Re: Debian-Med policy proposal: 64-bit & little-endian only* for new packages

Hi all, first of all thanks Michael for this idea and also for the elaborate proposal email that outlines the intended way to go quite well. [...] Support Debian-Med packages for 32-bit and/or big-endian architectures is not a good use of our limited resources. Agreed. [...] However, I

Re: Bug#1064291: marked as done (ITP: python-awkward -- manipulate JSON-like data with NumPy-like idioms)

Hi Andreas, [...] debian/rules override_dh_auto_build make[1]: Entering directory '/build/python-awkward-2.6.1' nox -s prepare nox > Running session prepare nox > Creating virtual environment (virtualenv) using python3 in .nox/prepare nox > python -m pip install build numpy packaging PyYAML

Bug#1064291: ITP: python-awkward -- manipulate JSON-like data with NumPy-like idioms

Package: wnpp Severity: wishlist Owner: debian-med@lists.debian.org X-Debbugs-Cc: debian-de...@lists.debian.org * Package name: python-awkward Version : 2.6.1 Upstream Contact: Jim Pivarski * URL : https://github.com/scikit-hep/awkward * License : BSD-3-clause

Re: Last call for any other location than Berlin (Was: Any suggestions for next Debian Med sprint (in person meeting)?)

Hi Andreas, Should I just clone the previous page, just updating the year and resetting the registration list? 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:

Re: Last call for any other location than Berlin (Was: Any suggestions for next Debian Med sprint (in person meeting)?)

Hi all, [...] Just lets fix it on this 16.2. water tower whoever will make it and 17-18 inside the kacher space provided by Saschas company. 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

Re: Last call for any other location than Berlin (Was: Any suggestions for next Debian Med sprint (in person meeting)?)

Hi all, I hope you have all had nice holidays, if that's a thing where you live :) 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

Re: Last call for any other location than Berlin (Was: Any suggestions for next Debian Med sprint (in person meeting)?)

Hi, [...] How about Feb 10-11, for example? My weekends are still free for now so it's your choice. I admit I'd prefer Feb. 17-18 over 10-11. Other opinions? Fine with me! Cheers Sascha OpenPGP_signature.asc Description: OpenPGP digital signature

Re: Last call for any other location than Berlin (Was: Any suggestions for next Debian Med sprint (in person meeting)?)

Hi Andreas, [...] did you managed to reserve a room for our sprint? 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 the booking.

Re: Any suggestions for next Debian Med sprint (in person meeting)?

Hi all, [...] I remember someone suggested Hamburg but it was not me. If the person who suggested this would speak up it would be nice. Otherwise I would ask Sascha to make suggestions when the known venue is open for our sprint. I wouldn't mind going somewhere else for a change... but i

Re: Any suggestions for next Debian Med sprint (in person meeting)?

Hi all, [...] No better idea from my part. The location in Berlin was actually fine and I cannot propose a better (also closer to me) place. Last time we discussed this, you evoked a place in Hamburg. Which would not change a lot of things for me compared to Berlin. I remember someone

Re: Unable to find source code for pbsv which would be helpful for cutesv autopkgtest

Hi Andreas, Unfortunately the upstream repository of pbsv does not contain any code and the issue tracker to contact upstream is deactivated. Any idea how to get the pbsv code? It looks like they are not distributing the code :/ There is a binary in the release section of the GitHub project

Re: Sprint can start Friday evening - who would like to join

Hi all, FYI the Vietnamese place (Viet Kitchen) around the corner has many vegan options and is quite good. https://goo.gl/maps/M7gwo7S97qpqs6ms6 See you on Friday! Sascha On 17.01.23 17:40, Andreas Tille wrote: Am Tue, Jan 17, 2023 at 04:05:59PM + schrieb Matus Kalas: I'll

Re: Sprint can start Friday evening - who would like to join

Hi Andreas, [...] So we have two options: 1. Meet 18:00 at Campus and go for dinner later 2. Have dinner at 18:00 and book the room starting at 19:00 I don't really have a preference here, whatever suits the others best. Cheers Sascha OpenPGP_signature Description: OpenPGP digital

Re: Sprint can start Friday evening - who would like to join

Hi Andreas, thanks for getting things started! on top of the small hotel at EUREF-Campus 22 there is a lounge for 8 persons. I can book this with Debian sponsored money for the evening - so we can meet there. Who would like to join and at what time do we want to meet? I would like to

