Dear all,
I have prepared an upload for the package uc-echo, of which autopkgtest was
failing on arm64 due to a (by default unsigned) char type being used to
store negative integer values.
I will forward this fix to upstream.
The package is in its Salsa repository [1].
Thanks in advance for
Hi Nilesh and Andreas,
Le 17/04/2020 à 19:21, Nilesh Patra a écrit :
>
>
> On Fri, 17 Apr 2020, 22:44 Pierre Gruet, <mailto:pgtdeb...@free.fr>> wrote:
>
> Dear all,
>
> I have prepared an upload for the package uc-echo, of which autopkgtest
&g
Hi Andreas,
Le 14/04/2020 à 18:53, Andreas Tille a écrit :
>>
>> If you have time, I would appreciate a review of the three packages, which
>> are in their three Salsa repositories.
>>
>> https://salsa.debian.org/med-team/sumaclust/
>> https://salsa.debian.org/med-team/sumatra
>>
Hi Andreas,
Le 20/04/2020 à 13:00, Andreas Tille a écrit :
> Hi Pierre,
>
> On Mon, Apr 20, 2020 at 11:29:04AM +0200, Pierre Gruet wrote:
>> I have just seen that sumalibs has successfully entered unstable and that
>> the automatic piuparts warnings have disappeared from i
Hi Andreas,
Le 09/04/2020 à 14:45, Andreas Tille a écrit :
> Hi Pierre,
>
> as you might have noticed the Debian package for sumalibs was just
> accepted. I've now built sumatra against this lib. I'd happily leave
> the maintenance of all suma* packages to you.
Yes, I noticed that sumalibs
Hi again,
Le 04/04/2020 à 10:14, Andreas Tille a écrit :
>
> I try to put high priority on newcomer contributions so I just take
> my time for a review. I can confirm that the tests are passing and
> thus we could upload the package as is.
Thanks a lot for the quick review!
> There is some
Hi Andreas,
Le 03/04/2020 à 22:26, Andreas Tille a écrit :
>
> I tried with a new paragraph at the beginning of "How to Contribute".
> Feel free to enhance that text!
I think this paragraph clarifies things a lot. Having explained rules this
way, there should be less hesitations.
>
> BTW,
Hi,
I have worked on sumaclust and pushed it on salsa [0] with version
``unreleased''.
Lines have been suppressed in the last patch because upstream has made the
necessary changes so that sumaclust builds.
I have also provided autopkgtests, which check the executable works fine in
a few simple
ian Med mailing list and
> would be really happy if you would answer there.
No problem about that, thanks for letting me know.
Please believe I did not intend to hide things, but only to reduce
noise. Next time I shall use the mailing list.
>
> On Wed, Apr 01, 2020 at 10:30:42PM +0200, P
Hi again,
Le 02/04/2020 à 10:28, Andreas Tille a écrit :
>
>> If I may add something: having read the policy some days ago, I feel it
>> lacks a kind of ``general habits'' section, like what you explained
>> above: is it casual/rude to begin working on a package that already has
>> uploaders who
Hi Andreas,
Le 25/04/2020 à 11:20, Andreas Tille a écrit :
> Hi again,
>
> perhaps also getting
>
>https://salsa.debian.org/med-team/libsis-jhdf5-java
>
> done would be helpful. I've pushed latest upstream but did not
> found the time to update the old patches to the new version.
>
Hi everyone,
I have been trying to package libsis-jhdf5-java, after Andreas imported the
last upstream version.
This package builds a java package with a .jar file and a jni package with
native code used by the .jar.
I have been able to:
- refresh patches;
- get rid of the private header
Hi,
I have packaged the new upstream version of jebl2 and made various changes.
Now the packaging is in Salsa [1], could someone please check and upload it
when time permits?
The changes are
* New upstream version 0.1+git20190308
* Deleting now useless patch source_8.patch
* Bumping
Hello Gilles,
Le 30/04/2020 à 23:17, Gilles Filippini a écrit :
>>>
>>> Thanks for checking; I had also seen that these tests did not run, this will
>>> have to be fixed. More important is the fact that I have put and arranged
>>> the piece of code of dh_auto_test override into a test in
>>>
Hi Gilles,
Le 01/05/2020 à 01:12, Gilles Filippini a écrit :
> Pierre Gruet a écrit le 30/04/2020 à 23:45 :
>> Thanks for looking at the issue and proposing a fix. It is very helpful!
