Hi,
I'm stumbling upon the license terms of a part of the code (which is
important enough so that the whole program really needs it) of the new
release of Jalview I am packaging: that part has a license identical to
BSD-3-clause except that clause 3 bas been changed to:
3. Redistributions
Hi Andreas and Steffen,
Le 28/11/2020 à 00:38, Steffen Möller a écrit :
Hi Pierre,
On 27.11.20 23:10, Andreas Tille wrote:
Hi Pierre,
On Fri, Nov 27, 2020 at 10:48:13PM +0100, Pierre Gruet wrote:
I'm stumbling upon the license terms of a part of the code (which is
important enough so
Hi,
I have worked on libsis-base-java, which FTBFS due to a IO error in
tests. Would you mind either reviewing [0] or giving me DM
rights?
dcut dm --uid "Pierre Gruet" --allow libsis-base-java
Thanks a lot,
Pierre
[0] https://salsa.debian.org/med-team/libsis-base-java
Hi,
I have worked on snap. Would you mind either reviewing [0] or giving me
DM rights?
dcut dm --uid "Pierre Gruet" --allow snap
Thanks a lot,
Pierre
[0] https://salsa.debian.org/med-team/snap
Hi Andreas and everyone,
Le 16/01/2021 à 12:45, Andreas Tille a écrit :
Hi folks,
since 2011 we are doing Debian Med developer sprints and it had turned
out that these events are very successfully. Due to the well known
situation in person meetings are not possible currently - but this
should
Hi Andreas,
Le 17/01/2021 à 17:52, Andreas Tille a écrit :
Hi Pierre,
On Sun, Jan 17, 2021 at 02:23:08PM +0100, Pierre Gruet wrote:
But I never took part to such event, so could you please give some examples
about possible outputs?
There is no dedicated output of our sprints. The major
.
Could you please either review them in Salsa or grant me DM rights?
dcut dm --uid "Pierre Gruet" --allow libjsonp-java pixelmed
Thanks a lot,
Pierre
Hi Andreas,
Le 27/01/2021 à 21:46, Andreas Tille a écrit :
Hi,
I've tried to upgrade picard-tools in Git. Unfortunately (and
admittedly not unexpected) the build time tests are failing:
...
Running Test: Test method
testForVcf(picard.vcf.processor.WidthLimitingDecoratorTest)
Gradle Test Exec
Hi Bruce and Andreas,
Le 05/02/2021 à 05:12, Bruce Walker a écrit :
Hi Andreas,
I am the upstream author of Pilon, and I built the new 1.24 release using a
modern 2.13.x Scala compiler and library (along with a java 11 JRE, previously
was java 8). I’m sure the issue is in those changes. I wil
Hi,
I have prepared an upload of the last upstream version of Jalview. True,
it is close to the soft freeze, but I have made thorough tests and
besides, no package depends on it.
Would you mind giving me DM rights to do the upload?
dcut dm --uid "Pierre Gruet" --allow jalview
M
of Jalview have been very helpful, special
thanks to them also!
Kind regards
Andreas.
Best regards,
Pierre
On Sat, Feb 06, 2021 at 10:25:38PM +0100, Pierre Gruet wrote:
Hi,
I have prepared an upload of the last upstream version of Jalview. True, it
is close to the soft freeze, but
Hi Nilesh,
Le 07/02/2021 à 15:30, Nilesh Patra a écrit :
Hi Pierre,
Thanks for your work on jalview. However, it seems that the autopkgtest
fails on i386, which will prevent migration to testing.
It looks like a memalloc problem so maybe this can be simply skipped. Or
if I'm mistaken, please
of 90?
The errors about no X11 display being set are non-fatal and look like
our problem upstream (well, Ben's perhaps 🙂 ) rather than Pierre's.
Yeah, no problem about this :)
Jim.
Thanks a lot,
Pierre
---
Hi,
I worked on drop-seq to correct its RC bug and add some minor improvements.
Would you mind reviewing or giving me DM rights?
dcut dm --uid "Pierre Gruet" --allow drop-seq
Many thanks,
Pierre
Hi Tássia and Andreas,
Le 21/02/2021 à 11:51, Andreas Tille a écrit :
Hi Tássia,
[...]
