Nabble - debian-med

FELIZ NATAL

2009-12-18T12:30:16Z

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Re: [Debian-med-packaging] dicomscope_3.6.0-1_i386.changes REJECTED

2009-12-17T14:42:07Z

Hi!

On Thu, Dec 17, 2009 at 8:13 PM, Barry deFreese <bdefreese@...> wrote:
> Ah, if the pdfs were generated from the source then that is OK and is my
> mistake. The lut files sound OK too. If those were the only two binary file
> types, we should be OK, just re-upload and I will fast-track it.

Just a suggestion, as this is the second or third time that I see this
happening: can't we get questions first and, if necessary, a reject
after?
Now it seems that it happens like this: reject the package and then
ask about it (and ask to reupload it when the doubts are answered).
It would save some time from the maintainers and also some bandwidth.

Thank you!

Best regards,
Nelson

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Re: dicomscope_3.6.0-1_i386.changes REJECTED

2009-12-17T14:13:09Z

Mathieu Malaterre wrote:

> I thought the situation for the pdf was ok (andreas could you
> confirm?). We described what they are in :
>
> $ cat doc-base.dscs
> $ cat doc-base.dsum
>
> As for the .lut file. Those are DICOM files:
>
>
> $ dcmdump dicomscope-3.6.0/DICOMscope/lut/philips256us.lut
>
> # Dicom-File-Format
>
> # Dicom-Meta-Information-Header
> # Used TransferSyntax: LittleEndianExplicit
> (0002,0000) UL 194 # 4, 1
> MetaElementGroupLength
> (0002,0001) OB 00\01 # 2, 1
> FileMetaInformationVersion
> (0002,0002) UI [1.2.276.0.7230010.3.1.0.1] # 26, 1
> MediaStorageSOPClassUID
> (0002,0003) UI [1.2.276.0.7230010.3.4.2139363186.15432.940262485.1] #
> 50, 1 MediaStorageSOPInstanceUID
> (0002,0010) UI =LittleEndianExplicit # 20, 1
> TransferSyntaxUID
> (0002,0012) UI [1.2.276.0.7230010.3.0.3.4.0] # 28, 1
> ImplementationClassUID
> (0002,0013) SH [OFFIS_DCMTK_340] # 16, 1
> ImplementationVersionName
>
> # Dicom-Data-Set
> # Used TransferSyntax: LittleEndianExplicit
> (2050,0010) SQ (Sequence with undefined length #=1) # u/l, 1
> PresentationLUTSequence
> (fffe,e000) na (Item with undefined length #=3) # u/l, 1 Item
> (0028,3002) US 256\0\12 # 6, 3
> LUTDescriptor
> (0028,3003) LO [Difference between GSDF and Philips Standard
> Display Curve] # 58, 1 LUTExplanation
> (0028,3006) US
> 0\22\43\65\87\109\131\152\174\195\217\238\260\281\302\324\345\366... #
> 512,256 LUTData
> (fffe,e00d) na (ItemDelimitationItem) # 0, 0
> ItemDelimitationItem
> (fffe,e0dd) na (SequenceDelimitationItem) # 0, 0
> SequenceDelimitationItem
>
>
> They were created by the dcmmklut program from DCMTK package.
>
> On Thu, Dec 17, 2009 at 8:04 PM, Barry deFreese <ftpmaster@...> wrote:
>> Hello maintainer,
>>
>> I am rejecting dicomscope for the following reasons:
>>
>> Several binary file types under the DICOMscope dir seem to have no source. For examples docs/*.pdf, lut/*.lut (These might be OK). and others.
>>
>> Thank you,
>>
>> Barry deFreese
>> Debian FTP Assistant
>>
>>
>>
>> ===
>>
>> Please feel free to respond to this email if you don't understand why
>> your files were rejected, or if you upload new files which address our
>> concerns.
>>
>>
>
>
>

Ah, if the pdfs were generated from the source then that is OK and is my
mistake. The lut files sound OK too. If those were the only two binary file
types, we should be OK, just re-upload and I will fast-track it.