>> I will thus look at it and investigate further the failures that remain.
>
> This packa
Hi Gilles,
Le 29/04/2020 à 17:53, Gilles Filippini a écrit :
> Andreas Tille a écrit le 29/04/2020 à 17:36 :
>> Hi Gilles,
>>
>> On Wed, Apr 29, 2020 at 05:10:38PM +0200, Gilles Filippini wrote:
>>>
>>> I've cloned the git repo and attempted a build. But the dh_auto_test
>>> part doesn't execute
Hi Andreas,
Le 24/04/2020 à 22:34, Andreas Tille a écrit :
> Hi Pierre,
>
> thanks a lot for your work. I usually would leave the commit ID inside
> the version number (so 0.1+git20190308.a98448e) since this would silence
> the new upstream available check - but I guess you thought about this
>
Hi Andreas,
Le 09/04/2020 à 23:01, Andreas Tille a écrit :
>>
>> My question is: as I understand /4.13 Embedded code copies/ in the Debian
>> policy, sumatra and sumaclust should use the libs in sumalibs to build, but
>> the code of those libs that is duplicated inside sumaclust should remain
>>
Hi Andreas,
Le 08/05/2020 à 22:51, Andreas Tille a écrit :
>
> If you think you might be able to care for the h5ar binary issue in the
> next couple of days I would delay the upload to fix the RC bug. I guess
> this will not have any practical drawback if the propagation of this
> package to
Hi Andreas and Gilles,
Andreas, I have just seen you uploaded my commits of libsis-jhdf5-java
to unstable, thanks for that!
I had not written to ask for it as I intended to do further changes
before the upload (the script h5ar in /usr/bin should be removed or
another jar should be compiled, as
Hi Andreas,
Le 07/05/2020 à 16:26, Andreas Tille a écrit :
> On Thu, May 07, 2020 at 09:43:11AM +0200, Andreas Tille wrote:
>> I also
>> think that observing autobuilders and possibly fix issues there in a
>> subsequent upload with your additional changes could be a good idea.
>
> As expected
Hi again,
Le 07/05/2020 à 16:26, Andreas Tille a écrit :
> On Thu, May 07, 2020 at 09:43:11AM +0200, Andreas Tille wrote:
>> I also
>> think that observing autobuilders and possibly fix issues there in a
>> subsequent upload with your additional changes could be a good idea.
>
> As expected
Hi Andreas,
Le 08/05/2020 à 22:05, Andreas Tille a écrit :
>
> Very nice. Thanks a lot for your work. I've built and installed the
> package. When noticing that there is no manpage for h5ar I intended to
> check whether it might be cheap to create one via help2man. However,
> this ended up
Hi Andreas,
Le 08/05/2020 à 22:51, Andreas Tille a écrit :
> Hi Pierre,
>
> On Fri, May 08, 2020 at 10:24:47PM +0200, Pierre Gruet wrote:
>>
>> Absolutely. This is part of the complementary tasks I was planning to do
>> (my Salsa push of yesterday was on
Package: wnpp
Severity: wishlist
Owner: Debian-med project
* Package name: distlib
Version : 0.9.1
Upstream Author : Peter N. Steinmetz
* URL : https://sourceforge.net/projects/statdistlib
* License : GPL-2
Programming Lang: Java
Description : Java
Control: retitle -1 ITP: libdistlib-java -- Java library of statistical
distribution functions
Hi Scott and Andreas,
Le 21/05/2020 à 06:44, Scott Kitterman a écrit :
> On Thursday, May 21, 2020 12:08:44 AM EDT Andreas Tille wrote:
>> At least the name of the binary package should be
>>
>>
Hi,
I have worked on artemis, which required some attention :-)
We now have the most recent upstream version and the RC bug is fixed.
Upstream now uses Maven for the build, which led to many changes.
https://salsa.debian.org/med-team/artemis
Could you please review and upload? My key is not in
Hi Andreas,
Le 02/09/2020 à 09:09, Andreas Tille a écrit :
> Hi Pierre,
>
> On Tue, Sep 01, 2020 at 10:54:52PM +0200, Pierre Gruet wrote:
>> I have worked on the packaging of igv 2.6.3+dfsg, which is in
>>
>> https://salsa.debian.org/med-team/igv
>>
>>
Hi,
Le 10/09/2020 à 17:11, Andreas Tille a écrit :
> Hi Steffen,
>
> On Thu, Sep 10, 2020 at 03:32:49PM +0200, Steffen Möller wrote:
>> libpicard-java needs an argparse class from the barclay library. This
>> was found by the intense build-time testing of the PIGx-scRNAseq.
