Re: request for r-cran packages

[Andreas Tille]

On Wed, Mar 20, 2019 at 05:31:01PM +0100, Tony Travis wrote:
> This is not a problem with Debian, it's really a problem with Ubuntu's
> relationship to Debian - Please feel free to tell me I would not have these
> problems if I used Debian :-)

I do not intend to repeat what I've said previously. ;-)
 
> I do understand, and thank you for uploading the three r-cran packages.

You are welcome.  Emmax is now also uploaded.  Please cross fingers
that ftpmaster is convinced by the d/copyright wording.

Kind regards

   Andreas. 

-- 
http://fam-tille.de

Re: request for r-cran packages

[Tony Travis]

On 20/03/2019 17:01, Andreas Tille wrote:

[...]
Well, I *personally* think that your decision to rely on those PPA and
hardly upgradable releases is asking for trouble at some point in time.
You are refusing the help of the men power of the Debian Med team who is
usually as quick as backports ftpmaster response to provide needed
backports.  But that's your decision and should not be discussed here.


Hi, Andreas.

I'm not refusing anyone's help!

This is not a problem with Debian, it's really a problem with Ubuntu's 
relationship to Debian - Please feel free to tell me I would not have 
these problems if I used Debian :-)


I only want to use Ubuntu LTS releases which, I now know, means I won't 
get all the up-to-date things you are contributing to Debian because LTS 
are not rolling releases. So, I'm making the same pragmatic choice that 
Tim Booth made in Bio-Linux 8 to use Michael Rutter's Ubuntu PPA's. I 
wish Ubuntu 18.04 had the up-to-date Debian packages, but it does not.



Sorry again about the false alarm asking Debian-Med to package the three R
libraries that I needed. They are fully supported in the CRAN 3.5 PPA.

Hope this doesn't put you off packaging PIQUE!


It seems I did not made my point clear enough.  PIQUE is depending from
those R packages and thus theses need to be packaged before PIQUE.
Luckily this is done and the packages are just waiting for ftpmaster.
The same is true for EMMAX (I mean the same way this is needed - thanks
to https://lists.debian.org/debian-med/2019/03/msg00085.html we hopefully
can make ftpmaster accepting it).

Please confirm that you understood that a package can only exist in
Debian if all its preconditions are packaged.


I do understand, and thank you for uploading the three r-cran packages.

Bye,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548http://minke-informatics.co.uk
mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk

Re: Debian-Med packaging of EMMAX

[Steffen Möller]

Excellent news, many thanks!

Steffen

On 20.03.19 14:29, Hyun Min Kang wrote:

Andreas - sorry for my oversight on the previous email. There is no
license attached with EMMAX, and you can consider it to be equivalent
to widely used public license (e.g. MIT license).

Hyun.
-
Hyun Min Kang, Ph.D.
Associate Professor of Biostatistics
University of Michigan, Ann Arbor
Email : hmk...@umich.edu 


On Wed, Mar 20, 2019 at 8:54 AM Andreas Tille mailto:ti...@debian.org>> wrote:

Hi again,

I stumbled upon some other software that needs emmax which brought
to my
attention that there was no final answer to the license question: 
Did you
decided for a free license for EMMAX which I might have missed?

Kind regards

        Andreas.

On Sun, Feb 11, 2018 at 04:27:45PM +0100, Tony Travis wrote:
> On 11/02/18 16:13, rhkra...@gmail.com
 wrote:
> > 
>
> Hi, Thanks for the correction :-)
>
> > On Sunday, February 11, 2018 06:03:23 AM Tony Travis wrote:
> >> I've been using EMMAX to teach GWAS under Bio-Linux, which
includes
> >> software packaged by the Debian-Med team. At present, we have to
> >> download the software from your website and install it during our
> >> training sessions. This works, but it would be a lot easier
if we could
> >> just install it as a package. Please let us know if you are
willing to
> >> allow EMMAX to be packaged by Debian-Med?
> >
> > Is the issue only permission to package, or is the issue a
free license for
> > the software?
>
> We would like to redistribute EMMAX in a standard Debian package
format
> and inform our users what they are allowed to do with the software,
> which requires it to have a free licence.
>
> Thanks,
>
>   Tony Travis.
>
>   (on behalf of the Debian-Med team)
>
> --
> Minke Informatics Limited, Registered in Scotland - Company No.
SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ,
Scotland (UK)
> tel. +44(0)19755 63548 http://minke-informatics.co.uk
> mob. +44(0)7985 078324       
mailto:tony.tra...@minke-informatics.co.uk

