On Sat, Apr 02, 2022 at 11:16:07PM +, Mohd Bilal wrote:
> Hello team,
>
> I've added autopkgtest for the package intake[1]. I've opened an MR[2] and
> would like someone to review my changes. I would also require sponsoring for
> my changes.
Uploaded, thanks for your work!
I did a minor cha
On Mon, Apr 04, 2022 at 04:58:53PM -, Mohd Bilal wrote:
> I would like to add autopkgtest for atropos[1] but I'm stuck with some .pyx
> files that the tests import from.
> I guess the tests require these C extensions to be built before running the
> test. I've tried building[2] the extensions
On Mon, Apr 04, 2022 at 08:16:07PM +0200, Andreas Tille wrote:
> In general I'd recommend to follow the packaging example of our team:
>
>
> https://salsa.debian.org/med-team/community/package_template/-/tree/master/debian/tests
Yes, the template is very helpful. But it should not be used wh
On Thu, Apr 07, 2022 at 10:37:24PM +0200, Andreas Tille wrote:
> Am Thu, Apr 07, 2022 at 06:52:47PM - schrieb Mohd Bilal:
> > I've enabled salsa ci and added autopkgtest for python-bioblend[1] .
> > Requesting someone to review and sponsor my changes.
>
> Looks good - uploaded.
I did an uplo
On Wed, Apr 13, 2022 at 09:49:35AM +0200, Andreas Tille wrote:
> Hi,
>
> if I remember correctly pyqi was packaged for qiime 1.x.
> It has no rdepends any more and I think we should remove it.
I got a few spare minutes so I fixed the RC bug.
> Does anybody think differently?
It is always good t
On 26 April 2022 1:16:06 pm IST, Andreas Tille wrote:
>Hi Xian,
>
>Am Tue, Apr 26, 2022 at 10:51:58AM +0800 schrieb 吴限:
>> I am Xian Wu, a senior student trying to find some challenging work to
>> prepare for my future graduate study.
Thanks for considering/contacting us!
>> Recently, I notic
Hi Xian,
On 29 April 2022 7:48:56 pm IST, "吴限" wrote:
>Hi, Nilesh!
>Thanks for your reply!
>I am willing to try my best to contribute my efforts to your packages. And
>yes, I think I may need some help about what to read and how to start.
Sure, I had given a sort of summary in this mail[1] a
Hi all,
I hereby welcome Mohammed Bilal for
the GSoC project
"Quality Assurance for Biological and Medical Applications inside Debian"
Congrats Bilal, I hope to have fun mentoring you on this project.
Feel free to ask any questions on the list.
--
Best,
Nilesh
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Hi and thanks for this
On Tue, May 24, 2022 at 12:01:22AM +0530, Mohd Bilal wrote:
> I've added autopkgtests for openslide[1]. Requesting someone to review and
> sponsor my changes.
Looks good, but have you created the image on your own - as you added
yourself as copyr holder[2]?
If not so, plea
[ CCing list again ]
On Tue, May 24, 2022 at 12:26:54AM +0530, Mohd Bilal wrote:
> On 5/24/22 00:17, Nilesh Patra wrote:
> > On Tue, May 24, 2022 at 12:01:22AM +0530, Mohd Bilal wrote:
> > > I've added autopkgtests for openslide[1]. Requesting someone to review and
&
On Tue, May 24, 2022 at 12:36:36AM +0530, Mohd Bilal wrote:
> I've updated the copyright as suggested.
Uploaded.
--
Best,
Nilesh
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Hi Martin,
On Sun, May 29, 2022 at 04:41:41PM +0900, Frith, Martin wrote:
> I hope it's ok for me to suggest packaging some of my software
That is very welcome. We also have LAST in our archive which you
authored.
> https://github.com/mcfrith/dnarrange
> https://gitlab.com/mcfrith/lamassemble
I
On Tue, May 31, 2022 at 10:10:45PM +0530, Mohd Bilal wrote:
> I've added autopkgtests for nifticlib[1]. Requesting someone to review
> and sponsor my changes.
Permissions granted, please wait for the mail to arrive.
Also, disable reprotest in salsa-ci before you upload.
