Re: bedtools version 2.18.0

[Andreas Tille]

Hi,

On Sat, Dec 14, 2013 at 07:23:08PM +0100, Thorsten Alteholz wrote:
> 
> DFSG 2 says that the source must be included. So if the PNG has been
> created, for example with gimp, there should be an XCF file
> available and part of the package ...

As long as the author of the graphic really stores it in XCF format.
Since we usually have less chances to really know what upstream has on
their harddisk I would not spent my time with pure speculation and spend
time / loose momentum with beeing overly picky about this since I can
not see in how far this is helpful for anybody.  I do not think that
DFSG was written in the mind of blocking us.

Kind regards

  Andreas.

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Fis-gtm accepted in unstable (Was: Packaging VistA - GT.M directories)

[Andreas Tille]

Hi,

finally we have a nice Christmas gift for all people dealing with VistA:
fis-gtm is now accepted in unstable.  Now it is time to work on
reasonable VistA packages and we *really* need to rely on upstream to
let this happen.  I think we should start now(ish) on this heavy task
since the time to next freeze is short (only less than 11 monthes and it
took us about two years to get fis-gtm in).  I'm offering all my help to
*guide* into Debian internals, *mentor* people who have VistA internal
knowledge oir whatever - but I personally can not take the lead in the
main packaging effort since I feel totally incapable doe to a lack of
even basic knowledge about this complex system.

Thanks to everybody who has helped to let fis-gtm packages become
available in official Debian

   Andreas.

On Sat, Jul 14, 2012 at 05:25:05PM +0200, Nicolas Barbier wrote:
> 2012/7/14 Luis Ibanez :
> 
> > Our first rough cut at the directory structure
> > for the VistA Debian package has been:
> >
> >
> > /var/lib/vista/
> > /var/lib/vista/r
> > /var/lib/vista/o
> > /var/lib/vista/g
> > /var/lib/vista/j
> > /var/lib/vista/logs
> > /var/lib/vista/inetd
> > /var/lib/vista/profile
> 
> (I apologize beforehand for being largely ignorant about the way
> Debian packages work. I also hope that this question hasn’t been asked
> and answered before.)
> 
> I have a problem understanding how the following would work:
> 
> * The package seems to contain files constituting a database (which
> seems to mean both data and code in an M context).
> * Those files are put in /var/, and are therefore probably expected to
> change during the normal course of operations (e.g., when VistA is
> being used by users).
> * Are those files therefore supposed to be considered “configuration
> files”? (Because package-provided non-configuration files are not
> supposed to be changed except by the package management system.)
> * If so, how are updates supposed to work? Do newer packages contain a
> full “pristine” version of a VistA database or rather files that
> describe how to update existing files (“KIDS patches”)?
> * Such a full pristine version seems to be required in any case,
> because otherwise I don’t see how users that install the newer package
> without upgrading from an older version would be able to get a VistA
> database.
> 
> I.e., I don’t understand how the mixture of user data (changed
> continuously) and code-like stuff (normally managed by the package
> management system) is going to be implemented by the package.
> 
> Are there other packages that had to solve a similar problem?
> 
> Nicolas
> 
> -- 
> A. Because it breaks the logical sequence of discussion.
> Q. Why is top posting bad?
> 
> 
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> 

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Re: Fis-gtm accepted in unstable

[Amul Shah]

Andreas,

> On Dec 15, 2013, at 1:18 PM, Andreas Tille  wrote:
> 
> Hi,
> 
> finally we have a nice Christmas gift for all people dealing with VistA:
> fis-gtm is now accepted in unstable.  

Excellent news!

Regarding fis-gtm, what work remains for the existing packaging? Off the top my 
head I know that we need man pages.

The next release will have some build changes for which I may need 
help/guidance from the good folks at Kitware. 

Thanks
Amul


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Re: Fis-gtm accepted in unstable

[Luis Ibanez]

This is great news !!

Many thanks for all your hard work on making this happen !

