Hi Mo,
On 2023-09-09 22:29, M. Zhou wrote:
I'm writing down my draft design for dh_pytorch here in order to hear
some comments or feedbacks. If you maintain a package that depends
on python3-torch or relevant pytorch packages, please let me have
your attention.
I maintain a pair of pytorch
Hi Kingsley,
On 2023-06-25 00:48, Kingsley G. Morse Jr. wrote:
You politely proposed using download date as
version for CCD.
You're smart.
Maybe you already know this, but Debian's Policy
Manual has a sub-sub-section called
"3.2.1. Version numbers based on dates"
If you haven't checked
Hi Maarten,
On 2023-06-23 20:22, Maarten L. Hekkelman wrote:
Although I agree that having an up-to-date CCD file is useful. And
having it installed by the system would even be better. But I wonder,
who is going to make new packages with the latest CCD file? That's a
task that needs to be
Hi Kingsley,
Thank you for your comments.
On 2023-06-23 10:17, Kingsley G. Morse Jr. wrote:
You politely and confidently invited comments.
1.) Thanks!
2.) I like your use of the concise "TL;DR" (ie:
"Too Long; Don't Read").
3.) Sometimes I shorten it even more, to "TLDR".
Thanks for
Hello,
TL;DR: I propose packaging frequently updated PDB Chemical Component
Dictionary. Reasons, technical solutions and limitations below.
PDB Chemical Component Dictionary (CCD) [1] is a single file (~400 MB
uncompressed) collection of small molecule components found in PDB
entries. It is
Hello,
On 2023-01-14 13:12, Rebecca N. Palmer wrote:
theano has been mostly abandoned upstream since 2018. (The Aesara fork
is not abandoned, but includes interface changes including the import
name, so would break reverse dependencies not specifically altered for it.)
Its reverse
Hi Andreas,
On 2022-06-18 15:42, Andreas Tille wrote:
> Is there some kind of "porting to latest tbb FAQ"? For instance I
> wonder how to fix issues like in twopaco[1] or the other bugs files
> against several packages. I personally have no idea how to deal
> about tbb and I'm wondering if
Hi Nilson,
On 2022-06-07 22:11, Nilson Silva wrote:
> I would like to know when the team will upload the new version of TBB to
> the debian repositories.
As Mo wrote, you may find onetbb/2021.5.0-9 in experimental. Transition
experimental -> unstable is in planning now, you may monitor the
Hi,
On 2022-04-28 13:12, Stephen Sinclair wrote:
> The last time I looked at Keras, there were some hard to fix issues
> and since it is my understanding that keras as a package outside of
> Tensorflow has reached end of life, it does not seem useful to try to
> maintain it.
At first glance
Hi Andreas,
On Wed, 27 Apr 2022, 16:48 Andreas Tille, wrote:
> seems Stephen is not active. If I where you I'd push the uploaded state
> to Git and upload the latest upstream version.
>
Thanks for suggestion - I will take care of keras then.
Best,
Andrius
>
Hello,
keras has recently dropped out of testing due to two RC bugs [1]. Both
of them seem quite easy to fix. However, repository on Salsa lacks
commits and tag for 2.3.1+dfsg-3. Stephen, could you please push them in
order to have up-to-date history on Salsa?
Moreover, newer upstream releases
Hi all,
Sorry I cannot keep up with all the developments. I have no idea how
shiny-server work, thus I would not be much of a help here, but I think
it is in good hands now :)
Replying only to Eric's summary of nodejs dependencies.
