Hi,
I have an invitation to have some talk with the title
Debian GNU/Linux for Scientific Research
Abstract:
Over the past decade, Enterprise Linux has dominated large-scale
research computing infrastructure. However, recent developments have
sparked increased interest in
package where I'm listed as Uploader. I'd be really happy about this.
Kind regards
Andreas.
Am Mon, Mar 11, 2024 at 03:47:42PM +0100 schrieb Andreas Tille:
> Hi R-pkg team members,
>
> as you might have possibly read I nominated myself for DPL for the next
> term[1]. I will pro
-
Date: Mon, 01 Apr 2024 07:32:34 -0700
From: Benjamin Redelings
To: bredelings/BAli-Phy
Cc: Andreas Tille , Author
Subject: Re: [bredelings/BAli-Phy] Test suite error in 4.0-beta7 (Issue #17)
Hi Andreas,
I finally did a beta9 release, so the issue should be fixed. Would you be able
to build beta9
Hi,
Am Mon, Apr 22, 2024 at 09:28:29AM +0200 schrieb Philip Hands:
> >> /usr/libexec/minio-client/bin/mc -> /usr/bin/mcli
>
> Might I suggest that the link goes the other way, so that the symlink
> lives in /usr/bin? That way the existence of the lib directory is
> somewhat self-documenting.
: Alexey Kozlov
To: amkozlov/raxml-ng
Cc: Andreas Tille , Author
Subject: Re: [amkozlov/raxml-ng] What libpll code is really needed (Issue #164)
> If I simply would package libpll-2 in the very place where libpll was
> packaged and I keep *that* name (without the -2) this would be
Hi Sebastian,
thank you for your work on t64 transition.
Am Thu, Apr 18, 2024 at 09:22:02PM +0200 schrieb Sebastian Ramacher:
I've spotted these Debian Med packages.
> gentle
> jellyfish
> quorum
> sbmltoolbox
No idea how we can help here. Please let us know if we can do
something.
> anfo
Am Wed, Apr 17, 2024 at 03:20:27PM +0300 schrieb Andrius Merkys:
> I have added the build-time test and filed the needed RM bugs + removed
> python-biopython test-dependency on emboss on s390x.
Thanks a lot
Andreas.
--
https://fam-tille.de
Am Tue, Apr 16, 2024 at 07:33:15PM +0530 schrieb Nilesh Patra:
> > I would suggest the following course of action for emboss:
> >
> > 1. Add a build-time test calling emboss executable(s). This way builds will
> > fail on s390x (and possibly other architectures) until #1069098 is fixed.
> >
> >
Hi folks,
by chance I looked at
https://qa.debian.org/developer.php?email=debian-med-packaging%40lists.alioth.debian.org
and realised:
main (1000)
;-)
Kind regards
Andreas.
--
https://fam-tille.de
Hi,
according to tracker[1] emboss is not migrating due to a test suite
error on s390x[2]. IMHO the appropriate thing to do is to also remove
s390x architecture - but we also need to care for all rdepends (again
after removing these for 32bit). Any volunteer to file the according
bugs?
I guess
Hi,
Am Wed, Apr 10, 2024 at 03:33:53PM -0700 schrieb Steven Eker:
> I like that solution since I believe there are 64-bit platforms where long
> is 32-bits. I've updated my development version thus:
>
> //
> // timeValue.tv_sec is 64-bit since Linux kernel 5.6 but GMP doesn't
> yet have
Hi,
I'd suggest to set
Build-Depends: architecture-is-64-bit, architecture-is-little-endian
and remove 32bit architectures of maude.
Kind regards
Andreas.
--
https://fam-tille.de
Hi,
Am Mon, Apr 01, 2024 at 09:12:49PM +0200 schrieb Sascha Steinbiss:
>
> > If there is agreement with this, then I would like an amend the
> > Debain-Med team policy to make it clear that we, as a community of
> > package maintainers and users, are okay with removing support for 32-bit
> >
Ping?
Am Sat, Dec 09, 2023 at 06:13:24PM +0100 schrieb Andreas Tille:
> Hi Amul,
>
> I realised that fis-gtm is lagging behind upstream some versions and the
> Debian packaged fis-gtm is featuring CVE-2021-44496 and CVE-2021-44504.