$ dcut dm --uid mdbi...@di
On Thu, Jun 02, 2022 at 10:57:26PM +0530, Mohd Bilal wrote:
> Thanks for the pointer ! I tried removing the usage of '__DATE__' via a
> patch
I think this is not right. Either also remove printing the last %s, so it
doesn't output any compilation date. Or properly subsitute compilation
date via SO
On Fri, Jun 03, 2022 at 10:33:27PM +0200, Étienne Mollier wrote:
> Please mark the package ready to upload to "unstable" instead of
> the current "UNRELEASED" in the d/changelog when you consider
> the package ready for upload, and I (or anyone beating me at
> it :) will upload that for you.
I jus
On Tue, Jun 07, 2022 at 10:31:23AM +0300, Andrius Merkys wrote:
> > This is perfectly in line with the request of ftpmaster to keep the
> > debian/ dir "sensibly" small and I'm pretty sure ftpmaster would have
> > been rejected the package if the data[...]
> To me this looks like an intricate evas
On Wed, Jun 08, 2022 at 05:26:18PM +0530, Mohd Bilal wrote:
> The upstream responded[1] to my query regarding the license of busco
> datasets. Looks like it uses a non-free license (CC-BY-ND-4.0).
Aw, crap!
> So I think adding this test data would make the package non-free. Seeking
> everyone's o
On Thu, Jun 09, 2022 at 06:34:20PM +0300, Andrius Merkys wrote:
> Interesting. I maintain a package with ~80 MBs in debian/. But again,
> maybe I will get a REJECT next time it has to clear NEW. It would be
> nice to have a rule of thumb to implement in lintian, but from [5] I
> gather this is not
Hi,
I have noticed that I am maintaining a number of packages inside
debian-med team i.e. mentioned in "Uploaders" field.
I feel that I do not have much of a personal interest in majority of
those packages (I am not a bioinformatic person) and I simply lack the bandwidth
to do timely maintainence
On 6/29/22 12:18 PM, Mathieu Malaterre wrote:
Hi there,
It turns out there are three CVEs associated with DCMTK version older
than 3.6.7.
*
https://www.hipaajournal.com/warning-issued-about-3-high-severity-vulnerabilities-in-offis-dicom-software/
Should we get in touch with debian-security to
On 6/29/22 3:27 PM, Mathieu Malaterre wrote:
On Wed, Jun 29, 2022 at 11:51 AM Nilesh Patra wrote:
On 6/29/22 12:18 PM, Mathieu Malaterre wrote:
Hi there,
It turns out there are three CVEs associated with DCMTK version older
than 3.6.7.
*
https://www.hipaajournal.com/warning-issued-about-3
On 7/4/22 5:28 PM, Mohd Bilal wrote:
Hello team,
I've added autopkgtest for biomaj3-cli[1]
Unfortunately that is not an autopkgtest, only a smoke test (which does nothing
more than an `import`)
Can you add in a proper test for it?
and gdcm[2]. Requesting someone to review and sponsor these
On 6/30/22 3:21 PM, Andreas Tille wrote:
Hi,
I'd like to point out to this serious bug. Steffen, would you mind
koordinating (not doing alone) an upgrade of the qiime infrastructure to
make sure everything will go smoothly?
This is breaking other stuff as well, IMHO this should be done soonish
On 7/7/22 2:14 PM, Mohd Bilal wrote:
On 7/4/22 19:54, Nilesh Patra wrote:
Unfortunately that is not an autopkgtest, only a smoke test (which does nothing
more than an `import`)
Can you add in a proper test for it?
Sorry. I added the smoke test by looking at other biomaj packages. I&#x
Package: ftp.debian.org
Severity: normal
X-Debbugs-Cc: debian-med@lists.debian.org
Hi,
nanopolish recently started depending on snow5lib which inturn depends
on streamvbyte.
streamvbyte does not build on s390x and so doesn't nanopolish.
nanopolish has virtually 0 users on s390x and hence I reque
Hi again,
On Sun, May 29, 2022 at 10:10:14PM +0900, Frith, Martin wrote:
> Wow, amazingly fast!!!
lamassemble fails its tests on i386 (see here[1]) -- could you fix accordingly?
