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. Do
Le 03/03/2015 17:17, Andreas Tille a écrit :
To make sure we will not loose track here: Could you provide either a
tarball of the freehep-aida source (or a rule how you did created it)?
I'd volunteer to spend some time into the packaging but I'm afraid I
might pick the wrong code and thus
Hi again,
On Sun, Feb 22, 2015 at 10:59:02PM +0100, Andreas Tille wrote:
At this point I think freehep aida/jaida should be packaged, then a new
colt-free package could be created using freehep-aida and the
modifications I made. This will allow you to free at least 3 packages
from
On Tue Feb 24 2015 at 2:23:26 AM Andreas Tille andr...@an3as.eu 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
On Sun Feb 22 2015 at 3:23:53 AM Andreas Tille andr...@an3as.eu 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
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
looked what
Hi Markus,
thanks for checking this.
On Sun, Feb 22, 2015 at 12:47:00AM +0100, Markus Koschany wrote:
Where could one find the aida code replacement on java.freehep.org? So
far I found
As far as I understood Emmanuel he has answered the question in his
mail.
There is something else you could try, you may remove the non free parts
of colt and try rebuilding the reverse dependencies with this stripped
down version. If it works you could then derive a new colt-free package
from this version.
Emmanuel Bourg
--
To UNSUBSCRIBE, email to
Hi Emmanuel,
On Sun, Feb 22, 2015 at 11:19:37AM +0100, Emmanuel Bourg wrote:
There is something else you could try, you may remove the non free parts
of colt and try rebuilding the reverse dependencies with this stripped
down version. If it works you could then derive a new colt-free package
On 2015-02-22, Andreas Tille andr...@an3as.eu wrote:
I tried the stupid approach and simply replaced the affected files
IAxis.java IHistogram*.java
by the equally named files I found in SVN. But this was probably to
simple and did not build. I guess this approached needs somebody who
On 22.02.2015 09:47, Andreas Tille wrote:
[...]
Whatever helps to get a free functionality of libcolt-java would be
really helpful.
I think Emmanuel has already pointed in the right directions. Just to
clarify what exactly is controversial or difficult and has to be done.
The *.java files
Hi Markus,
On Sun, Feb 22, 2015 at 06:11:47PM +0100, Markus Koschany wrote:
I think Emmanuel has already pointed in the right directions. Just to
clarify what exactly is controversial or difficult and has to be done.
The *.java files under src/hep/aida/ in Colt belong to the freehep-aida
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 the
Hi Emmanuel,
On Sun, Feb 22, 2015 at 01:01:39AM +0100, Emmanuel Bourg wrote:
I got a quick look and it seems some of these classes are available in
the aida and jaida modules of freehep. The main issue seems to be the
hep.aida.bin package, it doesn't exist in freehep and depends on Colt
Le 22/02/2015 09:41, Andreas Tille a écrit :
This would be really good news. I'd be really happy about this but I
personally have no idea what exactly needs to be done to approach it.
Any help would be more than welcome.
The classes of the Mahout fork reside in a different package. If they
On Sun, Feb 22, 2015 at 01:40:22AM +0100, Emmanuel Bourg wrote:
I just found out the Apache Mahout project maintains a fork of Colt [1],
they kept only the free bits. Maybe it could be used as a replacement
for the projects based on Colt that don't use the non free part?
This would be really
Hi Emmanuel,
On Sun, Feb 22, 2015 at 09:52:48AM +0100, Emmanuel Bourg wrote:
Le 22/02/2015 09:41, Andreas Tille a écrit :
This would be really good news. I'd be really happy about this but I
personally have no idea what exactly needs to be done to approach it.
Any help would be more
Le 22/02/2015 22:06, Andreas Tille a écrit :
As far as I understand ftpmaster everything needs to be removed in
src/hep/aida (including bin and ref).
Yes they are right, but except for the src/hep/aida/bin classes the
src/hep/aida ones can be replaced by their equivalent in freehep.
I
Hi Sune,
On Sun, Feb 22, 2015 at 06:12:55PM +, Sune Vuorela wrote:
On 2015-02-22, Andreas Tille andr...@an3as.eu wrote:
I tried the stupid approach and simply replaced the affected files
IAxis.java IHistogram*.java
by the equally named files I found in SVN. But this was
Hi Emmanuel,
On Sun, Feb 22, 2015 at 10:31:13PM +0100, Emmanuel Bourg wrote:
Le 22/02/2015 22:06, Andreas Tille a écrit :
As far as I understand ftpmaster everything needs to be removed in
src/hep/aida (including bin and ref).