>
>

--
http://fam-tille.de

Re: request for r-cran packages

[Andreas Tille]

On Wed, Mar 20, 2019 at 04:46:08PM +0100, Tony Travis wrote:
> 
> These, as with the out-of-date "Abyss" package in Ubuntu 18.04 all seem to
> be consequences of the same "no rolling release" policy of Ubuntu and do not
> reflect in any way a criticism of Debian. I've got backports enabled, but it
> makes no difference. As Steffen said, in an ideal world we would not need to
> use the PPA's, but as a practical way forward we need to because Ubuntu
> 18.04 is not going to sync with the latest Debian packages that, as you
> said, _are_ using R 3.5.

Well, I *personally* think that your decision to rely on those PPA and
hardly upgradable releases is asking for trouble at some point in time.
You are refusing the help of the men power of the Debian Med team who is
usually as quick as backports ftpmaster response to provide needed
backports.  But that's your decision and should not be discussed here.
 
> Sorry again about the false alarm asking Debian-Med to package the three R
> libraries that I needed. They are fully supported in the CRAN 3.5 PPA.
> 
> Hope this doesn't put you off packaging PIQUE!

It seems I did not made my point clear enough.  PIQUE is depending from
those R packages and thus theses need to be packaged before PIQUE.
Luckily this is done and the packages are just waiting for ftpmaster.
The same is true for EMMAX (I mean the same way this is needed - thanks
to https://lists.debian.org/debian-med/2019/03/msg00085.html we hopefully
can make ftpmaster accepting it).

Please confirm that you understood that a package can only exist in
Debian if all its preconditions are packaged. 

Kind regards

   Andreas.

-- 
http://fam-tille.de

Re: request for r-cran packages

[Tony Travis]

On 20/03/2019 16:36, Andreas Tille wrote:

On Wed, Mar 20, 2019 at 04:06:33PM +0100, Steffen Möller wrote:

I can package one or two of these R packages. Please direct me which one
I should address first.


None, all are in new as I wrote here

https://lists.debian.org/debian-med/2019/03/msg00075.html

I'd **strongly** recommend to everybody who wants to package GNU R
packages to read and understand this mail to save **a HUGE amount of
time** and by doing so also deliver policy conform and up to date
packaging.


Hi, Andreas.

I apologise for my ignorance but, in fairness to me, it was not clear 
why the Ubuntu 18.04 r-cran packages are so out of date and I did not 
fully appreciate the discussions that had gone on about deprecating R 
version 3.4 in Ubuntu 18.04 LTS. I know now, and I have taken action.


Thanks for your advice,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548http://minke-informatics.co.uk
mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk

Re: request for r-cran packages

[Steffen Möller]

On 20.03.19 16:36, Andreas Tille wrote:

On Wed, Mar 20, 2019 at 04:06:33PM +0100, Steffen Möller wrote:

I can package one or two of these R packages. Please direct me which one
I should address first.

None, all are in new as I wrote here

https://lists.debian.org/debian-med/2019/03/msg00075.html

I'd **strongly** recommend to everybody who wants to package GNU R
packages to read and understand this mail to save **a HUGE amount of
time** and by doing so also deliver policy conform and up to date
packaging.


Yup. I already used the R scripts of yours, but these salsa interaction
ones are really nice, too!

Many thanks

Steffen

Re: request for r-cran packages

[Tony Travis]

On 20/03/2019 16:32, Andreas Tille wrote:

On Wed, Mar 20, 2019 at 04:23:44PM +0100, Tony Travis wrote:

Probably trying to do too many things at once just now :-|

Please don't spend any time packaging the R libraries I requested, because
I'm going to use R 3.5 from now on.

Sorry about the false alarm, requesting packaging.


Wait a moment:  pique just needs some R packages, right?  A Debian
package of a GNU R package always builds against the latest packaged
version of R which is currently 3.5.3.  The three packages I uploaded to
new are built against this.  The packaging process itself does not
depend on the R version (funnily enough the only person who thinks so
is the R maintainer but he is de facto wrong in nearly all practical
cases and there were some flames about this ;-) ).

