Participation to Debian Med

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Participation to Debian Med

Cédric Lood

Hello everyone,


I am contacting you after having been lurking for some time the Debian Med project and would like to help out. I have some experience with using Linux (my own background being in CS and bioinfo), and I have an interest to learn the tricks of the trade behind the maintenance of packages. So far, I have been reading the project's group policy and discovered you had a mentoring program - I would like to enter that program if anyone would be willing to pair up.


You can reach me here, or via IRC (altersid on freenode/debian).


Looking forward to hear from you,


With kind regards,

Cedric

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Re: Participation to Debian Med

Andreas Tille-6
Hi Cédric,

thanks for your interest in Debian Med.

On Thu, Jul 13, 2017 at 01:21:24PM +0000, Cédric Lood wrote:
> I am contacting you after having been lurking for some time the Debian Med project and would like to help out. I have some experience with using Linux (my own background being in CS and bioinfo), and I have an interest to learn the tricks of the trade behind the maintenance of packages. So far, I have been reading the project's group policy and discovered you had a mentoring program - I would like to enter that program if anyone would be willing to pair up.

Sounds very good.
 
> You can reach me here, or via IRC (altersid on freenode/debian).

I admit I prefer communication via e-mail list but if needed I'm fine to
schedule IRC meetings outside office hours.  The only time when I'm
available on IRC fully is at DebConf - which will be in August. ;-)

You can find the mentoring program here

   https://wiki.debian.org/DebianMed/MoM

Feel free to pick some program that might be used by you but is not
yet packaged for Debian or pick from our todo list starting here

   https://blends.debian.org/med/tasks/bio#pkgvcs-debs

what you might consider interesting for your work and we can start
with the mentoring.
 
> Looking forward to hear from you,

Kind regards

      Andreas.

--
http://fam-tille.de

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Re: Participation to Debian Med

Cédric Lood
Hi Andreas,

Thank you for the answer - I am dealing with a fair share of sequencing data, and some of the programs I use are not packaged (as far as I know). So I would suggest tools that I use indeed, of which either Bandage [0] or Unicycler [1] may be a good start. I had a chance to help debug a bit Unicycler with Ryan (the author) and it was a very nice exchange.

Does that sound good? I can think of other suggestions should those prove too difficult.

With kind regards,
Cedric

[0] https://github.com/rrwick/Bandage/
[1] https://github.com/rrwick/Unicycler
________________________________________
From: Andreas Tille <[hidden email]>
Sent: Friday, July 14, 2017 9:06 AM
To: Cédric Lood
Cc: [hidden email]
Subject: Re: Participation to Debian Med

Hi Cédric,

thanks for your interest in Debian Med.

On Thu, Jul 13, 2017 at 01:21:24PM +0000, Cédric Lood wrote:
> I am contacting you after having been lurking for some time the Debian Med project and would like to help out. I have some experience with using Linux (my own background being in CS and bioinfo), and I have an interest to learn the tricks of the trade behind the maintenance of packages. So far, I have been reading the project's group policy and discovered you had a mentoring program - I would like to enter that program if anyone would be willing to pair up.

Sounds very good.

> You can reach me here, or via IRC (altersid on freenode/debian).

I admit I prefer communication via e-mail list but if needed I'm fine to
schedule IRC meetings outside office hours.  The only time when I'm
available on IRC fully is at DebConf - which will be in August. ;-)

You can find the mentoring program here

   https://wiki.debian.org/DebianMed/MoM

Feel free to pick some program that might be used by you but is not
yet packaged for Debian or pick from our todo list starting here

   https://blends.debian.org/med/tasks/bio#pkgvcs-debs

what you might consider interesting for your work and we can start
with the mentoring.

> Looking forward to hear from you,

Kind regards

      Andreas.

--
http://fam-tille.de

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Re: Participation to Debian Med

Andreas Tille-5
Hi Cédric,

On Fri, Jul 14, 2017 at 07:35:23AM +0000, Cédric Lood wrote:
> Thank you for the answer - I am dealing with a fair share of sequencing data, and some of the programs I use are not packaged (as far as I know). So I would suggest tools that I use indeed, of which either Bandage [0] or Unicycler [1] may be a good start. I had a chance to help debug a bit Unicycler with Ryan (the author) and it was a very nice exchange.

