New upstream jung on github seems to remove license issues( to be checked ).
We should go to github code for latest release.
Olivier
-- Forwarded message -
From: Joshua O'Madadhain
Date: dim. 17 janv. 2016 07:34
Subject: Re: Jung license
To: olivier sallou
On Thu, J
-- Forwarded message -
From: Andreas Tille
Date: lun. 18 janv. 2016 à 10:40
Subject: Re: Bug#810842: [a...@debian.org: Bug#810842: igv: libsam-java is
gone]
To: olivier sallou
On Mon, Jan 18, 2016 at 09:17:54AM +, olivier sallou wrote:
> Le lun. 18 janv. 2016 à 10
Hi Andreas,
I had no answer to my mail, is my answer clear enough ?
Olivier
Le lun. 18 janv. 2016 à 10:57, olivier sallou a
écrit :
>
>
> -- Forwarded message -
> From: Andreas Tille
> Date: lun. 18 janv. 2016 à 10:40
> Subject: Re: Bug#810842: [a...@debi
Le mer. 27 janv. 2016 14:17, Andreas Tille a écrit :
> Hi Olivier,
>
> On Wed, Jan 27, 2016 at 11:42:41AM +, olivier sallou wrote:
> > Hi Andreas,
> > I had no answer to my mail, is my answer clear enough ?
>
> Thanks for asking back - you might have missed
>
On 01/27/2016 02:36 PM, Andreas Tille wrote:
> On Wed, Jan 27, 2016 at 01:30:02PM +0000, olivier sallou wrote:
>> Le mer. 27 janv. 2016 14:17, Andreas Tille a écrit :
>>
>>> Hi Olivier,
>>>
>>> On Wed, Jan 27, 2016 at 11:42:41AM +, olivier sallou wr
Hi,
I made a quick build to test and build was successful. Did you fix your
issues in the meanwhile?
Le ven. 12 févr. 2016 à 16:31, Andreas Tille a écrit :
> Hi,
>
> I upgraded Git that was featuring version 2.0.1+dfsg.1 meanwhile to
> Build-Depend and use libngs-java. I think we should continu
Le jeu. 4 févr. 2016 à 14:26, Olivier Sallou a
écrit :
>
>
>
> Forwarded Message
> Subject: [Debian-med-packaging] Bug#813559: ngs-sdk: FTBFS: most
> platforms explicitly unsupported
> Resent-Date: Wed, 03 Feb 2016 07:03:01 +
> Resent-From: And
- Mail original -
> De: "Andreas Tille"
> À: debian-med@lists.debian.org
> Envoyé: Mardi 16 Février 2016 13:06:48
> Objet: Re: [Debian-med-packaging] Bug#813559: ngs-sdk: FTBFS: most platforms
> explicitly unsupported
>
> On Tue, Feb 16, 2016 at 11:29:2
Hi,
how can I get a programmatic list of debianmed packages, possibly by
section (bioinformatics ,...) ?
Thanks
Olivier
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key
On 03/14/2016 05:04 PM, Andreas Tille wrote:
> On Mon, Mar 14, 2016 at 04:38:08PM +0100, Olivier Sallou wrote:
>> how can I get a programmatic list of debianmed packages, possibly by
>> section (bioinformatics ,...) ?
