[Debian-med-packaging] Bug#777791: [PATCH] ball: ftbfs with GCC-5

[Andreas Tille]

Hi Danny,

thanks for your continuous work on this which is really appreciated.

On Tue, Jan 26, 2016 at 05:34:53PM +0100, Danny Edel wrote:
> I have had some spare time and spent it on the ball package.  I hope
> that helps you in getting the package back into Debian.
> 
> Some notes regarding the patch:
> 
> * I dropped the gcc5.patch, since it created an ambiguous overload of
> getline -- Upstream added one themselves in the meantime.

OK, fine - we should prefer the upstream patch.
 
> * The patches in debian/patches/backports/ are all cherry-picked from
> the upstream git repository at github.com/BALL-project/ball -- their
> first line will tell you the commit ID.  Take a look at the branch
> qt5_latest if they are not yet in master.
> They were created with git format-patch -1 <commit>, I hope that's all
> right.

Looks good.
 
> * The most problematic part was DOCKING/COMMON/poseClustering.h.  It
> seems to break with boost-1.56, because it assumes a certain class is
> copyable that has been adapted to c++11's "move" idea.
> The commit that breaks it is
> https://github.com/boostorg/graph/commit/cb26ccf
> 
> I have used a very crude workaround (I have defined a BOOST_* symbol
> suggesting that the compiler would not support moves), this needs to be
> properly ported to current boost by BALL upstream.  Please try to get in
> contact with upstream, and have them properly port the code.

Thanks for the warning.  You are right that we should contact upstream.
Hope they stopped their habit to simply ignores mails from Debian as I
had experienced in the last gcc transistion ...
 
> * The upstream code is also not yet ready for libeigen3 version 3.3
> (currently in beta) that drops some compatibility code.  I added a
> Build-Conflicts to make the buildd's aware of that.  This also needs to
> be ported by upstream.

Well, I realised the conflict which makes the build fail in the very
beginning:

The following packages have unmet dependencies:
 pbuilder-satisfydepends-dummy : Conflicts: libeigen3-dev (>= 3.3~) but 3.3~beta1-2 is to be installed.
Unable to resolve dependencies!  Giving up...

> In order to build the package anyway, I had to add to my sources.list a
> snapshot.debian.org containing the older version (its header-only, so
> it's compiled into the binary and does not generate a run-time
> dependency).  sources.list line containing a suitable old version:
> 
> deb http://snapshot.debian.org/archive/debian/20150924T154447Z sid main

Hmmmm, a bit hackish but I'll try to reproduce.  In any case this will
force us to contact upstream. ;-)
 
> * I activated the test suite in d/rules -- mainly because I was not sure
> if my crude workaround broke anything.
> On my test builds, the Socket_test sometimes™ failed.  Maybe there is a
> race condition, I don't know.  Could also be my old hardware bitrotting
> away...

OK.  Testing sounds always good.
 
> * Since I used the older libeigen, I set it as a "system" library in
> cmake, which prevents the compile log from generating warnings when
> eigen uses deprecated features  (just distracted me while working on
> ball, feel free to drop that patch).
> 
> 
> The patch is based against b915af8eff, which was today (jan 26) the
> current master in the debian-med repository.

Yupp, no change since our last mail exchange.
 
> After all this hacking, the package builds and the resulting .deb's seem
> usable to me, but I dont understand enough biochemics to make anything
> out of it : )

I admit that's the same for me.  I trust on the users of the package
to file bug reports. :_)
 
> I can't tell myself if the patch is of acceptable quality, please have a
> look over it before adopting.

Thanks for the warning.  I'll ask Steffen Möller who has personal
contact to upstream to discuss it there.

> Feedback would be much appreciated, this
> is my first non-trivial contribution.

Definitely non-trivial and really helpful.  Thanks a lot.

BTW, if you are actively seeking for other contribution for C++ issues:
The Debian Med team received recently several bugs containing

  FTBFS with GCC 6

in the bug subject.  Feel free to tackle whatever you might like to
work on at

  https://bugs.debian.org/cgi-bin/pkgreport.cgi?maint=debian-med-packaging@lists.alioth.debian.org

There are several (but not all bugs) we forwarded upstream.  There is
no point in looking into sitplus - here we need to package refectored
upstream from scratch.  Most others could need helping hands.
 
> I hope this helps,

Definitely.  Thanks a lot again

       Andreas.

-- 
http://fam-tille.de