Hi Sébastien
On 6/5/21 6:48 PM, Sébastien Jodogne wrote:
>> Thanks Nilesh for the permissions, I begun with upload of
>> orthanc 1.9.2+really1.9.1+dfsg-1 source changes. Sébastien, I
>> let you proceed with the plugins, since you seemed willing to do
>> it yourself.
>
> Great!
>
> Just an addit
Hi Steffen,
On 6/15/21 4:01 AM, Steffen Möller wrote:
> Hello,
>
> This was not really required for the pandemic, even though the author,
> David Goodsell, got some recent fame for his illustrations of the corona
> virus https://pdb101.rcsb.org/sci-art/goodsell-gallery/coronavirus
>
> Illustrate
Hi,
On 6/15/21 8:00 PM, Shruti Sridhar wrote:
> Hi,
>
> I have written autopkgtests for pilercr
> (https://salsa.debian.org/med-team/pilercr)
Excuse my lack of understanding, but the page you mentioned in d/README.test is
https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index
On opening
On 15/06/21 10:47 PM, Steffen Möller wrote:
> Hi Nilesh,
>
> Am 15.06.2021 um 12:29 schrieb Nilesh Patra:
> > Hi Steffen,
> >
> > On 6/15/21 4:01 AM, Steffen Möller wrote:
>> [..]
> > 1. Please consider to enable salsa CI for new packages with: salsa
On 6/17/21 12:12 PM, Shruti Sridhar wrote:
> Hi,
>
> The fasta files that I used are present as their examples.
> It can also be found on their repository here -
> (https://github.com/dcouvin/CRISPRCasFinder/blob/master/install_test/sequence.fasta)
>
> I modified this file a little for the t
Hi Shruti,
On 6/17/21 9:06 PM, Shruti Sridhar wrote:
> I had originally taken the data from the examples on the website [1] and I
> thought that the same data would be available on their github repository.
>
> But since the data is not the same, I have now changed it to the same
> sequence fro
On 17/06/21 03:45 PM, Aaron M. Ucko wrote:
> Nilesh Patra writes:
>
> > Since fetching it directly from a file location or a sort of API doesn't
> > seem the way out, writing a script directly looks not easy.
>
> Programmatic retrieval is very much pos
Hi,
On 20/06/21 01:22 PM, Steffen Möller wrote:
> Hello,
>
> I finally got around a revisit of
> g...@salsa.debian.org:med-team/mcaller.git . I think it is read to be
> uploaded, in the sense that it compiles nicely and does not give any
> testing errors.
I did the following changes:
* Do not c
Hi Andrius, Hi Andreas,
On Mon, 21 Jun 2021 at 11:27, Andrius Merkys wrote:
> Hello,
>
> On 2021-06-21 08:16, Andreas Tille wrote:
> >>> Repository data is changed during the tests, which I dislike, but ...
> >>> well ... we need to get somewhere.
> >> * And I dislike this as well, so I simply r
Hi Shruti,
On 30/06/21 09:15 PM, Shruti Sridhar wrote:
> Hello!
>
> I have written autopkgtests for seirsplus, salmid and mirtop.
>
> For mirtop, the tests pass for me in my chroot but seem to fail the
> pipeline [4]. Could you please take a look and let me know how I can
> proceed?
The error s
Hi Fabian,
On Mon, 5 Jul, 2021, 6:16 pm Fabian Klötzl, wrote:
> Hi folks,
>
> I have updated the phylonium package to v1.5. No big changes other than
> dropping the GSL dependency and Nilesh's improved autopkgtests.
>
Right now we are in deep freeze, and any changes except RC bug fixes should
b
Hi,
I was updating bustools to latest release (only making changes in salsa
for now due to freeze)
and I noticed that this new version has 3 dependencies which is vendored
along with it[1]
Since it is always better to use packaged libs, I decided to move with
this idea.