> grep-aptavail --field=Maintainer
&g
- Mail original -
> De: "Andreas Tille"
> À: debian-med@lists.debian.org
> Envoyé: Lundi 14 Mars 2016 17:45:42
> Objet: Re: how to get list of debianmed packages
>
> On Mon, Mar 14, 2016 at 05:15:50PM +0100, Olivier Sallou wrote:
> > > May be
Indeed, looks like incompatible classes between versions
Olivier
Le jeu. 24 mars 2016 17:28, Andreas Tille a écrit :
> Hi,
>
> I've just injected surankco[1] which failed to build with:
>
> jh_build --javacopts='-target 1.7' --javacopts='-source 1.7' surankco.jar
> src
> find src -name *.java -
I will have a look today
Le jeu. 24 mars 2016 18:44, olivier sallou a
écrit :
> Indeed, looks like incompatible classes between versions
>
> Olivier
>
> Le jeu. 24 mars 2016 17:28, Andreas Tille a écrit :
>
>> Hi,
>>
>> I've just injected surankco[1] w
Le ven. 25 mars 2016 à 07:00, olivier sallou a
écrit :
> I will have a look today
>
> Le jeu. 24 mars 2016 18:44, olivier sallou a
> écrit :
>
>> Indeed, looks like incompatible classes between versions
>>
>> Olivier
>>
>> Le jeu. 24 mars 2
Le mar. 16 févr. 2016 à 12:29, olivier sallou a
écrit :
> Le jeu. 4 févr. 2016 à 14:26, Olivier Sallou a
> écrit :
>
>>
>>
>>
>> Forwarded Message
>> Subject: [Debian-med-packaging] Bug#813559: ngs-sdk: FTBFS: most
>> platforms e
Le mar. 12 avr. 2016 à 16:16, Andreas Tille a écrit :
> Hi Aaron and Olivier,
>
> since there is a new upstream version since some time I tried my luck to
> upgrade the Debian packaging. I took the chance to migrate it to Git[1]
> since I'm hoping that some GSoC student might provide an autopkgt
Le mar. 12 avr. 2016 à 17:42, Andreas Tille a écrit :
> Hi Olivier,
>
> On Tue, Apr 12, 2016 at 03:33:43PM +, olivier sallou wrote:
> > > I imported the new upstream version and I **hope** I refreshed the
> quilt
> > > patches correctly. However, even the
Le mar. 12 avr. 2016 à 16:16, Andreas Tille a écrit :
> Hi Aaron and Olivier,
>
> since there is a new upstream version since some time I tried my luck to
> upgrade the Debian packaging. I took the chance to migrate it to Git[1]
> since I'm hoping that some GSoC student might provide an autopkgt
lfill the above wishes would be to use some
>> hosting platform (Github, SourceForge) and move the code there.
>>
>> Kind regards and thanks for considering a free license
>>
>> Andreas.
>>
>> [1] http://harvest.readthedocs.org/en/latest/content/parsnp.html
>>
- Mail original -
> De: "Dylan"
> À: "Debian Med Project"
> Envoyé: Lundi 18 Avril 2016 08:11:05
> Objet: Re: Request for sponsoring: beagle
>
> Hi,
> According to ftpmaster's comments, I removed the embedded copy of
> htsjdk and I patched some files to refer to the new htsjdk.
> But w
kag...@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
n.org/cgi-bin/bugreport.cgi?bug=822701
Olivier
On 05/04/2016 10:48 AM, Olivier Sallou wrote:
> HI,
> we can seen many removal messages related to fails to build against
> htslib 1.3.1.
>
> Has anyone already the "chance" to see what is going wrong? seels
> htslib
On 05/04/2016 11:29 AM, Andreas Tille wrote:
> Hi,
>
> On Wed, May 04, 2016 at 11:03:36AM +0200, Olivier Sallou wrote:
>> I don't understand however why bug is not fixed or lowered yet.
>>
>> [0]https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822701
> What I
On 05/04/2016 01:49 PM, Charles Plessy wrote:
> Le Wed, May 04, 2016 at 11:03:36AM +0200, Olivier Sallou a écrit :
>> Seems it should be fixed soon [0]
>>
>> Bug is still open, but samtools 1.3.1 should not be impacted anymore.
>> htslib 1.3.1 break samtools 1.3
Hi Charles,
seems that we have cross bugs/mails with samtools.
Has samtools been updated accordingly to match libhts >= 1.3.1 ? I understand
that yes from previous emails, but is described bug linked to the otherbug?
Thanks
Olivier
- Mail transféré -
> De: "Santiago Vila"
> À: "Debi
Eucalyptus. I presume that
> this situation is rather common and I would very much like to hear
> your
> opinions/experiences about it.
>
> Cheers,
>
> Steffen
>
>
>
>
>
> --
> Michael R. Crusoe
> Community Engineer & Co-founder
&g
not hesitate to ask if you have upload needs to
questions... :-)
Olivier
>
> And for sure there might be always open bugs to squash. ;-)
>
> Thanks a lot and happy uploading
>
> Andreas.