[1]:
https://ci.debian.net/data/autopkgtest/testing/i386/l/lamassemble/22546451/log.gz
--
Best,
Nilesh
signature.
On Mon, Jul 11, 2022 at 03:41:41PM +0900, Frith, Martin wrote:
> Do any of lamassemble's dependencies (e.g. mafft) fail tests?
No.
Neither mafft, nor last-align, links here[1,2]
[1]: https://ci.debian.net/packages/m/mafft/unstable/i386/
[2]: https://ci.debian.net/packages/l/last-align/unstable/i3
On 7/11/22 12:26 PM, Frith, Martin wrote:
Sorry I lack experience with this, so I have some questions...
No prob.
Were the tests passing before? Was there a specific update after which they
failed?
They were always failing on version 1.4.2 which is the only version I had every
uploaded.
Hi Martin and Katoh,
On Mon, Jul 11, 2022 at 06:40:51PM +0900, Frith, Martin wrote:
> Dear Nilesh and Debian Med
> (cc MAFFT author Katohさん)
>
> I have partly tracked down this lamassemble issue. First, I tested
> lamassemble on x86_64: the tests passed as expected. Then, I recompiled
> MAFFT aft
On 7/11/22 6:14 PM, Frith, Martin wrote:
Hi Nilesh,
after some searching and experimentation, I think `-ffloat-store` doesn't
always solve this floating point issue.
But this seems to solve it: `-msse2 -mfpmath=sse`.
Unfortunately I can't use these as it would violate i386 baseline that debia
On Mon, Jul 11, 2022 at 10:54:45PM +0530, Mohd Bilal wrote:
> Hello team,
>
> I have added autopkgtests for megadepth[1]. Requesting someone to review and
> sponsor my changes.
Good!
Thanks, uploaded. However please take in a look at my second-last commit, helps
package get cross-building. In thi
On Thu, Jul 14, 2022 at 08:04:10PM +0530, Mohd Bilal wrote:
> I've added autopkgtests for rockhopper[1]. The piuparts currently fails due
> to an issue with the pipeline[2] and had no problems when tested locally.
> Requesting someone to review and sponsor my changes.
Perfect.
Uploaded. Thanks, Bi
Hi,
I think at this point we *really* need to update qiime and friends. I am finding
it hard to keep q2cli 'limping' by cherry-picking changes from upstream.
If no-one volunteers, I will update qiime and q2-* in coming days/weeks.
On Sat, 16 Jul 2022 15:54:59 +0200 Lucas Nussbaum wrote:
> Sou
On 7/20/22 1:37 PM, Andreas Tille wrote:
Control: forwarded -1 https://github.com/PLAST-software/plast-library/issues/11
Control: tags -1 upstream
Control: tags -1 help
Am Tue, Jul 19, 2022 at 04:58:12PM + schrieb Matthias Klose:
Please try to fix the build with lto enabled, fixing the pack
On 7/20/22 1:27 PM, Mohd Bilal wrote:
Hello team,
I've added autopkgtests for emmax[1].Requesting someone to review and sponsor
my changes.
[1] - https://salsa.debian.org/med-team/emmax
Uploaded with minor nitpick, thanks Bilal.
--
Regards,
Nilesh
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On 7/20/22 2:34 PM, Andreas Tille wrote:
Am Wed, Jul 20, 2022 at 02:16:00PM +0530 schrieb Nilesh Patra:
I suppose it would be okay to wait to fix this bug, after we reach a concensus.
There are several packages that are breaking.
I admit I'm not specifically keen on fixing this actual
Hi Mattia,
On 7/20/22 7:52 PM, Mattia Rizzolo wrote:
On Wed, Jul 20, 2022 at 02:16:00PM +0530, Nilesh Patra wrote:
There is an ongoing discussion on -devel to not enable lto by default.
I suppose it would be okay to wait to fix this bug, after we reach a
concensus. There are several packages
On 7/24/22 12:55 PM, Étienne Mollier wrote:
* Is it still worth testing/fixing truspades, given that
getting it sorted does not look very obvious on first sight,
or should I just comment out truspades self-test in the
autopkgtest?