It has 3 dependencies: eig
On 11/07/21 10:04 PM, Steffen Möller wrote:
> Hello,
>
> I went a bit over packages listed in the "genome structure" tab
> https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit#gid=701092179
>
> and have
> surpyvor
Did the following things:
* Add missing buil
On Mon, 12 Jul 2021 at 16:48, Nilesh Patra wrote:
> On 11/07/21 10:04 PM, Steffen Möller wrote:
> > Hello,
> >
> > I went a bit over packages listed in the "genome structure" tab
> >
> https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgF
On 12/07/21 07:15 PM, Shruti Sridhar wrote:
> Hello!
>
> I have written autopkgtests for samblaster [1] and paraclu [2].
>
> For samblaster, the blhc fails during the ci pipeline. I tried fixing it by
> adding CPPFLAGS similar to what was done in this commit [3], but it did not
> seem to work. Ki
On 12/07/21 08:57 AM, Andreas Tille wrote:
> Lets wait for responses to the issue you opened first.
>
> 4. Asking bustools upstream why they picked this actual fork instead of
>liblbfgs. May be they can adapt to what we have packaged.
>
Opened an issue with bustools to track this[3]
> > [
On Mon, 12 Jul, 2021, 10:24 pm Nilesh Patra, wrote:
> On 12/07/21 08:57 AM, Andreas Tille wrote:
> > Lets wait for responses to the issue you opened first.
> >
> > 4. Asking bustools upstream why they picked this actual fork instead of
> >liblbfgs. May be the
>> However, this depends on the upsetplot package[1], which is not in the
>> archive -- can you please package this?
> Sorry, yes. Repeated offender, I admit.
Diane pushed the initial packaging for upsetplot to salsa, I finalised
this and uploaded.
Post that I uploaded the surpyvor package too, t
On Tue, 13 Jul 2021 at 13:14, Michael Banck wrote:
> Hi,
>
> On Mon, Jul 12, 2021 at 08:57:25AM +0200, Andreas Tille wrote:
> > On Sun, Jul 11, 2021 at 01:03:45PM +0530, Nilesh Patra wrote:
> > > I've thought of these (possible solutions):
> > >
>
Hi Steffen,
On Thu, 15 Jul 2021 at 00:21, Steffen Möller wrote:
> Hello,
>
> I had some fun with https://salsa.debian.org/med-team/ngmlr/ and helped
> upstream with the VA_ARGS in the preprocessor macros a bit more. This was
> all triggered by a division by 0 error that affected us locally and w
On 18/07/21 01:12 PM, Andreas Tille wrote:
> The packaging is not ready yet and after a quick view it might be caused
> by some ramxl issue where a different binary package name is expected.
> This needs further investigation I can not do right now (every other
> team member is kindly invited to st
On 7/18/21 7:04 PM, Andreas Tille wrote:
> Hi Nilesh,
>
> thanks a lot for fixing q2-phylogeny.
>
> On Sun, Jul 18, 2021 at 01:14:35PM +0000, Nilesh Patra (@nilesh) wrote:
>> + - Renamed binaries according to the names available in our distribution
>> ...
>>
On 19 July 2021 12:50:03 pm IST, Andrius Merkys wrote:
>Currently I am looking into ProMod3 [3], which seems to be the engine
>behind the great SWISS-MODEL service [4]. I seem to have figured out
>the
>dependencies, will go on to packaging next.
Let us know if you need help with packaging the
Hi,
It came to my notice that sambamba does not list copyright holders,
and copyrgiht holders of several files are missing.
I wonder if this is a RC bug, since I've seen a few of these earlier,
for example #823865
I fixed the copyright stuff, but along with that I did a bunch of other
changes:
On Wed, 21 Jul 2021 at 20:50, Andreas Tille wrote:
> Hi,
>
> On Wed, Jul 21, 2021 at 02:47:17AM +0530, Nilesh Patra wrote:
> >
> > I wonder if this is a RC bug,
>
> I'd consider it important and may be RC **after** bullseye release.
>
Why *after* release?
