Hi Michael,
On Tue, Feb 24, 2015 at 03:03:16PM +, Michael Crusoe wrote:
> >
> > I admit that I became optimistic after the latest discussion, that we
> > have good chances to see libcolt-java in main in a sensible time frame
> > (3-6 monthes ??). I'm definitely not sure about libjai-core-java
On Tue Feb 24 2015 at 2:23:26 AM Andreas Tille wrote:
> Hi Michael,
>
> On Mon, Feb 23, 2015 at 10:37:43PM +, Michael Crusoe wrote:
> > > To explain the problem: We need to build the package in the main
> > > universe and the build-dependency libcolt-java is missing there. I
> > > tried to
Hi Michael,
On Mon, Feb 23, 2015 at 10:37:43PM +, Michael Crusoe wrote:
> > To explain the problem: We need to build the package in the main
> > universe and the build-dependency libcolt-java is missing there. I
> > tried to simply drop this build-dependency (+libjai-core-java) and
> > looke
On Sun Feb 22 2015 at 3:23:53 AM Andreas Tille wrote:
> On Sun, Feb 22, 2015 at 08:50:37AM +0100, Andreas Tille wrote:
> >
> > That could be a workaround. Since you can not create such binary
> > packages from one source package you need to create different source
> > packages. I admit I'm fine
On Sun, Feb 22, 2015 at 08:50:37AM +0100, Andreas Tille wrote:
>
> That could be a workaround. Since you can not create such binary
> packages from one source package you need to create different source
> packages. I admit I'm fine if you ignore the contrib part for the
> moment if you only need
Hi Michael,
On Sun, Feb 22, 2015 at 01:20:55AM +, Michael Crusoe wrote:
>
> Fully aware. It looks like the parts of libjung-java that trinityrnaseq
> uses aren't the parts that use classes from libcolt-java. I'm going to
> split libjung-java into two packages, on main and one contrib.
That c
On Sat Feb 21 2015 at 8:20:55 PM Michael Crusoe
wrote:
> On Sat Feb 21 2015 at 4:19:41 PM Andreas Tille wrote:
>
>> Hi Michael,
>>
>> On Sat, Feb 21, 2015 at 08:54:50PM +, Michael Crusoe wrote:
>> > >
>> > > Uhmm, only for contrib since it depends libcolt-java. :-( :-( :-(
>> >
>> > Ugh.
>>
uot;
> *Cc:* debian-med@lists.debian.org
> *Betreff:* Aw: Re: Update on Trinityrnaseq packaging
>
> Hello,
>
>
> I added an express-doc package and uploaded. That was OK, I hope.
>
> @Andreas, I will address Transdecoder next.
>
> Concerning the git repository I faile
transdecoder went exceptionally smoothly.
Cheers,
Steffen
Gesendet: Sonntag, 22. Februar 2015 um 03:33 Uhr
Von: "Steffen Möller"
An: "Michael Crusoe"
Cc: debian-med@lists.debian.org
Betreff: Aw: Re: Update on Trinityrnaseq packaging
Hello,
I added an
subversion repository :)
Cheers,
Steffen
Gesendet: Dienstag, 17. Februar 2015 um 04:46 Uhr
Von: "Michael Crusoe"
An: debian-med@lists.debian.org
Betreff: Re: Update on Trinityrnaseq packaging
On Mon Feb 16 2015 at 11:09:37 AM Andreas Tille <andr...@an3as.eu> wrote:
On Sat Feb 21 2015 at 4:19:41 PM Andreas Tille wrote:
> Hi Michael,
>
> On Sat, Feb 21, 2015 at 08:54:50PM +, Michael Crusoe wrote:
> > >
> > > Uhmm, only for contrib since it depends libcolt-java. :-( :-( :-(
> >
> > Ugh.
> >
> > I've removed the bundled collections15 library via patching an
Hi Michael,
On Sat, Feb 21, 2015 at 08:54:50PM +, Michael Crusoe wrote:
> >
> > Uhmm, only for contrib since it depends libcolt-java. :-( :-( :-(
>
> Ugh.
>
> I've removed the bundled collections15 library via patching and updated
> control to use contrib.
Are you aware about the consequenc
On Tue Feb 17 2015 at 3:50:50 AM Andreas Tille wrote:
> Hi Michael,
>
> On Tue, Feb 17, 2015 at 03:46:09AM +, Michael Crusoe wrote:
> > On Mon Feb 16 2015 at 11:09:37 AM Andreas Tille
> wrote:
> > > > dependencies needing review & uploading to Debian:
> > > > - [ ] libjung-java
> >
> > Ready
On Tue, Feb 17, 2015 at 09:50:35AM +0100, Andreas Tille wrote:
> > > > - [ ] express
> >
> > Ready for sponsoring
>
> I'll have a look.
I had a look and pushed some small changes to fix some lintian issues
and uploaded.
Thanks for your preparation
Andreas.
--
http://fam-tille.de
-
Hi Michael,
On Tue, Feb 17, 2015 at 03:46:09AM +, Michael Crusoe wrote:
> On Mon Feb 16 2015 at 11:09:37 AM Andreas Tille wrote:
> > > dependencies needing review & uploading to Debian:
> > > - [ ] libjung-java
>
> Ready for sponsoring
Uhmm, only for contrib since it depends libcolt-java. :
On Mon Feb 16 2015 at 2:02:12 AM "Steffen Möller"
wrote:
>
> Hi Michael,
>
>
> > On Mon Feb 16 2015 at 5:46:42 PM Andreas Tille
> wrote:Hi Michael,
>
> On Mon, Feb 16, 2015 at 07:09:18AM +, Michael Crusoe wrote:
>
> >> I had some quick look into this and did some changed (please pull).