If it is unsupported then it probably isn't wo
On 7/26/22 5:38 PM, Pierre Gruet wrote:
Hi Andreas,
Le 26/07/2022 à 13:50, Andreas Tille a écrit :
Hi,
from my perspective the CMakeLists.txt of tiddit has not changed compared
to the last upstream version. Unfortunately the build fails[1] with
CMake Error at CMakeLists.txt:42 (add_execu
On 7/26/22 6:26 PM, Andreas Tille wrote:
Am Tue, Jul 26, 2022 at 06:19:38PM +0530 schrieb Nilesh Patra:
@Andreas, I suppose you will have to build it the pybuild-way now. Autopkgtests
will anyway help us verify
whether we are good :)
Right. Our quite good autopkgtest coverage helps a lot
Package: ftp.debian.org
Severity: normal
X-Debbugs-Cc: debian-med@lists.debian.org
Hi,
In recent upload of tiddit (new upstream release) it has started to depend on
python3-pysam.
python3-pysam is unavailable on s390x because of its dep bcftools not being
supported on the same arch.
Now, this is
Hi Andrius,
On Wed, 8 Jun 2022 08:59:13 +0300 Andrius Merkys wrote:
> Hello,
>
> rdflib will attempt to resolve any URL in @context in POSTed JSON-LD
> messages, leading to various probing and DDoS vectors, see the upstream
> discussion [1].
>
> [1] https://github.com/RDFLib/rdflib/issues/1844
At the moment, bolt-lmm seems to build only for amd64, i386 and ppc
I was trying to port it. I am able to get it building on arm64 box, but it does
not seem to run the right way. It seems to trigger the bolt command again while
trying to
make initial guess - don't know why.
I've committed the pa
On 8/1/22 7:18 PM, Mohd Bilal wrote:
Hello team,
I've added autopkgtest for plastimatch[1].Requesting someone to review and
sponsor the same.
Add in a "skip-not-installable" restriction as well before you upload.
$ dcut dm --uid mdbi...@disroot.org --allow plastimatch
Uploading commands file
CCing Mathieu for help on this.
On 8/4/22 1:32 AM, Mohd Bilal wrote:
gdcm[1] had an autopkgtest regression on s390x[2] which was preventing its
migration to testing. This was possibly due to the test data being encoded for
little endian hardware based on my understanding. So I've changed the t
On 8/4/22 2:42 PM, Andreas Tille wrote:
Hi Mathieu,
Am Thu, Aug 04, 2022 at 08:32:56AM +0200 schrieb Mathieu Malaterre:
It seems that pdflatex is exiting with exit code 1.
However, the pdf is rendered just fine, when I tried to compile and open it.
I am seeing a bunch of warnings in refman.log
On 8/8/22 5:50 PM, Mohd Bilal wrote:
On Sat, 6 Aug 2022 15:45:55 +0200 Paul Gevers wrote:
Source: zalign
Version: 0.9.1-6
Severity: serious
User: debian...@lists.debian.org
Usertags: fails-always
Dear maintainer(s),
You recently added an autopkgtest to your package zalign, great. However, it
On 8/8/22 6:20 PM, Mohd Bilal wrote:
On 8/8/22 18:05, Nilesh Patra wrote:
On 8/8/22 5:50 PM, Mohd Bilal wrote:
Hello Team,
I took a look at this and it seems the upstream[1] is not active anymore and
Ubuntu already has a long standing bug report[2] regarding the same issue which
hasn&#
On Tue, Aug 23, 2022 at 12:16:50AM +0530, Mohd Bilal wrote:
> Hello team,
>
> I've added autopkgtest for nipype[1] and also fixed the reprotest
> failures.Requesting someone to review my changes and sponsor the same.
- Is it possible to run build time tests also as autopkgtests along with your
s
On Fri, Aug 26, 2022 at 08:25:22PM +0530, Mohd Bilal wrote:
> Hello team,
>
> I've added autopkgtests for emperor[1]. Requesting someone to review and
> sponsor my changes.
done.
