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
ph
Welcome to the team.
+Emilien
Le 1 mars 2014 04:35, "Stephen Smith" a écrit :
> 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 ph
Hi Stephen,
On Fri, Feb 28, 2014 at 10:35:36PM -0500, Stephen Smith wrote:
> I wanted to express my interest in getting more involved in debian and
> possibly doing this with Andreas Tille through the MoM program.
That's great. I have added an entry for March 2014. :-)
> The package
> I would l
Great! Going through the process now.
Take care,
Stephen
On Sat, Mar 1, 2014 at 3:46 AM, Andreas Tille wrote:
> Hi Stephen,
>
> On Fri, Feb 28, 2014 at 10:35:36PM -0500, Stephen Smith wrote:
> > I wanted to express my interest in getting more involved in debian and
> > possibly doing this with
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
into ssh by passwordless login into alioth.
BTW, since I previously used SVN for the packaging and people are now
mov
Hi Stephen,
any opinion about SVN versus Git for phyutility 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 accept
Hi Andreas
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.
Take care,
Stephen
On Mon, Mar 3, 2014 at 1:17 PM, Andreas Tille wrote:
> Hi Stephen,
>
> any opinion about SVN versus Git for phyutility packaging?
>
> Ki
Hi Stephen,
On Mon, Mar 03, 2014 at 01:25:15PM -0500, 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' s
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/trunk/packages/phyutility/trunk phyutility
Gets this result:
declared svn repository at svn+
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/trun
Hi Andreas,
No problem. I am sure I added to the confusion there. I have added the bare
repo on Alitoh from "Pushing to git.debian.org, creating a new bare
repository on Alitoh." but haven't pushed yet. I have my local git repo
with the debian folder from the svn. For this part, "git import-orig
--
Hi Stephen,
On Mon, Mar 03, 2014 at 09:14:55PM -0500, Stephen Smith wrote:
> No problem. I am sure I added to the confusion there. I have added the bare
> repo on Alitoh from "Pushing to git.debian.org, creating a new bare
> repository on Alitoh." but haven't pushed yet. I have my local git repo
>
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 wrote:
> Hi Stephen,
>
> On Mon, Mar 03, 2014 at 09:14:55PM -0500, Stephen Smith wrote:
> > No problem. I am sure I added to the confusion the
Hi Stephen,
On Tue, Mar 04, 2014 at 01:17:17PM -0500, Stephen Smith wrote:
> All sounds good. OK, I have done an initial commit so you can check out
> where I am at.
I was really curious where you are at and thus I took the freedom to do
two commits:
1. Adapt changelog version to the injected
Hi Andreas
OK. When I do git-buildpackage (no arguments) in the directory I have been
working in, I get
dpkg-buildpackage -rfakeroot -D -us -uc -i -I
dpkg-buildpackage: source package phyutility
dpkg-buildpackage: source version 2.6-1
dpkg-buildpackage: source distribution UNRELEASED
dpkg-buildpa
Sorry, spoke too soon. I noted the missing dependencies there. Once
installed, it gets further and then fails at compile with
[javac]
phyutility/src/jebl/gui/trees/treeviewer_dev/TreePane.java:495: error:
reference to Painter is ambiguous, both interface javax.swing.Painter in
javax.swing and inter
Hi again,
OK, I believe I have fixed the code in phyutility (in the source repo not
the debian repo). Also, in noticing that code.google doesn't allow
downloads anymore, I moved it to github and added the new release. Now, it
seems I need to update the package but having some difficulty in the step
Hi Stephen,
On Tue, Mar 04, 2014 at 10:54:49PM -0500, Stephen Smith wrote:
> Hi again,
great to see your progress while I was sleeping. ;-)
> OK, I believe I have fixed the code in phyutility (in the source repo not
> the debian repo). Also, in noticing that code.google doesn't allow
> downloads
Hi Andreas,
I updated the changelog and committed and pushed after
git import-orig --pristine-tar phyutility_2_7_1.tar.gz
I haven't updated for uscan yet, but will do that in a bit. However,
on git-buildpackage, I am still getting the old tar although it is saying
it is getting the newer one. If I
Hi Stephen,
On Tue, Mar 04, 2014 at 10:54:49PM -0500, Stephen Smith wrote:
> Hi again,
> OK, I believe I have fixed the code in phyutility (in the source repo not
> the debian repo). Also, in noticing that code.google doesn't allow
> downloads anymore, I moved it to github and added the new releas
Hi Stephen,
On Wed, Mar 05, 2014 at 03:39:44PM -0500, Stephen Smith wrote:
> Hi Andreas,
> I updated the changelog and committed and pushed after
> git import-orig --pristine-tar phyutility_2_7_1.tar.gz
>
> I haven't updated for uscan yet, but will do that in a bit. However,
> on git-buildpackage
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 from uscan which doesn't have the jar. That has been updated
and pushed.