Yes they are right, but except for the src/hep/aida/bin
On Sat Feb 21 2015 at 8:20:55 PM Michael Crusoe michael.cru...@gmail.com
wrote:
On Sat Feb 21 2015 at 4:19:41 PM Andreas Tille andr...@an3as.eu wrote:
Hi Michael,
On Sat, Feb 21, 2015 at 08:54:50PM +, Michael Crusoe wrote:
Uhmm, only for contrib since it depends libcolt-java. :-(
Le 21/02/2015 22:32, Andreas Tille a écrit :
Unfortunately nobody in the team is skilled anough in Java to do the job
(or at least confirm that it is as simple as I assume) and thus I wonder
whether there is some kind soul on Debian Java having a look into this.
Hi Andreas,
I got a quick
On 21.02.2015 22:32, Andreas Tille wrote:
Hi Java programmers,
Hi Andreas,
I wonder whether you could help to replace some outdated code in
libcolt-java which has some old code from src/hep.aida.* which is LGPL
but no military exception. The code is old, was rewritten in
I just found out the Apache Mahout project maintains a fork of Colt [1],
they kept only the free bits. Maybe it could be used as a replacement
for the projects based on Colt that don't use the non free part?
Emmanuel Bourg
[1] https://github.com/apache/mahout/tree/master/math
--
To
repository :)
Cheers,
Steffen
Gesendet:Dienstag, 17. Februar 2015 um 04:46 Uhr
Von:Michael Crusoe michael.cru...@gmail.com
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:
Hi Michael
transdecoder went exceptionally smoothly.
Cheers,
Steffen
Gesendet:Sonntag, 22. Februar 2015 um 03:33 Uhr
Von:Steffen Mller steffen_moel...@gmx.de
An:Michael Crusoe michael.cru...@gmail.com
Cc:debian-med@lists.debian.org
Betreff:Aw: Re: Update on Trinityrnaseq packaging
Hello
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
On Sat Feb 21 2015 at 4:19:41 PM Andreas Tille andr...@an3as.eu 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
*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 failed to get the upstream/1.5.1 branch -
so I just
On Tue Feb 17 2015 at 3:50:50 AM Andreas Tille andr...@an3as.eu 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 andr...@an3as.eu
wrote:
dependencies needing review uploading to Debian:
- [ ]
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 consequences that
andr...@an3as.eu
To: debian-med@lists.debian.org
Subject: Re: Update on Trinityrnaseq packaging
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 andr...@an3as.eu wrote:
dependencies needing review uploading to Debian
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 andr...@an3as.eu wrote:
dependencies needing review uploading to Debian:
- [ ] libjung-java
Ready for sponsoring
Uhmm, only for contrib since it depends
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
--
To
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
On Mon Feb 16 2015 at 5:46:42 PM Andreas Tille andr...@an3as.eu 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
Hi Michael,
On Mon Feb 16 2015 at 5:46:42 PM Andreas Tille andr...@an3as.eu 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
On Mon Feb 16 2015 at 11:09:37 AM Andreas Tille andr...@an3as.eu 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
On Mon Feb 16 2015 at 2:02:12 AM Steffen Möller steffen_moel...@gmx.de
wrote:
Hi Michael,
On Mon Feb 16 2015 at 5:46:42 PM Andreas Tille andr...@an3as.eu
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
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:
-
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 comments
On Fri Feb 13 2015 at 2:31:21 PM Andreas Tille andr...@an3as.eu 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-origtargz
On Fri Feb 13 2015 at 10:37:29 AM Andreas Tille andr...@an3as.eu 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 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 path_to_original_download_source
Yeah, I had tried
On Thu Feb 12 2015 at 9:53:12 AM Andreas Tille andr...@an3as.eu 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
[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 they are
On Fri Feb 13 2015 at 12:55:49 AM Andreas Tille andr...@an3as.eu 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
- [ ] hardening-no-relro usr/lib/trinityrnaseq/Chrysalis/*
Needs investigation
- [ ] jar-not-in-usr-share usr/lib/trinityrnaseq/Butterfly/Butterfly.jar,
usr/lib/trinityrnaseq/util/support_scripts/ExitTester.jar
May be fixable with a move + symlink. Need to make sure that they are pure
Java
- [ ]
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
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