> It would be great if you could upgrade the
Hi Charles,
Am Fri, Mar 29, 2024 at 03:48:07PM +0900 schrieb Charles Plessy:
> > For the moment it would be easy to make sure at least new r-bioc-*
> > packages are restricted to the said architectures by adding this to
> > dh-r.
>
> I fully agree.
I've pushed an (only weakly tested) patch to
Hi,
I'm personally fine with Michaels suggestion in general.
Am Fri, Mar 29, 2024 at 10:13:40AM +0530 schrieb Nilesh Patra:
>
>
> On 28 March 2024 7:21:01 pm IST, "Michael R. Crusoe"
> wrote:
>
> There are also packages inside debian med umbrella which are not necessarily
> related to
Hi Emanuele.
Am Tue, Mar 19, 2024 at 12:16:16PM +0100 schrieb Emanuele Rocca:
> I've uploaded a NMU to DELAYED/2: https://bugs.debian.org/1067147
Thanks a lot for your attempt to help. In principle we have a team wide
low threshold NMU - so undelayed NMUs are fine. The kind of race
condition
Hi again,
sorry, I did not checked the situation.
Am Tue, Mar 19, 2024 at 10:34:13AM +0100 schrieb Andreas Tille:
> Testing removals are happening automatically if some RC bug exists
> for a certain time without pinging. Just writing some additional
> information to the bug in quest
Am Tue, Mar 19, 2024 at 09:52:49AM +0100 schrieb Jörg Riesmeier:
> Dear all,
>
> > Indeed, and there is a simple fix too, which has been uploaded to
> > experimental only so far:
>
> yes, there is a simple fix (that disables the error), but there is also a
> more fundamental fix that
Hi Sébastien,
Am Tue, Mar 19, 2024 at 09:44:04AM +0100 schrieb Sébastien Jodogne:
> > >
> > > On 2024-03-19 06:24, Sébastien Jodogne wrote:
> > > > Because of bug #1060104, a large majority of the packages related to
> > > > medical imaging have just disappeared from Debian Unstable.
To be
ot;Any team member can and *should* upload team
maintained packages no matter who is specified as Uploader." BTW, its
perfectly welcome to add additional IDs to Uploaders.
> Op Mon, Mar 11, 2024 at 03:47:42PM +0100 schreef Andreas Tille:
> >
>
> >
> > Joost van Baa
Hi Yaroslav,
Am Tue, Mar 12, 2024 at 03:50:22PM -0400 schrieb Yaroslav Halchenko:
> Let's keep DataLad under our (NeuroDebian) umbrella for now, since we
> are also upstream there and project is active. We are also
> working with Vasyl (CCed) to experiment with some semi-automation for
> package
Am Mon, Mar 11, 2024 at 10:29:30PM +0100 schrieb Étienne Mollier:
> The change turns out to be much more involved than I initially
> thought: we need to account for the build dependencies as well
> as the recommends, and tests don't go skipped that easily,
> because the control on skippable
Hi Yaroslav,
once we agreed that we should probably move all Neurodebian packages to
Debian Med to make it accessible for a bigger team. I was not really
active for some time in this attempt. However, bug #1065841 brought
datalad on my screen. I would love to see it maintained on Salsa either
Hi,
when trying to exclude clustalw and emboss from bioperl-run I learned
that its autopkgtest is failing for all architectures but amd64. The
reason is that the test wants to install pftools which is only available
on amd646. Thus all autopkgtests for other architectures are failing
with
Hi R-pkg team members,
as you might have possibly read I nominated myself for DPL for the next
term[1]. I will pronounce in my platform clearly that I will stop my
uploading activity to rather concentrate on my DPL tasks. I hope I will
be able to really stop myself from uploading in case I
Hi,
I'm working on some time_t side effects on the emboss package and by
doing so stumbled I upon the fact that i386 builds of packages with a
Build-Dependency on clustalw are failing. You can see an example in
Salsa CI for libbio-tools-run-alignment-clustalw-perl[1] which contains
The
Control: block -1 by 1065782
Hi Thorsten,
Am Mon, Mar 04, 2024 at 06:41:28PM + schrieb Thorsten Alteholz:
> there are still reverse dependencies that need to be taken care of:
>
> Checking reverse dependencies...
> # Broken Depends:
> emboss: jemboss
I think this is a false positive since
Hi Michael,
Am Thu, Mar 07, 2024 at 12:23:15PM +0100 schrieb Michael R. Crusoe:
> This is a great tip, thanks!