On 22/07/21 09:49 PM, Shruti Sridhar wrote:
> Hello!
>
> I have written autopkgtests for spaced [1].
>
> Kindly review,
Looks good!
Nilesh
signature.asc
Description: PGP signature
Hi,
I was adding in autopkgtests for q2-sample-classifier and I noticed that this
has a few
missing dependencies, which must be included for it to work properly.
$ grep -irn distutils
versioneer.py:1504:from distutils.core import Command
versioneer.py:1546:from distutils.command.bui
On 25/07/21 06:44 AM, Andreas Tille wrote:
> Hi Nilesh,
>
> thanks a lot for spotting this!
>
> On Sun, Jul 25, 2021 at 02:31:40AM +0530, Nilesh Patra wrote:
> >
> > All fixes in salsa
> >
> > Do you think it is fine uploading this now and filing a unbloc
Hi,
I committed a multi-orig tar to resfinder's salsa repository,
but the checkout does not seem to work as intended.
As seen in the CI, and I also cloned it in another directory and tried,
this ends with:
gbp:error: Error creating resfinder_4.1.5.orig.tar.bz2: Pristine-tar couldn't
checkout "r
On 7/26/21 12:01 AM, Nilesh Patra wrote:
> Hi,
>
> I committed a multi-orig tar to resfinder's salsa repository,
> but the checkout does not seem to work as intended.
>
> As seen in the CI, and I also cloned it in another directory and tried,
> this ends with:
>
Howdy
On 7/25/21 10:25 PM, Steffen Möller wrote:
> Hello,
>
> there is a 2021.4.0 version tagged that should be found by all the
> d/watch files but that was not the case for quite a number of the q2-*
> packages. I have updated them and gave them all a quick "uscan
> --verbose" to test.
Cool, t
On 7/26/21 12:47 AM, Andreas Tille wrote:
> On Mon, Jul 26, 2021 at 12:25:51AM +0530, Nilesh Patra wrote:
>>> I tried to re-create and re-import but that does not work either -- I'm
>>> not sure how to go about this.
>>> Please consider taking a look, any h
[Bringing Praveen into the loop who maintains fasttrack]
Hi Steffen,
On Tue, 27 Jul, 2021, 3:32 pm Steffen Möller,
wrote:
> Hello,
>
> fastx-toolkit https://tracker.debian.org/pkg/fastx-toolkit ran into a
> bug in one of its dependencies and was removed for that reason.
> ArrayExpressHTS still
On Tue, 27 Jul, 2021, 4:16 pm Nilesh Patra, wrote:
> and its reverse dependencies
>> like ArrayExpressHTS with it, then?
>
>
> Not needed for reverse dependencies, if we push those to ofiicial
> bullseye-backports.
>
Erm, correction here. Ofcourse,
On Tue, 27 Jul, 2021, 9:02 pm Steffen Möller,
wrote:
> Hello,
>
> This package is one of the closest that we have on our radar to suit
> virologists, to I went for CATCH from the broad institute at
> https://github.com/broadinstitute/catch . Conda has it already, does not
> surface on bio.tools,
Hi Steffen,
On Tue, 27 Jul 2021 at 23:05, Steffen Möller wrote:
> Hi Nilesh,
>
> Thank you tons for thinking along.
>
> It took me a bit but. Too long. The answer is that git does not lose the
> sensation of a file being a git lfs reference even when you download a
> tar.gz. For some reason I ha
On 28 July 2021 3:00:08 am IST, Nilesh Patra wrote:
>Hi Steffen,
>
>On Tue, 27 Jul 2021 at 23:05, Steffen Möller
>wrote:
>
>> Hi Nilesh,
>>
>> Thank you tons for thinking along.
>>
>> It took me a bit but. Too long. The answer is that git does not
Hi Steffen,
On 28/07/21 01:06 PM, Steffen Möller wrote:
> Hi Nilesh,
> > > The import of pristine-tar has worked after removing .gitattributes, but
> > > then the git lfs references were still in the tarball and the
> > > upstream branch. pristine-tar could be pushed, but then the other
> > >
On 29/07/21 09:40 PM, Shruti Sridhar wrote:
> Hello!
