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Re: [cilibrar@cilibrar.com: Bug#425278: ITP: libqsearch -- hierarchical clustering library using quartet tree reconstruction algorithm]

Dear Debian med team and Debian Mentors,

Thanks.  I am a little confused about how upstream authors are supposed to
use the mentors archive repository server.

I wanted to avoid mentors uploading because I  was under the impression that I
had to sign everything I uploaded to mentors. The reason I did not want to sign
my upload yet is because I am also upstream and
I don't want to release an "official" version 0.9.9 until I get more feedback since
there are big changes and I expect to make some last improvements. 
If I need to modify the orig.tar.gz I don't want to make another
version . . . is there any way to upload to mentors without signing the orig.tar.gz so
that I would not have to commit to the "final" version before getting any feedback
from other devs?  I am confused about how our process is supposed to work
optimally in this case.  Or am I supposed to just sign everything before even
submitting it for review to a small number of friends?  Then does it mean I
have to make a new version number every time I send a version to anybody
that is signed?  Am I being logical here or missing something basic?

I have already copied the debs for complear and dsc's etc to my server at [1]
and [2].

I am also Cc'ing the mentors list since Pabs asked for a URL and may be
interested in giving feedback.  Thanks for any help,


P.S.  I added internationalization to complearn in this version and am looking for some help to
make translations for NL, DE, RU, ES, and CN.

[1] http://cilibrar.com/~cilibrar/projsup/libqs/
[2] http://cilibrar.com/~cilibrar/projsup/libcomp/

On 5/21/07, Andreas Tille <tillea@rki.de> wrote:
[Full quote to debian-med list because I think there is no private
  content and you are adressing Debian-Med in some parts directly.]

On Mon, 21 May 2007, Rudi Cilibrasi, Ph.D. wrote:

> Dear Andreas,
> Thanks for your note.  I have seen Debian Med out of the corner of my eye
> for
> many months now and have been meaning to join one of these years.  I almost
> joined up with you guys because of another proto-package available from my
> private
> website packaging the nexus library [1].  This libnexus is not ready for
> prime
> time yet I guess but would appreciate feedback, help, comments, etc.
> I have also rewritten entirely my "complearn" package, now splitting it
> up into several smaller packages and going for a "panlingual" language
> binding approach using DBUS.  The net result is several new packages:
> libcomplearn now just does NCD
> libqsearch     contains maketree and associated quartet tree lib
> complearn-dbus contains a DBUS-based server to provide generic OO binding
> capability
> soon there will be very small ruby packages to finish the job of connecting
> to
> perl, python, ruby, java, etc easily and more importantly with a consistent
> interface across all languages.
> There is also another new deb package called
> complearn-mod-crypt that includes SHA1, SHA2, and MD5 hash function
> compression modules.
> I am wondering if there is anybody from the Debian Med team that would be
> willing to help review my packages before I upload them to mentors and

Well, to find out this you are best advised to keep the mailing list
debian-med@lists.debian.org CCed in mails like this.  IMHO, there is
no real need to look onto your work *before* you upload to mentors -
mentors is just the right place if you want somebody to look onto
your code.  So uploading and than posting the location to the mailing
list seems to be the best strategy.

> try to get somebody to sponsor them?

I think we have about three or four potential sponsors reading the
list so your chances are good to find a sponsor.

> I will have to do libcomplearn first
> since the API has been substantially enhanced and will have a few Conflicts:
> entries against old versions of complearn-gui and complearn-mpi I suppose.
> I will go ahead and join the debian med list now and hope I can make good
> progress getting these new packages rolling with the help of your team.

You are welcome


> Best
> regards,
> Rudi
> [1] http://cilibrar.com/~cilibrar/projsup/nex4/
> On 5/21/07, Andreas Tille < tillea@rki.de> wrote:
>> On Mon, 21 May 2007, Charles Plessy wrote:
>> > this is definitely interesting for us. I will tag the ITP, and subscribe
>> > to it.
>> Charles, thanks for spotting this.
>> Rudi, are you aware of the Debian-Med effort.  If you need a sponsor
>> just ask here.  Perhaps you like to join the Debian-Med mailing list
>> to stay in contact with other Debian users and developers that work
>> in the same field you are obviousely interested in.
>> Kind regards
>>             Andreas.
>> > ----- Forwarded message from Rudi Cilibrasi <cilibrar@cilibrar.com>
>> -----
>> >
>> > Date: Sun, 20 May 2007 18:10:02 +0200
>> > From: Rudi Cilibrasi <cilibrar@cilibrar.com>
>> > To: Debian Bug Tracking System <submit@bugs.debian.org >
>> > Subject: Bug#425278: ITP: libqsearch -- hierarchical clustering library
>> using quartet tree reconstruction algorithm
>> >
>> > Package: wnpp
>> > Severity: wishlist
>> > Owner: Rudi Cilibrasi <cilibrar@cilibrar.com>
>> >
>> >
>> > * Package name    : libqsearch
>> >  Version         : 0.9.9
>> >  Upstream Author : Rudi Cilibrasi <cilibrar@cilibrar.com>
>> > * URL             : http://www.complearn.org/
>> > * License         : BSD
>> >  Programming Lang: C
>> >  Description     : hierarchical clustering library using quartet tree
>> reconstruction algorithm
>> >
>> > libqsearch is a general-purpose data-mining library.  It creates a
>> > hierarchical clustering in the form of an unrooted binary tree based on
>> > an input square matrix of numbers.  No matter what kind of distance
>> > matrix you input into the system, it will search for the closest fitting
>> > unrooted binary tree that best represents the structural relationships
>> > between the objects as specified in the input matrix.  This package is
>> > useful with (and was once part of) the complearn package and is
>> > compatible with the text, CompLearn Binary, and Nexus file formats.  It
>> > outputs graphviz compatible .dot and Nexus format trees.  This system
>> > has been used for phylogenetic analysis of genetic sequences to
>> > reconstruct probable evolutionary histories, language analysis, and many
>> > other areas.
>> >
>> > -- System Information:
>> > Debian Release: 4.0
>> >  APT prefers unstable
>> >  APT policy: (500, 'unstable')
>> > Architecture: i386 (i686)
>> > Shell:  /bin/sh linked to /bin/bash
>> > Kernel: Linux 2.6.18-4-486
>> > Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
>> >
>> > ----- End forwarded message -----
>> >
>> > --
>> > Charles Plessy
>> > http://charles.plessy.org
>> > Wako, Saitama, Japan
>> >
>> >
>> > --
>> > To UNSUBSCRIBE, email to debian-med-REQUEST@lists.debian.org
>> > with a subject of "unsubscribe". Trouble? Contact
>> listmaster@lists.debian.org
>> >
>> >
>> >
>> --
>> http://fam-tille.de
> --
> Democracy is two wolves and a sheep deciding what to eat for lunch.
> Liberty is a well-armed sheep contesting the vote.


Democracy is two wolves and a sheep deciding what to eat for lunch.
Liberty is a well-armed sheep contesting the vote.
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