> [1] - https://salsa.debian.org/med-team/emperor
--
Best,
Nilesh
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On 8/23/22 13:45, Mohd Bilal wrote:
On 8/23/22 00:39, Nilesh Patra wrote:
- Is it possible to run build time tests also as autopkgtests along with your
sample test?
If so, please do so.
- The indentation is inconsistent across `concat' and `test_basic' function,
please fix this
a
On Sun, Aug 28, 2022 at 11:04:13PM +0530, Mohd Bilal wrote:
> Hello team,
>
> I've added autopkgtest for python-wdlparse[1]. Requesting someone to review
> and sponsor my changes.
Rather than printing the ast, it'd be better to `assert' it equal to expected
output.
Please make this change before
On Mon, Aug 29, 2022 at 01:21:43PM +0200, Steffen Moeller wrote:
> Thorsten is right - the qiime package should be arch-independent. But
> how do we then get it to migrate to testing?
>
> https://tracker.debian.org/pkg/qiime
>
> Upstream does not want to have 32bit installations, so they introduc
On Mon, Aug 29, 2022 at 05:15:04PM +0530, Nilesh Patra wrote:
> On Mon, Aug 29, 2022 at 01:21:43PM +0200, Steffen Moeller wrote:
> > Thorsten is right - the qiime package should be arch-independent. But
> > how do we then get it to migrate to testing?
> >
> > https://t
On Mon, Aug 29, 2022 at 11:18:07PM +0530, Mohd Bilal wrote:
> On 8/28/22 23:14, Nilesh Patra wrote:
> > Rather than printing the ast, it'd be better to `assert' it equal to
> > expected output.
> > Please make this change before you upload.
> >
> > It&#
On Wed, Aug 31, 2022 at 05:59:27PM +0530, Mohd Bilal wrote:
> Hello team,
>
> I've added autopkgtest for libncl[1]. Requesting a review and sponsor for my
> changes.
Granted you DM access.
Also, for the libbigwig upload you did yesterday, the autopkgtest
is failing on some archs.
Can you fix it?
Hi,
Pinfish is working fine in the archive(no bugs), but upstream has abandoned
the development and marked the repo as read-only[1]
Since this does not look very important, is it ok to file a removal request?
I am not a user of the package, nor a bioinformatics guy, hence looking for
opinions
i
On Mon, Sep 05, 2022 at 11:26:43PM +0530, Mohd Bilal wrote:
> Hello team,
>
> I've added autopkgtest for tvc[1]. Requesting someone to review and sponsor
> my changes.
Please also add a "exit 1" after you echo FAIL[2] otherwise this is a no-op.
The autopkgtest will keep passing even if the file i
On 9/5/22 23:50, Mohd Bilal wrote:
Hello team,
I tried adding autopkgtest for kmerresistance[1] but I'm getting an error when
using the installed binary.
I'm not able to run the binary with example data[2] from the package installed
via apt
But I'm able to run the command as expected if I bu
On Wed, Sep 14, 2022 at 02:07:51PM +0200, Andreas Tille wrote:
> Am Sun, Sep 04, 2022 at 11:07:12PM +0530 schrieb Nilesh Patra:
> > I am not a user of the package, nor a bioinformatics guy, hence looking for
> > opinions
> > if this is useful.
>
> In case you a
Hi,
There are some packages listed under our team and science team namespace
as listed below (I snipped the rest of the dd_list)
Please consider to port them to new wxwidgets if you happen to
work on these packages in near future.
And otherwise, help welcome in porting these, as we need to fix th
On Wed, Sep 14, 2022 at 03:53:42PM +0200, Andreas Tille wrote:
> Am Wed, Sep 14, 2022 at 06:23:58PM +0530 schrieb Nilesh Patra:
> > But I also strongly belive in removing software that no-one is using. I
> > agree
> > that our packages usually have low popcon values, b
On 14 September 2022 8:31:23 pm IST, Mohd Bilal wrote:
>Hello team \o/ ,
>
>I'm Mohammed Bilal and I've been the GSoC intern working with the Debian Med
>Team during 2022 and the one who've been bugging this mailing list for the
>past few months. [...]