Both are not yet packaged and both are looking like perfect MoM
candidates from *very* quick view.
 
> Does that sound good? I can think of other suggestions should those prove too difficult.

Yes, sounds good.  Simply put one of these into the table on the MoM
Wiki page (or if you do not want to register on Debian Wiki just tell me
which one you prefer as a start).

Kind regards

       Andreas.

--
http://fam-tille.de

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Re: Participation to Debian Med

Cédric Lood
Hi Andreas,

I am on the wiki - I wasn't sure if you'd take up the mentoring so I left that part blank. Anyhow, I'm gonna read the packaging documentation a bit more in details, but feel free to send me some pointers by emails.

Thanks in advance for the help,

Cedric
________________________________________
From: Andreas Tille <[hidden email]>
Sent: Friday, July 14, 2017 9:52 AM
To: [hidden email]
Subject: Re: Participation to Debian Med

Hi Cédric,

On Fri, Jul 14, 2017 at 07:35:23AM +0000, Cédric Lood wrote:
> Thank you for the answer - I am dealing with a fair share of sequencing data, and some of the programs I use are not packaged (as far as I know). So I would suggest tools that I use indeed, of which either Bandage [0] or Unicycler [1] may be a good start. I had a chance to help debug a bit Unicycler with Ryan (the author) and it was a very nice exchange.

Both are not yet packaged and both are looking like perfect MoM
candidates from *very* quick view.

> Does that sound good? I can think of other suggestions should those prove too difficult.

Yes, sounds good.  Simply put one of these into the table on the MoM
Wiki page (or if you do not want to register on Debian Wiki just tell me
which one you prefer as a start).

Kind regards

       Andreas.

--
http://fam-tille.de


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Re: Participation to Debian Med

Andreas Tille-5
Hi Cédric,

On Fri, Jul 14, 2017 at 07:56:05PM +0000, Cédric Lood wrote:
> I am on the wiki - I wasn't sure if you'd take up the mentoring so I left that part blank.

I added myself as mentor and also added the Git repository that will be
used.  I also changed the month to July - there is no need to wait until
August will start (and I promise I will not stop with the mentoring at
end of July ;-) ).

> Anyhow, I'm gonna read the packaging documentation a bit more in details, but feel free to send me some pointers by emails.

I'm hoping that the docs are sufficiently helpful and have no idea what
additional pointers would be needed.  Its better if you ask immediately
if you somehow feel struck.
 
Happy to do the mentoring

     Andreas.

--
http://fam-tille.de

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Re: Participation to Debian Med

Cédric Lood
Hi Andreas,

> I also changed the month to July - there is no need to wait until
August will start (and I promise I will not stop with the mentoring at
end of July ;-) ).

Thanks, actually I wasn't available in July, that is why I had put a starting date in August - no worries, I've changed it back :)

> I'm hoping that the docs are sufficiently helpful and have no idea what
additional pointers would be needed.  Its better if you ask immediately
if you somehow feel struck. Happy to do the mentoring

Great, you will hear from me then !

Best,
Cedric


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[MoM] bandage (Was: Participation to Debian Med)

Andreas Tille-5
Hi Cédric,

On Sun, Jul 30, 2017 at 03:52:00PM +0000, Cédric Lood wrote:
> > I'm hoping that the docs are sufficiently helpful and have no idea what
> additional pointers would be needed.  Its better if you ask immediately
> if you somehow feel struck. Happy to do the mentoring
>
> Great, you will hear from me then !

I have heard at least from Git commit list about your commits to bandage.

When I checked it out I have not yet seen any debian/ directory.  Either
you just have one locally but forgot to

     git add debian/

or you might wonder what to do next.  If the latter is the case my way to
start is to do

     svn export svn://anonscm.debian.org/svn/debian-med/trunk/package_template debian

which fetches some packaging template from SVN (you do NOT need to use
svn - these files are just there).  This gives you a generic template
for the packaging inside the team.  See also the relevant section in
Debian Med policy[1]

Hope these hints are helpful to keep you running - as I said previously:
Do not hesitate to ask any question you might stumble upon since this
usually enables you to find the solution more quickly.