>
> I've pushed commits that use the provisions from the
> architecture-properties package to clean up d/control for the following
> packages:
>
> abyss
> bazel-bootstrap
> bowtie
>
Hi,
Paul has sent me a valuable hint. I totally missed this information
but will try to fix all our packages that are only available for 64 bit
architectures according to this. I'm just bouncing this information
to the list in case I'm not the only one who missed this simple option
to exclude
Hi Sascha,
Am Sun, Feb 25, 2024 at 08:32:52PM +0100 schrieb Sascha Steinbiss:
> > nox > Creating virtual environment (virtualenv) using python3 in
> > .nox/prepare
> > nox > python -m pip install build numpy packaging PyYAML requests tomli
> > nox > Command python -m pip install build numpy
gt; Binary: python3-awkward python3-awkward-dbgsym
> Architecture: source amd64
> Version: 2.6.1-1
> Distribution: unstable
> Urgency: medium
> Maintainer: Debian Med Packaging Team
>
> Changed-By: Sascha Steinbiss
> Description:
> python3-awkward - man
Dear Emmanuel,
Am Thu, Feb 22, 2024 at 04:07:25PM +0100 schrieb Emmanuel Promayon:
> Thank for your time, patience and explanations!
You are welcome.
> Thank you very much for the explanation, the wiki update and the link to
> routine-update, that will probably my saviour in the future!
Hi Emmanuel,
Am Thu, Feb 22, 2024 at 07:48:53AM +0100 schrieb Emmanuel Promayon:
> I hope you had a great sprint (seems a lot was done, congrats!).
All was fine, thank you.
> I was wondering if any of you had any time to check the new CamiTK version
> package in between all of the bug fixing
Hi,
as reported in a qiime2 issue[1] there is some problem with Python3.12
in the tests of the q2-* packages which are all using the qiime package.
This problem is currently hidden from the tests made by Python3.12
porters but it became obvious now on Salsa CI[2]. I tried to fiddle
around a bit
Hi folks,
I'd suggest to have dinner tomorrow evening 18:00 at Viet Kitchen
(as last year):
https://www.openstreetmap.org/?mlat=52.47994=13.35216#map=19/52.47994/13.35216
(I've added this also to the Wiki)
See you either tomorrow or on Saturday
Andreas.
PS: For those who need to join
Am Mon, Feb 12, 2024 at 10:09:43PM -0500 schrieb Aaron M. Ucko:
> Andreas Tille writes:
>
> >Build-Depends libthread-pool 4.0.0 which does not build
> >for 32bit architectures[1]
>
> I see a fix in experimental:
>
> https://buildd.debian.org/statu
Hi,
the chain of dependencies for pinfish which creates the problem is
pinfish depends racon which in turn can't install its
Build-Depends libthread-pool 4.0.0 which does not build
for 32bit architectures[1]
My suggestion to solve the issue is to explicitly set
Architecture:
Hi folks,
today we should schedule our video conference but I will not make it
today and I think its better to meet next week at the sprint and invite
those who are not at site via Jitsi.
See you next week
Andreas.
--
http://fam-tille.de
ely assume that the world will not
see any version 0.10, IMHO.
Kind regards
Andreas.
> > Gesendet: Mittwoch, 07. Februar 2024 um 14:02 Uhr
> > Von: "Andreas Tille"
> > An: "Debian Med Project List"
> > Cc: "Steffen Möller&q
Hi again,
if there is no response of kind "Yes, please try to keep the Python
interface of ghmm" it will be removed soon.
Kind regards
Andreas.
Am Tue, Jan 30, 2024 at 07:58:34AM +0100 schrieb Andreas Tille:
> Hi Steffen (and two whom it might concern),
>
> when
Hi again,
I've filed bug #1062371
RM: emboss [armel armhf i386 hppa m68k powerpc sh4] -- ROM; No support of
32 bit architectures any more
Kind regards
Andreas.