>> ...
>> How shall
Hi Steffen,
Le 11/09/2020 à 02:23, Steffen Möller a écrit :
> Hi again,
>
> On 11.09.20 00:01, Pierre Gruet wrote:
>> Hi,
>>
>> Le 10/09/2020 à 17:11, Andreas Tille a écrit :
>>> Hi Steffen,
>>>
>>> On Thu, Sep 10, 2020 at 03:32:49PM
Hello,
Le 15/09/2020 à 09:02, Andrius Merkys a écrit :
> Hello,
>
> On 2020-09-15 09:50, Andreas Tille wrote:
>> Any idea what to do? Seems like a new dependency[2] but I want to make
>> sure whether I'm right here and whether we really need this since it
>> sounds pretty unrelated to that
Hi Steffen,
Le 11/09/2020 à 15:27, Steffen Möller a écrit :
> Hello again,
>
> [...]
>
> and the error prevails when minimizing the invocation as to
>
>
> ~/git/med-team/pigx/pigx-scrnaseq$ /usr/bin/java -XX:ParallelGCThreads=1
> -Xmx4G -Xss16M -Djava.io.tmpdir=/tmp -cp $PICARD_CLASSPATH -j
>
Hi,
I have worked on the packaging of igv 2.6.3+dfsg, which is in
https://salsa.debian.org/med-team/igv
This igv packaging still relies on its embedded jars. I have solved
build issues related to gradle, another one linked to the current
version of htsjdk (solves Grave bug on igv), and had to
Hi Andreas, hi everyone,
Le 11/09/2020 à 09:08, Andreas Tille a écrit :
> Hi,
>
> I tried to upgrade htsjdk[1] but unfortunately I got some build time
> test errors. It would be great if somebody could have a look.
>
I have looked and tried to build, which succeeded. Then I looked at the
log
Package: wnpp
Severity: wishlist
Owner: Debian-med project
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: sepp
Version : 4.3.10
Upstream Author : Siavash Mirarab
* URL : https://github.com/smirarab/sepp/
* License :
Hi Andreas,
Le 07/10/2020 à 22:43, Andreas Tille a écrit :
> Hi Pierre,
>
> On Wed, Oct 07, 2020 at 10:30:34PM +0200, Pierre Gruet wrote:
>> I have almost finished the initial packaging of sepp [0]. Beside the
>> sepp program, upstream also provides the tipp program i
Hi,
I have almost finished the initial packaging of sepp [0]. Beside the
sepp program, upstream also provides the tipp program in the same
tarball. Basically, tipp classifies sequences using sepp and a
collection of alignments and placements data and statistical methods.
People installing tipp
Hi,
I have finished the initial packaging of sepp [0]. Could someone please
review it and sponsor if everything is OK?
As discussed recently on the list, the binary package sepp includes
programs called sepp and tipp, the last one needing the user to download
a given dataset to be run. This is
Hi,
I have worked on jebl2 which has a new upstream version.
Would you mind either reviewing [0] or giving me DM rights?
dcut dm --uid "Pierre Gruet" --allow jebl2
Thanks a lot in advance,
Pierre
[0] https://salsa.debian.org/med-team/jebl2
Hi Paul,
Le 22/09/2020 à 22:11, Paul Gevers a écrit :
> Hi Pierre,
>
> On 22-09-2020 21:45, Pierre Gruet wrote:
>> Dear Debian CI project members,
>>
>> In Debian-med we have the package libsis-jhdf5-java. I can build it
>> inside or outside a chroot on my
Package: wnpp
Severity: wishlist
Owner: Debian-med project
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org
* Package name: icb-utils
Version : 2.0.1+git20161002.afee1d9
Upstream Author : Fabien Campagne
* URL :
Hi Andreas and Steffen,
Le 09/10/2020 à 18:37, Steffen Möller a écrit :
> ;) You win!
>
> Thanks!
>
> Steffen
>
> On 09.10.20 18:33, Andreas Tille wrote:
>> On Fri, Oct 09, 2020 at 06:32:55PM +0200, Steffen Möller wrote:
>>> @Andreas et al., I'll happily sponsor.