Kind regards

       Andreas.

[1] https://debian-med.alioth.debian.org/docs/policy.html#git-tips

--
http://fam-tille.de

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Re: [MoM] bandage (Was: Participation to Debian Med)

Cédric Lood
Hi Andreas,

> I have heard at least from Git commit list about your commits to bandage.
> Hope these hints are helpful to keep you running - as I said previously:
> Do not hesitate to ask any question you might stumble upon since this
> usually enables you to find the solution more quickly.

No worries, I have been a bit quiet on the ML, mainly because there is so much information available online in the various policies and blogs that I would feel silly asking trivial questions when I could just RTFM.

> When I checked it out I have not yet seen any debian/ directory.

I will be pushing it shortly.

With kind regards,
Cedric
________________________________________
From: Andreas Tille <[hidden email]>
Sent: Sunday, August 13, 2017 1:17 PM
To: Cédric Lood
Cc: [hidden email]
Subject: [MoM] bandage (Was: Participation to Debian Med)

Hi Cédric,

On Sun, Jul 30, 2017 at 03:52:00PM +0000, Cédric Lood wrote:
> > I'm hoping that the docs are sufficiently helpful and have no idea what
> additional pointers would be needed.  Its better if you ask immediately
> if you somehow feel struck. Happy to do the mentoring
>
> Great, you will hear from me then !

I have heard at least from Git commit list about your commits to bandage.

When I checked it out I have not yet seen any debian/ directory.  Either
you just have one locally but forgot to

     git add debian/

or you might wonder what to do next.  If the latter is the case my way to
start is to do

     svn export svn://anonscm.debian.org/svn/debian-med/trunk/package_template debian

which fetches some packaging template from SVN (you do NOT need to use
svn - these files are just there).  This gives you a generic template
for the packaging inside the team.  See also the relevant section in
Debian Med policy[1]

Hope these hints are helpful to keep you running - as I said previously:
Do not hesitate to ask any question you might stumble upon since this
usually enables you to find the solution more quickly.

Kind regards

       Andreas.

[1] https://debian-med.alioth.debian.org/docs/policy.html#git-tips

--
http://fam-tille.de


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Re: [MoM] bandage (Was: Participation to Debian Med)

Andreas Tille-5
Hi Cédric,

On Tue, Aug 15, 2017 at 06:02:42AM +0000, Cédric Lood wrote:
>
> No worries, I have been a bit quiet on the ML, mainly because there is so much information available online in the various policies and blogs that I would feel silly asking trivial questions when I could just RTFM.

MoM is about directing you quickly to the fine manuals and nobody will
blame you about trivial questions which frequently are not that tivial.
I'd like to smoothen your entry and shorten the time you need to dig
for proper information.
 
> > When I checked it out I have not yet seen any debian/ directory.
>
> I will be pushing it shortly.

Fine. :-)

Just let me know if you are seeking for more information

     Andreas.

--
http://fam-tille.de

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Re: [MoM] bandage

Cédric Lood
Hi Andreas,

> MoM is about directing you quickly to the fine manuals and nobody will
> blame you about trivial questions which frequently are not that tivial.
> I'd like to smoothen your entry and shorten the time you need to dig
> for proper information.

You are right of course, the debian project has an insane amount of documentation and I keep being sidetracked when reading it :)

> When I checked it out I have not yet seen any debian/ directory.

I have pushed a few commits just now, if you wanna have a look and will file a new ITP later today. As guideline, I am following very closely the Debian Med policy, as well as the guide for new maintainers.

Thank you for your time,

Cedric


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Re: [MoM] bandage

Andreas Tille-5
Hi Cédric,

thanks for pushing.

On Tue, Aug 15, 2017 at 11:25:33AM +0000, Cédric Lood wrote:
> > MoM is about directing you quickly to the fine manuals and nobody will
> > blame you about trivial questions which frequently are not that tivial.
> > I'd like to smoothen your entry and shorten the time you need to dig
> > for proper information.
>
> You are right of course, the debian project has an insane amount of documentation and I keep being sidetracked when reading it :)

Yes, MoM should be your personal shortcut through all this. ;-)
 
> > When I checked it out I have not yet seen any debian/ directory.
>
> I have pushed a few commits just now, if you wanna have a look and will file a new ITP later today. As guideline, I am following very closely the Debian Med policy, as well as the guide for new maintainers.