On 2022-03-27 06:20, Eric Brown wrote:
> So in summary, I think
Hi Nilesh,
On 2022-03-24 12:03, Nilesh Patra wrote:
> On 3/24/22 3:09 PM, Nilesh Patra wrote:
>> I figured out the problem. It is so because the debian package
>> node-send is patched[1]
>> to use node-mime-types instead of node-mime (not sure why)
>>
>> I just filed a bug report (with you in
Hi Nilesh,
On 2022-03-24 10:04, Nilesh Patra wrote:
> On Thu, Mar 24, 2022 at 08:41:01AM +0200, Andrius Merkys wrote:
>> Looking deeper into it, the problem seems to be that node-mime-types has
>> dropped define() in v2.0.0, as per
>> /usr/share/doc/node-mime-types/HISTO
Hi Nilesh,
On 2022-03-24 00:25, Nilesh Patra wrote:
> I uploaded rewire to NEW. On testing locally with rewire, I get:
>
> | TypeError: send.mime.define is not a function
> |at Object.
> (/home/nilesh/packages/shinyserv/shiny-server/lib/router/directory-router.js:27:11)
> |at
Hi Eric,
On 2022-03-23 16:25, Eric Brown wrote:
> Thank you Andrius, Andreas et al. for your work in getting
> node-sockjs-client in Debian testing. It appears that shiny-server
> (https://salsa.debian.org/science-team/shiny-server) may now have just
> one dependency left - node-rewire, which I'm
Hi Eric,
On 2022-02-27 22:36, Eric Brown wrote:
> Likewise, thank you very much! It’s exciting that the dependencies for
> shiny-server are coming together. Please note the upstream for
> sockjs-client responded to me and released 1.6.0 which also updates some
> other dependency versions.
You
Hello,
Replying to Nilesh and Andreas in the same mail.
On 2022-02-25 07:49, Andreas Tille wrote:
> Am Fri, Feb 25, 2022 at 03:09:36AM +0530 schrieb Nilesh Patra:
>>> Sure. It would be nice to get ACK from Pirate, though, as he owns the ITP.
>> I am a bit confused, why would you need ack from
On Thu, 24 Feb 2022, 22:21 Andreas Tille, wrote:
> Am Wed, Feb 23, 2022 at 06:10:24PM +0200 schrieb Andrius Merkys:
> > >
> https://github.com/sockjs/sockjs-client/commit/d9584abe2c7c913ce95a1aea29e5744dd85e1af4
> > > <
> https://github.c
Hi Eric,
On 2022-02-22 14:52, Eric Brown wrote:
> If I’m understanding the below correctly, it appears that the node-json3
> may already have been removed from the dependency socksjs-client, but
> the updated version is not released yet.
>
>
Hi Eric,
On 2022-02-22 14:52, Eric Brown wrote:
> If I’m understanding the below correctly, it appears that the node-json3
> may already have been removed from the dependency socksjs-client, but
> the updated version is not released yet.
>
>
Hi Eric,
On 2022-02-22 06:43, Eric Brown wrote:
> It appears that significant progress has been made in packaging the
> dependencies of shiny-server. I wonder if anyone is interested and
> able to revisit packaging shiny-server?
In past I have worked to package the dependencies of shiny-server.
Hello,
On 2022-02-09 20:28, Nilesh Patra wrote:
> $ reverse-depends libmmdb2-dev
> Reverse-Depends
> * libclipper-dev
> * libssm-dev
>
> $ reverse-depends libmmdb2-dev -b
> Reverse-Build-Depends
> * clipper
> * libccp4
> * molmodel
> * ssm
I have checked with ratt, all these build fine. Thus I
Hi Maarten,
On Wed, 9 Feb 2022, 18:26 Maarten L. Hekkelman,
wrote:
> Since you are the one who uploaded mmdb2 last: I've updated the package
> to include the latest version and committed that to salsa. But I believe
> I cannot upload this package so now I'm looking at you. (Or someone else
> in
On 2022-01-12 17:34, Gard Spreemann wrote:
> Andrius Merkys writes:
>> On 2022-01-11 16:14, Gard Spreemann wrote:
>>> I'm taking the liberty to forward this to the debian-ai list as well.
>>
>> Thanks. Highly relevant issue for debian-ai@ might be the retraining
Hi,
On 2022-01-11 16:14, Gard Spreemann wrote:
> I'm taking the liberty to forward this to the debian-ai list as well.