Re: sprint 2023

Hi Andreas and Olivier, thanks for the info! Question is who the sprint 'organizer' is ;) We do not have such a role, but I volunteer to contact DPL. Thanks a lot for taking care of this. I'm sorry but there's quite a bit of stuff on my plate at the moment. [...] So nothing more expected

Re: sprint 2023

Hi all, did sprint organizer asked for DDs  funding? Question is who the sprint 'organizer' is ;) I am providing the space, so are you also considering me the organizer in the sense of official communication? I was not aware of that, but if that's the case then please let me know how much

Re: Possibility of In-person sprints in 2023?

Hi again, [...] Thanks for confirming.  Sascha, did you had any success when asking for rooms we could use? I will bring it up again and let you know ASAP. I have been in touch with our front desk and it looks like a meeting at my employer here is doable in principle, given the same

Re: Possibility of In-person sprints in 2023?

Hi all, [...] Thanks for confirming. Sascha, did you had any success when asking for rooms we could use? I will bring it up again and let you know ASAP. Cheers Sascha

Re: Possibility of In-person sprints in 2023?

Hi all, just returned from a weekend of travel with no email and now catching up. 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

Re: 20 years of Debian Med list :-) and suggested sprint date

Hi all, > on Mon, 21 Jan 2002 11:59:11 +0100 the first mail to this list was > sent[1]. So somehow we can celebrate some anniversary. :-) Yay! =) [...]> I'd be happy if people who intend to join would confirm joining > the sprint and what date might be prefered. I don't really have a big

Re: apache arrow anyone?

Hi Steffen, [...] > I also think that the science-team's repository is where it should go. Done, now in https://salsa.debian.org/science-team/arrow. I have also added a README.Debian to summarize what is still open. I'd be more than happy to join in with some remaining tasks if there's a chance

Re: apache arrow anyone?

Hi Andreas, [...] > I'd recomment to move the packaging from satta to one of the > interested teams (either science or med or something that is close to > that audience). I'd be very happy to do that as I am a maintainer in both med and science. Just did not see the relevance for one of these

Re: apache arrow anyone?

Hi Andreas, On 23.08.21 13:3 [...] > I'd recomment to move the packaging from satta to one of the interested > teams (either science or med or something that is close to that audience). > > Kind regards and thanks a lot for your work on this > > Andreas. >

Re: apache arrow anyone?

Hi again, [...] > The rest of the story is that I considered my package ready to upload Ah, probably not -- taking a second look I apparently did not do the d/copyright yet. So not really ready to upload, some metadata polishing is still needed. Cheers Sascha

Re: apache arrow anyone?

Hi Steffen and Etienne, [...] >> Apache Arrow https://arrow.apache.org/faq/ knows how to efficiently >> handle large tabular data. And, while not in our distribution, it blocks >> some workflows for Debian Med. Arrow comes with interfaces to all the >> prominent languages, for the Med-workflows

Re: Autopkgtest fails for new upstream version of gubbins

Hi, > I injected latest version of Gubbins into Git. Some new Build-Depends were > needed > to run build time tests. I have no time to check the autopkgtest failures > right > now but it would be great if somebody could have a look. Looking at the release notes [0] and the Dockerfile [1], it

Re: Debian Med Sprint from February 18. to 21.

Hi all, [..] > I'd be happy if many members of the team would be able to take vaccation > from day job and free their time to > > * Lurk online face to face on our Jitsi channel[3] > * Lurk on IRC #debian-med > * May be other direct communication channels > * Be available for some ad hoc

Re: Kmc might cause iva autopkgtest fail on arm64

Hi, > run_kmc.sh: line 2: 5046 Segmentation fault kmc -fa -m4 -k95 -sf1 -ci25 > -cs100 -cx100 > /tmp/tmp.GkQzyocbDU/test/iva.out/tmp.common_kmers.8oo5afnl/reads.fa kmc_out > $PWD > /dev/null [...] > There are more Segmentation faults in connection with kmc later. > I think a

Re: [RFS] codonw

Hi Nilesh, >> I have added autopkgtests for codonw. It builds in a clean chroot with >> passing tests. >> My changes are pushed here[1]. >> Needs review and sponsorship. > > Cool, thanks! I will take a look. Uploaded, thanks! I have only added an additional d/changelog entry about the

Re: [RFS] codonw

Hi Nilesh, > I have added autopkgtests for codonw. It builds in a clean chroot with > passing tests. > My changes are pushed here[1]. > Needs review and sponsorship. Cool, thanks! I will take a look. Best regards Sascha signature.asc Description: Message signed with OpenPGP

Re: @DebianMed twitter account?