Moreover I realised that there seems to be another issue:
$ runXProtTestHPC
Error: Could not find or load main class es.uvigo.darwin.xprottest.XProtTestApp
Caused by: java.lang.NoClassDefFoundError:
org/
Hi Nilesh,
Le 24/03/2021 à 11:47, Nilesh Patra a écrit :
Hi Steffen,
Thanks for your reply. This is a lot of information, so I'll just quote
specific sections.
There are some tools that block many columns from being completed. To
mention here in particular are the workflow engines, and here i
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: snpeff
Version : 4.3t
Upstream Author : Pablo Cingolani
* URL : https://pcingola.github.io/SnpEff/
* License : LGPL
ource trees are now completely separated.
Do you (or someone else) know if SnpSift would be important to package?
Looking at the spreadsheet I am not sure it is worth packaging right now.
Thanks a lot
Andreas.
Best wishes,
Pierre
On Tue, Mar 30, 2021 at 12:24:18PM +0200, Pierre Gruet
Hi Steffen,
Le 30/03/2021 à 16:32, Steffen Möller a écrit :
Am 30.03.21 um 15:25 schrieb Andreas Tille:
Hi Pierre,
On Tue, Mar 30, 2021 at 01:16:17PM +0200, Pierre Gruet wrote:
Yes! It is almost ready and I'm happy about this :)
That's understandable considering the lot of wor
Hi everyone,
Le 31/03/2021 à 06:11, Andreas Tille a écrit :
In any case, I do not have push access in the blends-team
Please consider adding me in to the , or grant me maint access to this repo
Fixed.
Could someone please also grant me access to the blends-team (pgt)? I
made a request
Hi Andreas,
Le 08/04/2021 à 22:29, Andreas Tille a écrit :
Hi Pierre,
On Thu, Apr 08, 2021 at 05:28:15PM +0200, Pierre Gruet wrote:
Fixed.
Could someone please also grant me access to the blends-team (pgt)? I made a
request on Salsa some days ago but nothing has happened by now.
I added
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: capsule-nextflow
Version : 1.1.0
Upstream Author : Paolo di Tommaso
* URL : https://github.com/nextflow-io/capsule
* Licens
Hi Andreas and Nilesh,
Le 29/04/2021 à 16:44, Nilesh Patra a écrit :
On 4/29/21 7:24 PM, Andreas Tille wrote:
Hi Pierre,
On Thu, Apr 29, 2021 at 11:08:04AM +0200, Pierre Gruet wrote:
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian
Hi Andreas,
Le 30/04/2021 à 07:27, Andreas Tille a écrit :
Hi Pierre,
On Thu, Apr 29, 2021 at 08:34:58PM +0200, Pierre Gruet wrote:
Thanks for your kind words!
:-)
I met several issues with capsule, as the upstream author seems to build it
against jdk-8, and now in Debian we use openjdk
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: capsule-maven-nextflow
Version : 1.0.3.1
Upstream Author : Paolo di Tommaso
* URL : https://github.com/nextflow-io/capsule-
Dear all,
Those last weeks I spent quite a lot of time pushing forward the
packaging of nextflow. I wrote a few patches and pushed 5 dependencies
into NEW.
Now there remains quite a lot to do.
The biggest tasks would be to package the SDK of AWS [0] (which would
also benefit igv) and of M
Hi Steffen, Andreas and Noah,
Le 02/06/2021 à 19:27, Noah Meyerhans a écrit :
On Wed, Jun 02, 2021 at 09:45:05AM -0700, Ross Vandegrift wrote:
Let us start with a discussion where the sdk itself should be
team-maintained - cloud or med or java?
Personally, I'd opt for Java, since this seems li
Hi Steffen,
Le 02/06/2021 à 18:02, Steffen Möller a écrit :
Hello again,
Am 01.06.2021 um 13:03 schrieb Steffen Möller:
Hi Pierre,
Am 01.06.2021 um 11:46 schrieb Andreas Tille:
Hi Pierre,
thanks a lot for keeping us up to date.