I have checked your packaging and have some comments:

debian/upstream/metadata
   I simply pushed a syntax error and extended the authors
   field which is the one that is actively used on our tasks
   pages[1]

debian/changelog
   when using the suggested Debian Med template you need to
   replace some strings like the date stamp manually by
   the result of `date -R`.  You also need to add the package
   name and the version.  Otherwise any attempt to build the
   package will fail due to invalid d/changelog.

debian/copyright
   I simplified this file and pushed.  The general logic is
   that you start with some kind of general copyright paragraph
   featuring all files
     Files: *
   and afterwards you specify exceptions from this.

   The files is just missing two paragraphs for the used
   licenses which should specify the location of the full
   copies of the according licenses.  (Pick your favourite
   package as example how to specify this or ask back here
   if it might be not clear what I mean.)

debian/doc-base:
   This template can be most probably be removed.  I do not
   see that the software contains any extensive documentation.

debian/get-orig-source:
   Please remove this template since debian/watch should work.
   The script is only used if upstream does not follow sensible
   rules to provide a versioned tarball.

debian/watch
   Please remove all commented lines except the one for Github
   releases and make this point to
      https://github.com/rrwick/Bandage/releases
   Just a hint:  The debian/watch file is the first thing I'm
   fixing to get the upstream source right via uscan to see
   whether it can correctly download the source.

debian/rules
   After you have fixed everything (specifically the changelog
   file) you can try to build the package.  You should read the
   file README.md from upstream how to build.  It requires qmake
   which you need to specify in debian/control as a Build-Depends.

Hope these hints are helpful and enable you to continue easily.  Feel
free to ask here about any detail that might remain unclear.

Kind regards

        Andreas.

[1] https://blends.debian.org/med/tasks/bio

--
http://fam-tille.de

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Re: [MoM] bandage

Cédric Lood
Hi Andreas

> I have checked your packaging and have some comments:

> debian/upstream/metadata
>  I simply pushed a syntax error and extended the authors
>   field which is the one that is actively used on our tasks
 >  pages[1]

Thanks for noticing the mistake and fixing it.

> debian/changelog
>   when using the suggested Debian Med template you need to
>   replace some strings like the date stamp manually by
>   the result of `date -R`.  You also need to add the package
>   name and the version.  Otherwise any attempt to build the
>   package will fail due to invalid d/changelog.

I was waiting for the ITP to go through to get the bug#, but I guess
that is not required, so I pushed it and will fill it in later.

> debian/copyright
>   I simplified this file and pushed.  The general logic is
>   that you start with some kind of general copyright paragraph
>   featuring all files
>     Files: *
>   and afterwards you specify exceptions from this.

Got it.

>   The files is just missing two paragraphs for the used
>   licenses which should specify the location of the full
>   copies of the according licenses.  (Pick your favourite
>   package as example how to specify this or ask back here
>   if it might be not clear what I mean.)

I have added them, I wasn't so sure about the GPL2 vs GPL2+ and
likewise with GPL3 vs. GPL3+. Let me know whether this is correct.

For the bandage application files, the headers of the .cpp and .h indicate
version 3 or later, but for the OGDF files, the headers mention GPL2 or 3.

> debian/doc-base:
>   This template can be most probably be removed.  I do not
>   see that the software contains any extensive documentation.

Removed

> debian/get-orig-source:
>   Please remove this template since debian/watch should work.
>   The script is only used if upstream does not follow sensible
>   rules to provide a versioned tarball.

Removed

> debian/watch
>   Please remove all commented lines except the one for Github
>   releases and make this point to
>      https://github.com/rrwick/Bandage/releases
>   Just a hint:  The debian/watch file is the first thing I'm
>   fixing to get the upstream source right via uscan to see
>   whether it can correctly download the source.

Thanks for the hint.

> debian/rules
>   After you have fixed everything (specifically the changelog
>   file) you can try to build the package.  You should read the
>   file README.md from upstream how to build.  It requires qmake
>   which you need to specify in debian/control as a Build-Depends.

Alright, that is next on my list then.