So I guess it was correct that I uploaded the three R packages, right?


Hi, Andreas.

The problem lies with the Ubuntu 'Universe' repository, where all the R 
dependencies are for R version 3.4, even in Ubuntu 18.04 LTS (bionic).


These, as with the out-of-date "Abyss" package in Ubuntu 18.04 all seem 
to be consequences of the same "no rolling release" policy of Ubuntu and 
do not reflect in any way a criticism of Debian. I've got backports 
enabled, but it makes no difference. As Steffen said, in an ideal world 
we would not need to use the PPA's, but as a practical way forward we 
need to because Ubuntu 18.04 is not going to sync with the latest Debian 
packages that, as you said, _are_ using R 3.5.


CRAN is quite clear that R 3.5 is the supported version in Ubuntu bionic 
and, I admit, I didn't know that until I checked today when one of my 
colleagues in India was having problems installing PIQUE under Ubuntu 
18.04 and I started to investigate. In general, I go with whatever is in 
the Ubuntu repositories but, in this case, the repositories are out of 
date with CRAN and I need to use Michael Rutter's PPA's.


Sorry again about the false alarm asking Debian-Med to package the three 
R libraries that I needed. They are fully supported in the CRAN 3.5 PPA.


Hope this doesn't put you off packaging PIQUE!

Bye,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548http://minke-informatics.co.uk
mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk

Re: request for r-cran packages

[Andreas Tille]

On Wed, Mar 20, 2019 at 04:06:33PM +0100, Steffen Möller wrote:
> I can package one or two of these R packages. Please direct me which one
> I should address first.

None, all are in new as I wrote here

   https://lists.debian.org/debian-med/2019/03/msg00075.html

I'd **strongly** recommend to everybody who wants to package GNU R
packages to read and understand this mail to save **a HUGE amount of
time** and by doing so also deliver policy conform and up to date
packaging.

Kind regards

   Andreas.

-- 
http://fam-tille.de

Re: request for r-cran packages

[Andreas Tille]

On Wed, Mar 20, 2019 at 04:23:44PM +0100, Tony Travis wrote:
> Probably trying to do too many things at once just now :-|
> 
> Please don't spend any time packaging the R libraries I requested, because
> I'm going to use R 3.5 from now on.
> 
> Sorry about the false alarm, requesting packaging.

Wait a moment:  pique just needs some R packages, right?  A Debian
package of a GNU R package always builds against the latest packaged
version of R which is currently 3.5.3.  The three packages I uploaded to
new are built against this.  The packaging process itself does not
depend on the R version (funnily enough the only person who thinks so
is the R maintainer but he is de facto wrong in nearly all practical
cases and there were some flames about this ;-) ).

So I guess it was correct that I uploaded the three R packages, right?

Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: request for r-cran packages

[Steffen Möller]

On 20.03.19 16:19, Tony Travis wrote:

On 20/03/2019 16:06, Steffen Möller wrote:


On 20.03.19 13:48, Andreas Tille wrote:

Hi Tony,

On Wed, Mar 20, 2019 at 12:25:32PM +0100, Tony Travis wrote:

Yes, that would be great if you're willing, but I would struggle to
do it on
my own despite you explaining to me several times what to do...

Its a pleasure for me to look at this once you fixed

    https://github.com/tony-travis/PIQUE/issues/3

;-)



Hey, congrats, there is version 1.0!

I can package one or two of these R packages. Please direct me which one
I should address first.


Hi, Steffen.

I've decided to move to R 3.5 instead, because Michael Rutter's PPA
has the packages available for R 3.5 in Zenial and the 3.4 versions
are now deprecated starting from Ubuntu 18.04 LTS. I've just tested
installing PIQUE under Ubuntu-MATE 18.04 LTS with both of Michael's R
3.5 PPA's.

Sorry about the false alarm re: Packaging the R 3.4 libraries...


Well, 3.5 is the current version of R in Debian alike. Great to hear
your settled. Anyway, in some ideal world you would not need that PPA.