>> Ups, just receiving this.
Hi Andreas,
Le 13/10/2020 à 09:40, Andreas Tille a écrit :
> Hi Pierre,
>
> On Mon, Oct 12, 2020 at 09:34:04PM +0200, Pierre Gruet wrote:
>> I have worked on jebl2 which has a new upstream version.
>
> Ahhh, I did so yesterday evening without actually reading your ma
Hi Steffen and Andreas,
Le 25/08/2020 à 06:35, Andreas Tille a écrit :
> On Tue, Aug 25, 2020 at 12:12:04AM +0200, Steffen Möller wrote:
>> I created a "Java" tab on our spreadsheet. Would of course be great if
>> that sees some momentum. Took the freedom to also add Cytoscape. And if
>> I get
Hi Andreas,
Le 26/08/2020 à 07:13, Andreas Tille a écrit :
>>
>> BTW, snpeff depends on akka-actor, a (Scala+Java) library which still
>> has to be packaged, and I am afraid it will be blocked by the version of
>> Scala in Debian, itself being stuck to 2.11 as Scala build tool (SBT)
>> requires
Dear Maintainers,
For our information, do you know if it might be possible to unblock the
situation soon? Is there some ongoing work on sbt?
In Debian-med, we would be interested in having Scala 2.12 or 2.13 to
package the pre-dependency akka.
Thanks a lot in any case,
Best regards,
Pierre
Hi,
Le 21/08/2020 à 12:44, Andreas Tille a écrit :
> Hi Pierre,
>
> On Fri, Aug 21, 2020 at 11:32:47AM +0200, Pierre Gruet wrote:
>>> I injected the latest upstream version into Git. It does not include so
>>> many binary jar's any more but I think its trying to dow
Hi Andreas,
Le 24/08/2020 à 12:39, Andreas Tille a écrit :
> Hi Pierre,
>
> On Mon, Aug 24, 2020 at 12:08:28PM +0200, Pierre Gruet wrote:
>> Contrarily to what I wrote a few days ago, I do not think we are ready
>> to remove all included jars in igv.
>> For instan
gt;> Is this because sun.java2d.SunGraphicsEnvironment API has been deprecated,
>> or is it just that it is missing a dependency so it can't import the API? I
>> don't know much about Java packages, but if someone could point me in the
>> right direction, I might be able to help.
>
>
Hi Andreas,
Le 14/08/2020 à 23:35, Andreas Tille a écrit :
> Hi Pierre,
>
> On Fri, Aug 14, 2020 at 10:40:28PM +0200, Pierre Gruet wrote:
>> I had not heard of this deprecation issue and I don't think it matters
>> for us. It only causes warnings.
>>
>> C
Hi,
I have fixed some missing classpath entries for libdistlib-java and I
need to do a source-only upload for charts4j, which has just exited NEW.
Would you mine either reviewing them [0] [1] or giving me DM rights?
dcut dm --uid "Pierre Gruet" --allow libdistlib-java charts4j
(n
Hi Olivier and Andreas,
Le 23/09/2020 à 09:27, Andreas Tille a écrit :
> On Wed, Sep 23, 2020 at 08:08:01AM +0200, olivier sallou wrote:
>>> Given that you also have detailed knowledge in Java do you feel able
>>> to
>>> fix those 8 issues? That would really help several other packages.
>>
>> I
Hi,
Le 24/09/2020 à 11:27, Andrius Merkys a écrit :
> Hi Maarten,
>
> On 2020-09-24 12:21, Maarten L. Hekkelman wrote:
>> Suppose you want to submit two separate packages and one depends on the
>> other, do you have to wait with the second until the first has been
>> accepted and uploaded? Given
Hi Andreas,
Le 25/09/2020 à 11:22, Andreas Tille a écrit :
> Hi Pierre,
>
> On Fri, Sep 25, 2020 at 07:50:13AM +0200, Pierre Gruet wrote:
>>
>> I have fixed some missing classpath entries for libdistlib-java and I
>> need to do a source-only upload for charts4j
you
tested is indeed one upon which the build results of (Andreas and
ci.debian.net) and me are not the same.
>
>>
>> On Mon, Sep 21, 2020 at 11:31:21PM +0200, Pierre Gruet wrote:
>>> Thanks for providing me with this log file, it helps. I see 8
>>> failing
>
in their chroots
and got 8 failing tests, which is also the case of ci.debian.net [0].