   Luis



On Sun, Dec 15, 2013 at 3:43 PM, Amul Shah  wrote:

> Andreas,
>
> > On Dec 15, 2013, at 1:18 PM, Andreas Tille  wrote:
> >
> > Hi,
> >
> > finally we have a nice Christmas gift for all people dealing with VistA:
> > fis-gtm is now accepted in unstable.
>
> Excellent news!
>
> Regarding fis-gtm, what work remains for the existing packaging? Off the
> top my head I know that we need man pages.
>
> The next release will have some build changes for which I may need
> help/guidance from the good folks at Kitware.
>
> Thanks
> Amul
>
>

Re: Fis-gtm accepted in unstable

[Bhaskar, K.S]

Yes, thanks to all, and especially Andreas Tille, Amul Shah, Luis Ibañez 
and Brad King.


And now on to VistA, which I will try to take on.  Let me think about the 
right flavor, though.  There is a code convergence project to merge the 
various flavors ( http://www.osehra.org/group/code-convergence), and the 
question is whether to wait for that, or to start with WorldVistA EHR.


Regards
-- Bhaskar

On 12/15/2013 04:04 PM (US Eastern Time), Luis Ibanez wrote:

This is great news !!

Many thanks for all your hard work on making this happen !

   Luis



On Sun, Dec 15, 2013 at 3:43 PM, Amul Shah > wrote:


Andreas,

> On Dec 15, 2013, at 1:18 PM, Andreas Tille mailto:andr...@an3as.eu>> wrote:
>
> Hi,
>
> finally we have a nice Christmas gift for all people dealing with
VistA:
> fis-gtm is now accepted in unstable.

Excellent news!

Regarding fis-gtm, what work remains for the existing packaging?
Off the top my head I know that we need man pages.

The next release will have some build changes for which I may need
help/guidance from the good folks at Kitware.

Thanks
Amul




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Re: Fis-gtm accepted in unstable

[Luis Ibanez]

Yes ! now on to VistA.


FWIW, here is what I started crafting for it a while ago:

 https://github.com/luisibanez/debian-med-vista

It may help as a starting point for discussion.

It will have to be updated to catch up with the final settings
of the fis-gtm package.


Regarding the VistA version, fully agree with Bhaskar on
using building on the efforts of the code convergence group.


   Regards,


  Luis



On Sun, Dec 15, 2013 at 5:38 PM, Bhaskar, K.S wrote:

>  Yes, thanks to all, and especially Andreas Tille, Amul Shah, Luis Ibañez
> and Brad King.
>
> And now on to VistA, which I will try to take on.  Let me think about the
> right flavor, though.  There is a code convergence project to merge the
> various flavors ( http://www.osehra.org/group/code-convergence), and the
> question is whether to wait for that, or to start with WorldVistA EHR.
>
> Regards
> -- Bhaskar
>
>
> On 12/15/2013 04:04 PM (US Eastern Time), Luis Ibanez wrote:
>
> This is great news !!
>
>  Many thanks for all your hard work on making this happen !
>
> Luis
>
>
>
>  On Sun, Dec 15, 2013 at 3:43 PM, Amul Shah  wrote:
>
>> Andreas,
>>
>> > On Dec 15, 2013, at 1:18 PM, Andreas Tille  wrote:
>> >
>> > Hi,
>> >
>> > finally we have a nice Christmas gift for all people dealing with VistA:
>> > fis-gtm is now accepted in unstable.
>>
>> Excellent news!
>>
>> Regarding fis-gtm, what work remains for the existing packaging? Off the
>> top my head I know that we need man pages.
>>
>> The next release will have some build changes for which I may need
>> help/guidance from the good folks at Kitware.
>>
>> Thanks
>> Amul
>>
>>
>
> --
> GT.M - Rock solid. Lightning fast. Secure. No compromises.
>
>  _
> The information contained in this message is proprietary and/or
> confidential. If you are not the intended recipient, please: (i) delete the
> message and all copies; (ii) do not disclose, distribute or use the message
> in any manner; and (iii) notify the sender immediately. In addition, please
> be aware that any message addressed to our domain is subject to archiving
> and review by persons other than the intended recipient. Thank you.
>