Hi again, some news regarding this: > Does anyone know who owns and/or set up the @DebianMed twitter > account? At the moment it only tweets blog entry links, but it might > be useful to use it for other purposes as well.>> Trying to do account > recovery only revealed that the associated

@DebianMed twitter account?

Hi all, Does anyone know who owns and/or set up the @DebianMed twitter account [1]? At the moment it only tweets blog entry links, but it might be useful to use it for other purposes as well. Trying to do account recovery only revealed that the associated email address is:

Re: 2020 sprint travel cost reimbursement

Hi Steffen, > Hi Sascha, please reserve some ... 300? ... Euros for me - Travel plus > three nights. Okay, thanks for the information :) Anyone else? Otherwise I'd ask for approval of 600 EUR in total later today. Cheers Sascha > On 02.02.20 22:35, Sascha Steinbiss wrote:

Re: 2020 sprint travel cost reimbursement (was: Debian Med Sprint 2020 in Berlin?)

t; Olivier, I have already noted your request -- anyone else? > > Thanks! > Sascha > >> On 23.11.19 22:56, Sascha Steinbiss wrote: >>> Dear team, >>> >>> after some quick discussions with Andreas and Michael, I would be happy to >>> propose

2020 sprint travel cost reimbursement (was: Debian Med Sprint 2020 in Berlin?)

at if you want to request reimbursement via Debian for hotel costs, flights, or similar expenses, please let me know ASAP how much that will be so I can have the total amount pre-approved by the DPL. Thanks! Olivier, I have already noted your request -- anyone else? Thanks! Sascha > On 23.11.19 2

Debian Med Sprint, 8/9 Feb 2020, Berlin, Germany

Dear Debianistas, I am happy to announce that the next Debian Med sprint will take place in Berlin. The location would be the same as in the 2019 Berlin BSP. - when: Feb 8/9, 2020 - where: DCSO GmbH, EUREF-Campus 22, 10829 Berlin, Germany The venue is a modern office building in

Re: Debian Med Sprint 2020 in Berlin?

%20Med%20Sprint%20Feb%202020%2C%20Berlin On 23.11.19 22:56, Sascha Steinbiss wrote: > Dear team, > > after some quick discussions with Andreas and Michael, I would be happy to > propose Berlin as the next location for the annual sprint. I have checked > with my employer [1]

Re: debianmed sprint hotel

Hi all, > has anyone made an hotel choice for the sprint so that we can start > reservertions to be together if possible? FYI, here are some recommendations (from our wiki): - Within walking distance:

Bug#947954: ITP: vmatch -- large scale sequence analysis software

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss * Package name: vmatch Version : 2.3.0 Upstream Author : Stefan Kurtz * URL : http://vmatch.de * License : ISC Programming Lang: C Description : large scale sequence analysis software Vmatch

Re: [Debian-med-packaging] Bug#938565: Autopkgtest failing - any takers for Segmentation fault in bowtie (Was: Bug#938565: sspace: Python2 removal in sid/bullseye)

Hi, I've had another look at: > autopkgtest [15:40:05]: test example-tests: [--- > + which python > /usr/bin/python > + python > + which bowtie-build > /usr/bin/bowtie-build > + bowtie-build --help > Segmentation fault > autopkgtest [15:40:06]: test example-tests:

Re: Debian Med Sprint 2020 in Berlin?

Hi all, > If we agree to have the sprint in Berlin and also agreed on a date, I would > be happy to set up a wiki page. Wiki page is open! -> https://wiki.debian.org/Sprints/2020/Debian%20Med%20Sprint%20Feb%202020%2C%20Berlin Cheers Sascha signature.asc Description: OpenPGP digital

Debian Med Sprint 2020 in Berlin?

