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

[Andreas Tille]

Hi Carnë,

On Wed, Apr 19, 2017 at 10:12:53PM +0100, Carnë Draug wrote:
> >> [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).

I made some cosmetic changes - please pull.  If you add an ITP bug I'd
sponsor immediately.  Thanks for working on this.
 
> 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?).

I'm afraid I do not understand what you want to tell me here.  I
compared the code of Algorithm::SVM (from your packaging) with
Bio::Tools::SVMLoc from psortb source and there is quite some diff and a
separate name space.  I do not intend to change upstream code to a large
amount to sort this out without even a minor understanding of the
rationale behind this fork of Algorithm::SVM.

If you think I would need Algorithm::SVM as an extra Build-Depends
adding libalgorithm-svm-perl did not helped to change anything.

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

While I can confirm that the packaging of Algorithm::SVM looks fine I
totally fail to see how this would be helpful for psort.  I'd be happy
if you simply commit some change to psortb (or send me some git
format-patch I could apply) to make me better understand in code what
you want to suggest.

Thanks in any case for your help

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

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