Thank you Bilal for all the work you've
Package: ftp.debian.org
Severity: normal
X-Debbugs-Cc: debian-med@lists.debian.org
Hi,
khmer has assembly code in third_party/cqf and can't build on !amd64.
The maintainer/uploader reflected that in 3.0.0~a3+dfsg-3 d/ch entry[1]
but probably did not file a corresponding -rm bug for !amd64 archs.
On Wed, Sep 28, 2022 at 01:00:28PM +0200, Mathieu Malaterre wrote:
> Is there a way to (quickly) run the autopkgtests for dcmtk ?
These docs with autopkgtest package should help on that:
/usr/share/doc/autopkgtest/README.virtualisation-server.html
/usr/share/doc/autopkgtest/README
On Wed, Sep 28, 2022 at 01:56:17PM +0200, Mathieu Malaterre wrote:
> On Wed, Sep 28, 2022 at 1:34 PM Nilesh Patra wrote:
> > Since you already uploaded this package, debci ran on it.
> > Here's the link
> >
> > https://ci.debian.net/packages/d/dcmtk/
>
Hi,
I don't know how to go about it, but I suspect -devel might be a better list
for this since this is a general question and many package maintainers could be
using bitbucket sources.
On 29 September 2022 12:54:47 pm IST, Andreas Tille wrote:
>Hi,
>
>the watch file for metabat[1] used to wor
On 30 September 2022 10:57:16 am IST, Andreas Tille wrote:
>Am Thu, Sep 29, 2022 at 05:41:52PM -0400 schrieb Aaron M. Ucko:
>> Étienne Mollier writes:
>>
>> > I believe in the case of anfo, that warnings about auto_ptr /
>> > unique_ptr are red herrings. If I search for "error:"s, then I
>>
On 30.09.2022 20:00, Andreas Tille wrote:
Hi,
[...]
Strangely enough the autopkgtest is failing[4] (which was not the case
in my
local build.) Could anybody have a look?
I have just pushed a fix, which hopefully should fix this. You might
want to re-upload.
BTW, I noticed that the SOVERSI
On Fri, Sep 30, 2022 at 09:52:55PM +0200, Andreas Tille wrote:
> Am Fri, Sep 30, 2022 at 02:46:38PM + schrieb Nilesh Patra:
> >
> > I have just pushed a fix, which hopefully should fix this. You might want to
> > re-upload.
>
> I can't do this before Tuesday.
Hi,
I am on a VAC right now but happened to see this.
On Tue, Oct 04, 2022 at 01:38:49PM +, John Marshall wrote:
> On 1 Oct 2022, at 07:21, Nilesh Patra wrote:
> > I have fixed a bunch of things with htscodecs and htslib, both
> > of which were not building on !amd64.
On Fri, Oct 07, 2022 at 03:18:36PM +0200, Andreas Tille wrote:
> > Please upload if it looks ok to you.
>
> Is there any reason to stick to gcc-10. I'm not sure when this
> GCC version will be removed - but sooner or later this will be
> the case.
Becasue nvcc (This is a non-free compiler by nv
On 10 October 2022 11:50:14 am IST, Andreas Tille wrote:
>> If no one gets to it, asking for removal is a sensible option. It otherwise
>> imho becomes another time sapping package that no one cares about much.
>
>There was no volunteer to pick up the gcc-12 port of this package. So
>it seems
Hi,
On Thu, Oct 06, 2022 at 01:59:23AM +, John Marshall wrote:
> On 4 Oct 2022, at 15:31, Nilesh Patra wrote:
> > The thing that was causing failures on !amd64 was that there were amd64
> > specific symbols in debian/libhtscodecs2.symbols that were not matching on
> &g
Hi James,
On Wed, Oct 12, 2022 at 09:47:04AM +0100, James Bonfield wrote:
> On Wed, Oct 12, 2022 at 01:30:40AM +0530, Nilesh Patra wrote:
> > On Thu, Oct 06, 2022 at 01:59:23AM +, John Marshall wrote:
> > > If you omitted these internal symbols, there would be no problem
Hello,
On Mon, Oct 24, 2022 at 08:39:33PM +0200, Martin Uecker wrote:
>
> Hi Andreas and all,
>
> I updated the package and turned off some unit tests on
> i386 for now (and turned on other tests and made some
> other changes).