Sorry,

Barry deFreese
Debian FTP Assistant

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Re: dicomscope_3.6.0-1_i386.changes REJECTED

2009-12-17T13:46:05Z

I thought the situation for the pdf was ok (andreas could you
confirm?). We described what they are in :

$ cat doc-base.dscs
$ cat doc-base.dsum

As for the .lut file. Those are DICOM files:

$ dcmdump dicomscope-3.6.0/DICOMscope/lut/philips256us.lut

# Dicom-File-Format

# Dicom-Meta-Information-Header
# Used TransferSyntax: LittleEndianExplicit
(0002,0000) UL 194 # 4, 1
MetaElementGroupLength
(0002,0001) OB 00\01 # 2, 1
FileMetaInformationVersion
(0002,0002) UI [1.2.276.0.7230010.3.1.0.1] # 26, 1
MediaStorageSOPClassUID
(0002,0003) UI [1.2.276.0.7230010.3.4.2139363186.15432.940262485.1] #
50, 1 MediaStorageSOPInstanceUID
(0002,0010) UI =LittleEndianExplicit # 20, 1
TransferSyntaxUID
(0002,0012) UI [1.2.276.0.7230010.3.0.3.4.0] # 28, 1
ImplementationClassUID
(0002,0013) SH [OFFIS_DCMTK_340] # 16, 1
ImplementationVersionName

# Dicom-Data-Set
# Used TransferSyntax: LittleEndianExplicit
(2050,0010) SQ (Sequence with undefined length #=1) # u/l, 1
PresentationLUTSequence
(fffe,e000) na (Item with undefined length #=3) # u/l, 1 Item
(0028,3002) US 256\0\12 # 6, 3
LUTDescriptor
(0028,3003) LO [Difference between GSDF and Philips Standard
Display Curve] # 58, 1 LUTExplanation
(0028,3006) US
0\22\43\65\87\109\131\152\174\195\217\238\260\281\302\324\345\366... #
512,256 LUTData
(fffe,e00d) na (ItemDelimitationItem) # 0, 0
ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0
SequenceDelimitationItem

They were created by the dcmmklut program from DCMTK package.

On Thu, Dec 17, 2009 at 8:04 PM, Barry deFreese <ftpmaster@...> wrote:

> Hello maintainer,
>
> I am rejecting dicomscope for the following reasons:
>
> Several binary file types under the DICOMscope dir seem to have no source. For examples docs/*.pdf, lut/*.lut (These might be OK). and others.
>
> Thank you,
>
> Barry deFreese
> Debian FTP Assistant
>
>
>
> ===
>
> Please feel free to respond to this email if you don't understand why
> your files were rejected, or if you upload new files which address our
> concerns.
>
>

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Re: Pending upload: dicomscope / pixelmed

2009-12-14T08:22:14Z

On Mon, Dec 14, 2009 at 1:37 PM, Mathieu Malaterre
<mathieu.malaterre@...> wrote:
> Does anyone knows if there is something particular going on with NEW
> package ? dicomscope/pixelmed have not been uploaded (submitted ~3
> weeks ago).

Actually it can take months (so 3 week is normal) to new packages be
processed. It only depends on the available time of FTP masters and
FTP-assistants and/or how big the package is.

Best regards,
Nelson

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Pending upload: dicomscope / pixelmed

2009-12-14T07:37:37Z

Hi,

Does anyone knows if there is something particular going on with NEW
package ? dicomscope/pixelmed have not been uploaded (submitted ~3
weeks ago).

http://qa.debian.org/developer.php?login=debian-med-packaging@...#Pending%20uploads

Thanks,

--
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2009-12-10T03:12:10Z

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2009-12-09T16:15:33Z

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Re: pdb2pqr maintained by DebiChem team but in Debian Med repository?

2009-12-06T15:32:37Z

Le Sun, Dec 06, 2009 at 09:31:55PM +0100, Andreas Tille a écrit :
> On Sat, Dec 05, 2009 at 11:59:01PM +0100, Manuel Prinz wrote:
>
> > And what are the feeling towards the new source format? Is it OK with
> > the group to use 3.0 (whatever) or should I leave it at 1.0?
>
> Why not start using a new format if it is a new package. There are no
> certain numbers about packages using the new format but having some
> packages in this format let us gather some experience.

I am systematically converting the packages that have a direct benefit,
for instance the ones distributed as a bzipped tar archive (I like to use
exactly the same original tarball as Upstream). But note however that some
infrastructures like backports.org do not support the new formats yet.

Have a nice day,

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

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Re: pdb2pqr maintained by DebiChem team but in Debian Med repository?

2009-12-06T12:31:55Z

On Sat, Dec 05, 2009 at 11:59:01PM +0100, Manuel Prinz wrote:
> PDB2PQR also contains embedded copies of code which are not needed at
> all. The size might justify repacking. Any opinions on that?

In many cases it is a matter of taste. I'm personally in favour of
repackaging if it saves certain amount of code for download and
mirroring.

