plink Debian package that
is currently sitting in NEW?
Thanks, Faheem.

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Re: GDCM 2.0.9 is out !

2008-09-30T00:24:50Z

Steve,

On Tue, Sep 30, 2008 at 8:43 AM, Steve M. Robbins <steve@...> wrote:

> On Mon, Sep 29, 2008 at 10:01:33AM +0200, Mathieu Malaterre wrote:
>> On Mon, Sep 29, 2008 at 7:49 AM, Steve M. Robbins <steve@...> wrote:
>> > Hello Debian-Med folks,
>> >
>> > On Fri, Sep 26, 2008 at 10:58:29AM +0200, Mathieu Malaterre wrote:
>> >> This is mostly a bug fix release, anyone doing RLE compression / J2K
>> >> compression is suggested to upgrade to this version as it fixes quite
>> >> a few issues.
>> >
>> > I got thinking that it would be nice to have an up-to-date GDCM in
>> > Debian for ITK to link with. So I had a look at the sources in
>> > the debian-med SVN tree.
>> >
>> > After adding a few missing build-deps, I got 2.0.6 to build. Then I
>> > tweaked the debian/* files to build with 2.0.9. The C++ library
>> > packages look in reasonable shape. I'm not so sure about the other
>> > packages, however.
>> >
>> > In the python packages, for example, the sources are configured and
>> > built with both python 2.4 and 2.5, but only one of these seems to
>> > make it into the final package. I'll have a hack at these when I
>> > get some free time, but I'd really love it if someone else could
>> > fix it up for me.
>>
>> I am not sure I understand this one.
>>
>> I've just made a patch at the debian files:
>>
>> debian-med/trunk/packages/gdcm/trunk/debian
>> $ svn ci -m"BUG: Was missing some * character"
>> Password:
>> Sending debian/python-gdcm.install
>> Sending debian/python-vtkgdcm.install
>> Transmitting file data ..
>> Committed revision 2551.
>>
>>
>
>> Or are you saying that if someone has both python 2.4 and python 2.5
>> then at inspection time, cmake is picking the wrong version of python
>> ? This is easy to tell cmake which python to use. Just let me know if
>> this is what you mean. Thanks.
>
> If you have both 2.4 and 2.5 installed, then gdcm gets configured and
> built twice: once in debian/build-python2.4 and once in
> debian/build-python2.5.
>
> If this is intended, I'd expect all the build products to be
> packaged. It doesn't appear to be the case, however.

I send a post to debian-dev asking how to package python module and
was answered to have a look at the opensync package in experimental.
I simply copy/paste their 'rules' files and adapted the cmake line
only. If you believe this is wrong, please remove whatever version.
But you need to know that a python module build with python 2.4 will
link to python2.4 runtime shared lib, I do not know if this will work
with python 2.5

>
>> > It's a bit unusual to have the version number embedded in tool names
>> > (e.g. gdcmconv-2.0).
>> > My inclination is to drop the versioned names.
>> > Mathieu: do you have any objection to this?
>>
>> sure. How do you want the patch, I am not familiar with quilt and co.
>
> You can send me a simple patch and I'll put it into quilt form.

somehow this patch needs to be applied to the toplevel CMakeLists.txt:

https://gdcm.svn.sf.net/viewvc/gdcm/trunk/CMakeLists.txt?r1=4424&r2=4438&view=patch

And I have updated the rules file in debian med:

$ svn di
Index: rules
===================================================================
--- rules (revision 2550)
+++ rules (working copy)
@@ -48,6 +48,7 @@
-DCMAKE_C_COMPILER="/usr/bin/cc" \
-DCMAKE_C_FLAGS="-g -Wall -O2" \
-DCMAKE_SKIP_RPATH=ON \
+ -DGDCM_NO_EXECUTABLE_PROPERTIES=ON \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGDCM_BUILD_APPLICATIONS=ON \
-DGDCM_BUILD_SHARED_LIBS=ON \

$ svn ci -m"ENH: do not put prop on exe"
Password:
Sending debian/rules
Transmitting file data .
Committed revision 2558.

HTH
--
Mathieu

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Re: GDCM 2.0.9 is out !

2008-09-29T23:43:36Z

On Mon, Sep 29, 2008 at 10:01:33AM +0200, Mathieu Malaterre wrote:

> On Mon, Sep 29, 2008 at 7:49 AM, Steve M. Robbins <steve@...> wrote:
> > Hello Debian-Med folks,
> >
> > On Fri, Sep 26, 2008 at 10:58:29AM +0200, Mathieu Malaterre wrote:
> >> This is mostly a bug fix release, anyone doing RLE compression / J2K
> >> compression is suggested to upgrade to this version as it fixes quite
> >> a few issues.
> >
> > I got thinking that it would be nice to have an up-to-date GDCM in
> > Debian for ITK to link with. So I had a look at the sources in
> > the debian-med SVN tree.
> >
> > After adding a few missing build-deps, I got 2.0.6 to build. Then I
> > tweaked the debian/* files to build with 2.0.9. The C++ library
> > packages look in reasonable shape. I'm not so sure about the other
> > packages, however.
> >
> > In the python packages, for example, the sources are configured and
> > built with both python 2.4 and 2.5, but only one of these seems to
> > make it into the final package. I'll have a hack at these when I
> > get some free time, but I'd really love it if someone else could
> > fix it up for me.
>
> I am not sure I understand this one.
>
> I've just made a patch at the debian files:
>
> debian-med/trunk/packages/gdcm/trunk/debian
> $ svn ci -m"BUG: Was missing some * character"
> Password:
> Sending debian/python-gdcm.install
> Sending debian/python-vtkgdcm.install
> Transmitting file data ..
> Committed revision 2551.
>
>