Re: Fis-gtm accepted in unstable (Was: Packaging VistA - GT.M directories)

[Yaroslav Halchenko]

On Sun, 15 Dec 2013, Andreas Tille wrote:
> finally we have a nice Christmas gift for all people dealing with VistA:
> fis-gtm is now accepted in unstable.  
> >...<
> Thanks to everybody who has helped to let fis-gtm packages become
> available in official Debian

hip hip hoorray -- go Team! ;)

-- 
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Senior Research Associate, Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik


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Re: Fis-gtm accepted in unstable (Was: Packaging VistA - GT.M directories)

[Luis Ibanez]

On Sun, Dec 15, 2013 at 8:20 PM, Yaroslav Halchenko
wrote:

>
> On Sun, 15 Dec 2013, Andreas Tille wrote:
> > finally we have a nice Christmas gift for all people dealing with VistA:
> > fis-gtm is now accepted in unstable.
> > >...<
> > Thanks to everybody who has helped to let fis-gtm packages become
> > available in official Debian
>
> hip hip hoorray -- go Team! ;)
>
>


This is great news !

Many Thanks to all who helped make this happen !


Yes, let's move into packaging VistA.

Here is what we put together a while ago.

   https://github.com/luisibanez/debian-med-vista

It could be the beginning of the conversation.
It has to be updated now, to match the final form of the fis-gtm package,
and to match the latest representation of VistA in the github repository:

https://github.com/OSEHRA/VistA-M


Maybe we should plan a hackathon for this:-)


   Best


   Luis

Re: Fis-gtm accepted in unstable (Was: Packaging VistA - GT.M directories)

[Bhaskar, K.S]

Yaroslav, how could I forget to mention you in my thanks!  You drove 
several hours to our hackathon to help us get GT.M packaged.


Regards
-- Bhaskar

On 12/15/2013 08:20 PM (US Eastern Time), Yaroslav Halchenko wrote:

On Sun, 15 Dec 2013, Andreas Tille wrote:

finally we have a nice Christmas gift for all people dealing with VistA:
fis-gtm is now accepted in unstable.

...<

Thanks to everybody who has helped to let fis-gtm packages become
available in official Debian

hip hip hoorray -- go Team! ;)



--
GT.M - Rock solid. Lightning fast. Secure. No compromises.

_
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Re: Fis-gtm accepted in unstable (Was: Packaging VistA - GT.M directories)

[Yaroslav Halchenko]

On Sun, 15 Dec 2013, Bhaskar, K.S wrote:

> Yaroslav, how could I forget to mention you in my thanks! 
> You drove several hours to our hackathon to help us get GT.M packaged.

well -- that was so long ago now it seems, so it is not surprising
that those sweet memories about the hackathon were not as vivid ;-)

P.S. In general I like driving (unless multi-hour trips becomes
too often), so it was only a pleasure and not a hassle at all.  Thanks
again to Kitware for covering it up.

-- 
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Senior Research Associate, Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik


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Make Colt-lib: DynamicBin1D Thread safe.

[Malavika]

Hello,

I am using the Debian Colt library version 1.2.0 for some heavy
calculations and I see that my system deadlocks randomly. The simplified
test case to reproduce the deadlock is given below. The library is claimed
to be thread safe but deadlocks are found.


import hep.aida.bin.DynamicBin1D;
import cern.colt.function.DoubleDoubleFunction;
import cern.colt.matrix.DoubleFactory1D;
import cern.colt.matrix.DoubleFactory2D;
import cern.colt.matrix.DoubleMatrix1D;
import cern.colt.matrix.DoubleMatrix2D;
import cern.colt.matrix.DoubleMatrix3D;
import cern.jet.random.engine.RandomEngine;
public class OmenTestCase34 {


public static void main(String args[])
{
DynamicBin1D bin = new DynamicBin1D();
DynamicBin1D bin2 = new DynamicBin1D();
double[] v1 = { 1, 2, 3, 4, 5, 6, 7, 8, 9,10,  21,
22,23,24,25,26,27,28,29,30,31};
double[] v2 = {10,11,12,13,14,15,16,17,18,19,  20,
30,31,32,33,34,35,36,37,38,39};
bin2.addAllOf(new cern.colt.list.DoubleArrayList(v1));
bin2.addAllOf(new cern.colt.list.DoubleArrayList(v2));
CovarianceCalculator t1 = new CovarianceCalculator(bin,
bin2);
t1.start();
CorrelationCalculator t2 = new CorrelationCalculator(bin,
bin2);
t2.start();
}