> And what are the feeling towards the new source format? Is it OK with
> the group to use 3.0 (whatever) or should I leave it at 1.0?

Why not start using a new format if it is a new package. There are no
certain numbers about packages using the new format but having some
packages in this format let us gather some experience.

Kind regards

Andreas.

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Re: pdb2pqr maintained by DebiChem team but in Debian Med repository?

2009-12-05T14:59:01Z

Hi Michael!

Am Samstag, den 05.12.2009, 21:16 +0100 schrieb Michael Banck:
> Did you get around taking a look? Otherwise, if you could point me to a
> public list of issues, I could try to evaluate the new upstream release
> myself.

I did yesterday and uploaded an updated version a few minutes ago. Most
of the discussion happened privately, so there's no real place to get
yourself informed.

I hope that the package will pass NEW. Copyright is my only concern but
I check with other developers and the things listed should be
sufficient. There is a fallback solution in case it doesn't.

Also, the package needs several changes to improve quality. I'm going to
address them soon. The package is functional as is, though I do not
distribute the webserver part; I also have no motivation to support that
at all, since it is quite hackish and not worth the trouble, IMHO.

PDB2PQR also contains embedded copies of code which are not needed at
all. The size might justify repacking. Any opinions on that?

And what are the feeling towards the new source format? Is it OK with
the group to use 3.0 (whatever) or should I leave it at 1.0?

Best regards
Manuel

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Re: pdb2pqr maintained by DebiChem team but in Debian Med repository?

2009-12-05T12:16:40Z

Hi Manuel,

On Mon, Nov 02, 2009 at 10:09:21AM +0100, Manuel Prinz wrote:

> Hi Michael,
>
> On Sun, 2009-11-01 at 20:47 +0100, Michael Banck wrote:
> > pdb2pqr-1.5 just got released, FYI. Do you know whether it solves those
> > issues?
>
> I know of the release but did not have time to check yet. But sincerely
> hope so! :)
>
> I will have a look at it this evening or the day after.

Did you get around taking a look? Otherwise, if you could point me to a
public list of issues, I could try to evaluate the new upstream release
myself.

Thanks,

Michael

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Re: Dcmtk in Group maintenance

2009-12-03T03:13:15Z

Hi Andreas,

On Thu, Dec 3, 2009 at 9:11 AM, Andreas Tille <andreas@...> wrote:

> Hi,
>
> I just uploaded a lintian clean package of dcmtk which is compliant to
> our policy which is using quilt patches exclusively. While there is
> one minor problem if you build with debuild twice in a row you get some
> changes in config/config.guess which are not reverted by clean target
> which I do not understand because I do backups before - but I think we
> can ignore this for the moment.
>
> It would be great if all interested people would test the new packaging.

Will do ASAP !

> Moreover I wonder what to do with the snapshots Mathieu worked on in a
> SVN branch. I have no idea about upstream development but if it is
> ready for our users we should probably proceed with newer upstream based
> on the packaging I introduced.

The API changed (therefore ABI too), and thus package such as
dicomscope will not work anymore.
I would also wait until the team makes an official release (there has
been a couple of regression during those snapshot release).

> I hope that my work might make packaging more transparent and I did not
> introduced any error. Please check carefully just in case!
>
> Kind regards and thanks to Jürgen for his initial work (and hopefully
> you will continue on this as well)

Thanks for cleaning up the package !

Regards,
--
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Re: Dcmtk in Group maintenance

2009-12-03T00:11:36Z

Hi,

I just uploaded a lintian clean package of dcmtk which is compliant to
our policy which is using quilt patches exclusively. While there is
one minor problem if you build with debuild twice in a row you get some
changes in config/config.guess which are not reverted by clean target
which I do not understand because I do backups before - but I think we
can ignore this for the moment.

It would be great if all interested people would test the new packaging.

Moreover I wonder what to do with the snapshots Mathieu worked on in a
SVN branch. I have no idea about upstream development but if it is
ready for our users we should probably proceed with newer upstream based
on the packaging I introduced.

I hope that my work might make packaging more transparent and I did not
introduced any error. Please check carefully just in case!

Kind regards and thanks to Jürgen for his initial work (and hopefully
you will continue on this as well)

Andreas.

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Fwd: [Insight-users] Fedora-RHEL packages: Status of "Patented" and "Review" directories

2009-12-02T13:34:04Z

Just FYI

---------- Forwarded message ----------
From: Luis Ibanez <luis.ibanez@...>
Date: Wed, Dec 2, 2009 at 10:32 PM
Subject: Re: [Insight-users] Fedora-RHEL packages: Status of
"Patented" and "Review" directories
To: Mario Ceresa <mrceresa@...>
Cc: insight-users@...