Best,

Steffen

Re: Debian-Med packaging of EMMAX

[Hyun Min Kang]

Andreas - sorry for my oversight on the previous email. There is no license
attached with EMMAX, and you can consider it to be equivalent to widely
used public license (e.g. MIT license).

Hyun.
-
Hyun Min Kang, Ph.D.
Associate Professor of Biostatistics
University of Michigan, Ann Arbor
Email : hmk...@umich.edu


On Wed, Mar 20, 2019 at 8:54 AM Andreas Tille  wrote:

> Hi again,
>
> I stumbled upon some other software that needs emmax which brought to my
> attention that there was no final answer to the license question:  Did you
> decided for a free license for EMMAX which I might have missed?
>
> Kind regards
>
> Andreas.
>
> On Sun, Feb 11, 2018 at 04:27:45PM +0100, Tony Travis wrote:
> > On 11/02/18 16:13, rhkra...@gmail.com wrote:
> > > 
> >
> > Hi, Thanks for the correction :-)
> >
> > > On Sunday, February 11, 2018 06:03:23 AM Tony Travis wrote:
> > >> I've been using EMMAX to teach GWAS under Bio-Linux, which includes
> > >> software packaged by the Debian-Med team. At present, we have to
> > >> download the software from your website and install it during our
> > >> training sessions. This works, but it would be a lot easier if we
> could
> > >> just install it as a package. Please let us know if you are willing to
> > >> allow EMMAX to be packaged by Debian-Med?
> > >
> > > Is the issue only permission to package, or is the issue a free
> license for
> > > the software?
> >
> > We would like to redistribute EMMAX in a standard Debian package format
> > and inform our users what they are allowed to do with the software,
> > which requires it to have a free licence.
> >
> > Thanks,
> >
> >   Tony Travis.
> >
> >   (on behalf of the Debian-Med team)
> >
> > --
> > Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> > tel. +44(0)19755 63548http://minke-informatics.co.uk
> > mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk
> >
> >
>
> --
> http://fam-tille.de
>

Re: request for r-cran packages

[Tony Travis]

On 20/03/2019 16:19, Tony Travis wrote:

On 20/03/2019 16:06, Steffen Möller wrote:


On 20.03.19 13:48, Andreas Tille wrote:

Hi Tony,

On Wed, Mar 20, 2019 at 12:25:32PM +0100, Tony Travis wrote:
Yes, that would be great if you're willing, but I would struggle to 
do it on

my own despite you explaining to me several times what to do...

Its a pleasure for me to look at this once you fixed

    https://github.com/tony-travis/PIQUE/issues/3

;-)



Hey, congrats, there is version 1.0!

I can package one or two of these R packages. Please direct me which one
I should address first.


Hi, Steffen.

I've decided to move to R 3.5 instead, because Michael Rutter's PPA has 
the packages available for R 3.5 in Zenial [...]


Hi, Steffen.

Er, I meant "bionic" - Don't know where "Zenial" came from!

Probably trying to do too many things at once just now :-|

Please don't spend any time packaging the R libraries I requested, 
because I'm going to use R 3.5 from now on.


Sorry about the false alarm, requesting packaging.

Bye,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548http://minke-informatics.co.uk
mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk

Re: request for r-cran packages

[Tony Travis]

On 20/03/2019 16:06, Steffen Möller wrote:


On 20.03.19 13:48, Andreas Tille wrote:

Hi Tony,

On Wed, Mar 20, 2019 at 12:25:32PM +0100, Tony Travis wrote:
Yes, that would be great if you're willing, but I would struggle to 
do it on

my own despite you explaining to me several times what to do...

Its a pleasure for me to look at this once you fixed

    https://github.com/tony-travis/PIQUE/issues/3

;-)



Hey, congrats, there is version 1.0!

I can package one or two of these R packages. Please direct me which one
I should address first.


Hi, Steffen.

I've decided to move to R 3.5 instead, because Michael Rutter's PPA has 
the packages available for R 3.5 in Zenial and the 3.4 versions are now 
deprecated starting from Ubuntu 18.04 LTS. I've just tested installing 
PIQUE under Ubuntu-MATE 18.04 LTS with both of Michael's R 3.5 PPA's.


Sorry about the false alarm re: Packaging the R 3.4 libraries...