> Or are you saying that if someone has both python 2.4 and python 2.5
> then at inspection time, cmake is picking the wrong version of python
> ? This is easy to tell cmake which python to use. Just let me know if
> this is what you mean. Thanks.

If you have both 2.4 and 2.5 installed, then gdcm gets configured and
built twice: once in debian/build-python2.4 and once in
debian/build-python2.5.

If this is intended, I'd expect all the build products to be
packaged. It doesn't appear to be the case, however.

> > It's a bit unusual to have the version number embedded in tool names
> > (e.g. gdcmconv-2.0).
> > My inclination is to drop the versioned names.
> > Mathieu: do you have any objection to this?
>
> sure. How do you want the patch, I am not familiar with quilt and co.

You can send me a simple patch and I'll put it into quilt form.

-Steve

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Re: Name poll (Was: New name: Call for opinions)

2008-09-29T02:02:53Z

On Mon, 29 Sep 2008, David Paleino wrote:

> where "Change vote" is a link pointing to
> http://doodle.ch/edition.html?pollId=ggey86bvqnmcnuyb&participantName=David+Paleino&participantId=$id&credential=$credential
>
> (obviously, $id and $credential have been stripped off :) )
>
> I believe that just saving this link would let people changing the vote later...

Yes - but this does not work for people who forgot to save the link ...

Kind regards

Andreas.

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Re: Name poll (Was: New name: Call for opinions)

2008-09-29T01:12:45Z

On Mon, 29 Sep 2008 09:54:28 +0200 (CEST), Andreas Tille wrote:

> On Fri, 26 Sep 2008, Andreas Tille wrote:
>
> > So we decided to remove all votes from the
> > current ballot next Monday morning
>
> This happened now because nobody showe up who found a way to change
> a vote on doodle.

Well, I have. It's simple, and clearly stated :)

I've just voted, and this showed up at the top of the page:

"Thanks, David Paleino, the data has been saved. Change vote"

where "Change vote" is a link pointing to
http://doodle.ch/edition.html?pollId=ggey86bvqnmcnuyb&participantName=David+Paleino&participantId=$id&credential=$credential

(obviously, $id and $credential have been stripped off :) )

I believe that just saving this link would let people changing the vote later...

Kindly,
David

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Re: GDCM 2.0.9 is out !

2008-09-29T01:01:33Z

On Mon, Sep 29, 2008 at 7:49 AM, Steve M. Robbins <steve@...> wrote:

> Hello Debian-Med folks,
>
> On Fri, Sep 26, 2008 at 10:58:29AM +0200, Mathieu Malaterre wrote:
>> This is mostly a bug fix release, anyone doing RLE compression / J2K
>> compression is suggested to upgrade to this version as it fixes quite
>> a few issues.
>
> I got thinking that it would be nice to have an up-to-date GDCM in
> Debian for ITK to link with. So I had a look at the sources in
> the debian-med SVN tree.
>
> After adding a few missing build-deps, I got 2.0.6 to build. Then I
> tweaked the debian/* files to build with 2.0.9. The C++ library
> packages look in reasonable shape. I'm not so sure about the other
> packages, however.
>
> In the python packages, for example, the sources are configured and
> built with both python 2.4 and 2.5, but only one of these seems to
> make it into the final package. I'll have a hack at these when I
> get some free time, but I'd really love it if someone else could
> fix it up for me.

I am not sure I understand this one.

I've just made a patch at the debian files:

debian-med/trunk/packages/gdcm/trunk/debian
$ svn ci -m"BUG: Was missing some * character"
Password:
Sending debian/python-gdcm.install
Sending debian/python-vtkgdcm.install
Transmitting file data ..
Committed revision 2551.

Or are you saying that if someone has both python 2.4 and python 2.5
then at inspection time, cmake is picking the wrong version of python
? This is easy to tell cmake which python to use. Just let me know if
this is what you mean. Thanks.

> It's a bit unusual to have the version number embedded in tool names
> (e.g. gdcmconv-2.0).

That's the only AFAIK to be able to support the same tool with
different library version, right ? Pretty much just like gcc is doing.
Anyway GDCM 1.x is not being supported anymore, so it's not likely
that it will make it into debian. And since I am not planning on
having a gdcm 2.2 at the moment, I guess a single version of the tools
should be ok.