>
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENN
- Mail original -
> De: "Michael Crusoe"
> À: "Debian Med Project List"
> Envoyé: Mercredi 8 Juin 2016 14:58:34
> Objet: NETTAB 2016 abstract deadline extended to June 30th
> Solicited topics http://www.igst.it/nettab/2016/submissions/topics/
> I think a presentation on what Debian (Me
also be limited.
Olivier
>
>> With the same focus? Or more medical?
> Personally I probably wouldn't be too interested in medical or research
> applications as I tend to focus more on the technical/infrastructure
> aspect. But that's just me, YMMV. I can imagine
nd others). So not easy to fit in Debian as all
dependencies not to be Debian packages.
Olivier
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 63
-- Forwarded message -
From: Debian FTP Masters
Date: mar. 21 juin 2016 à 15:33
Subject: bytecode_0.92.svn.20090106-2_amd64.changes ACCEPTED into unstable
To: Debian Java Maintainers ,
Olivier Sallou
Accepted:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256
Format: 1.8
Date
On 06/22/2016 11:29 AM, Andreas Tille wrote:
> Hi,
>
> On Thu, Jun 16, 2016 at 05:07:18PM +0200, Olivier Sallou wrote:
>>> Vezi Tweetul lui @natefoo:
>>> https://twitter.com/natefoo/status/743306923026440194
>>>
>>> https://depot.galaxyproject.
values to upstream/metadata does not make
> things user visible automatically. We need to patch tasks pages / other
> things to let the data show up.
would be nice indeed to get metadata info visible directly from the web
or via a debian command like apt-meta package_source_name ;-)
>
Hi Charles,
http://upstream-metadata.debian.net/ seems unavailable, connections
remain waiting.
Olivier
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83
- Mail original -
> De: "Michael Crusoe"
> À: "Olivier Sallou"
> Cc: "Debian Med Project List" , "Nate Coraor"
>
> Envoyé: Lundi 27 Juin 2016 21:04:21
> Objet: Re: Galaxy project producing their own Debian packages
>
- Mail original -
> De: "Charles Plessy"
> À: debian-med@lists.debian.org
> Envoyé: Mardi 28 Juin 2016 03:25:12
> Objet: Re: http://upstream-metadata.debian.net/
>
> Le Mon, Jun 27, 2016 at 04:21:23PM +0200, Andreas Tille a écrit :
> > On Mon, Jun 27,
I'm at the Galaxy Community Conference sitting next to Nate Coraor.
>>
>> Nate is enthusiastic about Galaxy becoming properly packaged for
>> Debian. He is well aware of how hacky his current package is :-)
>>
>> On Thu, Jun 16, 2016 at 11:07 AM, Oli
opla,
>>
>> I'm at the Galaxy Community Conference sitting next to Nate Coraor.
>>
>> Nate is enthusiastic about Galaxy becoming properly packaged for
>> Debian. He is well aware of how hacky his current package is :-)
>>
>> On Thu, Jun
On 06/28/2016 04:34 PM, Olivier Sallou wrote:
> by the way, as they are all python packages, should we handle them in
> DebianMed or Python team ?
>
> On 06/28/2016 03:20 PM, Steffen Möller wrote:
>> This is great! That custom fokr of pysam reads as if one wants to avoid
>&
Hi,
just to let you know that I will manage this package update by the end of
the month.
Olivier
-- Forwarded message -
From: Fabian Sievers
Date: ven. 1 juil. 2016 à 17:08
Subject: Clustal Omega Release 1.2.2
To: ,
Hi Olivier and Tille,
Please find the code for the newest v
: 829...@bugs.debian.org
To: Olivier Sallou
Thank you for filing a new Bug report with Debian.
This is an automatically generated reply to let you know your message
has been received.
Your message is being forwarded to the package maintainers and other
interested parties for their
python-dictobj is in archive
-- Forwarded message -
From: Debian FTP Masters
Date: lun. 4 juil. 2016 à 15:00
Subject: python-dictobj_0.4-1_amd64.changes ACCEPTED into unstable, unstable
To: Debian Med Packaging Team ,
Olivier Sallou
Accepted:
-BEGIN PGP SIGNED MESSAGE
Conference sitting next to Nate Coraor.