Thanks. Highly relevant issue for debian-ai@ might be the retraining of
the neural network model. In addition to being pre-trained, the model
itself is licensed under
Hi,
On 2022-01-11 15:47, PICCA Frederic-Emmanuel wrote:
> I would like to know if you are aware of an effort to package alphafold[1] on
> Debian ?
Some time ago there was a thread on debian-med@ [2], but I do not recall
how did it end.
Moreover, I noticed some interest in compiling alphafold
Hi Nilesh,
On 2021-11-04 13:13, Nilesh Patra wrote:
> On Thu, Nov 04, 2021 at 11:48:45AM +0200, Andrius Merkys wrote:
>> Maybe separate mailing lists could be enough? In the end
>> upstreams mostly work on one-two source packages, and even if they
>> become DMs they d
Hi Ole,
On 2021-11-03 13:52, Ole Streicher wrote:
> Andrius Merkys writes:
>> problem: How would we define what is math software? What would be done
>> with interdisciplinary software? For example, I maintain two packages,
>> spglib and voronota, which deal with cryst
Hi Andreas,
On 2021-11-03 17:55, Andreas Tille wrote:
> Am Wed, Nov 03, 2021 at 01:26:34PM +0200 schrieb Andrius Merkys:
>>> No notes, Andreas came up with this idea in debconf, you could find it on
>>> videos.debian.net.
>>> But anyways, I have the following poin
very positive about).
>
> Am Sat, Oct 30, 2021 at 06:18:28PM +0530 schrieb Nilesh Patra:
>> Hi Andrius,
>>
>> Thanks for replying. See below :-
>>
>> On Sat, Oct 30, 2021 at 10:33:02AM +0300, Andrius Merkys wrote:
I am skipping most of your replies to Nile
Hi Nilesh,
On 2021-10-30 15:48, Nilesh Patra wrote:
Thanks for replying. See below :-
Thanks for answering my concerns, and sorry for the long silence.
On Sat, Oct 30, 2021 at 10:33:02AM +0300, Andrius Merkys wrote:
I agree with Anton here. I do not see how further fragmentation of
debian
On 2021-10-30 14:45, Anton Gladky wrote:
> I do not see any benefits from creating a one-more team. It decreases
> definitely bus-factor of the package, will unlikely increase their quality
> and for end-users it is mostly not visible, in what team it is maintained.
>
> Sure, feel free to create
Hi,
On 2021-10-29 20:31, Torrance, Douglas wrote:
> During the Debian Science BoF at this year's DebConf, there was some
> discussion of creating a team devoted to packaging mathematical software.
I agree with Anton here. I do not see how further fragmentation of
debian-science could benefit it.
Hi François,
On 2021-10-03 12:50, François Mazen wrote:
> I've just packaged the last version of ceres package and I've pushed it
> to the salsa repo [1], and to mentors [2].
>
> Could someone review the package? The tricky part may be the transition
> of the lib package from libceres1 to
Hi,
On 2021-05-12 15:49, Gard Spreemann wrote:
> It is my understanding that fields in d/u/metadata are meant to be
> case-insensitive (according to [1]). Yet, Lintian seems to complain
> about "Cite-as", but not "Cite-As". Is this a Lintian bug, or a
> documentation bug, or a me-bug?
The
Hi Markus,
On 2021-04-28 16:17, Markus Blatt wrote:
> I have recently posted an ITP (bug )for this software
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=987381
Thanks a lot an interesting ITP, and welcome to the team!
Just a couple of comments on points not addressed by Anton:
> - For
On 2021-03-10 02:38, George N. White III wrote:
> On Mon, 8 Mar 2021 at 12:36, Andrius Merkys <mailto:mer...@debian.org>> wrote:
> Many users will not look into e-mail addresses. They will search online
> using the name of the software, and will arrive at the same deve
Hi,
On 2021-03-08 15:44, Albert van der Horst wrote:
> I don't see the problem here. If there is a bug in an old version supplied
> with Debian, the bug report lands with Debian.