> My inclination is to drop the versioned names.
> Mathieu: do you have any objection to this?

sure. How do you want the patch, I am not familiar with quilt and co.

thanks!
--
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Re: Name poll (Was: New name: Call for opinions)

2008-09-29T00:54:28Z

On Fri, 26 Sep 2008, Andreas Tille wrote:

> So we decided to remove all votes from the
> current ballot next Monday morning

This happened now because nobody showe up who found a way to change
a vote on doodle.

> and start voting again about
> the suggestions which are known at this point in time.

For the record:

12 votes: Debian Spins
11 votes: Debian Remix
10 votes: Debian Pure Blends

All other suggestions got less than 8.4 (70% of 12) votes and thus
would be below the limit I suggested for a potential condorset voting
in case we have no clear winner (I would not regard the result above
as a clear winning situation).

> This is
> the reason why I post to all these lists:
>
> If you have an additional suggestion just suggest it *NOW*.

There were no additional suggestions with the syntax I asked you
to use until now (I hope that there was no technical reason for
this - some network restructuring at my institute might have delayed
some mails but this should have been sorted out since hours).

So please go now to

http://doodle.ch/ggey86bvqnmcnuyb

and vote about a name. I would apreciate if you use firstname
and surname. It makes it easier to identify people in case of
questions.

Kind regards

Andreas.

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Re: GDCM 2.0.9 is out !

2008-09-29T00:14:01Z

On Mon, 29 Sep 2008, Steve M. Robbins wrote:

> In the python packages, for example, the sources are configured and
> built with both python 2.4 and 2.5, but only one of these seems to
> make it into the final package.

I had not yet time to dive into this but reading your mail here I would
suggest to go only with python 2.5.

Kind regards

Andreas.

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Re: BioCocoa

2008-09-28T23:49:57Z

On Mon, 29 Sep 2008, Charles Plessy wrote:

> It is indeed necessary to do the development work on the unstable
> version of Debian, because this is where the binary packages will be
> compiled. Actually, for packages that are not too complex, it is often
> possible to do the development on testing or even stable. In that case,
> it is necessary to double-check that everything works fine on unstable
> as well. Some package, for instance many perl modules, provide
> regression tests that are ran at build time and that fit this role very
> well. For graphical applications, chroots or virtual machines are
> needed.

I might add that the pbuilder package provides a very reasonable access
to a chroot environment for building packages. If you are keen on keeping
your stable system and just want to build the package. In case of
biococoa this might be insufficient because testing under a graphical
environment seems to be required - but perhaps you can do the build on
your day to day computer running stable and test on a "not so important"
computer with unstable. (As a side note: current testing = Lenny will
be released in the near future and can be considered stable for most
applications.)

To clarify the issue with biococoa.app: I putted this package under
maintainership of the Debian Med packaging team because it was orphaned
(=not maintained by the initial maintainer any more) but is interesting
for the Debian Med project - so I wanted to keep it for the users of
Debian Med. I admit I'm really uneducated about the whole framework
and never had any experience with the gnustep framework. So I do not
really qualify to fix any problems which might occure which is actually
a quite bad situation. So I'm *really* happy that you are interested
in working on Debian packages and I would like to give any possible
support to enable you to build the packages successfully. Just do not
hesitate to ask here in any case.

Kind regards and thanks for your interest in Debian Med

Andreas.

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Re: GDCM 2.0.9 is out !

2008-09-28T22:49:00Z

Hello Debian-Med folks,

On Fri, Sep 26, 2008 at 10:58:29AM +0200, Mathieu Malaterre wrote:
> This is mostly a bug fix release, anyone doing RLE compression / J2K
> compression is suggested to upgrade to this version as it fixes quite
> a few issues.

I got thinking that it would be nice to have an up-to-date GDCM in
Debian for ITK to link with. So I had a look at the sources in
the debian-med SVN tree.

After adding a few missing build-deps, I got 2.0.6 to build. Then I
tweaked the debian/* files to build with 2.0.9. The C++ library
packages look in reasonable shape. I'm not so sure about the other
packages, however.

In the python packages, for example, the sources are configured and
built with both python 2.4 and 2.5, but only one of these seems to
make it into the final package. I'll have a hack at these when I
get some free time, but I'd really love it if someone else could
fix it up for me.

It's a bit unusual to have the version number embedded in tool names
(e.g. gdcmconv-2.0). My inclination is to drop the versioned names.
Mathieu: do you have any objection to this?

Best regards,
-Steve

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Re: BioCocoa

2008-09-28T22:12:54Z

Le Sun, Sep 28, 2008 at 11:09:18AM -0700, Scott Christley a écrit :
> I think I figured it out. There are two other distributions, testing
> aka lenny, and unstable aka sid, so I need to upgrade my system to one
> of these to get more recent versions of packages. I'm using virtual
> machines so I will likely maintain one for each.

Hi Scott,

It is indeed necessary to do the development work on the unstable
version of Debian, because this is where the binary packages will be
compiled. Actually, for packages that are not too complex, it is often
possible to do the development on testing or even stable. In that case,
it is necessary to double-check that everything works fine on unstable
as well. Some package, for instance many perl modules, provide
regression tests that are ran at build time and that fit this role very
well. For graphical applications, chroots or virtual machines are
needed.

Have a nice day,

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

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