On Tue, Jun 01, 2021 at 10:49:11AM +0200, Pierre Gruet wrote
Hi Shruti,
Le 21/07/2021 à 17:18, Andreas Tille a écrit :
Hi Shruti,
On Wed, Jul 21, 2021 at 01:32:35PM +0530, Shruti Sridhar wrote:
I am working on writing autopkgtests for logol [1] and the test passes in
my chroot but fails the pipeline
I could reproduce this locally with autopkgtest-vir
Hi everyone,
Recently there has been quite a lot of movement around the packaging of
gatk:
- I listed the dependencies to be packaged in our common spreadsheet, in
the Java sheet, on lines 61 to 78. I think some of them should reveal
optional, but I also see at some point we will be blocked
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: libgoby-java
Version : 3.3.1
Upstream Author : Institute for Computational Biomedicine
* URL : https://github.com/CampagneLa
Hi Andreas,
Le 09/09/2021 à 08:31, Andreas Tille a écrit :
Hi Pierre (and others)
when trying to build the latest version of pilon[1] I get:
...
scalac -classpath /usr/share/java/htsjdk.jar -d pilon.jar
src/main/scala/org/broadinstitute/pilon/*
src/main/scala/org/broadinstitute/pilon/BamFile.
Hi Tony,
Le 23/09/2021 à 22:06, Tony Travis a écrit :
On 23/09/2021 17:16, Steffen Möller wrote:
[...]
You would install both the source tree (with the Debian folder) and
install the binary. Then run
sh debian/tests/run-unit-test
from the source directory.
Hi, Steffen.
Please forgive my ig
Hi Andreas,
Le 27/09/2021 à 17:26, Andreas Tille a écrit :
Hi Pierre,
I was running routine-update on igv and as usually some patches did not
applied. There is no urgent pressure to upgrade the package but its
raising a signal that the watch file is not working (due to changes on
github). The
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: tipp
Version : 1.0
Upstream Author : Siavash Mirarab
* URL : https://github.com/TeraTrees/TIPP
* License : GPL-3
P
HI Andreas,
Le 28/09/2021 à 07:11, Andreas Tille a écrit :
Hi Pierre,
On Mon, Sep 27, 2021 at 08:38:34PM +0200, Pierre Gruet wrote:
Actually the situation is a bit complicated with igv:
- I am waiting for libgoby-java to exit NEW so that I can upload the version
currently packaged to main
Hi Maarten,
Le 29/09/2021 à 17:28, Andreas Tille a écrit :
Should I add a call to this update script in the post install hook? Having
500MB of data in Debian that's probably updated the very next day after
installation seems very inconvenient, right?
I'm not sure whether we have example sol
Hi Andreas,
Thanks for forking the thread and launching this conversation.
Le 01/10/2021 à 08:48, Andreas Tille a écrit :
Hi,
Am Thu, Sep 30, 2021 at 02:10:50PM +0200 schrieb Pierre Gruet:
My concern with this is the average user might not even know about the
README.Debian file and could
Hi,
Le 01/10/2021 à 16:52, Andreas Tille a écrit :
Hi,
I intended to update pilon to its latest upstream version but
got:
scalac -classpath /usr/share/java/htsjdk.jar -d pilon.jar
src/main/scala/org/broadinstitute/pilon/*
src/main/scala/org/broadinstitute/pilon/BamFile.scala:24: error: object
Hi Andreas,
Le 12/10/2021 à 09:59, Andreas Tille a écrit :
Hi Pierre,
I realised that you updated Git of drop-seq to fix the watch file. I
simply uploaded basically as is to have a proper signal in our tools
that there is a new upstream version. Unfortunately I realised that
there seems to be
Hi again,
Le 12/10/2021 à 15:24, Andreas Tille a écrit :
Am Tue, Oct 12, 2021 at 12:12:43PM +0200 schrieb Pierre Gruet:
Thanks for pointing this out; I looked at it and saw biojava has not been a
dependency of drop-seq until now. It seems version 2.4.1 is the first to
need biojava. So I will
Hi again,
Le 12/10/2021 à 18:58, Andreas Tille a écrit :
Hi Pierre,
Am Tue, Oct 12, 2021 at 03:29:33PM +0200 schrieb Pierre Gruet:
I have added biojava4 as a dependency, then some paths had to be changed
because upstream relies on a far outdated version of biojava, and then I had
to revise
Hi Andreas,
Le 13/10/2021 à 07:38, Andreas Tille a écrit :
Hi Pierre,
Am Tue, Oct 12, 2021 at 09:13:49PM +0200 schrieb Pierre Gruet:
Cool. I also think we should pimp biojava4 watch file to return the last
upstream source of biojava4 and than also provide biojava5. We will soon
see
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: biojava5-live
Version : 5.4.0
Upstream Author : BioJava Developers
* URL : https://www.biojava.org/
* License : LGP
Hi Andreas,
Le 09/11/2021 à 07:55, Andreas Tille a écrit :
Hi Pierre,
thanks a lot for all your work on this.