Am Wed, Jan 31, 2024 at 07:53:26AM +0100 schrieb Andreas Tille:
> Hi again,
>
> besides my suggested solution to
Hi Tony,
Am Wed, Jan 31, 2024 at 09:57:32AM + schrieb Tony Travis:
> The only people I know still using 32-bit software are doing BLAST etc on
> older Raspberry Pi's. However, AFAIK, the default Raspberry Pi OS (based on
> Debian Bullseye) is 32-bit even though the newer Raspberry Pi have
/ReleaseGoals/64bit-time
Am Fri, Jan 26, 2024 at 10:44:09AM +0100 schrieb Andreas Tille:
> Hi Charles,
>
> I wonder how we can properly solve this bug. In the early stage of
> Emboss packaging obviously the packages
>
>libajax6,
>libajax6-dev,
>
Hi Steffen (and two whom it might concern),
when Israel has written the autopkgtest for ghmm it turned
out that there are several issues with the Python3 interface.
In Matrix Nilesh raised the perfectly valid question:
The py interface is living off a patch from py2to3 and is (very)
Hi Xavier,
Am Mon, Jan 29, 2024 at 06:34:54PM +0100 schrieb Komolehin Israel:
> > Would it be useful for you if I added these files to the github
> > repository?
>
> Yes. That would be great.
I consider this specifically helpful since you could add a test
in the upstream archive which is
Hi Rebecca,
Am Sun, Jan 21, 2024 at 03:29:21PM + schrieb Rebecca N. Palmer:
>
> Hence, doing this transition now would involve breaking some reverse
> dependencies with no known fix, but given the number of packages involved,
> trying to wait until they're all fixed is rather likely to
Hi,
this is the call for the next video meeting of the Debian Med team
that are an established means to organise the tasks inside our team.
Meetings usually take us only 15-20min depending what we are talking
about and how many people are joining. The next meeting is tomorrow
Hi,
the Debian Med team will held its yearly in person meeting from Friday,
February 16 (evening) until Sunday, February 18 (evening) in Berlin.
For more detailed information please visit the Wiki page[1] and if you
like to join our small meeting with bug squashing (may be Python 3.12
bug fixing
Hi,
Am Wed, Jan 03, 2024 at 12:41:23PM +0100 schrieb Sascha Steinbiss:
> > This would be very convenient. I'd take over to ask DPL for budget
> > confirmation once the list of attendees needing travel support is
> > fixed.
>
> Done: https://wiki.debian.org/Sprints/2023/DebianMed2024
Thanks a
Am Wed, Jan 03, 2024 at 10:44:03AM +0100 schrieb Sascha Steinbiss:
>
> I can see in our internal calendar that the room has been booked for
> 17./18.2.
>
> > We should setup an according Wiki page quickly (but I will not be
> > possible to do this today).
>
> Should I just clone the previous
Hi,
Am Sat, Dec 30, 2023 at 11:39:35PM +0100 schrieb Étienne Mollier:
> > > I'd love to fix 17-18. February (or lets meet at 16.2. February evening
> > > inside the water tower like last year.)
Just lets fix it on this 16.2. water tower whoever will make it and
17-18 inside the kacher space
Am Sat, Dec 30, 2023 at 04:28:39PM +0100 schrieb Étienne Mollier:
>
> autopkgtest-pkg-python can be requested to use only one python3
> version by specifying the X-Python3-Version field in d/control,
> first paragraph. It is a consequence of autopkgtest-pkg-python
> using `py3versions
Am Sat, Dec 30, 2023 at 04:27:31PM +0530 schrieb Nilesh Patra:
> > I can try to do so but I'm afraid we will run into the same issue as
> > for libsbml[1].
>
> No, we won't. There are no autopkgtests for the python wrapper. If
> autopkgtests for this
> are added, we should just run the same for
Am Sat, Dec 30, 2023 at 01:19:32PM +0530 schrieb Nilesh Patra:
> > Sure. Feel free to implement this - I'm just not available for the next
> > couple of days.
>
> This is the currently existing solution itself. Only additional change needed
> is to
> replace python3-all-dev with python3-dev in
Hi Lance,
Am Fri, Dec 29, 2023 at 10:36:54PM +0700 schrieb Lin Qigang:
> While I do not plan to close any more before the new year, I enjoyed joining
> this year's bug squashing advent. Thank you again to all of my sponsors and
> those who offered help.
It was a pleasure to work with you. In
Am Wed, Dec 27, 2023 at 09:43:19PM +0100 schrieb Steffen Möller:
> > for teaching and meeting reasons.
> >
> > But as I just wrote, 17-18 also works.
