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
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,
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:
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
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
for
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.
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
as
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 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 as
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
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 of
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
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. Hopefully
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 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
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
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 phyutility.
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 the tasks
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
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 will
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
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
a
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 release.
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
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
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
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
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 to 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 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
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 accepted for
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 andr...@an3as.eu wrote:
Hi Stephen,
any opinion about SVN versus Git for phyutility
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'
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
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://
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
with
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 like
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
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
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