Hi Mario,

Thanks a lot for your efforts on packaging ITK for Fedora.

1) About the Patented directory:

It is not worth the trouble,

just exclude it.

We must get rid of it as soon as we can, anyways.

We shouldn't provide free advertisement for those
who decided to acquire 20-years monopolies for
excluding others from the use of ideas.

In fact, for some of the examples there, (the ICP,
the (20 year-long monopoly) "patent" has expired,
and the method is back in the public domain,
where it should have always been, given that
the US Congress have never authorized the
use of Patents for software. Even the
US Supreme Court made clear that only Congress
had the power for making such determination.
Not to mention that they have repeatedly clarified
that Algorithms are NOT patentable, because they
are equivalent to Mathematics and to Laws of
Nature.

It has been only the misguided decisions of the
US Court of Appeals of the Federal Circuit (CAFC)
that have brought the patent system to it current
mess.

With about 170,000 software patents being awarded,
it is practically impossible to write any piece of software
without infringing on somebody else's "imaginary property".

Nobody should own Mathematics.

Hopefully, now that the Bilsky case has been ruled
in the Supreme Court
( http://en.wikipedia.org/wiki/In_re_Bilski)
we may see some rational sense coming back to the
US Patent Office, and hopefully the CAFC will be
re-populated with more diverse Judges, as the
US National Academy of Science has recommended:
http://www7.nationalacademies.org/ocga/testimony/Patent_System_Overhaul.asp

2) About the Review directory:

Strictly speaking,
you must exclude it as well.

The copyright of many of the files in this directory
has not been officially transferred to the Insight
Software Consortium. Most of them have been
moved from the Insight Journal, but still the
copyright and license status is unclear.

We should focus on moving files from this
directory into the toolkit itself during the following
months.

Regards,

Luis

----------------------------------------------------------------------------------
On Wed, Dec 2, 2009 at 11:44 AM, Mario Ceresa <mrceresa@...> wrote:

> Hello everybody,
> things move slowly on the Fedora package front but moves!
> The reviewer asked me about possible copyright issues for the Review -
> Patented folders in the ITK build tree (ver 3.16).
>
> https://bugzilla.redhat.com/show_bug.cgi?id=539387#c6
>
> We agreed not to include Patented, but I'd like to include at least
> Review in the rpm because is needed for wrapitk (If I'm not
> mistaking).
>
> Does anyone know if the Review folder (or a subset of it) is
> compatible with one of these licenses?
>
> http://fedoraproject.org/wiki/Licensing#SoftwareLicenses
>
> Thanks and regards,
>
> Mario
>
> 2009/11/17 Mario Ceresa <mrceresa@...>:
>> Hello everybody,
>> first of all, thanks for the great work done: I've been happily using
>> both ITK and WrapITK for a while and also received a lot of help from
>> this mail list.
>>
>> Still I'm a bit confused about the packaging status: are there any
>> prebuilt packages available for Fedora/RHEL?
>> I noticed that while there are WrapITK packages for Debian/Ubuntu,
>> there seem to be none for Fedora/RHEL.
>>
>> Is there anyone interested in using binaries for this distributions?
>> If so, I would be more than happy to contribute back a package for the
>> two of them, or help anyone else who is working on it. Just let me
>> know!
>>
>> Thanks and regards,
>>
>> Mario
>>
> _____________________________________
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>
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>
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2009-11-28T19:58:04Z

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Re: Dcmtk in Group maintenance

2009-11-27T02:40:59Z

On Fri, Nov 27, 2009 at 11:11:48AM +0100, Juergen Salk wrote:
>
> I have to admit that I'm somewhat perplexed now. After our
> discussion back in May last year [1] and also after checking the

Uhm, sorry for the confusion. It's just my bad memory!

> I have to apologize for any misunderstanding on my side that
> might have caused this deadlock condition. What am I supposed to
> do in order to resolve this issue?

Just waiting and I apologize for not continuiong in this issue
after you just confirmed and I forgot to check the changelog in
SVN.

I'll keep in touch and update my mind

Andreas.

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Re: Dcmtk in Group maintenance

2009-11-27T02:11:48Z

Andreas Tille <andreas@...> wrote:

> I wonder if you might agree to maintain dcmtk in the Debian Med
> team. This package is one of the last one which is relevant for
> Debian Med not in group maintenance. IMHO we could fix #553495
> and commit to SVN (or at your preference to git).