You are welcome! Indeed I am very pleased this long-term target of mine
is now reached!
I intended to do a source-only upload and when doing so at least fixing
the watch file (I re
Hi Andreas,
Le 09/11/2021 à 18:29, Andreas Tille a écrit :
Hi Pierre,
Am Tue, Nov 09, 2021 at 06:02:39PM +0100 schrieb Pierre Gruet:
If you are not able to reproduce I can send a full build log. It would
be fine for me if you would just fix - build - upload yourself. I just
wanted to help
Hi,
Le 10/11/2021 à 15:14, Andreas Tille a écrit :
Hi,
I realised that libjung-java "smells"[1] and in fact it was not uploaded
a long time and has some maintenance issues. I tried to build the
current state in Git but it fails the API fails to build. I hope this is
not a big issue for a Java
Hi Nilesh,
Le 23/11/2021 à 19:11, Nilesh Patra a écrit :
Hi,
It looks like profphd has a open RC bug for a little over two years by now,
and upstream looks dead.
It has only reverse-recommends, no reverse-(build-)depends
$ reverse-depends profphd
Reverse-Recommends
* norsnet
* norsp
* profbval
Hi,
Newest picard-tools is in unstable, and I fixed the two bugs the source
package had!
Best,
Pierre
RC bug in sight is now fixed!
Forwarded Message
Subject: Bug#1001681: marked as done (sight: FTBFS in unstable)
Date: Thu, 16 Dec 2021 06:21:03 +
From: Debian Bug Tracking System
Reply-To: 1001...@bugs.debian.org
To: Pierre Gruet
Your message dated Thu, 16 Dec 2021 06
Hi Andreas,
On 09/09/2021 14:21, Andreas Tille wrote:
Hi Pierre,
thanks a lot for your educated answer.
On Thu, Sep 09, 2021 at 12:48:33PM +0200, Pierre Gruet wrote:
Any hint how to fix this?
Well, /maybe/ we could patch this last pilon version to use Scala 2.11 with
it... but I see there
Hi Andreas,
On 18/12/2021 08:52, Andreas Tille wrote:
Hi Pierre,
Am Fri, Dec 17, 2021 at 11:27:50PM +0100 schrieb Pierre Gruet:
I have just uploaded latest upstream version of pilon to unstable, together
with a fix for the scala issues showing up. Normally we would have had to
update scala
Hello Lance,
On 21/12/2021 14:33, Lance Lin wrote:
Debian Medical Team,
I have started looking at adding autopkgtest suites for a variety of packages.
Two of the packages (hinge, pique) require very large data sets to run their
included examples. The sizes are several GB. It also looks like t
Control: tags -1 unreproducible help
Hi,
Currently I am not able to reproduce the issue on my computer nor on
several machines of the Debian project.
I shall investigate further a bit later, but so far looking at a diff
between the provided build log and mine has not helped.
The warning me
Hi Andreas,
On 23/12/2021 17:27, Andreas Tille wrote:
Thanks Pierre for your work. :-)
Maintainer: Debian Med Packaging Team
Changed-By: Pierre Gruet
Closes: 1002155
Changes:
libgoby-java (3.3.1+dfsg2-6) unstable; urgency=medium
.
* Adding --no-parallel flag to dh_auto_test to avoid
Hi Andreas,
On 23/12/2021 19:42, Andreas Tille wrote:
Hi Pierre,
Am Thu, Dec 23, 2021 at 05:42:24PM +0100 schrieb Pierre Gruet:
You're welcome! Thanks for your help on this.