>
> I have written autopkgtests for yanagiba[1] and unc-fish[2].
>
> The yanagiba package seems to fail the ci pipeline. The error seems to be
> from -
>
> dpkg: yanagiba-build-deps: dependency problems, but configuring anyway as
> you request
On 31/07/21 11:23 AM, Shruti Sridhar wrote:
> > yanagiba is almost ready, since you downloaded data from ncbi database,
> > can you write a script for fetching data by running it?
> > Just like the way I did it for pilercr[5]
> > I don't have a good idea of navigating this file at the right locatio
On 31/07/21 03:57 PM, Shruti Sridhar wrote:
> Hello!
>
> I have written autopkgtests for ecopcr[1] and python-gtfparse[2].
>
> Kindly review,
Both look good. Thanks!
Nilesh
signature.asc
Description: PGP signature
Hi Steffen,
Apologies for delay in replying
>> 3) Since we are pretty close to a release, would it be a better idea to
>> upload it to NEW post release?
> I do not see why not both could be submitted together. The version that
> pigx-rnaseq depends on should be in.
OK, uploaded this to NEW aft
On 31/07/21 11:49 PM, Shruti Sridhar wrote:
> Hello!
>
> I have written autopkgtests for estscan[1] and blasr[2].
>
> Blasr seems to fail build in the ci pipeline[3].
> Could you please review and take a look and let me know how to proceed?
estscan looks good.
For blasr,
1) Copyright is incompl
On 1 August 2021 4:16:13 pm IST, Shruti Sridhar
wrote:
>>
>> For blasr,
>>
>> 1) Copyright is incomplete, you also need to add in a "License:" for
>> your files.
>> You can also see it in lintian warning here[4]
>>
>> 2) i386 build failure is legit, so you could simply disable the salsa CI
>>
On 8/1/21 4:57 PM, Shruti Sridhar wrote:
> Hello!
>
> I have written autopkgtests for segemehl[1].
> The package was failing blhc and reprotrest in the pipeline. I managed to fix
> the blhc error
Great! You seem to have understood the concept :)
> but I am a little stuck on how to begin fix
On 8/1/21 8:17 PM, Steffen Möller wrote:
> Hello,
>
> I just prepared a package for https://github.com/google/ml_collections on
> https://salsa.debian.org/python-team/packages/python-ml-collections.
I did a few changes, all commits should be self explanatory.
Only bit of an _ugly change_ I had
On 2 August 2021 2:28:13 am IST, "Steffen Möller"
wrote:
>Heya,
>
>@Nilesh, concerning extra files for testing I am just fine. Thank you
>for doing this.
Do you think it's good to go for an upload?
If yes, I'll sign and dput
Nilesh
On 8/2/21 6:30 PM, Andreas Tille wrote:
> Hi Shruti,
>
> On Mon, Aug 02, 2021 at 04:50:36PM +0530, Shruti Sridhar wrote:
>> I have written autopkgtests for perm[1]
>>
>> The package initially failed blhc in the pipeline but when I fixed the
>> error [2]
Congratulations, you found a security iss
On 8/2/21 6:44 PM, Nilesh Patra wrote:
>>> the autopkgtest which was initially working fails [3].
>>
>> The autopkgtest says:
>>
>> Info 3: Sortubg buckets using 2 CPUs
>> .
>> *** buffer overflow detected ***
On 8/2/21 2:53 PM, Steffen Möller wrote:
>
> On 02.08.21 07:28, Nilesh Patra wrote:
>>
>> On 2 August 2021 2:28:13 am IST, "Steffen Möller"
>> wrote:
>>> Heya,
>>>
>>> @Nilesh, concerning extra files for testing I am just fine. Than
On 8/2/21 3:46 AM, Steffen Möller wrote:
> Hello,
>
> I know, PyRosetta is not free enough to be packaged, but I hope to eventually
> revive an older project that uses it and would like to run it on Debian. It
> seems like just two packages are missing - billiard, which I have just
> address
On 8/4/21 11:49 PM, Shruti Sridhar wrote:
> Hello!