I have updated the watch, updated phyutility which now compile
Hi Andreas,
Been playing around a lot more with pbuilder and the like and I believe I
have it right. For some reason my lintian call wasn't calling the location
of the changes files. Everything is getting put
in /var/cache/pbuilder/result/ but I do have a deb and things seem ok other
than a few thi
Hi Stephen,
On Wed, Mar 05, 2014 at 04:53:33PM -0500, Stephen Smith wrote:
> Thanks for all that info. I had definitely missed some of those.
If you think something is missing in the policy document or should be
enhanced to better fit a newcomers need any patch would be more than
welcome.
> I c
Hi Stephen,
On Wed, Mar 05, 2014 at 09:28:39PM -0500, Stephen Smith wrote:
> Hi Andreas,
> Been playing around a lot more with pbuilder and the like and I believe I
> have it right. For some reason my lintian call wasn't calling the location
> of the changes files. Everything is getting put
> in /
Good Evening Andreas:
For this debian-med project, is it important where a git repository
is kept for a particular package ? I would guess that as long as
it is a public git resource it can be anywhere ?
--Hiram
--
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of
Hi Stephen,
any news from your side?
On Thu, Mar 06, 2014 at 08:57:13AM +0100, Andreas Tille wrote:
> Further needed changes:
>
> - When I created the packaging debhelper compatibility level was 8
> Please increade debian/compat to 9 (and adjust the debhelper version
> in debian/contro
Hi Andreas
Responses inline below
> any news from your side?
yeah, sorry about the bit of silence there. I got bogged down in some
work things. Anyway, back on track.
> On Thu, Mar 06, 2014 at 08:57:13AM +0100, Andreas Tille wrote:
> > Further needed changes:
> >
> > - When I created the pac
Hi Stephen,
On Wed, Mar 12, 2014 at 09:19:10PM -0400, Stephen Smith wrote:
> > any news from your side?
>
> yeah, sorry about the bit of silence there. I got bogged down in some
> work things. Anyway, back on track.
:-)
> > I noticed you have changed debian/compat but you will definitely get
Hi Stephen,
On Sat, Mar 15, 2014 at 07:28:01AM -0400, Stephen Smith wrote:
> > > By take over do you mean just rerun dch --create -v 2.7.3 --package
> > > phyutility? Or dch -i ?
>
> This one is done. Just did the --create.
The result is exactly what I mean.
> Waiting for the number and then
> 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. Obviou
Hi 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 th
Hi Stephen,
thanks to Andreas I learned today that I need to write more emails and
that phyutility is going to be uploaded soon.
Before this upload, can you please have a closer look at the (yet)
incomplete contents of debian/copyright.
Would it make sense to create a separate package from the
Hi Thorsten
I would be happy to take a look at the copyright contents. However, I am
a bit new to this so not exactly sure which bits are missing. Not trying
to be dense, just not sure. Maybe Andreas or you could point me in the
right direction and I can fix things. Aha, the copyright needs the jeb
Hi Andreas
OK, I got the smtp worked out and the bug report got filed. Hopefully
things look ok. There was also the query about the copyright. Wondering
what I need to do there but happy to do what I need.