>
> If you or somebody else could sponser an upload, this
> would b
On Mon, Oct 24, 2022 at 09:20:21PM +0200, Martin Uecker wrote:
> Am Dienstag, den 25.10.2022, 00:41 +0530 schrieb Nilesh Patra:
> > Hello,
> >
> > On Mon, Oct 24, 2022 at 08:39:33PM +0200, Martin Uecker wrote:
> > > Hi Andreas and all,
> > >
> > >
On Tue, Oct 25, 2022 at 09:36:33AM +0200, Andreas Tille wrote:
> Hi,
>
> the new version of nthash needs btllib which was luckily accepted very
> quickly by ftpmaster. Now I "just" need to declare in CMakeLists.txt
> that the Debian packaged btllib should be used and as usually I failed
> in doin
On Tue, Oct 25, 2022 at 12:07:46PM +0200, Andreas Tille wrote:
> Hi Nilesh,
>
> Am Tue, Oct 25, 2022 at 02:49:25PM +0530 schrieb Nilesh Patra:
> > On Tue, Oct 25, 2022 at 09:36:33AM +0200, Andreas Tille wrote:
> > > Hi,
> > >
> > > the new versio
On Wed, Oct 26, 2022 at 11:56:28AM +0200, Martin Uecker wrote:
> Thank you! It seems this is working correctly
> on all archs.
>
> I also finalized the bart-view update. Can
> you upload it as well?
I had done so, thanks!
--
Best,
Nilesh
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On Thu, Oct 27, 2022 at 11:37:39AM +0200, Andreas Tille wrote:
> Hi Andrius,
>
> Am Thu, Oct 27, 2022 at 12:00:59PM +0300 schrieb Andrius Merkys:
> > I have just pushed a fix. Please check if that works for you as well.
>
> Hmmm, this results in
I pushed something via which I get:
| uscan info:
Hi,
I suppose sprints in 2021 and 2022 have been virtual so far due to COVID.
There were some COVID related sprints in 2020 as well.
Is there a possibilty to have an in-person debian-med sprint in 2023?
Would someone be interested in it, or so?
Thanks!
--
Best,
Nilesh
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Package: ftp.debian.org
Severity: normal
X-Debbugs-Cc: debian-med@lists.debian.org
Hi,
libnthash-dev binary package from src:nthash has changed its arch
from all to any, because it now also ships a static lib along with
it, hence please remove the arch:all binary for this binary package.
Thanks!
Package: ftp.debian.org
Severity: normal
X-Debbugs-Cc: debian-med@lists.debian.org
Hi,
nthash has recently started to build-depend on btllib, which is
not supported on 32-bit and probably on big-endian systems as well.
The upstream has also confirmed the same:
https://github.com/bcgsc/b
On Fri, Nov 04, 2022 at 11:08:05PM +0100, Andreas Tille wrote:
> I injected the new version of kalign into Git. Unfortunately the file
> layout has changed and the files that were patched in the currently
> packaged version do not exist any more[1]. It would be great if you
> could update the pat
On Sun, Nov 06, 2022 at 04:12:18AM +0530, Nilesh Patra wrote:
> On Fri, Nov 04, 2022 at 11:08:05PM +0100, Andreas Tille wrote:
> > I injected the new version of kalign into Git. Unfortunately the file
> > layout has changed and the files that were patched in the currently
> >
On Fri, Nov 04, 2022 at 10:23:25PM +0100, Andreas Tille wrote:
> Hi,
>
> I tried to update the Debian package of proteinortho to 6.1.2 but I'm running
> into a failure:
> [...]