>
> Nate is enthusiastic about Galaxy becoming properly packaged for
> Debian. He is well aware of how hacky his current package is :-)
>
> On Thu, Jun 16, 2016 at 11:07 AM, Olivier Sallou
> mailto:olivier.sal...@irisa.fr>> wrote:
>
- Mail original -
> De: "Andreas Tille"
> À: "Debian Med Project List"
> Envoyé: Jeudi 28 Juillet 2016 14:43:27
> Objet: Java question: How to query picard-tools for --version
>
> Hi,
>
> I'm struggling to package metaBIT[1] and I'm currently stumbling upon
> the fact that it is query
- Mail original -
> De: "Andreas Tille"
> À: "Debian Med Project List"
> Envoyé: Jeudi 28 Juillet 2016 16:00:14
> Objet: Benchmarking adapters
>
> Hi folks
>
> when trying to package AdapterRemoval[1] (packaging will show up in Git
> soon) I spotted some benchmarking suite[2] featurin
- Mail original -
> De: "Andreas Tille"
> À: "Debian Med Project List"
> Envoyé: Jeudi 28 Juillet 2016 14:43:27
> Objet: Java question: How to query picard-tools for --version
>
> Hi,
>
> I'm struggling to package metaBIT[1] and I'm currently stumbling upon
> the fact that it is query
- Mail original -
> De: "Andreas Tille"
> À: "Debian Med Project List" , "Olivier Sallou"
> , "Aaron M. Ucko"
>
> Envoyé: Mardi 2 Août 2016 11:43:13
> Objet: New version of ncbi-blast+ available
>
> Hi Aaron and Olivier,
- Mail original -
> De: "Andreas Tille"
> À: debian-med@lists.debian.org
> Cc: "Aaron M. Ucko"
> Envoyé: Mardi 2 Août 2016 22:54:16
> Objet: Re: New version of ncbi-blast+ available
>
> Hi Aaron,
>
> On Tue, Aug 02, 2016 at 04:03:48PM -0400, Aaron M. Ucko wrote:
> > > I gonna have a l
- Mail original -
> De: "Andreas Tille"
> À: debian-med@lists.debian.org
> Envoyé: Mercredi 3 Août 2016 11:00:51
> Objet: Re: New version of ncbi-blast+ available
>
> On Wed, Aug 03, 2016 at 10:42:14AM +0200, Olivier Sallou wrote:
> > > I just
- Mail original -
> De: "Andreas Tille"
> À: "Olivier Sallou"
> Cc: debian-med@lists.debian.org
> Envoyé: Mercredi 3 Août 2016 11:25:57
> Objet: Re: New version of ncbi-blast+ available
>
> On Wed, Aug 03, 2016 at 11:09:17AM +0200, Olivier Sa
nd though it is
the expected one.
you did not pushed your updates with new upstream release?
Olivier
>
> Kind regards
>
> Andreas.
>
> - Forwarded message from Andreas Tille -
>
> Date: Wed, 3 Aug 2016 18:10:40 +0200
> From: Andreas Tille
> To: Olivi
Thank you!
Le mer. 3 août 2016 à 21:37, Aaron M. Ucko a écrit :
> olivier sallou writes:
>
> > you did not pushed your updates with new upstream release?
>
> I asked about that earlier; he said that he had been concerned that he
> might have incorrectly refreshed the exi
Hi,
I see that clustalo is unrealeased in git repo (changelog) in version
1.2.2-1 though I see version 1.2.2-1 is uploaded in debian.
I was about to upload new release 1.2.3, but I'd like to check status
with you before
Olivier
--
Olivier Sallou
IRISA / University of Rennes 1
Camp
)' is
ambiguous
It seems a cast to double or float is necessary for your log2 calls. As
I do not know what is the type of your data, I did not try any conversion.
for code like q.tr[i][I2I]=log2(q.tr[i][I2I]/sum);
It may be related to gcc (v6) version or related libraries.