I would like to know if there have already been such problems with tests
failing in some chroots and passing in others; if so, would you have
examples or pointers to provide us with?
Many thanks in advance,
Pierre Gruet
Hi Paul,
Thanks for the quick answer!
Le 22/09/2020 à 22:11, Paul Gevers a écrit :
> Hi Pierre,
>
> On 22-09-2020 21:45, Pierre Gruet wrote:
>> Dear Debian CI project members,
>>
>> In Debian-med we have the package libsis-jhdf5-java. I can build it
>> inside o
Hi,
Le 21/09/2020 à 09:01, Andreas Tille a écrit :
> On Tue, Sep 15, 2020 at 04:04:49PM -0400, Aaron M. Ucko wrote:
>> Andrius Merkys writes:
>>
>>> AFAIR, buildds are not guaranteed to have running X sessions, thus I
>>> suggest skipping these tests (most likely by using patches).
>>
>> For
Hi Andreas,
Le 28/09/2020 à 19:47, Andreas Tille a écrit :
> Hi Pierre,
>
> On Mon, Sep 28, 2020 at 06:07:43PM +0200, Pierre Gruet wrote:
>>> That's true but according to my experience the issue did not occured
>>> on the build daemons.
>>>
>>> Ap
Hi again Andreas,
Le 28/09/2020 à 21:36, Andreas Tille a écrit :
> On Mon, Sep 28, 2020 at 08:23:11PM +0200, Pierre Gruet wrote:
>
>> I have a question about "best practices": last uploaded version of
>> beast2-mcmc is 2.6.3+dfsg-2, but I will need to repack t
Hi Andrius,
Le 29/09/2020 à 07:57, Andrius Merkys a écrit :
> Hi Pierre,
>
> On 2020-09-28 22:47, Pierre Gruet wrote:
>> Thanks for your advice! Nevertheless, this seems to rank before the
>> current version number, as
>>
>> echo "2.6.3+dfsg-2,2.6.3+dfsg1-
Hi,
I have worked on beast2-mcmc: autopkgtests have been added, which came
along with some patches.
Would you mind either reviewing [0] or giving me DM rights?
dcut dm --uid "Pierre Gruet" --allow beast2-mcmc
Thanks a lot in advance,
Pierre
[0] https://salsa.debian.org/med-team/beast2-mcmc
Hi Andreas,
Le 21/09/2020 à 13:34, Andreas Tille a écrit :
> Hi Pierre,
>
> On Mon, Sep 21, 2020 at 10:32:54AM +0200, Pierre Gruet wrote:
>> Le 21/09/2020 à 08:43, Andreas Tille a écrit :
>>
>> Some days ago, I worked on gatk. The most recent upstream tarball i
Hi,
I have packaged libdistlib-java, which is a Java implementation of
several cdf, pdf, quantile and simulation functions from R, originally
written in C.
This was announced in ITP bug #961158.
Would it be possible to have a review? It would be precious, as this is
my first initial packaging!
Dear all,
Lastly I have begun packaging Java software needed as dependencies of
snpeff, that we would need in Debian Med as it is related to genes and
proteins.
I have thus worked on a Java library related to cdf, pdf and random
variates generation: libdistlib-java. It is currently in NEW.
Now
Hi Andreas,
Le 30/05/2020 à 07:51, Andreas Tille a écrit :
> Hi Pierre,
>
> On Fri, May 29, 2020 at 11:48:39PM +0200, Pierre Gruet wrote:
>>
>> Lastly I have begun packaging Java software needed as dependencies of
>> snpeff, that we would need in Debian Me
Hi Andreas,
Le 25/05/2020 à 23:12, Andreas Tille a écrit :
> Hi Pierre,
>
> On Mon, May 25, 2020 at 10:47:58PM +0200, Pierre Gruet wrote:
>> I have packaged libdistlib-java, which is a Java implementation of
>> several cdf, pdf, quantile and simulation functions from R,
Hi,
Le 21/09/2020 à 08:43, Andreas Tille a écrit :
> Hi again,
>
> [...]
>
> I once tried git-lfs for gatk but failed. Could anybody fix the
> gatk repository (may be create a new one since as far as I understand
> its necessary for git-lfs to declare this at creation time)? I gave
> up last
Hello,
I have prepared the package icb-utils [0], which is a dependency of
goby, itself needed to move igv from non-free to main...
