[Debian-med-packaging] Debian package for vsearch

Torbjørn Rognes torognes at ifi.uio.no
Fri Feb 20 09:25:09 UTC 2015

Hi Roland

On 19 Feb 2015, at 22:05, Roland Fehrenbacher <rf at q-leap.de<mailto:rf at q-leap.de>> wrote:

"T" == Torbjørn Rognes <torognes at ifi.uio.no<mailto:torognes at ifi.uio.no>> writes:

Hi Torbjørn,

   T> Hi Andreas
On 18 Feb 2015, at 23:29, Andreas Tille <andreas at an3as.eu<mailto:andreas at an3as.eu>> wrote:

Thank you. We will consider all patches and potentially
integrate all of them into a future version of vsearch. As far
as I can see now they all seem to be fine. I will inform you
when they have been integrated.

Thanks, that would be very helpful.

   T> We have already integrated the patches related to the manual and
   T> the code. What remains are those patches that apply to the
   T> Makefile(s). We will handle these together with the other changes
   T> that we want to make to the Makefile relating to reading
   T> compressed files using the zlib or bzip2 libraries.

please write your Makefile such that it will simply use the existing
zlib or bzip2 libraries on the system. Bundling the zlib or bzip2 code
with your own code makes life more difficult from the packaging point of
view (we'll have to create a modified source package without those

Hm. We were planning to do exactly what you do not recommend. But we might reconsider. We planned to include the source of zlib and bzip2 in the src directory and link their object files directly into vsearch. They seem quite stable.

We have already included the code from Google CityHash (https://code.google.com/p/cityhash/).

We think it would make life easier for those who compile and use vsearch, because then we can make sure that both of these libraries are part of vsearch and that they use the correct version of the libraries. In my experience the availability and version of these libraries vary a lot from system to system, and I had problems compiling vsearch without updating at least one of them.

Why do you have to remove these libs from the package if we include them?

- Torbjørn



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