> What do you think?

Hi Andreas,

I have to admit that I'm somewhat perplexed now. After our
discussion back in May last year [1] and also after checking the
the package changelog in SVN [2] I was under the perception that
DCMTK already went into group maintenance. This is actually one
of the reasons that made me step back from the first row with a
quiet conscience.

I have to apologize for any misunderstanding on my side that
might have caused this deadlock condition. What am I supposed to
do in order to resolve this issue?

Best regards - Juergen

[1] http://lists.debian.org/debian-med/2008/05/msg00023.html ff.
[2] http://svn.debian.org/wsvn/debian-med/trunk/packages/dcmtk/trunk/debian/changelog?rev=2800&sc=1

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R-cran-psy in Debian Med team?

2009-11-27T00:19:02Z

Hi Chris,

you might have noticed that your r-cran-psy package is part of the
Debian Med task psychology:

http://debian-med.alioth.debian.org/tasks/psychology

While browsing this page I realised that no Homepage field is mentioned
in the debian/control file and the package is not group maintained. I
wonder whether you are interested in maintaining the package in the
Debian Med team where also other people are working on psychology
related packages. The advantage in this probably low maintenance
package which seems to be orphaned upstream would be that in cases like
the R 2.10 rebuild could be done in a coordinated effort.

Moreover I would really like if you would bring in some competence in
this field into the Debian Med team.

Whatever you decide it would be great if you would at least add the
Homepage field to debian/control in your next upload.

Kind regards

Andreas.

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Dcmtk in Group maintenance

2009-11-26T23:12:59Z

Hi Jürgen,

I wonder if you might agree to maintain dcmtk in the Debian Med team.
This package is one of the last one which is relevant for Debian Med
not in group maintenance. IMHO we could fix #553495 and commit to
SVN (or at your preference to git).

What do you think?

Kind regards

Andreas.

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Article in Genome Biology: Searching for SNPs with cloud computing.

2009-11-25T06:48:19Z

Dear all,

Here are an abstract and a link to an article in Genome Biology where free
software is used in a cloud to analyse human genetic polymorphisms:

Open AccessSoftware

Searching for SNPs with cloud computing

Ben Langmead email, Michael C Schatz email, Jimmy Lin email, Mihai Pop email
and Steven L Salzberg email

Genome Biology 2009, 10:R134doi:10.1186/gb-2009-10-11-r134
Published: 20 November 2009
Abstract (provisional)

As DNA sequencing outpaces improvements in computer speed, there is a critical
need to accelerate tasks like alignment and SNP calling. Crossbow is a
cloud-computing software tool that combines the aligner Bowtie and the SNP
caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data
comprising 38-fold coverage of the human genome in three hours using a 320-CPU
cluster rented from a cloud computing service for about $85. Crossbow is
available from http://bowtie-bio.sf.net/crossbow.

http://genomebiology.com/2009/10/11/R134

Have a nice day,

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Re: Can backports be built with backports ?

2009-11-24T12:15:36Z

Charles Plessy schrieb am Tuesday, den 24. November 2009:

Hi,

*snip*
> If I package ExtUtils::Manifest, let it go in testing, and if you then accept a
> backport of it, will it be possible to build a bioperl backport using it? Said
> differently, do the backports buildds use backports.org to satisfy dependancies
> not in Lenny? (Sorry I did not manage to find the information).
Of course they can. The same rules as for experimental apply (if there is a
version in stable and bpo add a versioned build-dep to your package).

Alex

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Re: Can backports be built with backports ?

2009-11-24T07:26:28Z

On 24 Nov 2009, at 2:20 pm, Charles Plessy wrote:

> I would like to backport the bioperl package as well (a bigger
> beast), and it
> needs ExtUtils::Manifest >= 1.52 to build (but not to run). However
> Lenny's
> perl-modules package does not provide such a high version.

Hehe, hi Charles. Now you know why, when I discussed this with you a
couple of years ago at Debconf, that I said I didn't use Debian
packaged sequencing packages. All the dependencies are a nightmare,
the scientists always want the very latest of this, and simultaneously
some ancient version of that, and they want multiple versions of
everything installed simultaneously. It's a nightmare.