>
> I'd opt for the earlier date, so we have a bit of a break before some of us I
> expect to bump into each other again in Hamburg if Holger's
Am Fri, Dec 29, 2023 at 11:35:41AM +0530 schrieb Nilesh Patra:
> On a brief look, it does not seem easy and would mean maintaining a debian
> specific
> patch for ever which maybe non-trivial for future versions.
>
> Can we not support just the default python3-dev?
Sure. Feel free to implement
Hi,
Am Thu, Dec 28, 2023 at 03:28:54PM +0530 schrieb Nilesh Patra:
>
> Fixed the build. Now it fails at dh_missing due to python stuff not being
> installed.
> I am not sure if you want to create a new bin pkg with python wrapper or not
> - so I
> leave the onus of finalizing it onto you.
Hi,
libargparse was accepted by ftpmaster. Now meson code needs to be
adjusted to create a proper cmake input file to use the Debian packaged
version of libargparse (may be even that needs some cmake helper to be
detected properly). Currently I do not have time to care for this[1]:
Hi,
I think bug #1059214 was my last one in this years Advent bug squashing.
Thanks to all who joined. For those who missed the fun for whatever
reason there are some "add build support for loongarch64" and some
"Fails to build source after successful build" low hanging fruits left.
;-)
For
Hi Israel,
Am Sat, Dec 23, 2023 at 08:07:22PM +0100 schrieb Komolehin Israel:
> I worked on Python-iow package by providing autopkgtest and providing a
> patch to fix some issues with the upstream test. CI was successful.
Nice.
> I would like this package to be reviewed as the test fails with
Hi Yaroslav,
Am Thu, Dec 21, 2023 at 03:52:26PM -0500 schrieb Yaroslav Halchenko:
> So a solution would be to revert going to monitor github and then reimport
> source. I do not think it is worthwhile packaging nwb-schema at this point
> since small and unlikely we would bother packaging any
Hi Yaroslav,
I bumped pynwb to its latest upstream version a couple of times. It was
not release in any stable release since o-o-stable since the package was
always in a bad state. Popcon is pretty low[1] - but we do not see any
Ubuntu users here so may be that's a weak metric.
My recent
Hi Sascha,
Am Thu, Dec 21, 2023 at 03:13:04PM +0100 schrieb Sascha Steinbiss:
>
> Absolutely! See [1] -- for February or early March we could have the room on
> weekends without a problem. I am now waiting for you guys to come up with a
> suggestion for possible specific dates so I can finalize
Hi Sasccha,
did you managed to reserve a room for our sprint? It would be nice if
we know in advance to arrange travel for those who do not come from
close by.
Kind regards and have a nice CHristmas
Andreas.
Am Mon, Nov 20, 2023 at 06:12:47PM +0100 schrieb Andreas Tille:
> Hi Sas
Hi Étienne,
Am Wed, Dec 20, 2023 at 08:51:34PM +0100 schrieb Étienne Mollier:
> And with this, I will probably wind down my activity for the
> remaining of the year
Thanks a lot for all your work and have a nice Christmas
Andreas.
--
http://fam-tille.de
Hi Andrius,
Am Wed, Dec 20, 2023 at 08:27:31AM +0200 schrieb Andrius Merkys:
> On 2023-12-19 18:51, Debian Bug Tracking System wrote:
> > [ Komolehin Israel Timilehin ]
> > * Added autopkgtest to check hmmer and prodigal integration (Closes:
> > #1010653)
>
> Thanks for working on this.
Hi Pierre,
Am Tue, Dec 12, 2023 at 09:09:46PM +0100 schrieb Pierre Gruet:
> You're welcome! I am astonished to see it cleared NEW in one hour anf a half,
Yes, I had to double check when I've seen this. Very nice
> I had not even the time to prepare my Advent Calendar email related to it.
the runpaths so that private shared libraries can be found
* Fixing spelling mistakes
* Using python3 instead of python in shebangs
* Fixing Lintian override syntax
* Overriding Lintian warnings about spelling errors due to false positives
.