However, it's great to have PIQUE packaged!

Bye,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548http://minke-informatics.co.uk
mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk

Re: PIQUE packaging (Was: request for r-cran packages)

[Tony Travis]

On 20/03/2019 16:04, Andreas Tille wrote:

Hi Tony,

On Wed, Mar 20, 2019 at 01:48:05PM +0100, Andreas Tille wrote:

Yes, that would be great if you're willing, but I would struggle to do it on
my own despite you explaining to me several times what to do...


Its a pleasure for me to look at this once you fixed

https://github.com/tony-travis/PIQUE/issues/3


That was quick. :-)


Hi, Andreas.

I've also pushed some changes for Ubuntu 18.04 LTS that were pending, 
and I tested installation using Michael Maruter's R 3.5 PPA instead of 
using the 3.4 versions in the Ubuntu repos, because the r-cran packages 
that I want are supported for R 3.5 in Ubuntu 'bionic' and thinking of 
the future, I want to move everything to R 3.5 for Bio-Linux...



Here are my next questions:

   1. Could you please join me in bothering the emmax author again?
  That's definitely a prerequisite for PIQUE packaging.


Yes, of course, but my work-around is just to download it.


   2. Is there any description of PIQUE that could be used as long
  description for the package.  I've checked doc/pique_manual.odt
  but despite its filename it says it is the ParSNP manual
  (btw, parsnp is packaged) and doc/pique_tutorial.odt does
  also not contain anything that would enlighten me about PIQUE
  at first sight.
  Feel free to simply replace the FIXME in
   https://salsa.debian.org/med-team/pique/blob/master/debian/control


Yes, I'll sort that out: We called it "ParSNP" at first, but I 
subsequently discovered that someone has already used that name!



   3. I do not see any need to install the files in etc/profile.d or
  am I missing something?


That's only there because, at present, PIQUE is installed in:

  /usr/local/pique

If it's packaged and installed using "apt" they are not needed.

Thanks for packaging PIQUE,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548http://minke-informatics.co.uk
mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk

Re: Debian-Med packaging of EMMAX

[Andreas Tille]

Dear Hyun,

thanks a lot for the very quick response.  I will link in the Debian
copyright file to this mail which is publicly archived in the mailing
list archive.  I hope that will be acceptable for the Debian ftpmaster.

Kind regards

  Andreas.

On Wed, Mar 20, 2019 at 09:29:00AM -0400, Hyun Min Kang wrote:
> Andreas - sorry for my oversight on the previous email. There is no license
> attached with EMMAX, and you can consider it to be equivalent to widely
> used public license (e.g. MIT license).
> 
> Hyun.
> -
> Hyun Min Kang, Ph.D.
> Associate Professor of Biostatistics
> University of Michigan, Ann Arbor
> Email : hmk...@umich.edu
> 
> 
> On Wed, Mar 20, 2019 at 8:54 AM Andreas Tille  wrote:
> 
> > Hi again,
> >
> > I stumbled upon some other software that needs emmax which brought to my
> > attention that there was no final answer to the license question:  Did you
> > decided for a free license for EMMAX which I might have missed?
> >
> > Kind regards
> >
> > Andreas.
> >
> > On Sun, Feb 11, 2018 at 04:27:45PM +0100, Tony Travis wrote:
> > > On 11/02/18 16:13, rhkra...@gmail.com wrote:
> > > > 
> > >
> > > Hi, Thanks for the correction :-)
> > >
> > > > On Sunday, February 11, 2018 06:03:23 AM Tony Travis wrote:
> > > >> I've been using EMMAX to teach GWAS under Bio-Linux, which includes
> > > >> software packaged by the Debian-Med team. At present, we have to
> > > >> download the software from your website and install it during our
> > > >> training sessions. This works, but it would be a lot easier if we
> > could
> > > >> just install it as a package. Please let us know if you are willing to
> > > >> allow EMMAX to be packaged by Debian-Med?
> > > >
> > > > Is the issue only permission to package, or is the issue a free
> > license for
> > > > the software?
> > >
> > > We would like to redistribute EMMAX in a standard Debian package format
> > > and inform our users what they are allowed to do with the software,
> > > which requires it to have a free licence.
> > >
> > > Thanks,
> > >
> > >   Tony Travis.
> > >
> > >   (on behalf of the Debian-Med team)
> > >
> > > --
> > > Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> > > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> > > tel. +44(0)19755 63548http://minke-informatics.co.uk
> > > mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk
> > >
> > >
> >
> > --
> > http://fam-tille.de
> >