That's not to say that I don't think you and the Debian Med team are
doing a fabulous job. I'm just saying I really don't envy you. Me, I
just install all this crap on an NFS server and be done with it. Our /
software central NFS server now contains more than 600GB of various
versions of software the scientists want. Actually, I don't install
most of it. Fortunately, they're allowed to build their own stuff,
which makes my life a bit simpler (and accounts for a lot of the size
- multiple installs for different groups of different versions of
apache, tomcat, bioperl, ssaha, blast, you name it)

Still 600GB is nothing in the world of next-gen sequencing, n'est-ce
pas? We've got a 0.5 petabyte Lustre filesystem just as a staging
area for the sequencers... 600GB is less than one disk spindle.

Tim

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company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.

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Re: Can backports be built with backports ?

2009-11-24T06:26:00Z

Le 24 nov. 09 à 15:20, Charles Plessy a écrit :

> Said differently, do the backports buildds use backports.org to
> satisfy dependancies
> not in Lenny? (Sorry I did not manage to find the information).

AFAICT, they do. It's not so uncommon to package build-dependencies,
for instance debhelper.

T.

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Can backports be built with backports ?

2009-11-24T06:20:17Z

Hi Alexander, thank you for the fast answer!

Le Tue, Nov 24, 2009 at 06:55:55AM +0100, Alexander Wirt a écrit :

> Charles Plessy schrieb am Monday, den 23. November 2009:
>
> > I have another question… The package I tried to upload is ‘bwa’, which has a
> > popcon score of less than ten, but of course a bright future :) It seems to
> > contradict directly your rule ‘Please only upload package with a noteable
> > userbase’. My purpose in this upload is to offer backports from a highly
> > trustable environment, in order to help the creation of ‘cloud’ images based
> > on Lenny but with the latest software in my speciality. Would such packages
> > be accepted ? (I am their maintainer in Debian).
> Even after reading the description I don't have a clue what to do with that
> application :). But go ahead.

I just uploaded bwa to bp.o's NEW queue. bwa is part of a bunch of packages
related to ‘next-generation sequencing’, that is about sequencing (our)
genomes. Not to mention that it is useful for my work, I also hope that by
supporting free software in this area it will help to build a good world, in
opposition to a ‘Brave New World’ !

I would like to backport the bioperl package as well (a bigger beast), and it
needs ExtUtils::Manifest >= 1.52 to build (but not to run). However Lenny's
perl-modules package does not provide such a high version.

If I package ExtUtils::Manifest, let it go in testing, and if you then accept a
backport of it, will it be possible to build a bioperl backport using it? Said
differently, do the backports buildds use backports.org to satisfy dependancies
not in Lenny? (Sorry I did not manage to find the information).

Have a nice day,

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

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Re: [Pkg-exppsy-maintainers] Team maintenance of Praat?

2009-11-24T06:12:29Z

On Tue, Nov 24, 2009 at 10:59:23PM +0900, Charles Plessy wrote:

> Le Tue, Nov 24, 2009 at 02:39:05PM +0100, Andreas Tille a écrit :
> > On Tue, Nov 24, 2009 at 08:22:36AM -0500, Michael Hanke wrote:
> > >
> > > praat is essential for psychological research on speech perception. The
> > > package should live where it would get the most attention -- regardless
> > > of the name of the team. ExpPsy can take it. However, we are probably
> > > the smallest of all candidate teams. So, if there is a chance that it
> > > would be better off staying in -science or -med that would be the
> > > preferred choice, IMHO.
> >
> > Considering the fact that ExpPsy maintainers are also close to Debian
> > Med and Debian Science it is finally not really important in which
> > repository the package might end up. So I probably will move on with
> > Debian Med except somebody disagrees.
>
> In addition, all DDs have write access to the Debian Med repostitories… So
> after the moving has been officialised by an upload, ‘debcheckout -a praat’
> will allow all of us to work on this package. In case some guest accounts from
> the ExpPsy need access, we can grant write access to all the ExpPsy team
> through ACLs.

Thanks. It should all be fine if it lives in -med.

Michael

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Re: [Pkg-exppsy-maintainers] Team maintenance of Praat?

2009-11-24T05:59:23Z

Le Tue, Nov 24, 2009 at 02:39:05PM +0100, Andreas Tille a écrit :

> On Tue, Nov 24, 2009 at 08:22:36AM -0500, Michael Hanke wrote:
> >
> > praat is essential for psychological research on speech perception. The
> > package should live where it would get the most attention -- regardless
> > of the name of the team. ExpPsy can take it. However, we are probably
> > the smallest of all candidate teams. So, if there is a chance that it
> > would be better off staying in -science or -med that would be the
> > preferred choice, IMHO.
>
> Considering the fact that ExpPsy maintainers are also close to Debian
> Med and Debian Science it is finally not really important in which
> repository the package might end up. So I probably will move on with
> Debian Med except somebody disagrees.