Thanks
Olivier
Olivier
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
- Mail original -
> De: "Sascha Steinbiss"
> À: "Aaron M. Ucko"
> Cc: 834...@bugs.debian.org
> Envoyé: Samedi 27 Août 2016 16:56:28
> Objet: [Debian-med-packaging] Bug#834862: Bug#834862: hisat2: FTBFS on
> non-x86: -msse2 (and often -m32) unrecognized
>
> Hi Aaron,
>
> >> I’l
Hi mickael,
Do you have any news regarding next debianmed sprint?
Are a date and place/town decided?
We need some time to find cheap travel prices, and debian pre approval for
expenses.
You also need to ask for a budget approval to debian dpl to allow further
reimbursements to dd.
Thanks
Olivie
Hi Mickael,
sorry but I had to update my availabilities, I am not anymore available on
18th and 25th.
But from previous poll I see that 11th was also ok for a majority.
If this is ok for others, I'd prefer the 11th to participate.
Of course, stick to the majority.
Thanks
Olivier
would
> also be great to see progress on packaging the various implementations
> <https://github.com/common-workflow-language/common-workflow-language#implementations>
> .
>
>
> 2016-11-12 0:11 GMT+02:00 olivier sallou :
>
> Hi Mickael,
> sorry but I had to update my
- Mail original -
> De: "Andreas Tille"
> À: "Debian Med Project List"
> Envoyé: Mardi 15 Novembre 2016 17:14:33
> Objet: Help needed to package manta which needs samtools >= 1.2 and libbam.a
>
> Hi folks,
>
> I have injected manta[1] into packaging Git. Upstream contains several
> p
Hi mickael,
Wiki sprint page specifies location to be constanta, romania. From previous
discussions i think we decided it would be bucarest, am i correct? if yes,
could you update wiki page with uptodate info?
Thanks
Olivier
HI,
I have updated (locally) patches for the new release of ncbi-blast+.
However I face an error during import of new sources in git:
gbp import-orig --pristine-tar ../ncbi-blast+_2.5.0.orig.tar.gz
Upstream version is 2.5.0
Merging to 'master'
Automatic merge failed
Error detected, will roll
On 12/01/2016 02:37 PM, olivier sallou wrote:
> HI,
> I have updated (locally) patches for the new release of ncbi-blast+.
> However I face an error during import of new sources in git:
>
> gbp import-orig --pristine-tar ../ncbi-blast+_2.5.0.orig.tar.gz
>
> Upst
>>
> I tried to apply your hint to ncbi-tools6[1] but this does not change
> anything:
>
> ncbi-tools6(master) $ LC_ALL=C git merge upstream/6.1.20120620
> Already up-to-date.
>
> Did I missinterpreted your hint?
>
> Kind regards
>
> Andreas.
>
>>> [1] https://anonscm.debian.org/git/debian-med/ncbi-tools6.git
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Le dim. 4 déc. 2016 00:26, Dylan a écrit :
Hi Iain,
Since I maintain some Fitbit related packages, I will take this one.
Best regards,
Dylan
Ok.
Honestly i do not remind why i did an upload
Olivier
2016-12-03 20:09 GMT+01:00 Iain R. Learmonth :
> Hi Oliver,
>
> I'm no longer using a FitB
Hi mickael,
Are 13/15 january the final dates for the sprint? Can we go for travel
reservation (after dpl approval) ?
Time is close. .. Do you have an hotel location for the sprint? Did you get
news about working at night ?
Olivier
be interested to
join (even for a key signing).
Olivier
Le ven. 16 déc. 2016 à 07:03, olivier sallou a
écrit :
> Hi mickael,
> Are 13/15 january the final dates for the sprint? Can we go for travel
> reservation (after dpl approval) ?
>
> Time is close. .. Do you have an hotel l
Hi mickael,
Can you ping us when you have approval from dpl for the sprint? I will
check fir plane tickets right after
Olivier
Hi,
DPL has approved debianmed sprint, we can go for reservations.
Remains the hotel with double rooms to share rooms and manage between us
who share rooms.
Olivier
Hi Michael,
did also check with the working location for wifi access ?
For the hotel, it would also be better to get one with wifi.
And merry christmas :-)
Olivier
hi Andreas,
I had a look at your build issues after switching to git and new code is
based on a more recent jmol version (14.6.2) than before. Previous was on
1.3.0.14.