Dear team, after some quick discussions with Andreas and Michael, I would be happy to propose Berlin as the next location for the annual sprint. I have checked with my employer [1] and they agreed to let us use their space for the weekend. The location would be the same as in the 2019 Berlin

Re: Bug#944299: ITP: phylonium -- Fast and Accurate Estimation of Evolutionary Distances

Hi Fabian, you should be able to push now. Cheers Sascha On 11/8/19 10:41 AM, Fabian Klötzl wrote: > Hi all, > > I started packaging phylonium locally. However, I can't push to salsa > because of some "default branch" issue. As I am only a "Developer" for > that repo, I can't change it my

Re: Bug#944299: ITP: phylonium -- Fast and Accurate Estimation of Evolutionary Distances

Sorry, I meant: I made you a maintainer so you can set up the repo by yourself. Cheers S. On 11/8/19 11:12 AM, Sascha Steinbiss wrote: > Hi Fabian, > > you should be able to push now. > > Cheers > Sascha > > On 11/8/19 10:41 AM, Fabian Klötzl wrote: >> Hi

Re: Source uploads not processing?

Hi Mattia, [...] >> I've gotten no error messages about my GPG signatures or emails about lack >> of authorization. > > That's the clear sign of a gpg problem. Indeed from the queued log: > Jul 23 17:13:34 processing /prokka_1.13.7+dfsg-1_source.changes > Jul 23 17:13:34 GnuPG signature

Re: Pizzly keeps complaining about missing pthreads library - any idea anyone?

Hi Steffen, > Please someone help me out. Pizzly is lintian clean when built > "regularly" on my desktop but fails with > > /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_8a4be.dir/link.txt > --verbose=1 > /usr/bin/c++  -g -O2 -fdebug-prefix-map=/build/pizzly-0.37.3=. >

Re: Wham aligner package name - just wham? wham-align?

Hi Steffen, > I have no exact idea why alignment tools are all given such short names. > We have http://last.cbrc.jp/ as last-align with is. Should I do the same > for wham and name the package wham-align? That's what I did for lambda [1] and lambda2 [2] as well. Keeps the namespace clean and

Re: Sprint preparation

Hi Andrius, hi all, first of all thanks for your quick reply! > To reach the apartments [1] one has to take the bus 3G at the airport > terminal (the airport is very small, bus station is just outside). A > paper ticket has to be bought from the driver, it should cost €1. > It's better to pay in

Re: Should lambda-align v2 replace v1 or be its own Debian package?

Hi Michael, [...[ > Other than the lack of full test suite that we had with v1.0.x [1], I > think this is ready for sponsorship for the NEW queue. Hmm, but the rest of the tests (the ones currently run in your package on salsa) are supposed to succeed? They fail for me: [...] debian/rules

Re: Should lambda-align v2 replace v1 or be its own Debian package?

Hi Michael, [...] > Pursuant to that I split off the v2.0.0 packaging: > https://salsa.debian.org/med-team/lambda-align2 [...] > I think this is ready for sponsorship for the NEW queue. Could you please make sure that we have an ITP for that? I'll take a look tomorrow then, try to address Hannes'

Re: Should lambda-align v2 replace v1 or be its own Debian package?

Hi, just my 2 cents. I introduced Lambda into Debian some time ago just out of interest but looking at the uploads, Michael has done more work recently... So here are just a few comments from me. [...] >> However, there are no references from other Debian packages to >> lambda-align's binaries,

Re: htslib: FTBFS on i386: 2 tests fail

Hi all, >> test_vcf_api: >> /<>/test/test-vcf-api /tmp/JMIB5wVvT_/test-vcf-api.bcf >> bcf_get_format_float didn't produce the expected output. >> >> .. failed ... >> >> test_vcf_sweep: >> /<>/test/test-vcf-sweep /tmp/JMIB5wVvT_/test-vcf-api.bcf >> >> The outputs differ: >>

Re: DebianMed Sprint in Vilnius?

Hi all, > This sounds awesome, I'm already looking forward! :-D So am I :) [...] > 2019 Mar 09-11   best, with the additional advantage of 3 free days in > Lithuania (if that is the requirement from the co-working facility) I would probably welcome doing this a bit later this yeas as well, to

Re: Who will go to DebConf 18 in Taiwan?

