Bug#784863: Debian package for kmer -- test suites

Hi, Afif-

I'm a little slow on packaging up a release, sorry. It's on the to do list with a decent priority, but not getting much time yet. The paying projects are being unruly.

From the kmer repo, I've created four releases by removing select top level directories. For 'meryl' the directories are:

Make.include
Make.rules
Makefile
README.compiling
README.meryl
configure.sh
libbio
libkmer
libmeryl
libseq
libutil
meryl

No changes to Make* are needed. This is the package needed for wgs-assembler. The other three are for ATAC, ESTmapper and sim4db (which exists already).

I've wanted to get rid of kazlib for a long time, and I think it is only used by the atac package. Before you expend too much effort on modifications, lets see if the meryl component will compile without it. IIRC, it's used only in class 'bigQueue' in libutil. I wanted to replace it with STL, but last time I looked, it wasn't a drop-in replacement.

The test suite(s) are probably quite low level, and not very good. A functional test should find any major problems. I can't think of any gotchas for reviving the tests though.

On Tue, May 19, 2015 at 4:00 AM, Afif Elghraoui <afif@ghraoui.name> wrote:

Hello again,

As I've been looking to modify kmer to use an unmodified version of kazlib as already packaged in Debian, I first started checking out your test suite to make sure there is a chance of detecting potential issues due to such a change.

I see, however, that the test suite is not in very good shape. I may be able to help you get it working again if it's a matter of some shuffling around in the interfaces used by the drivers. Is there anything I should be aware of before undertaking this?

Thanks for your cooperation with this effort.
Afif

PS: In CC on this email, we have the Debian Med list and the packaging log for kmer in Debian.

--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name