Fortunatly debian jmol release is 14.6.4.
so jmol needs to be udpated to latest and d/control must require jmol >=
14.6.4. I upda
Hi,
Mickael could not manage the hotel location and won't be back to Romania
before some days.
So, I have made a reservation at an hotel not far from the Faculty of
Biology and quite well located. It is not expensive and has twin bed rooms
for those willing to share rooms. It also has a restaurant
Le mer. 28 déc. 2016 11:01, Andreas Tille a écrit :
> Hi Olivier,
>
> On Wed, Dec 28, 2016 at 07:57:57AM +, olivier sallou wrote:
> > Hi,
> > Mickael could not manage the hotel location and won't be back to Romania
> > before some days.
> > So, I have
- Mail original -
> De: "Sascha Steinbiss"
> À: "Andreas Tille"
> Cc: debian-med@lists.debian.org
> Envoyé: Mercredi 28 Décembre 2016 12:23:21
> Objet: Re: DebianMed sprint hotel proposal
>
> Hi Andreas,
>
> >> I have also just booked a room at that hotel. They’re really inexpensive
>
Hi michael,
What is the plan for the sprint, on friday morning and evening (depending
on our different arrival times) ? I suppose we will all meet at the hotel
to go to the university work room together?
Olivier
ll met at the airport at about 14:00 we
> might checkin
> into our hotels and ping you via GMail chat then.
>
> > I've updated the wiki with some local travel advice
> > https://wiki.debian.org/Sprints/2017/DebianMed2017#Getting_there
> <https://
-- Forwarded message -
From: olivier sallou
Date: sam. 14 janv. 2017 à 09:27
Subject: Bug#851342: ITP: baitfisher -- package for designing hybrid
enrichment probes
To: sub...@bugs.debian.org
Package: wnpp
Severity: wishlist
Owner: Olivier Sallou
* Package name: baitfisher
Le lun. 16 janv. 2017 à 17:54, Aaron M. Ucko a écrit :
> Great, thanks!
>
upload in progress, wiki at Paris CDG is better than in Bucarest :-)
Olivier
>
> -- Aaron
>
> olivier sallou writes:
>
> > Hi,
> > Package is almost ready, i should upload tomorrow.wi
anyway push to unstable ?
I kept some packages update aside 'till now due to the freeze.
Olivier
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9
- Mail original -
> De: "Andreas Tille"
> À: "Debian Med Project List" , "Debian Java
> List"
> Envoyé: Samedi 6 Mai 2017 09:23:27
> Objet: Help needed for tn-seqexplorer Java package
>
> Hi,
>
> I intend to package tn-seqexplorer[1]. I have removed all JAR files
> upstream included
rds
>
> Andreas.
>
>
>> [1] https://anonscm.debian.org/git/debian-med/tn-seqexplorer.git
>> [2] https://anonscm.debian.org/git/pkg-java/libexternalsortinginjava-java.git
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel
On 05/09/2017 01:20 PM, Andreas Tille wrote:
> Hi Olivier,
>
> On Tue, May 09, 2017 at 11:46:51AM +0200, Olivier Sallou wrote:
>>> $ tn-seqexplorer
>>> Exception in thread "main" java.lang.NullPointerException
>>> at sun.awt.S
I updated in git repo but did not pushed.
Olivier
Forwarded Message
Subject:[Debian-med-packaging] Bug#863159: zstd: New upstream version
with multithreading support
Resent-Date:Mon, 22 May 2017 19:03:20 +
Resent-From:Andreas Kotes , Andreas Kotes
Resent-
- Mail original -
> De: "Sascha Steinbiss"
> À: "Olivier Sallou"
> Cc: "Debian Med Project List"
> Envoyé: Mercredi 24 Mai 2017 18:11:32
> Objet: Re: [Debian-med-packaging] Bug#863159: zstd: New upstream version with
> multithreading
- Mail original -
> De: "Nadiya Sitdykova"
> À: "Debian Med Project List"
> Envoyé: Jeudi 24 Août 2017 04:30:20
> Objet: gatb-core packaging
> Hello Andreas,
> I decided at least to try to package gatb-core.