[ Andreas Tille ]
* Fix watch file
Hi Aaron,
Am Sun, Dec 10, 2023 at 06:30:01PM -0500 schrieb Aaron M. Ucko:
>
> Because env/common.cmake doesn't actually try to use a system
> installation:
>
> #check_include_file_cxx(mbedtls/md.h HAVE_MBEDTLS_H)
> set(HAVE_MBEDTLS_H 0) # TODO: disabling system mbedtls since it may be
>
Hi Aaron,
Am Sat, Dec 09, 2023 at 08:23:26PM -0500 schrieb Aaron M. Ucko:
>
> AFAICT, the immediate problem is that label_online_tests.patch refers to
> at least one removed or renamed test:
>
> CMake Error at test/internal/vdb-diff/CMakeLists.txt:42
> (set_tests_properties):
>
Hi Aaron,
I've spent some time into the new version of sra-sdk and tried to adapt
the patches to the new upstream version. Salsa CI was not working at
the time of pushing so there is no build log but if you might like to
try on your side you will notice that my attempt failed. I'd be super
Hi Amul,
I realised that fis-gtm is lagging behind upstream some versions and the
Debian packaged fis-gtm is featuring CVE-2021-44496 and CVE-2021-44504.
It would be great if you could upgrade the Debian package to the latest
upstream version.
Kind regards,
Andreas.
--
http://fam-tille.de
Hi,
this is the call for the next video meeting of the Debian Med team
that are an established means to organise the tasks inside our team.
Meetings usually take us only 15-20min depending what we are talking
about and how many people are joining. The next meeting is tomorrow
Control: reassign -1 snippy
Control: retitle -1 Wrong calls of snpEff
Control: tags -1 upsteam
Control: forwarded -1 https://github.com/pcingola/SnpEff/issues/510
Thanks to snpEff upstream I've found a solution[1] for the problem
reported above. I've also added a conscise test case[2] which was
Hi Nilesh,
Am Wed, Dec 06, 2023 at 02:00:52AM +0530 schrieb Nilesh Patra:
> Sometimes just tagging upstream author does wonders :)
I hope I'll keep that trick in mind! ;-)
> They have replied and the (upstream) bug has been closed.
> BTW, are you able to still reproduce (without any fixes for
Hi Étienne,
Am Sun, Dec 03, 2023 at 03:54:57PM +0100 schrieb Étienne Mollier:
> > Please leave some low hanging fruits for me! ;-P
>
> I see at least four screenful worth of low hanging fruits in the
> bug tracking system affecting Debian Med packages, if not more.
> That should be plenty for
Hi Pierre and Étienne,
Am Sun, Dec 03, 2023 at 11:55:05AM +0100 schrieb Étienne Mollier:
> Hi,
>
> Pierre Gruet, on 2023-12-03:
> > Fixing minor bugs #1043696, #1045612, #1046315, #1046647, #1046802,
> > #1046809, #1047000, #1048408, #1049745. Not crucial, but they offer the
> > opportunity to
Hi,
closed #1057132 yesterday and #1057253 today.
For those who might consider reporting closed bugs here too much noise
we can also report it on our Matrix channel[1].
In any case I'd like to announce here that Étienne has fixed this year
more bugs than I in Debian Med team. I'm absolutely
: Andreas Tille
We believe that the bug you reported is fixed in the latest version of
jellyfish1, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed
Hi folks,
until 2021 we had the nice bug squashing advent calendar manually
maintained by Thorsten Alteholz. Since Thorsten confirmed that this
manual work is draining time from his other tasks for Debian mainly his
ftpmaster task. I'd like to thank Thorsten again for all his effort -
even mor
Hi,
we tried to package snippy which has uncovered a bug in SnpEff which we
have reported upstream[1] with some easily verificable data set and
command line. Unfortunately we did not had any response from upstream.
We even would consider to revert SnpEff version to a working one without
this
Hi Pierre,
I realised that you've fixed bug #1054675 (thanks for doinig so) but
that several architectures are failing to build[1] which I do not
understand when looking at the build logs. Since there was a new
upstream version I imported this and tried to adapt the patches.
Unfortunately the
Hi Sascha,
thanks a lot for checking the know venue.
Am Mon, Nov 20, 2023 at 03:27:35PM +0100 schrieb Sascha Steinbiss:
> > I wouldn't mind going somewhere else for a change... but i can
> > surely ask if we can have another weekend in February.
Same for me - I would like to meet at any
Am Thu, Nov 16, 2023 at 11:07:11AM +0100 schrieb Steffen Möller:
> > I wouldn't mind going somewhere else for a change... but i can surely
> > ask if we can have another weekend in February.