}
class CovarianceCalculator extends Thread {
DynamicBin1D l2;
DynamicBin1D l3;
public CovarianceCalculator(DynamicBin1D bin, DynamicBin1D bin2) {
l2 = bin;
l3 = bin2;
}

public void run() {
System.out.println(l3.covariance(l2));
}
}

class CorrelationCalculator extends Thread {
DynamicBin1D l2;
DynamicBin1D l3;
public CorrelationCalculator(DynamicBin1D bin, DynamicBin1D bin2) {
l2 = bin;
l3 = bin2;
}

public void run() {
System.out.println(l2.correlation(l3));
}
}

Regards,
Malavika


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Bug#732264: ITP: probabel -- Toolset for Genome-Wide Association Analysis

[L.C. Karssen]

Package: wnpp
Severity: wishlist
Owner: "Debian Med team" 

* Package name: probabel
  Version : 0.4.1
  Upstream Author : L.C. Karssen 
* URL : http://www.genabel.org/packages/ProbABEL
* License : GPL
  Programming Lang: C, C++, Perl
  Description : Toolset for Genome-Wide Association Analysis

The ProbABEL package is part of the GenABEL project for analysis of genome-wide
 data. ProbABEL is used to run GWAS. Using files in filevector/DatABEL format
 even allows for running GWAS on computers with only a few GB of RAM.


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Re: looking for a review for pycorrfit

[Simon Kainz]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Am 2013-12-13 16:40, schrieb Alex Mestiashvili:
> Hi All,
> 
> I am looking for a review for my package pycorrfit [0], ITP
> #730640. Lintian is clear, but I am pretty sure there are hidden
> issues :)
> 
> Also I am not sure what to do with png images in doc-src/Images
> directory. There are svg files as well, but I haven't managed to
> correctly convert the svg files to png. It would be great if you
> would give me ideas or examples.
> 
> Thanks, Alex
> 
> 
> [0]
> http://anonscm.debian.org/gitweb/?p=debian-med/pycorrfit.git;a=summary
>
> 
> 
Hi!

The manpage mentions documentation it at

/usr/share/doc/pycorrfit/PyCorrFit_doc.pdf.gz

which is not true.


skainz@foo:~$ dpkg -L pycorrfit |grep pdf
/usr/share/pyshared/pycorrfit_doc/PyCorrFit_doc.pdf
/usr/lib/python2.7/dist-packages/pycorrfit_doc/PyCorrFit_doc.pdf

Please fix that.

Regards,

Simon



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Re: Fis-gtm accepted in unstable

[Andreas Tille]

Hi,

On Sun, Dec 15, 2013 at 06:41:47PM -0500, Luis Ibanez wrote:
> Yes ! now on to VistA.
> 
>  https://github.com/luisibanez/debian-med-vista

If this is Debian packaging related it might make sense to move it to

  git://git.debian.org/git/debian-med/vista.git

If it might fullfill other purposes we should try to follow the
established sheme to import a pristine-tar and add the debian/ dir.
 
> Regarding the VistA version, fully agree with Bhaskar on
> using building on the efforts of the code convergence group.

I agree that code convergence sounds like a reasonable idea.  However,
as experience shows, convergence always takes its time.  So we should
have a close eye where this convergence is moving and doing the
packaging stuff in parallel (perhaps with potentional influence on the
convergence code) to be finished with the packaging quite at the same
time uf such a convergence release.

Kind regards

 Andreas.