> The Debian Med Group Policy suggests to add the package to the "task" file,
- Mail original -
> De: "Andreas Tille"
> À: debian-med@lists.debian.org
> Envoyé: Mercredi 23 Août 2017 19:04:01
> Objet: Re: FOSDEM devroom
>
> Hi Sébastien,
>
> On Wed, Aug 23, 2017 at 02:06:19PM +0200, Sébastien Jodogne wrote:
> > Dear all,
> >
> > The next edition of FOSDEM will
- Mail original -
> De: "Andreas Tille"
> À: "Debian Med Project List"
> Envoyé: Mardi 29 Août 2017 23:05:50
> Objet: Python-pysam 0.12 released, could someone please care?
Can't test now, but it seems that config.h should come from htslib, which is
included in upstream (but we use de
- Mail original -
> De: "Andreas Tille"
> À: debian-med@lists.debian.org
> Envoyé: Jeudi 14 Septembre 2017 19:05:21
> Objet: Help finding authors needed (Was: License of cluster3 becomes
> unspecified since you are linking to a
> non-existing URL)
>
> Hi list,
>
> both contacts of the
never made it. Meeting Debian Med people there might
>> be a good reason to go.
> I am too busy to attend myself, sadly.
>
> Best,
>
> Steffen
>
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
CC list mail sent to bug.
- Mail transféré -
> De: "Olivier Sallou"
> À: 877...@bugs.debian.org
> Envoyé: Mercredi 11 Octobre 2017 11:58:44
> Objet: [Debian-med-packaging] Bug#877590: Bug#877590: Please help
> upgrading htsjdk (Was: Bug#877590
ontainers at regular interval, based of course on a
Debian container image.
But those will not be *official* debian containers, just an initiative
to make them available.
>
> *Non-library, non-dev, non-service. Basically the command line tools
> used by researchers to perform data anal
.
upstream makes use of tags to filter some tests.
Thanks
Olivier
On Wed, Oct 11, 2017 at 12:05:28PM +0200, Olivier Sallou wrote:
>
> Failure seems related to not finding the *tags* extension to Test.
> Seems introduced by scalatest , one of the plugins loaded by graddle.
> sc
htsjdk and other dependent packages are marked for removal.
The patch I uploaded recently (in git repo) fixed the testng issue, but
I did not tested the package itself and I had to disable tests to get
package done.
The patch indeed fix compilation issues, but introduce gradle testing
issues.
T
adle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
>> at
>> org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:45)
>> at
>> org.gradle.api.internal.tasks.execu
On 10/31/2017 03:05 PM, Olivier Sallou wrote:
> testng maven definition needs to be modified in build.graddle to match
> testng debian pom.
>
> Following patch fix the compilation for tests:
>
> --- a/build.gradle
> +++ b/build.gradle
> @@ -32,7
htsjdk and picard-tools test issues are gradle related.
After some deeper tests and discussions with debian-java team, it
appears the errors faced in testing (after the patches I proposed on
testng) are related to the gradle version on debian.
Someone in java team should upgrade to an upper release
Hi,
I uploaded patched version of htsjdk and picard-tools to fix serious bugs
and prevent their removal (and removal of their reverse dependencies)
I switched bugs severity to normal but keep bugs open as a reminder as part
of the fix is to disable unit tests (due to gradle 3.2 issue that will be
iscosnp as reference for comparison?
>
> Kind regards
>
> Andreas.
>
>
> [1] http://colibread.inria.fr/software/discosnp/
> [2] https://lists.debian.org/debian-med/2017/10/msg00025.html
>
--
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
On 11/15/2017 09:44 AM, Andreas Tille wrote:
> Hi Olivier,
>
> On Wed, Nov 15, 2017 at 09:18:36AM +0100, Olivier Sallou wrote:
>>> Assuming that we will manage to finalise gatb-core in the near future
>>> (Olivier, you might like to talk to upstream regarding dropin
Hi,
I see that biopython has been patched to prevent removal, but it seems to
be stuck in unstable
20 days old (needed 5 days)
missing build on mips64el: python-biopython, python3-biopython (from
1.70+dfsg-2)
old binaries left on all: python-biopython-doc, python-biopython-sql,
python3-biopython-s
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