Not necessary. Many users cannot tell whether a bug is caused by
upstream code or Debian packaging. Many users do
On 2021-01-27 11:06, Andreas Tille wrote:
> In any case you should run `yamlling` on the result. I think there
> are also some lintian checks applied.
Indeed lintian does some checks:
$ grep debian/upstream/metadata -lR /usr/share/lintian/tags/
Hi Gard,
On 2021-01-23 12:01, Gard Spreemann wrote:
> I took a stab at it for one package. Does this seem sane?
>
> https://salsa.debian.org/gspr/hera/-/blob/2749a47cad5b1b25f4c5cd219db2db907bd4ddc7/debian/upstream/metadata
Seems OK to me. I am not aware of any validation tool for d/u/metadata,
Hi Gard,
On 2021-01-22 15:09, Gard Spreemann wrote:
> I've been meaning to add upstream's bibliography data to some of my
> packages. My understanding [1] is that this should be done through
> d/upstream files, but it is also my impression that DEP-12 has stalled a
> bit.
>
> What is the current
Hi Doug,
Yesterday I reviewed and uploaded your packaging of nauty 2.7r1+ds-1.
Thanks a lot for your work!
Best,
Andrius
On 2020-07-09 09:10, PICCA Frederic-Emmanuel wrote:
> done
Thanks!
Andrius
Hello,
Could someone with appropriate rights delete empty repository science-team/ete3
from salsa? This one has been named incorrectly, and was replaced with
med-team/python-ete3.
Thanks,
Andrius
On 2020-07-03 13:50, zhao feng wrote:
> Thanks for your help. I can build the package on buster and bullyseye.
> Which distribution do you use? I find the version of softwares like
> python is quite new.
The package fails to build on clean sid chroot. Most likely some Python
dependencies are
Hello,
On 2020-07-02 17:23, zhao feng wrote:
> ok, the warning has been fixed by 3.1.1-3
Thanks for fixing lintian issues. I have cloned your repository, tried
to build it, and ran into the following problem:
dh_auto_test -O--buildsystem=pybuild
pybuild --test -i python{version} -p
Hi,
I have tried building the package from the packaging repository on
salsa, however, 'upstream' and 'pristine-tar' branches are missing
there. Could you please push them with 'salsa push' or 'git push --all
&& git push --tags'?
On 2020-07-02 11:03, zhao feng wrote:
> feng@debian:~/ete$ lintian
Hello,
On 2020-06-30 11:56, zhao feng wrote:
> To access further information about this package, please visit the
> following URL:
>
> https://mentors.debian.net/package/ete
mentors.debian.net report lintian errors for this package. These have to
be addressed prior to sponsoring.
Best
Hi Pierre,
On 2020-04-26 12:39, Pierre Gruet wrote:
> Absolutely, the only non-Haskell reverse dependency is the binary bibutils.
> I have already filed a blocking bug, which I am going to raise to RC, and I
> will write to the list following your advice.
bibutils themselves should be fine.
Hi Pierre,
On 2020-04-25 15:53, Pierre Gruet wrote:
> The release team has just asked to go ahead after I submitted a transition
> bug [1]; I have prepared the upload to unstable in Salsa [2] (with
> UNRELEASED distribution), would you please mind uploading it, as you kindly
> offered?
Done.
Hi Pierre,
On Tue, 14 Apr 2020, 18:54 Pierre Gruet, wrote:
> Thanks a lot for reviewing my work, correcting this mistake and uploading
> the package to experimental!
>
Happy to help!
I will now wait for it to exit NEW and then launch the transition procedure.
Sure! Ping me when you need an
Hi Pierre,
On 2020-04-08 19:59, Pierre Gruet wrote:
> Some days ago I worked on the packaging of bibutils, which is maintained in
> the team. I had to bump the SONAME and therefore I ask for sponsorship to
> put it in *experimental* in order to begin a transition procedure, having
> identified
Hi Steffen,
On 2020-04-08 20:03, Steffen Möller wrote:
> My GPG key expired, could someone please source-only upload Rick's
> AMDGPU utils from
> https://salsa.debian.org/science-team/ricks-amdgpu-utils/ ? I have run
> it through cowbuilder.