In addition, all DDs have write access to the Debian Med repostitories… So
after the moving has been officialised by an upload, ‘debcheckout -a praat’
will allow all of us to work on this package. In case some guest accounts from
the ExpPsy need access, we can grant write access to all the ExpPsy team
through ACLs.

Have a nice day,

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

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Re: [Pkg-exppsy-maintainers] Team maintenance of Praat?

2009-11-24T05:50:40Z

* Andreas Tille <andreas@...> [2009-11-24 14:39]:

> Raphael, you had a lot of other packages. Any other targets for
> Debian Med or Debian Science we might have missed?

The huge majority of the packages were co-maintained. From the few ones
that I maintained alone, no one besides praat should interest the
debian-med and -science teams.

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Re: [Pkg-exppsy-maintainers] Team maintenance of Praat?

2009-11-24T05:39:05Z

On Tue, Nov 24, 2009 at 08:22:36AM -0500, Michael Hanke wrote:
>
> praat is essential for psychological research on speech perception. The
> package should live where it would get the most attention -- regardless
> of the name of the team. ExpPsy can take it. However, we are probably
> the smallest of all candidate teams. So, if there is a chance that it
> would be better off staying in -science or -med that would be the
> preferred choice, IMHO.

Considering the fact that ExpPsy maintainers are also close to Debian
Med and Debian Science it is finally not really important in which
repository the package might end up. So I probably will move on with
Debian Med except somebody disagrees.

Raphael, you had a lot of other packages. Any other targets for
Debian Med or Debian Science we might have missed?

Kind regards

Andreas.

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Re: Team maintenance of Praat?

2009-11-24T05:34:51Z

On Tue, Nov 24, 2009 at 01:42:37PM +0100, Rafael Laboissiere wrote:
> The praat package may also interest the members of the Debian Science
> Team.

I finally don't mind which team takes over but regarding the fact that
Rafael retired any of the teams in question should step in soon. What
do Experimental Psychology Maintainers think? If they have no interest
I'll take over and put it either in Debian Med or Debian Science.

> At any rate, the praat package should not remain abandoned in Debian. It
> is highly actively maintained upstream and has a good user basis among
> speech scientists.

Thanks for the information.

> Thanks for taking care of this.

Sure. Thanks for packaging it for Debian in the first place

Andreas.

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Re: [Pkg-exppsy-maintainers] Team maintenance of Praat?

2009-11-24T05:22:36Z

On Tue, Nov 24, 2009 at 01:42:37PM +0100, Rafael Laboissiere wrote:

> * Andreas Tille <andreas@...> [2009-11-24 13:24]:
>
> > The package praat is listed as part of the psychology task of Debian
> > Med[1]. I wonder if it might make sense to put it under group
> > maintenance of either the Experimental Psychology Maintainers team
> > (fits probably best) or if there is no interest in the Debian Med team.
> > This might be helpful to make sure that we are not lagging behind
> > upstream (if there is no reason to stick to a certain version which
> > should be mentioned on the tasks page).
> >
> > Rafael, what do you think about this? We would welcome new team
> > members and have good experience in team maintenance.
>
> The praat package may also interest the members of the Debian Science
> Team.
>
> At any rate, the praat package should not remain abandoned in Debian. It
> is highly actively maintained upstream and has a good user basis among
> speech scientists.

+1

praat is essential for psychological research on speech perception. The
package should live where it would get the most attention -- regardless
of the name of the team. ExpPsy can take it. However, we are probably
the smallest of all candidate teams. So, if there is a chance that it
would be better off staying in -science or -med that would be the
preferred choice, IMHO.

Michael

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Re: Team maintenance of Praat?

2009-11-24T04:42:37Z

* Andreas Tille <andreas@...> [2009-11-24 13:24]:

> The package praat is listed as part of the psychology task of Debian
> Med[1]. I wonder if it might make sense to put it under group
> maintenance of either the Experimental Psychology Maintainers team
> (fits probably best) or if there is no interest in the Debian Med team.
> This might be helpful to make sure that we are not lagging behind
> upstream (if there is no reason to stick to a certain version which
> should be mentioned on the tasks page).
>
> Rafael, what do you think about this? We would welcome new team
> members and have good experience in team maintenance.

The praat package may also interest the members of the Debian Science
Team.

At any rate, the praat package should not remain abandoned in Debian. It
is highly actively maintained upstream and has a good user basis among
speech scientists.

Thanks for taking care of this.

Cheers,

--
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Team maintenance of Praat?

