Re: [MoM] incorporating phyutility into the packages

2014-04-08 Thread Stephen Smith
Hi Thorsten No, libmatrixExp.so isn't used for anything here. Is there a way to remove that in the debian package or do I need to do it in the original phyutilty and push a new version? Take care, Stephen On Tue, Apr 01, 2014 at 02:55:44PM +0200, Thorsten Alteholz wrote: Hi Stephen, lintian

Re: [MoM] incorporating phyutility into the packages

2014-03-25 Thread Stephen Smith
Hi Andreas, If you would have called `lintian -I -i` it would have told you that there were some minus signes inside the manpage where hyphens are expected. Since I was fixing syntactical issues before I did so for now as well. Just a recommendation to use lintian extensively the next time.

Re: [MoM] incorporating phyutility into the packages

2014-03-25 Thread Stephen Smith
, but is there one for med? I might see if there are orphaned things that would also be interesting. Take care, Stephen On Tue, Mar 25, 2014 at 06:32:59PM +0100, Andreas Tille wrote: Hi Stephen, On Tue, Mar 25, 2014 at 01:22:19PM -0400, Stephen Smith wrote: If you would have called `lintian -I -i

Re: [MoM] incorporating phyutility into the packages

2014-03-24 Thread Stephen Smith
Hi Thorsten There were a number of others and they have been added to the copyright file. Thanks for the catch. Take care, Stephen On Sun, Mar 23, 2014 at 03:47:18PM +0100, Thorsten Alteholz wrote: Hi Stephen, On Thu, 20 Mar 2014, Stephen Smith wrote: Hopefully, yes! I have tracked down

Re: [MoM] incorporating phyutility into the packages

2014-03-24 Thread Stephen Smith
Hi Andreas, So far for the syntactical things in the manpage, but there is some missing content. The DESCRIPTION section is somehow suboptimal and you are refering to the documentation - but where is this. At least not in the package and thus a link would be helpful. Please also provide a

Re: [MoM] incorporating phyutility into the packages

2014-03-23 Thread Stephen Smith
Hi Thorsten Ah! Sorry, missed those. Will add and look closer for any others. Take care, Stephen On Sun, Mar 23, 2014 at 03:47:18PM +0100, Thorsten Alteholz wrote: Hi Stephen, On Thu, 20 Mar 2014, Stephen Smith wrote: Hopefully, yes! I have tracked down as best I can, all the authors

Re: [MoM] incorporating phyutility into the packages

2014-03-20 Thread Stephen Smith
, Andreas Tille wrote: Hi Stephen, On Sun, Mar 16, 2014 at 10:49:40PM -0400, Stephen Smith wrote: OK, I got the smtp worked out and the bug report got filed. Hopefully things look ok. That's fine. Just a hint for the future: I usually use the short description (in this case

Re: [MoM] incorporating phyutility into the packages

2014-03-16 Thread Stephen Smith
Stephen, On Sat, Mar 15, 2014 at 04:48:00PM -0400, Stephen Smith wrote: Yup. Please note that I pushed another change to point to Git i nthe Vcs URLs (I simply forgot this after the move from SVN to Git). Great! Got it. Hmmm, I need to check why it is not yet rendered at the tasks

Re: [MoM] incorporating phyutility into the packages

2014-03-15 Thread Stephen Smith
Yup. Please note that I pushed another change to point to Git i nthe Vcs URLs (I simply forgot this after the move from SVN to Git). Great! Got it. Hmmm, I need to check why it is not yet rendered at the tasks page (but should!). Hm, wondering if I did something wrong here. Obviously

Re: [MoM] incorporating phyutility into the packages

2014-03-05 Thread Stephen Smith
your same setup that you sent along last time but clearly something is up there). I will let you know what I find. Take care, Stephen On Wed, Mar 5, 2014 at 3:53 PM, Andreas Tille andr...@an3as.eu wrote: Hi Stephen, On Wed, Mar 05, 2014 at 03:39:44PM -0500, Stephen Smith wrote: Hi Andreas

Re: [MoM] incorporating phyutility into the packages

2014-03-05 Thread Stephen Smith
of what would be the best way to do that? Take care, Stephen On Wed, Mar 5, 2014 at 4:53 PM, Stephen Smith black...@gmail.com wrote: Hi Andreas, Thanks for all that info. I had definitely missed some of those. I can definitely remove the jar from the package. I will just move to taking the tag