>
> I have written autopkgtests for bamkit[1]
The python3-pysam should be in Depends field of d/control, it is not a
test-only dependency
And aw crap, this missing dependency will affect user experience :(
I guess I'll push your changes also
Hi,
Note: This is for *after* release
last-align saw some major overhauls in the later versions post 1179,
which had me almost fully re-write the patches and do more than trivial
changes to rest of the files
It'd be great if someone could review them and give an ACK. I do not
want to keep the re
Hi Andreas,
On 8/6/21 1:52 AM, Andreas Tille wrote:
> Hi,
>
> On Thu, Aug 05, 2021 at 07:33:14PM +0530, Nilesh Patra wrote:
>>
>> last-align saw some major overhauls in the later versions post 1179,
>> which had me almost fully re-write the patches and do more than tr
> [...]
Do you need some help?
> Q2-taxa needs a bit of
>cleanup with the JavaScript it is shipping. But otherwise, I tend to
>think we are done.
I believe I made q2-taxa ready for its entry to the archive. What $cleanup does
it need exactly?
On 8 August 2021 2:57:46 am IST, "Steffen Möller"
wrote:
>
>On 07.08.21 22:13, Nilesh Patra wrote:
>>> [...]
>> Do you need some help?
>
>There is a partial dependency of
>https://salsa.debian.org/med-team/gneiss (dep of q2-gneiss) on
>https://g
On 8/10/21 3:49 PM, Steffen Möller wrote:
> Hello again,
> I just pushed Pillow to s.d.o/python-team/packages/python-pillow.
https://tracker.debian.org/pkg/pillow
:)
Again in archive, please consider to close ITP and purge repo. Please consider
doing an apt-file find/search when you do a packa
On 8/12/21 4:06 PM, Steffen Möller wrote:
> Hello,
>
> TL;DR: Qiime tutorial is directly usable with the packages in salsa for
> 2020.11.1, no need for anything redundant from Debian. We need to work on
> JavaScript to get q2-diversity into main.
Done and pushed, please take look and let me k
On 8/13/21 11:46 PM, Steffen Möller wrote:
>
> On 12.08.21 20:12, Steffen Möller wrote:
>>> BTW, q2-diversity (Build-+)Depends on q2-emperor which again depends on
>>> python3-emperor which are not in the archive. And both do not look ready
>>> for upload yet (in interim state)
>>> If you make
On 8/19/21 5:52 PM, Steffen Möller wrote:
> Dear all,
>
> This is another small dependency nagging me:
> https://salsa.debian.org/python-team/packages/pytest-ordering
>
> pytest-3 does not find the local module when runnig cowbuilder, but it
> is just fine with gbp or dpkg-buildpackage. Does t
On Thu, 19 Aug, 2021, 8:12 pm Steffen Möller,
wrote:
>
> On 19.08.21 15:37, Nilesh Patra wrote:
> >
> > On 8/19/21 5:52 PM, Steffen Möller wrote:
> >> Dear all,
> >>
> >> This is another small dependency nagging me:
> >> https:/
Recently I added autopkgtest to the latest version of resfinder, which uses
kma_index binary from src:kma package. That started failing on
32 bit architectures[1]
I reported the same upstream, and upstream says that kma could never work
properly on 32-bit arches, see here[2]
However, kma had bee
On 8/23/21 9:00 PM, Nilesh Patra wrote:
> Recently I added autopkgtest to the latest version of resfinder, which uses
> kma_index binary from src:kma package. That started failing on
> 32 bit architectures[1]
>
> I reported the same upstream, and upstream says that kma c
Hi Michael,
You did simde trick[1] for last-align a long time ago (which saw a major
overhaul later), to make it building across multiple arches, many thanks
for that!