That's team work, isn't it? ;-)
Sure ! :)
BTW, if you are seeking new challanges: It would b
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: megan-ce
Version : 6.21.1
Upstream Author : Daniel Huson
* URL : https://github.com/danielhuson/megan-ce
* License
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: malt
Version : 0.5.2
Upstream Author : Daniel Huson
* URL : https://github.com/danielhuson/malt
* License : GPL-3+
[redirecting to debian-med@lists.debian.org for information]
Hi Andreas,
Le 22/01/2022 à 16:43, Andreas Tille a écrit :
Thanks a lot Pierre for fixing it quickly in a new upload. Its a
great step forward if we have this package.
Thanks also to Thorsten for checking
You're welcome! Thanks fo
Hi again Andreas,
Le 22/01/2022 à 21:24, Andreas Tille a écrit :
Hi Pierre,
Am Sat, Jan 22, 2022 at 08:37:54PM +0100 schrieb Pierre Gruet:
Le 22/01/2022 à 16:43, Andreas Tille a écrit :
Thanks a lot Pierre for fixing it quickly in a new upload. Its a
great step forward if we have this
Dear all,
Le 24/01/2022 à 16:09, Andreas Tille a écrit :
Hi folks,
on Mon, 21 Jan 2002 11:59:11 +0100 the first mail to this list was
sent[1]. So somehow we can celebrate some anniversary. :-)
Great :-) Happy to celebrate this!
Since 11 years we are doing team sprints - preferably face to
Hi Andreas,
Le 28/01/2022 à 22:30, Andreas Tille a écrit :
Am Fri, Jan 28, 2022 at 10:11:27PM +0100 schrieb pgtdeb...@free.fr:
If you want, I would be happy to package pdfbox-graphics2d. I can do that
very soon.
Else, please tell me if you start something :-)
I've just collected a basic debi
Hi Andreas,
Le 28/01/2022 à 22:42, Andreas Tille a écrit :
Am Fri, Jan 28, 2022 at 10:11:27PM +0100 schrieb pgtdeb...@free.fr:
If you want, I would be happy to package pdfbox-graphics2d. I can do that
very soon.
Else, please tell me if you start something :-)
I've pushed
https://salsa.
Hi,
Le 28/01/2022 à 22:42, Andreas Tille a écrit :
Am Fri, Jan 28, 2022 at 10:11:27PM +0100 schrieb pgtdeb...@free.fr:
If you want, I would be happy to package pdfbox-graphics2d. I can do that
very soon.
Else, please tell me if you start something :-)
I've pushed
https://salsa.debian.o
Hi Andreas,
Le 03/02/2022 à 10:31, Andreas Tille a écrit :
Hi,
Am Sat, Jan 22, 2022 at 09:49:32PM +0100 schrieb Pierre Gruet:
I did the upload -- I agree autopkgtests would be valuable, still. Yet I
remember the tests I did when designing the package last Spring, and I feel
providing a
Hi again,
Le 03/02/2022 à 22:22, Andreas Tille a écrit :
Am Thu, Feb 03, 2022 at 02:42:40PM +0100 schrieb Pierre Gruet:
Yes, just before looking at king/libpdfbox-graphics2d-java I was updating
snpeff and seeing if I could turn some unit tests into autopkgtests -- and I
trust I can, this is
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: rockhopper
Version : 2.0.3
Upstream Author : Brian Tjaden
* URL : https://cs.wellesley.edu/~btjaden/Rockhopper
* License
Hi,
Le 12/02/2022 à 06:42, Andreas Tille a écrit :
Very cool!
You're welcome!
Eventually, all the .class files in the archive were just igv and its
dependencies, so that I could remove all of them and have igv as the
sole dependency of the binary package :-)
Best regards,
--
Pierre
Hi everyone,
To give a bit of context: I am currently writing autopkgtests for
htsjdk, which is one Java library we maintain in the team. Those
autopkgtests should test reverse-dependencies to ease upgrades of htsjdk.
When designing such tests, I would need data to run, let's say, artemis
or
Hi Andrius,
Le 18/02/2022 à 17:21, Andrius Merkys a écrit :
Hi Pierre,
On 2022-02-18 17:52, Pierre Gruet wrote:
To give a bit of context: I am currently writing autopkgtests for
htsjdk, which is one Java library we maintain in the team. Those
autopkgtests should test reverse-dependencies to
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: snpsift
Version : 5.1
Upstream Author : Pablo Cingolani
* URL : https://pcingola.github.io/SnpEff/ss_introduction/
* Licens
Package: wnpp
Severity: wishlist
Owner: Debian med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: aeonbits-owner
Version : 1.0.12
Upstream Author : Luigi R. Viggiano
* URL : http://owner.aeonbits.org/
* License : B
Hello everyone,
I need your advice on a packaging issue I am meeting right now.