-- 
http://fam-tille.de

Re: request for r-cran packages

[Steffen Möller]

On 20.03.19 13:48, Andreas Tille wrote:

Hi Tony,

On Wed, Mar 20, 2019 at 12:25:32PM +0100, Tony Travis wrote:

Yes, that would be great if you're willing, but I would struggle to do it on
my own despite you explaining to me several times what to do...

Its a pleasure for me to look at this once you fixed

https://github.com/tony-travis/PIQUE/issues/3

;-)



Hey, congrats, there is version 1.0!

I can package one or two of these R packages. Please direct me which one
I should address first.

Best,

Steffen

PIQUE packaging (Was: request for r-cran packages)

[Andreas Tille]

Hi Tony,

On Wed, Mar 20, 2019 at 01:48:05PM +0100, Andreas Tille wrote:
> > Yes, that would be great if you're willing, but I would struggle to do it on
> > my own despite you explaining to me several times what to do...
> 
> Its a pleasure for me to look at this once you fixed
> 
>https://github.com/tony-travis/PIQUE/issues/3

That was quick. :-)

Here are my next questions:

  1. Could you please join me in bothering the emmax author again?
 That's definitely a prerequisite for PIQUE packaging.

  2. Is there any description of PIQUE that could be used as long
 description for the package.  I've checked doc/pique_manual.odt
 but despite its filename it says it is the ParSNP manual
 (btw, parsnp is packaged) and doc/pique_tutorial.odt does
 also not contain anything that would enlighten me about PIQUE
 at first sight.
 Feel free to simply replace the FIXME in
  https://salsa.debian.org/med-team/pique/blob/master/debian/control

  3. I do not see any need to install the files in etc/profile.d or
 am I missing something?

Kind regards

   Andreas.

-- 
http://fam-tille.de

Re: Debian-Med packaging of EMMAX

[Andreas Tille]

Hi again,

I stumbled upon some other software that needs emmax which brought to my
attention that there was no final answer to the license question:  Did you
decided for a free license for EMMAX which I might have missed?

Kind regards

Andreas.

On Sun, Feb 11, 2018 at 04:27:45PM +0100, Tony Travis wrote:
> On 11/02/18 16:13, rhkra...@gmail.com wrote:
> > 
> 
> Hi, Thanks for the correction :-)
> 
> > On Sunday, February 11, 2018 06:03:23 AM Tony Travis wrote:
> >> I've been using EMMAX to teach GWAS under Bio-Linux, which includes
> >> software packaged by the Debian-Med team. At present, we have to
> >> download the software from your website and install it during our
> >> training sessions. This works, but it would be a lot easier if we could
> >> just install it as a package. Please let us know if you are willing to
> >> allow EMMAX to be packaged by Debian-Med?
> > 
> > Is the issue only permission to package, or is the issue a free license for 
> > the software?
> 
> We would like to redistribute EMMAX in a standard Debian package format
> and inform our users what they are allowed to do with the software,
> which requires it to have a free licence.
> 
> Thanks,
> 
>   Tony Travis.
> 
>   (on behalf of the Debian-Med team)
> 
> -- 
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> tel. +44(0)19755 63548http://minke-informatics.co.uk
> mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk
> 
> 

-- 
http://fam-tille.de

Re: request for r-cran packages

[Andreas Tille]

Hi Tony,

On Wed, Mar 20, 2019 at 12:25:32PM +0100, Tony Travis wrote:
> 
> Yes, that would be great if you're willing, but I would struggle to do it on
> my own despite you explaining to me several times what to do...

Its a pleasure for me to look at this once you fixed

   https://github.com/tony-travis/PIQUE/issues/3

;-)
 

Kind regards

  Andreas.