> >>
On Mon Feb 16 2015 at 11:09:37 AM Andreas Tille wrote:
> Hi Michael,
>
> On Mon, Feb 16, 2015 at 07:09:18AM +, Michael Crusoe wrote:
> > To-do:
> > dependencies needing review & uploading to Debian:
> > - [ ] libjung-java
>
Ready for sponsoring
> > - [ ] rsem
>
Has a dependency that I jus
Hi Michael,
> On Mon Feb 16 2015 at 5:46:42 PM Andreas Tille wrote:Hi
>Michael,
On Mon, Feb 16, 2015 at 07:09:18AM +, Michael Crusoe wrote:
>> I had some quick look into this and did some changed (please pull).
>> Thanks for the changes. I realised that some large files are installed i
On Mon Feb 16 2015 at 5:46:42 PM Andreas Tille wrote:
> Hi Michael,
>
> On Mon, Feb 16, 2015 at 07:09:18AM +, Michael Crusoe wrote:
> >
> > To-do:
> > dependencies needing review & uploading to Debian:
> > ...
> > - [ ] transdecoder
>
> I had some quick look into this and did some changed (pl
Hi Michael,
On Mon, Feb 16, 2015 at 07:09:18AM +, Michael Crusoe wrote:
>
> To-do:
> dependencies needing review & uploading to Debian:
> ...
> - [ ] transdecoder
I had some quick look into this and did some changed (please pull).
I realised that some large files are installed into
/usr/
Hi Michael,
On Mon, Feb 16, 2015 at 07:09:18AM +, Michael Crusoe wrote:
> To-do:
> dependencies needing review & uploading to Debian:
> - [ ] libjung-java
> - [ ] rsem
> - [ ] express
> - [ ] transdecoder
OK, just ping me if one or more are ready for sponsering.
> - [ ] jaligner
Just upload
Done:
parafly has been submitted to the NEW queue (tille)
Trinity has a man page (tille)
hardening-no-relro usr/lib/trinityrnaseq/Chrysalis/* fixed
jar-not-in-usr-share usr/lib/trinityrnaseq/Butterfly/Butterfly.jar
update to release 2.0.4
To-do:
dependencies needing review & uploading to Debian:
-
On Fri Feb 13 2015 at 10:37:29 AM Andreas Tille wrote:
> Hi Michael,
>
> On Thu, Feb 12, 2015 at 11:03:48PM +, Michael Crusoe wrote:
> > > > Nothing coming up. Probably Broad Foundation employees / interns. I
> think
> > > > they are covered by the existing entry.
> > >
> > > Finally it does
On Fri Feb 13 2015 at 2:31:21 PM Andreas Tille wrote:
> On Thu, Feb 12, 2015 at 11:03:48PM +, Michael Crusoe wrote:
> > > a cleaned up archive. You can get this by
> > >
> > > debian/rules get-orig-source
> > >
> > > ... or if you want to save your bandwidth via
> > >
> > > mk-origta
On Thu, Feb 12, 2015 at 11:03:48PM +, Michael Crusoe wrote:
> > a cleaned up archive. You can get this by
> >
> > debian/rules get-orig-source
> >
> > ... or if you want to save your bandwidth via
> >
> > mk-origtargz --repack --compress xz
> >
>
> Yeah, I had tried that; I get this
Hi Michael,
On Thu, Feb 12, 2015 at 11:03:48PM +, Michael Crusoe wrote:
>
> > [Reply to list only]
>
> We are oppositely calibrated :-D I prefer to be CC'd even when I am a
> subscriber and you don't.
Well, I've got my calibration as a beginner @lists.debian.org.
Sometimes you get rude comm
On Fri Feb 13 2015 at 12:55:49 AM Andreas Tille wrote:
> [Reply to list only]
>
We are oppositely calibrated :-D I prefer to be CC'd even when I am a
subscriber and you don't.
> On Thu, Feb 12, 2015 at 09:42:45PM +, Michael Crusoe wrote:
> > > > - [ ] binary-without-manpage usr/bin/Trinity
[Reply to list only]
Hi Michael,
On Thu, Feb 12, 2015 at 09:42:45PM +, Michael Crusoe wrote:
> > ...
> > code I have seen (not too much admittedly) had extra *.so files in
> > /usr/lib. If you are unsure asking on debian-j...@lists.debian.org is
> > the best way to clarify.
>
> Upon review
On Thu Feb 12 2015 at 9:53:12 AM Andreas Tille wrote:
> On Thu, Feb 12, 2015 at 12:16:57AM +, Michael Crusoe wrote:
> > - [ ] hardening-no-relro usr/lib/trinityrnaseq/Chrysalis/*
> > Needs investigation
>
> While fixing this is nice to have I would not insist on it for sponsoring
> the packag
On Thu, Feb 12, 2015 at 12:16:57AM +, Michael Crusoe wrote:
> - [ ] hardening-no-relro usr/lib/trinityrnaseq/Chrysalis/*
> Needs investigation
While fixing this is nice to have I would not insist on it for sponsoring
the package.
> - [ ] jar-not-in-usr-share usr/lib/trinityrnaseq/Butterfly/Bu
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