However, I had a conversation with the upstream maintainer here[2] and it
seems like that patch might not be needed anymore - alth
htslib is triggering a number of removals, triggering a lot of noise among
several packages.
I do see commits from Steffen for a new upstream version -- is someone at it?
If not, does it make sense to cherry pick the two patches from here[1] and
upload with these? -- Additionally, would someone
On Thu, 26 Aug 2021 at 17:03, Étienne Mollier wrote:
> Hi there,
>
> I had a quick look at the autoconf issue, but I now witness a
> slightly different symptom of ftbfs. I'm considering to push
> some newer upstream versions and upload to experimental, to have
> a picture of the situation; begin
Hi Dylan,
On 15 August 2021 1:31:21 pm IST, "Dylan Aïssi" wrote:
>Hi Steffen, hi Andreas,
>
>Le jeu. 5 août 2021 à 06:18, Andreas Tille a écrit :
>> Sure. We need a transition. Dylan (in CC) was kind enough to trigger
>> this in the past and we should do so right after the release (I'm
>> a
Hi Maarten,
On 9/3/21 8:31 PM, Maarten L. Hekkelman wrote:
> I'm trying to update the libzeep package and stumbled upon the following.
>
> libzeep uses documentation generated by boostbook which uses quickbook and
> doxygen amongst others. Now this setup creates an HTML page containing the
> u
On 9/3/21 10:45 PM, Maarten L. Hekkelman wrote:
> Tried to use my fresh new powers as a maintainer today.
Nice, and congrats!
> That worked well, until I tried to update the SONAME one of my libraries
> (libzee> The version currently in Debian is version 5.0.2 and has SONAME 5.
> The current
https://www.debian.org/doc/manuals/developers-reference/pkgs.html#binary-only-nmu
[2]:
https://www.debian.org/doc/manuals/developers-reference/pkgs.html#source-nmus-vs-binary-only-nmus-binnmus
Cheers,
--
Nilesh Patra
Debian Developer, Uploading
⢀⣴⠾⠻⢶⣦⠀
⣾⠁⢠⠒⠀⣿⡁
⢿⡄⠘⠷⠚⠋ nil...@deb
On 9/13/21 11:07 PM, Steffen Möller wrote:
>
> On 13.09.21 18:27, Nilesh Patra wrote:
>> r-cran-gprofiler2, last missing dep of pigx-rnaseq has been accepted some
>> hours ago.
> This is great news. Thank you for the upload. I just installed it. Was
> not aware that gprof
he team-stuff that I do. Hence, I
removed myself from Uploaders field
and uploaded.
That said, I'm even motivated to remove myself from uploaders in med-packages
which I don't have any interest in,
and which has co-maintainers. Let's see.
Thanks again for your efforts
On Fri, 17 Sept 2021 at 22:48, Vincent Danjean wrote:
> On 17/09/2021 15:40, Vincent Danjean wrote:
> >I built the package locally, installed it and executed the
> > debian/tests/run-unit-test manually.
> >No errors occurred (with gcc from up-to-date unstable, ie
> > gcc=4:10.2.1-1 and gc
On 9/29/21 6:42 PM, Maarten L. Hekkelman wrote:
> Everyone and their grandmother is currently working on getting libcifpp
> through the ballot. Very much appreciated. But I just managed to release
> version 2.0.
>
> Now what.
>
> Should I wait until the dust settles and libcifpp-data is accep
On 10/1/21 5:40 PM, Steffen Möller wrote:
> Hi all,
>
> I just got
>
> [...]
$ salsa update_repo --ci-config-path debian/salsa-ci.yml
med-team/long-read-assembler
$ echo $?
0
Works okay for me. There is some local problem for you
> I
On 10/11/21 3:17 PM, Andreas Tille wrote:
Hi Shayan,
I tried to upgrade shasta to the latest upstream version. Unfortunately
the autopkgtest fails with:
[...]