2009-11-24T02:37:51Z

Hi,

The package praat is listed as part of the psychology task of Debian
Med[1]. I wonder if it might make sense to put it under group
maintenance of either the Experimental Psychology Maintainers team (fits
probably best) or if there is no interest in the Debian Med team. This
might be helpful to make sure that we are not lagging behind upstream
(if there is no reason to stick to a certain version which should be
mentioned on the tasks page).

Rafael, what do you think about this? We would welcome new team
members and have good experience in team maintenance.

Kind regards

Andreas.

[1] http://debian-med.alioth.debian.org/tasks/psychology

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Re: Update on WrapITK and debian

2009-11-24T00:51:48Z

On Tue, Nov 24, 2009 at 8:09 AM, Steve M. Robbins <steve@...> wrote:

> On Mon, Nov 23, 2009 at 06:45:06PM +0100, Mathieu Malaterre wrote:
>> Steve,
>>
>> I thought I should give an update.
>> I have been trying for the past weeks to get WrapITK working without
>> Review. I have to admit I never succeeded (see all my attempt
>> commented out in the patch file). I do not say it is not possible, I
>> am saying this is really hard.
>
> I didn't see the commented-out patch. What is the difficulty?

You have to comment out entire groups. Filters are re-groupped
together assuming Review is ON.

@@ -0,0 +1,25 @@
+--- insighttoolkit-3.4.0.orig/Wrapping/WrapITK/CMakeLists.txt 2009-11-09
14:28:31.000000000 +0100
++++ insighttoolkit-3.4.0/Wrapping/WrapITK/CMakeLists.txt.old 2009-11-09
14:28:13.000000000 +0100
+@@ -145,8 +145,8 @@
+ Denoising
+ DistanceMap
+ EdgesAndContours
+- FFT
+- FFTW
++ #FFT
++ #FFTW
+ Filtering
+ IntensityFilters
+ Interpolators
+@@ -156,9 +156,9 @@
+ Morphology
+ #Patented
+ PixelMath
+- Registration
++ #Registration
+ Resize
+- Review
++ #Review
+ SegmentationAndThreshold
+ SegmentationValidation
+ SimpleFilters

Some filters even internally uses itkFlatStructuringElement or
itkKernelImageFilter to provide basic wrapping functionalities.

@@ -102,7 +112,8 @@
get-orig-source: $(UPSTREAM_SRC).tar.gz
tar xzf $(UPSTREAM_SRC).tar.gz
find $(UPSTREAM_SRC) -name CVS -o -name Patented | xargs rm -rf
- rm -rf $(UPSTREAM_SRC)/Code/Review
+ #rm -rf $(UPSTREAM_SRC)/Code/Review
+ #find $(UPSTREAM_SRC)/Code/Review -type f | grep -v
itkComposeRGBAImageFilter | grep -v itkFlatStructuringElement | grep
-v itkKernelImageFilter | grep -v itkSharedMorphologyUtilities | grep
-v itkBoxImageFilter | grep -v itkVanHerkGilWermanDilateImageFilter |
grep -v itkVanHerkGilWermanErodeDilateImageFilter | grep -v
itkBresenhamLine | grep -v itkVanHerkGilWermanUtilities | xargs rm -rf
mv $(UPSTREAM_SRC) $(DEBIAN_SRC_DIR)
GZIP=-9 tar czf $(DEBIAN_SRC_TAR) $(DEBIAN_SRC_DIR)

> Could we get upstream help for this?

I have CC Gaetan, he mentionned that building without Review will be very hard.
The point being that at any time Review will be integrated into the
main source. Until REVIEW option is properly handled in WrapITK, I
think this will not be a task upstream will handle.

>> Let me know what you think of including Review in ITK.
>
> I'd really prefer not to do so, as Review provides no guarantee
> of license suitability nor stability.

Ok.

thanks,
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Re: Update on WrapITK and debian

2009-11-23T23:09:49Z

On Mon, Nov 23, 2009 at 06:45:06PM +0100, Mathieu Malaterre wrote:
> Steve,
>
> I thought I should give an update.
> I have been trying for the past weeks to get WrapITK working without
> Review. I have to admit I never succeeded (see all my attempt
> commented out in the patch file). I do not say it is not possible, I
> am saying this is really hard.

I didn't see the commented-out patch. What is the difficulty?
Could we get upstream help for this?

> Let me know what you think of including Review in ITK.

I'd really prefer not to do so, as Review provides no guarantee
of license suitability nor stability.

Regards,
-Steve

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