I am in the course of packaging gatk-bwamem-jni [0], providing a native
interface which allows one to use bwa (Debian packaged [1]) from Java
code. Fine.
But the upstream of gatk-bwamem-jni relies on a version of
Hi Nilesh,
Thanks for the quick answer. Your advice is much appreciated, as always.
Le 13/03/2022 à 15:46, Nilesh Patra a écrit :
On 3/13/22 8:05 PM, Pierre Gruet wrote:
What should I do? My proposal would be to design a multiple upstream
tarball for gatk-bwamem-jni: original one + the
Hi Andrius,
Thanks for looking at my issue.
Le 14/03/2022 à 06:03, Andrius Merkys a écrit :
Hi Pierre,
On 2022-03-13 16:35, Pierre Gruet wrote:
My proposal would be to design a multiple upstream tarball for
gatk-bwamem-jni: original one + the sources at the tip of the Apache2
branch of bwa
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: gatk-fermilite
Version : 1.2.1
Upstream Author : Broad Institute
* URL : https://github.com/broadinstitute/gatk-fermilite-jn
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: http-nio
Version : 0.1.0
Upstream Author : Daniel Gomez-Sanchez
* URL : https://github.com/lbergelson/http-nio
* License
Hi Guillem,
Le 28/03/2022 à 13:43, Guillem Jover a écrit :
Hi!
On Sat, 2022-03-26 at 14:59:17 +0100, Pierre Gruet wrote:
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: http-nio
Version
1-07 15:25:19.0
+0100
+++ artemis-18.1.0+dfsg/debian/changelog2022-02-28 18:24:58.0
+0100
@@ -1,3 +1,9 @@
+artemis (18.1.0+dfsg-7) UNRELEASED; urgency=medium
+
+ * Changing coordinates of biojava, which is now Maven-packaged
+
+ -- Pierre Gruet Mon, 28 Feb 2022 18:2
Hi Olivier, Andreas, Steffen,
Le 28/03/2022 à 17:54, Steffen Möller a écrit :
On 28.03.22 17:15, Andreas Tille wrote:
Am Mon, Mar 28, 2022 at 04:42:15PM +0200 schrieb olivier sallou:
...
that's fine for me
Thanks a lot for this effort
Many thanks - brings some memories back!
Steffen
Th
Hi everyone,
Le 24/06/2022 à 22:15, Étienne Mollier a écrit :
[...]
In the light of Andreas' own time shrinking, my id is also
available if need be (disregarding the fact that I felt having
the head underwater in the past few months myself). I'll try to
add myself systematically when interven
Hi Andreas and tony,
Le 01/07/2022 à 19:13, tony mancill a écrit :
On Thu, Jun 30, 2022 at 05:06:50PM +0200, Andreas Tille wrote:
Hi Pierre (and others)
I injected latest version of milib which moved to gradle even in some
versions before. My extremely weak attempt to switch to gradle failed
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: gatk-bwamem
Version : 1.0.4
Upstream Author : Broad Institute
* URL : https://github.com/broadinstitute/gatk-bwamem-jni/
* L
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: genomicsdb
Version : 1.4.3
Upstream Author : Intel Health and Lifesciences
* URL : https://www.genomicsdb.org/
* License
Hi Andreas,
Le 26/07/2022 à 13:50, Andreas Tille a écrit :
Hi,
from my perspective the CMakeLists.txt of tiddit has not changed compared
to the last upstream version. Unfortunately the build fails[1] with
CMake Error at CMakeLists.txt:42 (add_executable):
No SOURCES given to
Hello Flavien,
We have just had this bug report on sight:
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1016276
My last upload of sight was 15 days ago with no issue. Anyway, if you
have some time to look at it, it will be useful!