Can you (or somebody else) have a look?
Hi,
I have fixed this, and pushed my changes to salsa. However, lintian
complains about s
Hi,
On Thu, 14 Oct, 2021, 1:05 pm Andreas Tille, wrote:
> Hi Aaron,
>
> I updated golang-github-dataence-porter2 since uscan failed parsing
> upstream (there were no tags and I switched to git mode). Unfortunately
> the autopkgtest fails in my pbuilder chroot. Can you (or anybody else
> who is
Hi Shayan,
On 10/15/21 12:59 AM, Shayan Doust wrote:
Hello all,
It ran fine today, so it looks like you beat me to fixing it.
Unfortunately my faculty now blocks connections via the SMTP port, so email
communications are more difficult. That is, until I set up a method around it.
Damn, what
Hi,
python3-pysam seems to lag several versions behind in the archive -- is there
something blocking it?
I updated to a newer release than the one committed in salsa and everything
works smooth.
If there is no good reason for holding an upload, and the update looks good,
please upload, or giv
On 10/15/21 2:01 AM, Andreas Tille wrote:
Hi Nilesh,
Am Fri, Oct 15, 2021 at 01:17:52AM +0530 schrieb Nilesh Patra:
python3-pysam seems to lag several versions behind in the archive -- is there
something blocking it?
I updated to a newer release than the one committed in salsa and everything
On 10/15/21 11:06 AM, Andreas Tille wrote:
Cool. Did you used ratt or something else?
ruby-team/meta script: https://salsa.debian.org/ruby-team/meta -- I always
vouch for this one.
Here is the rebuild output(please check the entire mail since there are a few
questions at the end):
rebuild
On 10/15/21 11:33 AM, Nilesh Patra wrote:
Update:
===> pyvcf
Fixed and uploaded. This problem was due to new setuptools.
===> cnvkit
This looked like a flaky failure, and probably it was due to tests running in
parallel.
I uploaded with what I considered sensible
I have re-con
On 10/15/21 7:16 PM, Andreas Tille wrote:
Hi Rebecca
and whoever might care. As usual snakemake is troublesome to upgrade.
I have injected the latest version into Git but there are lots of
failed tests. It would be great if someone could care about this.
Looking at the log, many failures see
On 10/15/21 9:27 PM, Andreas Tille wrote:
Hi Flavien,
Am Fri, Oct 15, 2021 at 09:46:46AM +0200 schrieb Flavien Bridault:
Cmake 21 reached testing, so that's all clear for me. You may upload the new
version of the package.
I'm afraid you have installed some Build-Depends on your testing system
Hi,
The new version of fastp B-D on libisal-dev, whick is available only on amd64,
arm64 and kfreebsd-amd64
Due to this, fastp is no longer able to build on archs it was able to build on,
earlier.
And as a direct consequence, testing migration is stalled.
I am not sure of the best way to proc
On 10/16/21 12:08 PM, Andrius Merkys wrote:
Hi Nilesh,
On 2021-10-16 08:54, Nilesh Patra wrote:
The new version of fastp B-D on libisal-dev, whick is available only on
amd64, arm64 and kfreebsd-amd64
Due to this, fastp is no longer able to build on archs it was able to
build on, earlier.
And
On 10/16/21 12:39 PM, Nilesh Patra wrote:
The intuitive solution to me seems to make libisal-dev build on the
remaining architectures. Do you know why it is limited to amd64, arm64
and kfreebsd-amd64?
I am not aware. But the library looks specifically for processors with intel
support
Hi Thomas,
On 10/16/21 4:07 PM, Graham Inggs wrote:
Hi,
Did you look into the source package? isal is written in assembly
language...
I see at least an erasure_code/ppc64le directory.
I did a quick test build in Ubuntu and the package built and passed
its tests on armhf, ppc64el and riscv64,
On 10/18/21 12:13 AM, Rebecca N. Palmer wrote:
On 15/10/2021 14:46, Andreas Tille wrote:
Hi Rebecca
and whoever might care. As usual snakemake is troublesome to upgrade.