> Hope these hints are helpful and enable you to continue easily.  Feel
> free to ask here about any detail that might remain unclear.

Very useful, thanks a lot for the feedback!

With kind regards,
Cedric


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Re: [MoM] bandage

Andreas Tille-5
Hi Cédric,

On Tue, Aug 15, 2017 at 04:03:42PM +0000, Cédric Lood wrote:
>
> > debian/upstream/metadata
> >  I simply pushed a syntax error and extended the authors
> >   field which is the one that is actively used on our tasks
>  >  pages[1]
>
> Thanks for noticing the mistake and fixing it.

You are welcome - that's actually the purpose of MoM.
 
> I was waiting for the ITP to go through to get the bug#, but I guess
> that is not required, so I pushed it and will fill it in later.

It is perfectly fine (inside the Debian Med team) to start without the
ITP.  Its not the generally recommended behaviour but we are talking
about very rarely used packages and we are coordinating here internally
inside the team who cares.  So the sense of an ITP to stop somebody else
to do duplicated work is basically void in our case.  In case you might
be interested to package a great game from scratch or some basic
library I'd recommend to do the ITP first.
 
> > debian/copyright
> >   I simplified this file and pushed.  The general logic is
> >   that you start with some kind of general copyright paragraph
> >   featuring all files
> >     Files: *
> >   and afterwards you specify exceptions from this.
>
> Got it.

I've seen the commits and I pushed another fix.  We are using some
reserved names (see the URL in the first line of the copyright file).
 
> >   The files is just missing two paragraphs for the used
> >   licenses which should specify the location of the full
> >   copies of the according licenses.  (Pick your favourite
> >   package as example how to specify this or ask back here
> >   if it might be not clear what I mean.)
>
> I have added them, I wasn't so sure about the GPL2 vs GPL2+ and
> likewise with GPL3 vs. GPL3+. Let me know whether this is correct.

It is the "+" version when the text says "or later".
 
> For the bandage application files, the headers of the .cpp and .h indicate
> version 3 or later, but for the OGDF files, the headers mention GPL2 or 3.

Ahhh, so my fix was wrong it should then rather be

    GPL-2 or GPL-3

I was just checking the text you inserted into d/copyright and did not
really checked the license text.

BTW, OGDF is a third party code copy which is not really a good idea.
I did a search

   $  apt-cache search ogdf
  libogdf-tulip-4.8-0 - Open Graph Drawing Framework shared library, built for Tulip
  libtulip-ogdf-4.8 - Tulip graph library - OGDF runtime

which sounds pretty close.  I have no idea what that tulip thingy might
be.  Would you please check whether the source package of this package
is containing the same or at least compatible source?  You can get it by

  $ apt-cache showsrc libtulip-ogdf-4.8 | grep ^Package:

to know in what source package it is and than

  $ apt-get source tulip

The name of the maintainer rings some bell in my mind since he is also a
member of the Debian Science team.  May be this stuff might make sense
in Debian Science.  In case the code copy of OGDF inside bandage is
something else it might make sense to consider to package it separately
from bandage.  Please do some research for the homepage and source that
might be available and I'll check what might be the best way to go.

(I'll just leave you this task to learn what tasks belong to proper
package maintenance.  I'm not sure what we decide to for the final
bandage package.)

> > debian/watch
> >   Please remove all commented lines except the one for Github
> >   releases and make this point to
> >      https://github.com/rrwick/Bandage/releases
> >   Just a hint:  The debian/watch file is the first thing I'm
> >   fixing to get the upstream source right via uscan to see
> >   whether it can correctly download the source.
>
> Thanks for the hint.

Well, you deleted a bit to much.  The template contained some regular
expression after this URL.  That is needed.  Please restore the rest of
the line and replace "PREFIX" by the 'v' upstream is using.  As a
general rule the watch file expression should match the download URL.
You can see this in your browser.  The version number should be a
regular expression.  You can read more about watch files in Debian
Wiki[1].  The template in SVN is just assembling the possible watch file
entries to enable straightforward access without consulting the Wiki.
:-P
 
> > debian/rules
> >   After you have fixed everything (specifically the changelog
> >   file) you can try to build the package.  You should read the
> >   file README.md from upstream how to build.  It requires qmake
> >   which you need to specify in debian/control as a Build-Depends.
>
> Alright, that is next on my list then.