This was an issue w/ building in parallel. I have fixed it, but the last test in
autopkgtest does not work, which tries
On Sun, Nov 06, 2022 at 03:45:30PM +0530, Nilesh Patra wrote:
> On Fri, Nov 04, 2022 at 10:23:25PM +0100, Andreas Tille wrote:
> > Hi,
> >
> > I tried to update the Debian package of proteinortho to 6.1.2 but I'm
> > running
> > into a failure:
> >
On 6 November 2022 7:44:45 pm IST, Nilesh Patra wrote:
>On Sun, Nov 06, 2022 at 03:45:30PM +0530, Nilesh Patra wrote:
>> On Fri, Nov 04, 2022 at 10:23:25PM +0100, Andreas Tille wrote:
>> > Hi,
>> >
>> > I tried to update the Debian package of protein
On Wed, Nov 16, 2022 at 11:25:02AM +0100, Andreas Tille wrote:
> Am Tue, Nov 15, 2022 at 09:16:53PM +0100 schrieb Paul Gevers:
> > 2022/11/15 09:16:56 Cannot find the mcxdeblast executable, please ensure its
> > in your PATH
The error is here ^^^
mcl has stopped vendoring mxcdeblast since your las
On Wed, Nov 16, 2022 at 05:30:21PM +0530, Nilesh Patra wrote:
> On Wed, Nov 16, 2022 at 11:25:02AM +0100, Andreas Tille wrote:
> > Am Tue, Nov 15, 2022 at 09:16:53PM +0100 schrieb Paul Gevers:
> > > 2022/11/15 09:16:56 Cannot find the mcxdeblast executable, please ensure
>
On 11/16/22 18:30, Andreas Tille wrote:
Control: tags -1 pending
Am Wed, Nov 16, 2022 at 05:35:12PM +0530 schrieb Nilesh Patra:
$ debdiff mcl_14-137+ds-9.dsc mcl_22-282+ds-1.dsc 2>/dev/null | wc -l
51040
That's quite a lot of lines. Something definitely changed.
And I found out what
On Thu, Nov 17, 2022 at 10:19:46PM +0100, Étienne Mollier wrote:
> Maarten L. Hekkelman, on 2022-11-17:
> > Looking for an appropriate name I inadvertently created a project on salsa
> > called libcfg. That clashes with a package already in Debian and I'm not
> > allowed to remove that repository a
On Fri, Nov 18, 2022 at 10:27:43PM +0100, Étienne Mollier wrote:
> Hi Greg,
>
> Gregory Sharp, on 2022-11-18:
> > Thank you, you are correct! Yahoo blocked your direct e-mail, but it also
> > blocked the one from debian-med which is not good.
>
> Things that happen I guess. For what it's worth
On Wed, Nov 23, 2022 at 09:01:40PM +0100, Andreas Tille wrote:
> python-cobra
It seems like that the interpreter is having trouble referencing the
name variable. I tried using getName instead of that which gets the
test passing but I'm not very sure if it serves the purpose well.
Pushed this chan
On Fri, Nov 25, 2022 at 06:04:29PM +0100, Andreas Tille wrote:
> Hi,
>
> I upgraded rampler to the latest upstream version. CMakeLists.txt
> has changed and I'm not sure whether I've properly adjusted the
> patch. I thinks the error message
>
> CMake Error in CMakeLists.txt:
> Imported target
Source: python-biopython
Version: 1.79+dfsg-3
Severity: serious
X-Debbugs-Cc: debian-med@lists.debian.org
Control: block 1024855 by -1
Control: block 1024858 by -1
Hi,
biopython in unstable does not vendor bindings for python3.11, due to which
augur and busco fail their autopkgtest.
Thanks,
Nile
On Tue, Nov 29, 2022 at 08:23:59PM +0100, Andreas Tille wrote:
> Hi,
Hi,
> I tried to upgrade spoa but the build[1] fails with
> [...]
> Any idea what might be wrong here would be great.
I did get this rolling past that point but now the build fails due to
d-shlibs, which I am not very familiar
On 1 December 2022 12:54:07 pm IST, Andreas Tille wrote:
>Hi folks,
>
>just to give an example of announcing a squashed bug here. ;-)
I wonder if it could be nice to make a wiki page instead and add in bugs there
date-wise if hosting the calendar isn't a possibility?
I'm ok with announcing o
Hi,
There are a bunch of LTO based bugs that have been filed. The packages
that had "real" issues (as in with the code) with LTO have been fixed.
Now most of what is left is changes in symbols, which fails with
dpkg-gensymbols,
which is just a change with compiler opt, and likely nothing more
an
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