-- 
http://fam-tille.de

Re: request for r-cran packages

[Tony Travis]

On 20/03/2019 11:59, Andreas Tille wrote:

Hi Tony,

On Tue, Mar 19, 2019 at 10:02:17PM +0100, Tony Travis wrote:

I need three r-cran packages that are not in the Debian-Med-based Ubuntu
archive for my PIQUE GWAS pipeline:


https://github.com/tony-travis/PIQUE


Thanks for the feature request (BTW, should we try to package
PIQUE itself as well?)
[...]


Hi, Andreas.

Yes, that would be great if you're willing, but I would struggle to do 
it on my own despite you explaining to me several times what to do...


I've been advising some colleagues in India to stop using Bio-Linux 8 
and switch to Ubuntu-MATE 18.04 + med-bio instead and they reported the 
issue. TBH, I had forgotten that I did a manual work-around on my own 
servers.


Thanks,

  Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548http://minke-informatics.co.uk
mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk

Re: request for r-cran packages

[Andreas Tille]

Hi Tony,

On Tue, Mar 19, 2019 at 10:02:17PM +0100, Tony Travis wrote:
> I need three r-cran packages that are not in the Debian-Med-based Ubuntu
> archive for my PIQUE GWAS pipeline:
> 
> > https://github.com/tony-travis/PIQUE

Thanks for the feature request (BTW, should we try to package
PIQUE itself as well?)
 
> I would like to request Debian-Med packaging of:
> 
>   r-cran-forecast
>   r-cran-uroot
>   r-cran-fracdiff
> 
> These are not present in the Ubuntu 18.04 LTS repository...

Just to explain what's needed to do:

   $ prepare_missing_cran_package forecast

This creates ready to `git buildpackage` repositories of r-cran-forecast
and r-cran-fracdiff (which is a precondition for r-cran-forecast).

   $ cd ../CRAN_prospective/r-cran-fracdiff

I manually fixed d/copyright of r-cran-fracdiff and did

   $ git buildpackage
   $ inject-into-salsa-git
   $ itp_from_debian_dir "This package is a precondition for r-cran-forecast"

This resulted in ITP bug #925131.  Close bug

   $ dput r-cran-fracdiff_1.4-2-1_amd64.changes

Copy deb from r-cran-fracdiff to my extra pbuilder mirror.

   $ cd ../r-cran-forecast

manually fixed d/copyright and d/control (needs injecting r-cran-fracdiff
into Build-Depends since at the time of packaging creation this dependency
did not existed yet)

   $ git buildpackage
   $ inject-into-salsa-git

Check autopkgtest and learn that r-cran-uroot is needed to pass this test

   $ prepare_missing_cran_package uroot
   $ cd ../r-cran-uroot

manually fixed d/copyright and (extremely unusually in R packages)
needed work around some build issue.  Uroot can work with CUDA but we
can not support this feature in official Debian since this is only in
non-free.  I added README.Debian explaining the fact and if needed how
to deal with it.

   $ git buildpackage
   $ inject-into-salsa-git
   $ itp_from_debian_dir "This package is needed to run the test suite of 
r-cran-forecast"

This resulted in ITP bug #925133.  Close bug

 

   $ dput r-cran-uroot_2.0-9-1_amd64.changes
   $ cd ../r-cran-forecast
   $ itp_from_debian_dir

This resulted in ITP bug #925137 which I just uploaded to new.

You see (with the exception of uroot which is an extremely rare
exception) creating the R packages is extremely easy using the existing
R toolset (in package dh-r - itp_from_debian_dir was used from Git since
the extension to right send a bug report was added after freeze but it
was simple enough anyway).  The time to write all steps down was
basically duplicating the time for the actual work (if uroot would
have been more simple the relation for writing it down would be even
worse),  I took that effort to give some practical example how to
work with the existing tool set.

> I manually downloaded these versions from Michael Rutter's PPA:
> 
> > https://launchpad.net/~marutter/+archive/ubuntu/c2d4u
> 
>   r-cran-forecast_8.4-3cran1ppa0bionic0_amd64.deb
>   r-cran-uroot_2.0-9-3cran1ppa0bionic0_amd64.deb
>   r-cran-fracdiff_1.4-2-3cran2ppa0bionic0_amd64.deb

Thanks for the links.  I admit I ignored these since we need source
packages anyway and getting a policy conform source package of latest
upstream versions including autopkgtests is done obviously faster than
doing research where to find the source package and possibly update the
packaging to latest standards.
 