Done.
Best,
Andrius
On 2019-04-25 16:45, Emmanuel Arias wrote:
> If you need work, meanwhile you can create your own repo.
> Then, when you have privileges you can transfer the repo.
Sure, thanks.
Andrius
--
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 V
ook declined)
error: failed to push some refs to
'g...@salsa.debian.org:science-team/coot-reference-structures.git'
Could I be promoted to Maintainer status? My Salsa login is 'merkys'.
Thanks,
Andrius
--
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
e to look into it. I'm
not common with bzr.
Best,
Andrius
--
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania
ius
--
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania
ces'
indication for it. Or do I miss something?
Best,
Andrius
--
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania
On 05/05/2018 12:44 PM, PICCA Frederic-Emmanuel wrote:
> Can you do this before the upload ?
Done. I hope I did it right. Debug symbols package descriptions now contain
correct Breaks and Replaces records.
Best,
Andrius
--
Andrius Merkys
Vilnius University Institute of Biotechnol
nd let me know should
anything fail.
Best,
Andrius
--
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania
-dev mailing list. Let's hear what they
will say.
> then I will upload the packages, once I build them with sbuild :))
Great!
Thanks,
Andrius
--
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania
upload updated mmdb, ssm, clipper and libccp4 packages to
unstable if they are OK? If not, let me know what should I fix.
Thanks,
Andrius
On 05/02/2018 07:25 PM, PICCA Frederic-Emmanuel wrote:
> It would be nice tu update all these library to the lateste versions :))
--
Andrius Merkys
Viln
On 05/02/2018 07:25 PM, PICCA Frederic-Emmanuel wrote:
> It would be nice tu update all these library to the lateste versions :))
OK, I'll see what I can do :)
Best,
Andrius
--
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania
Hello,
On 05/02/2018 07:21 PM, PICCA Frederic-Emmanuel wrote:
> Not enough time from my side :((. If you want to take care of this. It is ok
> for me.
sure, I would like to give it a try. Will you help me with uploading the
packages once they're ready?
Best,
Andrius
--
Andrius
to build
successfully for me, therefore, I guess the transition could be initiated. mmdb
>= 2 is a build dependency of coot, which I would like to see in Debian one day.
Best wishes,
Andrius
--
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10
as you find it ready, tell us, and we can import it into the group space
> from there. Then we can also adjust the projects permissions if necessary.
thanks for the explanation. I prefer creating projects in my personal workspace
and asking to be moved after they are done.
Best,
Andrius
--
Dear Boris,
On 04/12/2018 11:27 AM, Boris Pek wrote:
> It is briefly described in Debian Science Policy Manual:
> https://science-team.pages.debian.net/policy/#idm145
thanks for the link. I was not aware of this change of the policy.
Best wishes,
Andrius
--
Andrius Merkys
Vilnius Univ
projects. How can I contribute new packages on
salsa?
Best wishes,
Andrius
--
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania
sted to join the Team and
now I am able to push my commits.
Best regards,
Andrius
--
Andrius Merkys
PhD student at Vilnius University Institute of Biotechnology, Saulėtekio al. 7,
room V325
LT-10257 Vilnius, Lithuania
-team/cod-tools.git
andrius@tasmanijos-velnias cod-tools $ git push
GitLab: You are not allowed to push code to this project.
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
I have signed up on salsa.debian.org (@merkys-guest) and set up my SSH
key
pe of Debian Science or DebiChem. I'd like to suggest you should
> maintain the package in either of this team.
>
> Kind regards
>
>Andreas.
>
> On Wed, Jun 07, 2017 at 04:33:49PM +0300, Andrius Merkys wrote:
>> Package: wnpp
>> Severity: wishlist
>&
72 matches
Mail list logo