It is a NEW source package and thus would need a review and upload when
time permits.
Thanks a lot in advance,
Pierre
[0]
Hello,
icb-utils has just exited NEW; I have prepared a source-only
upload.
Would you mind either reviewing [0] or giving me DM rights?
dcut dm --uid "Pierre Gruet" --allow icb-utils
Thanks a lot in advance,
Pierre
[0] https://salsa.debian.org:med-team/icb-utils
Hi Andreas,
Le 29/07/2020 à 21:52, Andreas Tille a écrit :
> Hi Pierre,
>
> On Wed, Jul 29, 2020 at 05:36:29PM +0200, Pierre Gruet wrote:
>> I have prepared an upload of libgtextutils in
>>
>> https://salsa.debian.org/med-team/libgtextutils
>>
>> It solv
Hi Andreas,
Congratulations for getting this opportunity to talk about our work!
Personally, I have worked on
* Sumaclust (and its close relatives Sumatra and Sumalibs);
* Dependencies of Snpeff, which is part of the Covid-19 task.
Bye,
Pierre
Le 28/07/2020 à 08:43, Andreas Tille a écrit :
>
Hi Andreas,
Le 26/07/2020 à 22:28, Andreas Tille a écrit :
> Hi Pierre,
>
>
>> While I am at it:
>> - if aparapi cannot enter Debian, I should be able to deactivate the
>> module of apfloat that uses it, as this module is not part of the main
>> code. I have got a similar issue for the module
Hi,
I have packaged the new upstream version of libdistlib-java (taking into
account many of our patches!), which lies in
https://salsa.debian.org/med-team/libdistlib-java
If time permits, could you please look at it and upload?
Many thanks in advance,
Pierre
Hello,
I have prepared an upload of snap, fixing the gcc-10 FTBFS:
https://salsa.debian.org/med-team/snap
I have let 2 Lintian warnings, one of them stating a policy violation
due to traversing link usr/lib/debian-med/bin/snap -> usr/bin/snap-hmm .
While I understand this link is useful for
Package: wnpp
Severity: wishlist
Owner: Debian-med project
* Package name: libaparapi-java
Version : 2.0.0
Upstream Author : Gary Frost, Syncleus, Inc.
* URL : http://aparapi.com/
* License : Apache-2.0
Programming Lang: Java
Description : framework
Dear all,
I have pushed the initial packaging of libaparapi-java to Salsa [0], I
would need a review and an upload if time permits.
This is a dependency of apfloat (to be packaged), which is a dependency
of SpnEff that we would like to get packaged.
libaparapi-java builds two binary packages.
Hi Andreas,
Le 26/06/2020 à 18:14, Andreas Tille a écrit :
> On Fri, Jun 26, 2020 at 05:33:30PM +0200, Pierre Gruet wrote:
>>> Did you noticed that I've just injected
>>>
>>> https://salsa.debian.org/java-team/libapfloat-java
>>>
>>> (and stop
Hi Andreas,
Le 25/06/2020 à 22:49, Andreas Tille a écrit :
> Hi Pierre,
>
> On Thu, Jun 25, 2020 at 10:20:46PM +0200, Pierre Gruet wrote:
>> I have pushed the initial packaging of libaparapi-java to Salsa [0], I
>> would need a review and an upload if time permits.
>
>
Hi Emmanuel,
Le 22/06/2020 à 16:30, Andreas Tille a écrit :
> Hi Emmanuel,
>
> On Mon, Jun 22, 2020 at 10:57:15AM -0300, Emmanuel Arias wrote:
>> I would be happy to help on artemis. Obviously I will need
>> a more experienced developer helping me. :)
>
> I'll try hard to answer any question
Hello everyone,
I am currently beginning packaging aparapi, which is a Java API to
execute Java code on a GPU. In Debian Med, we need it as dependency of
the dependency apfloat of SnpEff.
This package relies on a JNI (native code) package which the same
upstream develops as aparapi-native.
Yet
Hello,
Le 04/06/2020 à 22:36, Thorsten Glaser a écrit :
> On Thu, 4 Jun 2020, Mechtilde wrote:
>
>> This is an outdated information. You can collect all source tar.gz
>> together in to one orig.tar.xz. In the d/gbp.conf you configure a
>
> DON’T DO THAT.