> Unfortunately, they are no longer available for 'bionic (18.04 LTS).

The packages are now in new queue and we need to wait until ftpmaster
has processed these.  As you know I'm not informed about how these can
make it to bionic.

Kind regards,

   Andreas.

-- 
http://fam-tille.de

Re: Outreachy current

[Andreas Tille]

Hi Liubov,

thanks a lot for your comments.  I have no idea whether there is some
point in making you an official co-mentor but if you see some advantage
for you in adding you officially that would be perfectly fine for me.

On Wed, Mar 20, 2019 at 10:43:43AM +0100, Liubov Chuprikova wrote:
> But in case there are other unreleased changes in the package (for example,
> you have added new test data), as Andreas mentioned already, you may need
> pbuilder or sbuild to build packages in a chroot environment and then to
> run tests. I am using sbuild, so I put a couple of useful links below
> related to sbuild [2][3].

Regarding sbuild:  It is used on Debian autobuilders and by several
developers.  I personally never managed to set it up properly (obviously
Liubov was more successfully than me ;-) ).  You can alternatively use
pbuilder (which also builds a package in a chroot environment.  For your
specific purpose I also do not see any harm if you build your private
packages using debuild from devscripts (which is faster but might
include installing lots of Build-Depends on your local machine which you
do not want.  In short: Try to follow Liubov's hints.  In case you might
run into trouble there are alternatives to get you up and running
quickly.
 
> If you have any questions, feel free to ask.

Thanks a lot for your help

 Andreas.
 
> [1] https://people.debian.org/~mpitt/autopkgtest/README.running-tests.html
> [2] https://wiki.debian.org/mk-sbuild
> [3] https://wiki.debian.org/sbuild
> [4] https://github.com/liubovch/vagrant-debianVM/blob/master/playbook.yml
> [5] https://ci.debian.net/doc/file.TUTORIAL.html

-- 
http://fam-tille.de

Re: Outreachy current

[Liubov Chuprikova]

Hi Saira,

I am glad to know there is a new potential Outreachy student! :-)

On Tue, 19 Mar 2019 at 09:13, Andreas Tille  wrote:

> On Mon, Mar 18, 2019 at 11:11:11PM +, Saira Hussain wrote:
>
> > What's the best way to use autopkgtest locally to emulate the test? As I
> currently
> > only treat them as  sh scripts and test manually.
>
> I admit I do it that way most of the time. ;-)  I also added a pbuilder
> hook for testing.  Pbuilder is a tool which builds Debian packages in a
> minimalistic chroot environment and thus the test is done in a chroot
> (but obviously did not fetched that last error - no idea why).
>
> I once followed
>
>https://wiki.debian.org/DebianScience/Debci
>
> (see paragraph "Configure your system to run autopkgtest using lxc")
> but dealing with those lxc containers was not always easy and after I
> had some trouble I stopped this again (lazy me :-().
>
> I've put Liubov (last years outreachy student) in CC - may be she has
> some additional hints.
>

In case, you haven't found this already, here [1] you can read how to run
autopkgtest using different virtualizations (it's almost the same actually
that is in /usr/share/doc/autopkgtest directory). I am using schroot, but I
cannot say that it's the best choice since I haven't tried others. It's up
to you what to choose :-)

Most of the time you don't need to build the packages locally, just run the
tests you wrote with packages from distribution:

autopkgtest -B packages/mysrc -- *virt-server*

But in case there are other unreleased changes in the package (for example,
you have added new test data), as Andreas mentioned already, you may need
pbuilder or sbuild to build packages in a chroot environment and then to
run tests. I am using sbuild, so I put a couple of useful links below
related to sbuild [2][3]. You may find some configuration examples in my
ansible recipies [4]. Here is some additional information on writing
autopkgtests that was useful for me [4].

If you have any questions, feel free to ask.

Have fun and all the best,
Liuba.

[1] https://people.debian.org/~mpitt/autopkgtest/README.running-tests.html
[2] https://wiki.debian.org/mk-sbuild
[3] https://wiki.debian.org/sbuild
[4] https://github.com/liubovch/vagrant-debianVM/blob/master/playbook.yml
[5] https://ci.debian.net/doc/file.TUTORIAL.html