Best wishes,
--
Pierre
OpenPGP_signature
Descri
Hi Aaron and Andreas,
Le 11/10/2022 à 15:06, Aaron M. Ucko a écrit :
Andreas Tille writes:
I wanted to set you "Owner" of the Debian Med team repository since this
is the maximum power. I realised you are owner. So either someone has
beaten me and just did so or something is wrong if you ca
Hi Aaron,
Le 12/10/2022 à 04:48, Aaron M. Ucko a écrit :
Pierre Gruet writes:
Indeed, this warning should be overridden, usually I do so and add a
pointer to the discussion in
https://lists.debian.org/debian-java/2018/06/msg00021.html in the
comment in the .lintian-overrides file.
Got it
Hi Aaron,
Le 14/10/2022 à 02:05, Aaron M. Ucko a écrit :
Pierre Gruet writes:
I have just pushed some changes. I adopted the -- I believe -- least
invasive solution by creating a new package libngs-jni which depends
on the shared lib package (not the -dev one), only ships a symlink to
the
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: biojava6-live
Version : 6.0.5
Upstream Author : BioJava Developers
* URL : https://biojava.org
* License : LGPL-2.1
Package: wnpp
Severity: wishlist
Owner: Debian-med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: libmjson-java
Version : 1.4.0
Upstream Author : Miami-Dade County
* URL : https://bolerio.github.io/mjson/
* License
Hi Andreas,
Le 24/10/2022 à 09:58, Andreas Tille a écrit :
Hi Pierre,
I've updated beast2-mcmc in Git but the new upstream version fails to
build[1] which has hopefully a simple fix.
Thanks for drawing my attention on this issue. I pushed the effort
forward, but now half of the tests are fai
Hi,
Le 26/10/2022 à 10:35, Andreas Tille a écrit :
Hi Mathieu,
Am Wed, Oct 26, 2022 at 08:10:42AM +0200 schrieb Mathieu Malaterre:
On Wed, Oct 26, 2022 at 7:53 AM Andreas Tille wrote:
Hi,
in the bug log there is some discussion to drop C# and Java VTK
bindings. This would mean to drop the
Hi Andreas,
Le 26/10/2022 à 11:24, Andreas Tille a écrit :
Hi Pierre,
Am Wed, Oct 26, 2022 at 10:41:51AM +0200 schrieb Pierre Gruet:
[1] https://salsa.debian.org/med-team/gdcm/-/jobs/3427720
This is really just a missing include dir, as the problematic header is in
/usr/lib/jvm/default-java
Hi everyone,
Le 01/11/2022 à 16:35, Andreas Tille a écrit :
Hi,
this is the call for the next video conference of the Debian Med team
[...]
For those who are interested in hot topics we want to tackle, here
are some items:
- RC bugs
- Pushing latest versions of our software
While I
Hi everyone,
Le 29/10/2022 à 21:28, Nilesh Patra a écrit :
Hi,
I suppose sprints in 2021 and 2022 have been virtual so far due to COVID.
There were some COVID related sprints in 2020 as well.
Is there a possibilty to have an in-person debian-med sprint in 2023?
Would someone be interested in i
Hi,
Le 22/11/2022 à 14:38, Andreas Tille a écrit :
Hi Sascha,
Am Tue, Nov 22, 2022 at 12:38:21AM +0100 schrieb Sascha Steinbiss:
I have been in touch with our front desk and it looks like a meeting at my
employer here is doable in principle, given the same conditions as last
time. So I guess
Hi Andreas,
Le 25/11/2022 à 10:57, Andreas Tille a écrit :
Hi,
I just realised that libsbml moved to Github. After fixing the watch
file I tried to package the latest upstream version. Unfortunately
the build fails and I see the lines
/builds/med-team/libsbml/debian/output/source_dir/src/bin
Hi Andreas,
Le 27/11/2022 à 07:07, Andreas Tille a écrit :
Hi Pierre,
when fixing the watch file I stumbled upon an autopkgtest error[1].
Do you have an idea what might be wrong here?
My guess is there is a missing jar in the manifest of the jar shipped by
libmilib-java, which I updated two
Hi Andreas,
Le 27/11/2022 à 07:07, Andreas Tille a écrit :
Hi Pierre,
when fixing the watch file I stumbled upon an autopkgtest error[1].
Do you have an idea what might be wrong here?
At last I found classpath issues in the build, and I could provide a
cleaner way to build the jar which was
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