Fine.
 
> > Hope these hints are helpful and enable you to continue easily.  Feel
> > free to ask here about any detail that might remain unclear.
>
> Very useful, thanks a lot for the feedback!

You are welcome as said above.  I'm happy that it was helpful.

Kind regards

       Andreas.


[1] https://wiki.debian.org/debian/watch 

--
http://fam-tille.de

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Re: [MoM] bandage

Cédric Lood
Hi Andreas,

> > debian/watch

> Well, you deleted a bit to much.  The template contained some regular
> expression after this URL.  That is needed.  Please restore the rest of
> the line and replace "PREFIX" by the 'v' upstream is using.  As a
> general rule the watch file expression should match the download URL.
> You can see this in your browser.  The version number should be a
> regular expression.  You can read more about watch files in Debian
> Wiki[1].  The template in SVN is just assembling the possible watch file
> entries to enable straightforward access without consulting the Wiki.

Thanks, I have fixed the file and tested it with uscan, it seems fine now.

> BTW, OGDF is a third party code copy which is not really a good idea.
> I did a search

>   $  apt-cache search ogdf
>  libogdf-tulip-4.8-0 - Open Graph Drawing Framework shared library, built for Tulip
>  libtulip-ogdf-4.8 - Tulip graph library - OGDF runtime

> which sounds pretty close.  I have no idea what that tulip thingy might
> be.  Would you please check whether the source package of this package
> is containing the same or at least compatible source?  You can get it by

>  $ apt-cache showsrc libtulip-ogdf-4.8 | grep ^Package:

> to know in what source package it is and than

>  $ apt-get source tulip

> The name of the maintainer rings some bell in my mind since he is also a
> member of the Debian Science team.  May be this stuff might make sense
> in Debian Science.  In case the code copy of OGDF inside bandage is
> something else it might make sense to consider to package it separately
> from bandage.  Please do some research for the homepage and source that
> might be available and I'll check what might be the best way to go.

> (I'll just leave you this task to learn what tasks belong to proper
> package maintenance.  I'm not sure what we decide to for the final
> bandage package.)

I did a bit of research, and what is copied in the bandage repository corresponds to a subset of the OGDF source files [0]. OGDF is meant to be a library for applications that have to draw graphs [1]. It is hard to estimate how small a subset the bandage application uses, but it seems rather limited in terms of files. After cloning OGDF, I found that the core application consists of 346 cpp files, in 50 folders. Bandage has 34 cpp files in 6 subfolders of the OGDF-specific folder - some of the files have been modified by the upstream author to fit to the bandage application.

As for Tulip [2] , it has a plugin that allows to use the different layout algorithms provided by the OGDF library, but that seems to be about it [3]. Inspection of the source code did not reveal further files that would be related to the OGDF library (aside from this plugin).

Let me know what you think about this,

With kind regards,
Cedric

[0] https://github.com/ogdf/ogdf
[1] www.ogdf.net/doku.php/ogdf:faq
[2] tulip.labri.fr/TulipDrupal/
[3] https://hal.archives-ouvertes.fr/hal-01359308/document
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Re: [MoM] bandage

Cédric Lood
In reply to this post by Andreas Tille-5
> > > debian/rules
> > >   After you have fixed everything (specifically the changelog
> > >   file) you can try to build the package.  You should read the
> > >   file README.md from upstream how to build.  It requires qmake
> > >   which you need to specify in debian/control as a Build-Depends.

> >Alright, that is next on my list then.

> Fine.

Alright, the package builds. There are minor problems that I have mentioned to the upstream author but that can easily be corrected. The first one is the omission of a necessary qt library atop of the qtbase5-dev [0] (for this I have sent him a pull request). And the second one is a problem with the file used by qmake to generate a makefile. The file, called "Bandage.pro", has a set of INCLUDE variables that result in a build failure when using the generated makefile. I noticed the upstream author has fixed that in the dev branch, so I just mentioned it to him via an existing request for a new release [1].

I think the first problem can be easily fixed on our side by including the proper library in the debian/control - Build-Depends field. For the second problem, I guess a patch is in order?