Hi Andreas, > I'll be there. Who else from the team? I won't this year. Maybe next? :) > A Debian Med BoF with life stream is scheduled > > https://debconf18.debconf.org/talks/39-debian-med-bof/ Will watch it -- will check when to set my alarm. Cheers Sascha

CMake help: pthread linking issue

Hi again, [...] > I am trying to update salmon [1] to the latest upstream version, but it > won't build for reasons I can not really track down well. It uses CMake > as the build system, which I am really not familiar with and to me feels > a bit like magic incantations to me that mostly work if

CMake help: pthread linking issue

Dear mentors, I am trying to update salmon [1] to the latest upstream version, but it won't build for reasons I can not really track down well. It uses CMake as the build system, which I am really not familiar with and to me feels a bit like magic incantations to me that mostly work if you use

Re: salsa.d.o merge_requests for pristine-tar and upstream?

Hi Steffen, if I see that correctly this is just a default hook that GitLab does -- offer to open merge requests for each pushed branch. I don't think that fits too well with how we do things: for example, proposing an upstream update via regular merge requests would require all three separate

Re: uploading libzstd...

Hi Mattia, thanks for diving into this! Just quickly replying as my name was mentioned... [...] > Alex Mestiashvili, Sascha Steinbiss, Kevin Murray: there are a bunch of > patches without Forwarded header, that seems like have been there for a > while. Please do some upstrea

Re: pynast did not migrate to salsa?

Hi Steffen and Andreas, >> I cannot find the pynast repository on salsa. Any ideas? The entry on  the >> med/bio task page points to its previous location on alioth and I cannot >> find it on salsa. > > I simply forgot to push after the local SVN to Git migration. So the > package never existed

Re: RFS: andi

Hi Fabian, > I prepared a new package for andi, now on salsa [1]. However, I am sure, > I must have done something wrong, because the packaging was surprisingly > smooth. I can sponsor this, but it seems that the 0.12 orig tarball is missing in the pristine-tar branch. Could you please push this

Re: Salsa migration of Debian Med team packages

Hi Dylan, [...] > I think all R packages (r-*) can be removed from the Debian Med > repository, they moved into the Debian R team repository [1] some > weeks ago [2]. Thanks for the hint. I will remove those repositories from the Debian Med namespace tomorrow if there are no objections from the

Re: Salsa migration of Debian Med team packages

Hi all, [...] >> Do we also want the automatic tag-pending assignment hook? > > I would say so. I think the only reason we didn't have them before was > that nobody got around to adding it. OK, I see. I'm currently enabling this hook on all repositories migrated yesterday. Cheers Sascha

Re: Salsa migration of Debian Med team packages

Hi all, >> Picking a random repository, I noticed no integration was enabled. >> Can I suggest: >> + email on push to dipa...@tracker.debian.org ¹ >> + irc notification to #debian-med >> + tagpending hook > > Cool, didn't know these were already existing and usable. :) > Will look into this

Re: Salsa migration of Debian Med team packages

Hi Mattia, yay, thanks for your hints! > Picking a random repository, I noticed no integration was enabled. > Can I suggest: > + email on push to dipa...@tracker.debian.org ¹ > + irc notification to #debian-med > + tagpending hook Cool, didn't know these were already existing and usable. :)

Salsa migration of Debian Med team packages

Dear Debian Med team, here's a quick hello from the Debian Med sprint in Barcelona! I used the first day of the sprint to migrate the team packaging repositories from Alioth to Salsa, resulting in almost 1200 new Salsa repos in the Debian Med group [1]. The Alioth repositories are now locked, any

Re: Hotel for Debian Med Sprint

Hi Steffen,I just need to call in tomorrow morning again for special conditions forus as a group. If you cannot wait then book tonight, otherwise I proposeyou wait for the official green light tomorrow. I'll then also update the website.Great, I will wait — thanks for taking care of

Re: Date shift: Sprint moving to 10-12/2/2018, was: Debian Med Sprint 26-28/1/2018 in Barcelona

Hi all, [...] >> I wonder whether it would be possible to have our Sprint *before* the >> ELIXIR meeting. I do not question your point above but I have strong >> private reasons to keep the weekend 10./11. February 2018 free. If >> anybody else would be in a similar situation (and the ELIXIR

Re: [Debian-med-packaging] Bug#871513: muscle FTCBFS: hard codes the build architecture compiler g++

Hi Helmut, > Updating the patch to use $(CXX) fixes the build. Please consider > applying the attached patch. Thanks, I would be happy to take a look and upload this. However, it looks like the git repo on Alioth doesn't seem to have the latest commits/tags for the latest uploaded version. I'd

