[Debian-med-packaging] Psortb has errors in Perl testsuite

[Carnë Draug]

On 19 April 2017 at 19:37, Andreas Tille <tille at debian.org> wrote:
> On Wed, Apr 19, 2017 at 03:52:30PM +0100, Carnė Draug wrote:
> [...]
>> There was one other
>> issue that may be important too about being able to build for 32 bit
>> with recent versions of perl [6].
>
> I was hoping that this change which I turned into a quilt patch[7] would
> solve the issue.  Unfortunately this does not help.  The file libsvm.cpp
> is just compiled inside the resulting Makefile and thus the library is
> lacking the respective symbols.  Patch [7] does not do the trick
> unfortunately.
>
> Any other hints?
>
> Kind regards
>
>        Andreas.
>
>> [4] https://rt.cpan.org/Public/Bug/Display.html?id=79106
>> [5] https://rt.cpan.org/Public/Dist/Display.html?Name=Algorithm-SVM
>> [6] https://rt.cpan.org/Public/Bug/Display.html?id=79754
>
> [7]
> https://anonscm.debian.org/cgit/debian-med/psortb.git/tree/debian/patches/fix_build_Algorithm-SVM.patch

To help with this, I have packaged Algorithm::SVM [8], and unbundled
libsvm from it with the patches from Fedora.  The changes seem to make
autopkgtest happy in sid-amd64 (Algorithm::SVM has a test unit).

Note that even if you decide against unbundling Algorithm::SVM out of
psortb, psortb is still dependent on it.  The module
Bio::Tools::SVMLoc, which is part of psortb, uses Algorithm::SVM and
not the bundled version in Bio::Tools::PSort::SVMLoc (I guess the Loc
means local to the psortb?).

Can you check if my attempt at packaging Algorithm::SVM works for you
or if you still have any issue?

Carnë

[8] https://anonscm.debian.org/cgit/pkg-perl/packages/libalgorithm-svm-perl.git/