Thanks for your help,
Cedric

[0] https://github.com/rrwick/Bandage/blob/master/README.md#-ubuntu
[1] https://github.com/rrwick/Bandage/issues/44
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Re: [MoM] bandage

Andreas Tille-5
In reply to this post by Cédric Lood
Hi Cédric,

On Sat, Aug 19, 2017 at 03:28:04PM +0000, Cédric Lood wrote:
>
> Thanks, I have fixed the file and tested it with uscan, it seems fine now.

I confirm it is working now.  I have fixed pristine-tar branch since you
used for some reason uper case file name which is not allowed since it
needs to match the source package name.
 
> > (I'll just leave you this task to learn what tasks belong to proper
> > package maintenance.  I'm not sure what we decide to for the final
> > bandage package.)
>
> I did a bit of research, and what is copied in the bandage repository corresponds to a subset of the OGDF source files [0]. OGDF is meant to be a library for applications that have to draw graphs [1]. It is hard to estimate how small a subset the bandage application uses, but it seems rather limited in terms of files. After cloning OGDF, I found that the core application consists of 346 cpp files, in 50 folders. Bandage has 34 cpp files in 6 subfolders of the OGDF-specific folder - some of the files have been modified by the upstream author to fit to the bandage application.

Adapting third party code is a really bad idea.  Please try to contact
bandage upstream that it would be better if he would forward the changes
that are needed for bandage to OGDF upstream.

For the sake of keeping it simple for now I'd suggest to keep the code
copy but teach upstream anyway to possibly do the right thing in some
later version of the package.
 
> As for Tulip [2] , it has a plugin that allows to use the different layout algorithms provided by the OGDF library, but that seems to be about it [3]. Inspection of the source code did not reveal further files that would be related to the OGDF library (aside from this plugin).

Thanks for the clarification.
 
When I try to build bandage in a pbuilder chroot as recommended by
Debian Med policy I get:

...
   dh_auto_configure
        qmake -makefile -nocache "QMAKE_CFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/build/bandage-0.8.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/build/bandage-0.8.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_RELEASE=-g -O2 -fdebug-prefix-map=/build/bandage-0.8.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "QMAKE_CXXFLAGS_DEBUG=-g -O2 -fdebug-prefix-map=/build/bandage-0.8.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" QMAKE_LFLAGS_RELEASE=-Wl,-z,relro QMAKE_LFLAGS_DEBUG=-Wl,-z,relro QMAKE_STRIP=: PREFIX=/usr
Can't exec "qmake": No such file or directory at /usr/share/perl5/Debian/Debhelper/Dh_Lib.pm line 330.
...


It is caused by a missing Build-Depends featuring the qmake executable.
Just let me know if you need further hints regarding this issue.

Kind regards

        Andreas.

> [0] https://github.com/ogdf/ogdf
> [1] www.ogdf.net/doku.php/ogdf:faq
> [2] tulip.labri.fr/TulipDrupal/
> [3] https://hal.archives-ouvertes.fr/hal-01359308/document
>

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Re: [MoM] bandage

Andreas Tille-5
In reply to this post by Cédric Lood
On Sun, Aug 20, 2017 at 06:19:02AM +0000, Cédric Lood wrote:
>
> > Fine.
>
> Alright, the package builds. There are minor problems that I have mentioned to the upstream author but that can easily be corrected. The first one is the omission of a necessary qt library atop of the qtbase5-dev [0] (for this I have sent him a pull request). And the second one is a problem with the file used by qmake to generate a makefile. The file, called "Bandage.pro", has a set of INCLUDE variables that result in a build failure when using the generated makefile. I noticed the upstream author has fixed that in the dev branch, so I just mentioned it to him via an existing request for a new release [1].
>
> I think the first problem can be easily fixed on our side by including the proper library in the debian/control - Build-Depends field. For the second problem, I guess a patch is in order?
Yes, there are missing Build-Depends, which need to be fixed (as I
tried to point out in my answer to your other mail).  And, yes, patches
are for sure in order.  Please use quilt for this.

Kind regards

       Andreas.
 
> [0] https://github.com/rrwick/Bandage/blob/master/README.md#-ubuntu
> [1] https://github.com/rrwick/Bandage/issues/44
>

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