>
> MUTs (multi-origtgz) were invented
Hi,
I just realized there was a strange paragraph in the ATTRIBUTIONS.md
file in libaparapi-java root folder :
https://salsa.debian.org/med-team/libaparapi-java/-/blob/master/ATTRIBUTIONS.md
It seems to be restrictive and perhaps annoying for us.
Afterwards I saw that Andreas had already
Hello,
C++11 introduced references on rvalues, which basically allows to use a
non-constant reference on a temporary object (ie waiting for
affectation). Before, temporary objects could only be references by a
const reference.
Thus, from there, it becomes a problem to have two implicit
Hi,
I have prepared an upload of libgtextutils in
https://salsa.debian.org/med-team/libgtextutils
It solves RC bug #925745 and makes the package lintian-clean. I have
also added a C++-filtered symbols file.
Could you please review when time permits?
All the best,
Pierre
Hi Steffen,
Le 27/07/2020 à 12:19, Steffen Möller a écrit :
> Hello,
>
> I had felt much like informing upstream about yanosim in Debian but
> somehow it does not migrate. I don't really get this since the build is
> just fine. Is it a runtime dependency? And why isn't the site clearly
>
Hi Andreas,
Le 26/07/2020 à 17:22, Andreas Tille a écrit :
> Hi Pierre,
>
>>
>> https://github.com/aparapi/aparapi/issues/50
>
> I've pinged that issue.
>
Thanks!
>
>> Yet I packaged libaparapi-java and we sent it in NEW, where it currently
>> lies. Sorry for not seeing it before.
>
>
Hello everyone,
I have packaged the new upstream version of jebl2, available in the
repository
https://salsa.debian.org/med-team/jebl2
Could you please see and upload? Apart the new upstream version, there
is just an update of the compat level.
Regards,
Pierre
Hi Andreas,
Le 27/11/2020 à 09:22, Andreas Tille a écrit :
Hi Pierre,
On Thu, Nov 26, 2020 at 10:11:14PM +0100, Pierre Gruet wrote:
>> [...]>>
- HTTP logs on the Jalview website
We record IP addresses of machines which access the web site, either via
the browser when
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.
Hi Nilesh and Andreas,
Le 26/11/2020 à 17:14, Andreas Tille a écrit :
Hi Nilesh,
On Thu, Nov 26, 2020 at 06:00:38PM +0530, Nilesh Patra wrote:
It seems that libsis-jhdf5-java hasn't migrated to testing due to build
failure on s390x, log attached[1]
This is preventing a chain of other packages
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 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
Hello,
I'm currently on the packaging of Jalview. I would like to get some
advice as Jalview upstream is collecting statistics on its use through
the Internet. Basically this amounts to 4 things, I'm quoting/commenting
their documentation:
- HTTP logs on the Jalview website
We record
Hi everyone,
I have fixed the RC bug in igv. Would you mind either reviewing [0] or
giving me DM rights?
dcut dm --uid "Pierre Gruet" --allow igv
Thanks a lot,
Pierre
[0] https://salsa.debian.org/med-team/igv
Hi,
artemis had only a superficial autopkgtest not marked as such. I have
marked it and provided another autopkgtest running some build tests.
Would you mind either reviewing [0] or giving me DM rights?
dcut dm --uid "Pierre Gruet" --allow artemis
Thanks a lot,
Pierre
Hi,
Le 15/11/2020 à 18:16, Andreas Tille a écrit :
>
>>
>> This may be worth a sidenote - bcbio to me is something metaphorical. We
>> have it in the distribution already. And now we work to get all the
>> runtime-dependencies in to make it functional. And snpEff is pretty high
>> up (it
Hi again,
Le 18/11/2020 à 15:59, Pierre Gruet a écrit :
> Hi Andreas,
>
>
> Le 18/11/2020 à 11:09, Andreas Tille a écrit :
>> Hi Pierre (and others)
>>
>> I tried to update libjloda-java but the build fails with
>>
>> ...
>> compile:
>>
Hi Andreas,
Le 18/11/2020 à 11:09, Andreas Tille a écrit :
> Hi Pierre (and others)
>
> I tried to update libjloda-java but the build fails with
>
> ...
> compile:
> [javac] Compiling 360 source files to
> /build/libjloda-java-2.0/antbuild/modules/jloda
> [javac] error: the unnamed
considering packaging aparapi itself, but it
would impose restrictions on other software that might be bundled with it.
We will discuss it with upstream and consider packaging later.
Pierre Gruet
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