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Re: Flexbar source code?

On 21/01/13 21:17, Andreas Tille wrote:

[...]
Before I come to the tarball itself:  I do not consider it a clever way
if you exchange provate mails with upstream author and by doing so
proxying mail discussion.  Upstream can post in public to the list (his
mail address will be uncovered to spammers thought) without subscribing
and we can CC him.


Hi, Andreas.
I was in contact with Johannes Röhr, one of the the upstream authors, before suggesting that we package "Flexbar" for Debian-Med. My initial contact with you about "Flexbar" was off-list and, as you suggested, I moved our conversation about it onto the Debian-Med list.
I volunteered to do the packaging because Johannes is too busy. It seems strange to me that you expect an upstream author to take part in online discussions when they are not the package maintainer, but I'll ask Johannes if he will join in the discussion about "Flexbar" here. 


For the tarball itself I have two remarks:

   1. It would be a good idea to include a file COPYING containing the
      license statement.

   2. A really large part of the source tarball is a convenience copy of
      the seqan library which is also packages in seqan-dev package.
      Usually we try strongly to build packages against Debian packaged
      libraries and thus I would be very happy if we could drop the
      seqan code (by at the same time tweaking src/CMakeLists.txt to
      regard the Debian packaged seqan.)  Unfortunately the included
      copy has some indifferent state - it is way younger than the latest
      official seqan release (1.3.1) which is packaged.  So the question
      remains whether flexbar will really build with Debian's seqan
      package.  It is the duty of the Debian maintainer of flexbar to
      find this out (either by testing himself or by asking upstream.)
I've discussed this with Johannes already off-list, and I was able to compile his source release unmodified on Bio-Linux 7/Ubuntu 12.04 LTS. 


apt-cache policy seqan-dev
seqan-dev:
  Installed: 1.3.1-0ubuntu1
  Candidate: 1.3.1-0ubuntu1
  Version table:
 *** 1.3.1-0ubuntu1 0
        500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ precise/main amd64 Packages
        100 /var/lib/dpkg/status
     1.3-1ubuntu2 0
        500 http://gb.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages
If Johannes is willing to join in the discussion, I will let him continue. Otherwise, I'll post a summary of my off-list discussions with him about "Flexbar" dependencies. 

Bye,

  Tony.
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