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Re: Fis-gtm accepted in unstable (Was: Packaging VistA - GT.M directories)

[Andreas Tille]

On Sun, Dec 15, 2013 at 08:39:36PM -0500, Luis Ibanez wrote:
> It could be the beginning of the conversation.
> It has to be updated now, to match the final form of the fis-gtm package,
> and to match the latest representation of VistA in the github repository:
> 
> https://github.com/OSEHRA/VistA-M
> 
> 
> Maybe we should plan a hackathon for this:-)

No idea whether Scotland is to far from the centre of mass of VistA
developers but as you can see here:

   https://wiki.debian.org/DebianMed/Meeting/Aberdeen2014

there is some free space left in the Debian Med sprint hotel. :-)

Kind regards

 Andreas.

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Re: Make Colt-lib: DynamicBin1D Thread safe.

[Andreas Tille]

Hi Malavika,

thanks for your problem report about the Debian packaged libcolt-java.
In general it is advised to use the

   reportbug

tool to issue this kind of bug reports since it submits more detailed
information (like for instance the JVM you are using).

Moreover in the specific case of colt it seems to be a concern for the
upstream developer.  I included the address that is known to us in CC
but we had trouble contacting Wolfgang Hoschek in the past which we
tried seriosly since libcolt-java contains src/hep.aida.* which has no
free license.  The code does not seem to be maintained any more since
we did not got any answer so far.

For sure we try to deal in cases where upstream is not responding also
in Debian to add patches but I must admit at least for myself that my
Java knowledge is so low that I do not even understand the problem you
want to demonstrate with the code below.  What do we need to do with
this code what is your result and what result would you expect instead?
Could you possibly provide a patch which solves your problem?

Kind regards

Andreas.

On Mon, Dec 16, 2013 at 09:51:27AM +0400, Malavika wrote:
> Hello,
> 
> I am using the Debian Colt library version 1.2.0 for some heavy
> calculations and I see that my system deadlocks randomly. The simplified
> test case to reproduce the deadlock is given below. The library is claimed
> to be thread safe but deadlocks are found.
> 
> 
> import hep.aida.bin.DynamicBin1D;
> import cern.colt.function.DoubleDoubleFunction;
> import cern.colt.matrix.DoubleFactory1D;
> import cern.colt.matrix.DoubleFactory2D;
> import cern.colt.matrix.DoubleMatrix1D;
> import cern.colt.matrix.DoubleMatrix2D;
> import cern.colt.matrix.DoubleMatrix3D;
> import cern.jet.random.engine.RandomEngine;
> public class OmenTestCase34 {
> 
> 
> public static void main(String args[])
> {
> DynamicBin1D bin = new DynamicBin1D();
> DynamicBin1D bin2 = new DynamicBin1D();
> double[] v1 = { 1, 2, 3, 4, 5, 6, 7, 8, 9,10,  21,
> 22,23,24,25,26,27,28,29,30,31};
> double[] v2 = {10,11,12,13,14,15,16,17,18,19,  20,
> 30,31,32,33,34,35,36,37,38,39};
> bin2.addAllOf(new cern.colt.list.DoubleArrayList(v1));
> bin2.addAllOf(new cern.colt.list.DoubleArrayList(v2));
> CovarianceCalculator t1 = new CovarianceCalculator(bin,
> bin2);
> t1.start();
> CorrelationCalculator t2 = new CorrelationCalculator(bin,
> bin2);
> t2.start();
> }
> 
> }
> class CovarianceCalculator extends Thread {
> DynamicBin1D l2;
> DynamicBin1D l3;
> public CovarianceCalculator(DynamicBin1D bin, DynamicBin1D bin2) {
> l2 = bin;
> l3 = bin2;
> }
> 
> public void run() {
> System.out.println(l3.covariance(l2));
> }
> }
> 
> class CorrelationCalculator extends Thread {
> DynamicBin1D l2;
> DynamicBin1D l3;
> public CorrelationCalculator(DynamicBin1D bin, DynamicBin1D bin2) {
> l2 = bin;
> l3 = bin2;
> }
> 
> public void run() {
> System.out.println(l2.correlation(l3));
> }
> }
> 
> Regards,
> Malavika
> 
> 
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> 

-- 
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