Re: [MoM] incorporating phyutility into the packages

2014-03-04 Thread Stephen Smith
All sounds good. OK, I have done an initial commit so you can check out where I am at. Take care, Stephen On Tue, Mar 4, 2014 at 2:12 AM, Andreas Tille andr...@an3as.eu wrote: Hi Stephen, On Mon, Mar 03, 2014 at 09:14:55PM -0500, Stephen Smith wrote: No problem. I am sure I added

Re: [MoM] incorporating phyutility into the packages

2014-03-04 Thread Stephen Smith
in the steps for this. I have tried git-import-orig with the new tar as well as git-import-orig --pristine-tar as well as pristine tar alone and it still seems to grab the older tar when doing git-buildpackage. What am I missing? Thanks Stephen On Tue, Mar 4, 2014 at 7:46 PM, Stephen Smith black

Re: [MoM] incorporating phyutility into the packages

2014-03-03 Thread Stephen Smith
packaging? Kind regards Andreas. On Sat, Mar 01, 2014 at 05:56:58PM +0100, Andreas Tille wrote: Hi, On Sat, Mar 01, 2014 at 09:31:12AM -0500, Stephen Smith wrote: Great! Going through the process now. Just accepted for the Debian Med team. Please confirm that you can ssh

Re: [MoM] incorporating phyutility into the packages

2014-03-03 Thread Stephen Smith
, Stephen Smith wrote: I definitely use git more than svn. I would prefer to move it to git and have been looking at the docs for doing that correctly. Seeking http://debian-med.alioth.debian.org/docs/policy.html for the keyword 'git' should give you all answers how to do so. Please let me

Re: [MoM] incorporating phyutility into the packages

2014-03-03 Thread Stephen Smith
wrote: Hi Stephen, On Mon, Mar 03, 2014 at 04:47:46PM -0500, Stephen Smith wrote: Hi Andreas I seem to be having a bit of a problem in converting this from subversion to git. Checking out from svn seems fine This command: debcheckout --user blackrim-guest svn:// svn.debian.org/debian-med

[MoM] incorporating phyutility into the packages

2014-02-28 Thread Stephen Smith
Hi, I wanted to express my interest in getting more involved in debian and possibly doing this with Andreas Tille through the MoM program. The package I would like to start helping get into the system is phyutility - a program that is useful for formatting and postprocessing of sequence data and

Re: Source code of phyutility

2012-02-15 Thread Stephen Smith
Hi Andreas, Derby requirement should be gone. Hope that helps and let me know if you run into any other issues. Take care, Stephen On 01/31/2012 10:21 AM, Andreas Tille wrote: Hi Stephen, On Tue, Jan 31, 2012 at 09:52:32AM -0500, Stephen Smith wrote: No problems. How about I just change

Re: Source code of phyutility

2012-01-31 Thread Stephen Smith
the derby bit for now and continue as free and the next iteration will no longer have it. Stephen On 01/31/2012 03:12 AM, Andreas Tille wrote: On Mon, Jan 30, 2012 at 12:31:04PM -0500, Stephen Smith wrote: There is now a basic ant build file included and I released a new version. Thanks

Re: Source code of phyutility

2012-01-29 Thread Stephen Smith
Hi Andreas, Great! I have the source on http://code.google.com/p/phyutility. I switched to git and it should be relatively easy to see the main branch. I would be very happy to help however I can. And I am currently working on some bug fixes, etc. Please let me know how best to help in terms

Re: MUMmer patches and Artistic license.

2009-07-28 Thread Boyd Stephen Smith Jr.
. -- Boyd Stephen Smith Jr. ,= ,-_-. =. b...@iguanasuicide.net ((_/)o o(\_)) ICQ: 514984 YM/AIM: DaTwinkDaddy `-'(. .)`-' http://iguanasuicide.net/\_/ signature.asc Description: This is a digitally signed message part.

Re: MUMmer patches and Artistic license.

2009-07-28 Thread Boyd Stephen Smith Jr.
In 200907281303.42301@iguanasuicide.net, Boyd Stephen Smith Jr. wrote: In 20090728163525.gc31...@an3as.eu, Andreas Tille wrote: On Sun, Jul 12, 2009 at 10:50:10PM +0900, Charles Plessy wrote: This patch is a good idea -- fixed length buffers are rarely considered user-friendly. However

Re: MUMmer patches and Artistic license.

2009-07-06 Thread Boyd Stephen Smith Jr.
Stephen Smith Jr. ,= ,-_-. =. b...@iguanasuicide.net ((_/)o o(\_)) ICQ: 514984 YM/AIM: DaTwinkDaddy `-'(. .)`-' http://iguanasuicide.net/\_/ signature.asc Description: This is a digitally signed message part.