>
> Hamburg would also be fine with me. Important for the med team is
> increasingly also what the ML
Hi,
this is the call for the next video meeting of the Debian Med team
that are an established means to organise the tasks inside our team.
Meetings usually take us only 15-20min depending what we are talking
about and how many people are joining. The next meeting is tomorrow
Hi Pierre,
Am Fri, Nov 10, 2023 at 05:48:13PM +0100 schrieb Pierre Gruet:
> > its autumn so we should prepare for winter. For Debian Med winter is
> > the time where we usually do our in person meeting. The last meetings
> > were in a perfectly fitting location in Berlin and I for myself would
Am Wed, Nov 08, 2023 at 06:50:25PM +0100 schrieb Étienne Mollier:
>
> I reran three or four times the autopkgtest on arm64 on my host
> with no issues. The rerun on official CI also went fine in a
> very reasonable time[1]. CI history of jellyfish[2] reveals two
> occurrences of this issue
Hi Étienne,
Am Wed, Nov 08, 2023 at 09:44:22AM +0100 schrieb Étienne Mollier:
> > I'd like to rewrite bcftools autopkgtest according to the model of
> > samtools. However, we need a new binary package bcftools-test which I
> > rather delay util the set of packages has migrated to testing.
>
>
Am Tue, Nov 07, 2023 at 10:27:04PM +0100 schrieb Étienne Mollier:
>
> Yup, there may be some tight coupling between samtools and
Samtools and bcftools uploaded.
> python-pysam, but the latter's upgrade will be needed for the
> upcoming python 3.12 transission anyway.
I've seen the bug report
Hi Étienne,
Am Mon, Nov 06, 2023 at 10:30:04PM +0100 schrieb Étienne Mollier:
> I kind of forgot an htslib upload to experimental in version
> 1.18 for like two months, and which had no excuses[1] for
> lingering like that. I will have some time on Wednesday to do
> things, and I considered the
Hi,
its autumn so we should prepare for winter. For Debian Med winter is
the time where we usually do our in person meeting. The last meetings
were in a perfectly fitting location in Berlin and I for myself would
be fine to meet there again. If someone knows better option (also
better for
Hi Tony,
Am Wed, Nov 01, 2023 at 05:11:41PM + schrieb Tony Travis:
>
> Sorry, the attached screenshot with your picture on it is what I read, but I
> didn't notice that it was the upstream README.md.
O, dear, if I would have written all the stuff where Github
instances put my picture on
Am Wed, Nov 01, 2023 at 10:02:24AM + schrieb Tony Travis:
> I didn't say that you gave advice "to use bioconda": I said that I had
> followed your advice 'about installing "canu" under "bioconda3"'.
>
> I needed to fix the problem we encountered with "canu" installed from the
> Debian-Med
Hi Tony,
Am Tue, Oct 31, 2023 at 11:13:13AM + schrieb Tony Travis:
> What's the status of "canu"?
Since canu has a test suite issue on arm64 a bug was filed[1].
Since we have no idea about this issue the forwarded the problem
upstream[2].
> The "canu" package in Debian-Med appears to be
Hi Sébastien,
Am Tue, Oct 31, 2023 at 10:46:15AM +0100 schrieb Sébastien Jodogne:
>
> Please however could you explain me how to execute autopkgtests on my
> development Debian, without having to recompile the package from scratch
> everytime I try to modify the "debian/test/*" files?
Generally
Hi Santiago,
Am Fri, Oct 20, 2023 at 02:43:57PM +0200 schrieb Santiago Vila:
> One more question: I didn't get the hang of gbp to build
> the package at first, so I put the orig.tar.xz below the working
> directory and used good old "dpkg-buildpackage -S", since
> I know dpkg-buildpackage is
Am Fri, Oct 20, 2023 at 04:51:57PM +0530 schrieb Nilesh Patra:
>
> > (B) Yes, but only if you don't keep the package in a half-fixed state,
> > i.e. only if you do all that at nearly the same time, including the tag
> > and the new upload, so that we don't have changes in master
> > without their
Hi,
Am Fri, Oct 20, 2023 at 08:44:26AM +0100 schrieb Oyindamola Olatunji:
> I am working on adding autopkgtest to the orthanc-python package. Whenever
> I run the test locally, it gets stuck in execution and doesn't seem to give
> an output.
>
> Here is the autopkgtest:
>
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