Re: [Help] Failed to upgrade bcftools to version 1.5

Hi all, > Well, I was going to branch off a separate branch from the > debian/1.4.1-2 tag, add the patches, build and upload 1.4.1-3 from > there, and then just add the changelog entry to the current master (as > the patches should already been in the latest upstream code, right?). > If one wants

Re: [Help] Failed to upgrade bcftools to version 1.5

Hi all, [...] >> The remaining bugs blocking the transition are augustus (bug #869126) and >> bcftools (bug #868958). Sascha has already pushed the augustus changes to >> git, and it just needs an upload. The two fixes for bcftools are in the bug >> report, someone should review them and

Bug#869969: ITP: gfapy -- flexible and extensible software library for handling sequence graphs

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@debian.org> * Package name: gfapy Version : 1.0.0 Upstream Author : Giorgio Gonnella * URL : https://github.com/ggonnella/gfapy * License : ISC Programming Lang: Python Descr

Re: CI for probalign needs sponsoring from other sponsor [Outreachy]

Hi Nadiya, > I added autopkgtest test-suite for probalign package. > I would really appreciate your help in uploading. Done, thanks for your contribution! :) Cheers Sascha signature.asc Description: OpenPGP digital signature

Re: CI for abyss needs sponsoring from other sponsor [Outreachy]

Hi Nadiya, > I added simple autopkgtest test for abyss package. > Your help in uploading will be very much appreciated. Cool, many thanks! I just took a look and I’m going to upload with some minor modifications. BTW, your autopkgtest revealed that there apparently still was a missing

Re: Please fix bugs

Hi all, > On 6/27/17 9:34 PM, Andreas Tille wrote: >> as I stated on debian-private list I will not be able to fix bugs in the >> next two weeks. I have the feeling we are currently receiving way more >> than we are fixing. It would be really cool if you could run some kind >> of inofficial

Re: [Debian-med-packaging] Bug#863159: zstd: New upstream version with multithreading support

Hi, > On 24 May 2017, at 14:57, Olivier Sallou wrote: > > I updated in git repo but did not pushed. Thanks for that! I had a look at this this morning as well but given that I am traveling at the moment I also only found the time to merge the new version locally but

Re: spades updated to 3.10.1 in git

Hi Michael, > It will need sponsoring once sketch has been released Thanks! I was taking a shot at this myself a while ago but ran into random segfaults after adjusting patches. Nice to see that there's some progress. Would be happy to take a look and sponsor the upload when it's time. Cheers

Re: upload to unstable during freeze ?

Hi Olivier, > I see some uploads to unstable during the freeze. I understood it was > not expected as fixes that need to go to "next stable" go through > uploads to unstable. > > While this should not be an issue for packages that do not present > issues at this time, I'd like to know if we

Re: Patching fermi-lite to enable packaging libSeqLib

Hi Andreas, as a previous uploader of ariba and fermi-lite, I'll see if I can contribute to this discussion. > to package the latest version of freebayes (version 1.0.2 is in new, > latest upstream is 1.1) a new library libSeqLib is needed. I started > with the packaging[1] and managed to build

Re: pbcommand new upstream

Hi Afif, >> OK, thanks for the confirmation. I’ll update to the latest version of >> pbcommand then. > > Many thanks for updating pbcommand--but don't forget to push the final > changes and tag. :) [x] Done. BTW, I've seen that you updated and uploaded kineticstools -- I just finished getting

Re: libzstd 1.1.2 contains embedded zlib fork

Hi Kevin, thanks for your email. >> I was looking to update libzstd to the current upstream version 1.1.2. >> Besides some minor changes to the patches I had to make, I also noticed that >> it now includes an embedded copy of some zlib code, which -- according to the >> inline comments -- was

Re: pbcommand new upstream

Hi Afif, thanks for getting back to me so quickly. >> What would you suggest, package the current version now that we need it? You >> have got more experience with the PB tools and how likely they are to break >> APIs across versions — do you think it’s a good idea? > > Yes, I think it should

pbcommand new upstream

Hi Afif, at the sprint I’m currently trying to update kineticsTools to a recent version. However, it also requires a newer version of pbcommand, which we missed to keep up-to-date as upstream are not tagging their GitHub releases [1]. It is possible to manually track the upstream versions by

libzstd 1.1.2 contains embedded zlib fork

Hi Kevin, here on the Debian Med sprint I was looking to update libzstd to the current upstream version 1.1.2. Besides some minor changes to the patches I had to make, I also noticed that it now includes an embedded copy of some zlib code, which -- according to the inline comments -- was