Take care,
Stephen
On Sun, Mar 16, 2014 at 11:32:19AM +0100, Andreas Tille wrote:
> Hi Stephe
Hi Stephen,
On Sun, Mar 16, 2014 at 10:38:44PM -0400, Stephen Smith wrote:
> I would be happy to take a look at the copyright contents. However, I am
> a bit new to this so not exactly sure which bits are missing. Not trying
> to be dense, just not sure.
The fact that Thorsten was talking about j
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
simple analyses or modifications on
Hi Stephen,
On Sun, 16 Mar 2014, Stephen Smith wrote:
I would be happy to take a look at the copyright contents. However, I am
a bit new to this so not exactly sure which bits are missing.
In debian/copyright the maintainer must document the copyright holder
and license of all files in the so
Hi Thorsten,
On Mon, Mar 17, 2014 at 11:37:38AM +0100, Thorsten Alteholz wrote:
>
> >As for jebl being a separate package, it is a bit complicated. The original
> >one is no longer maintained (http://sourceforge.net/projects/jebl/) though
> >this older one is the one that is included in phyutilit
Hi Stephen,
ans news from phyutility packaging?
Kind regards
Andreas.
On Mon, Mar 17, 2014 at 09:04:32AM +0100, 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. Hopefull
Hopefully, yes! I have tracked down as best I can, all the authors of
the original JEBL and the LGPL version that it was under. These have
been added to the copyright. The removal of the dep of jebl2 was pushed
and the adding of the bug number was done. So, I think that is it? Let
me know if there
Hi Stephen,
On Thu, Mar 20, 2014 at 10:05:16PM -0400, Stephen Smith wrote:
> Hopefully, yes! I have tracked down as best I can, all the authors of
> the original JEBL and the LGPL version that it was under. These have
> been added to the copyright.
Looks good to me.
> The removal of the dep of j
Hi Stephen,
On Thu, 20 Mar 2014, Stephen Smith wrote:
Hopefully, yes! I have tracked down as best I can, all the authors of
the original JEBL and the LGPL version that it was under. These have
been added to the copyright.
sorry for not being more verbose, the jebl directory was just one examp
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
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 dow
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 provi
Hi Stephen,
On Mon, Mar 24, 2014 at 10:09:45PM -0400, Stephen Smith wrote:
> I believe I have solved these issues and expanded the content to a more
> meaningful manpage. I think the synopsis was close but made some edits
> and the same for the description. I added some examples and more info
> fo
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
> t
Hi Stephen,
On Tue, Mar 25, 2014 at 01:22:19PM -0400, Stephen Smith wrote:
> > 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
> >
In that case, I might like to try some other packages. Might try this
one (treePL divergence time analysis for phylogenies) published here
http://www.ncbi.nlm.nih.gov/pubmed/22908216
but will think about it. Also, I see there is a list of packages for
debian as a whole that need help, but is there
Hi Stephen
On Tue, Mar 25, 2014 at 01:44:52PM -0400, Stephen Smith wrote:
> In that case, I might like to try some other packages. Might try this
> one (treePL divergence time analysis for phylogenies) published here
> http://www.ncbi.nlm.nih.gov/pubmed/22908216
> but will think about it.
That's
Hi Stephen,
lintian tells me something about:
W: phyutility: incompatible-java-bytecode-format Java7 version (Class format:
51
I am not a Java expert, but wouldn't this make the package unusable on
standard Debian?
Do you need src/jade/lib/libmatrixExp.so for anything?
Thorsten
--
To U
Hi Stephen,
I guess Thorsten was asking this question wearing his ftpmaster hat.
Any comment to his question?
Kind regards
Andreas.
On Tue, Apr 01, 2014 at 02:55:44PM +0200, Thorsten Alteholz wrote:
> Hi Stephen,
>
> lintian tells me something about:
> W: phyutility: incompatible-jav
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
Hi Stephen,
On Tue, Apr 08, 2014 at 10:19:07PM -0400, Stephen Smith wrote:
> 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?
There is the option to use "
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