I have injected the latest version into Git but there are lots of
failed tests. It would be great if someone could care abo
Hi Steffen,
On Mon, 18 Oct 2021 at 01:06, Steffen Möller wrote:
>
> On 17.10.21 21:19, Nilesh Patra wrote:
>
> Yeah, snakemake has now moved to pulp 2.0. pulp had another rev-dep on
> congress which is now removed from archive.
> pulp is maintained in openstack, and I sent ou
Hi Steffen,
On Mon, 18 Oct 2021 at 01:41, Steffen Möller wrote:
>
> On 17.10.21 21:39, Nilesh Patra wrote:
>
> Hi Steffen,
>
> On Mon, 18 Oct 2021 at 01:06, Steffen Möller
> wrote:
>
>>
>> On 17.10.21 21:19, Nilesh Patra wrote:
>>
>> Yeah, snake
On Mon, Oct 18, 2021 at 01:32:30AM +0200, Steffen Möller wrote:
> Hi Nilesh,
> Uploaded.
Thanks a lot, but,
You seemed to have done a binary upload, I now did a source-only so it migrates.
I also took the liberty to add myself to uploaders, since this is a LP based
package,
which I would be inter
On Tue, 19 Oct, 2021, 8:15 pm olivier sallou,
wrote:
> On Mon, 2021-10-18 at 12:30 +0200, Andreas Tille wrote:
> > Hi,
> >
> > I wanted to update python-biom-format, but the build time test ends
> > up in
> >
> >
> > FAILED
> > biom/tests/test_table.py::TableTests::test_from_hdf5_custom_parsers -
On Tue, 19 Oct 2021 at 22:37, Andreas Tille wrote:
> > I wonder if it's a problem with the the version of h5py in the archive?
> > Because these seem to run fine upstream.
> >
> > Might be worth raising this problem upstream?
>
> Its worth trying IMHO. Would you volunteer to do so?
>
https://gi
On 10/20/21 12:40 AM, Steffen Möller wrote:
Update follows. There is an uninstallable file in the tests folders. I
am now separating -tests and -doc.
Thanks, but that'd go a trip to NEW. It'd be nice if you can fix it in the
single-source
package only, for now. -- So as to not stall migration.
On Wed, 20 Oct 2021 at 00:57, Steffen Möller wrote:
>
> On 19.10.21 21:12, Nilesh Patra wrote:
> > On 10/20/21 12:40 AM, Steffen Möller wrote:
> >> Update follows. There is an uninstallable file in the tests folders. I
> >> am now separating -tests and -doc.
> &
On Wed, 20 Oct 2021 at 03:32, Steffen Möller wrote:
> I just ran into this. Will package this with the Python team now.
>
Cool, meanwhile I hacked around, and got it to work somehow,
if you could please do a review and upload, that'd be great!
We can remove the hack when the new package connect
On 20 October 2021 6:26:29 am IST, "Steffen Möller"
wrote:
>Snakemake is working for me with python3-connection-pool installed, so I
>have uploaded.
>
>Best,
>
>Steffen
I had uploaded with my hack, and autopkgtests work in salsa CI.
I think we simply revert the hack when we have connection po
Package: wnpp
Severity: normal
X-Debbugs-Cc: debian-med@lists.debian.org
Hi,
I currently have no interest in maintaining unifrac, which
is a bit cumbersome to maintain (the new update being an example)
and it doesn't motivate me enough to keep maintaining it.
Should you feel motivated, feel free
On Wed, 03 Mar 2021 16:11:37 + Matthias Klose wrote:
BRNN/RNNs/Options.h:69:5: error: ISO C++17 does not allow dynamic exception
specifications
69 | throw(BadOptionSetting);
| ^
BRNN/RNNs/Options.h:143:5: error: ISO C++17 does not allow dynamic exception
specifications
1
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