Re: Sprint organisation

Hi all, > I did a walk through of the space today, a snowy 10 minute walk from the > hotel. Yay! > Good news on the Wi-Fi! > > http://www.speedtest.net/my-result/a/2527663676 Sounds good. It looks like most of you will already be arriving on Thursday... so I guess I will meet you at the

Re: DebianMed sprint hotel proposal

Hi Andreas, >> I have also just booked a room at that hotel. They’re really inexpensive and >> it looks like there are still rooms left :) > > I also tried a reservation and while the page lists empty rooms I failed > in registering using their web interface. I've just send an e-mail and >

Re: DebianMed sprint hotel proposal

Hi all, > > So, I have made a reservation at an hotel not far from the Faculty of > > Biology and quite well located. It is not expensive and has twin bed rooms > > for those willing to share rooms. It also has a restaurant if needed. > > Thanks a lot for steping in. Indeed, thanks Olivier for

Re: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: Fails to build from source since bioperl upgrade has broken libbio-graphics-perl)

BTW, [1] here was: https://github.com/sanger-pathogens/Roary/issues/196 Cheers Sascha > On 17 Dec 2016, at 23:28, Sascha Steinbiss <sa...@debian.org> wrote: > > Hi all, > > thanks for checking these. > >>> roary >> >> Build, however when trying to

Re: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: Fails to build from source since bioperl upgrade has broken libbio-graphics-perl)

Hi all, thanks for checking these. >> roary > > Build, however when trying to simulate the test suite via > > cd t/data/genbank_gbff > roary -f out *.gff > > Please cite Roary if you use any of the results it produces: >Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong,

Re: Sponsoring request: beagle

Hi Dylan, I just took a look and uploaded. Thanks, Sascha > On 4 Oct 2016, at 22:01, Dylan wrote: > > Hi, > I have updated beagle. Could someone upload it to unstable? > > Thank you. > > Best regards, > Dylan >

Bug#838856: ITP: ruby-rgfa -- Ruby library for handling GFA files

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@debian.org> * Package name: ruby-rgfa Version : 1.2 Upstream Author : Giorgio Gonnella <gonne...@zbh.uni-hamburg.de> * URL : https://github.com/ggonnella/rgfa * License : ISC Prog

Re: Again help needed to upgrade picard-tools

Hi, >> ... >> Results: FAILURE (1833 tests, 1832 successes, 1 failures, 0 skipped) >> ... >> Any ideas from someone with more detailed insight? > > We needed to exclude some tests since internet access is needed. I have > not checked the lot of output but this might be the case here as well >

Re: Again help needed to upgrade picard-tools

Hi all, > seems I always have trouble with picard-tools. I have injected new > upstream version in Git but it fails to build. The upgrade of > libhtsjdk-java went fine but it would be great if somebody could have a > look at picard-tools. Something in the build system changed; I patched it

Re: Build directories sneaking into Makefiles installed as examples

Hi, >> I have found some more instances, and I have added some workarounds removing >> these problematic fields from the Makefile [2] to let them use the default >> if required — however, I am wondering whether these Makefiles should be >> installed at all. Cleaning them up would add quite a

Build directories sneaking into Makefiles installed as examples

Hi all, when trying to fix some packages that have recently become unreproducible after adding build path variations, I have noticed that a common case is that some of these variations make it into Makefiles that have been generated by automake from upstream’s Makefile.in. Some of these

Re: Could somebody please check ncbi-tools6 (Was: [GSOC] Todo List)

Hi Andreas, > On Mon, Aug 22, 2016 at 02:20:08PM +0200, Sascha Steinbiss wrote: >> BTW you don’t need to install your test data to be used in the autopkgtest, >> as tests will always be run with an decompressed source tree present, >> including the debian directory

Re: Could somebody please check ncbi-tools6 (Was: [GSOC] Todo List)

he test, see git repo. Cheers Sascha > > Best Regards > > > Canberk Koç > about.me/canberkkoc > > > 2016-08-22 13:49 GMT+03:00 Sascha Steinbiss <sa...@tetrinetsucht.de>: > Hi Andreas, > > I’ll take a look. > > Cheers > Sascha > &g

Re: Could somebody please check ncbi-tools6 (Was: [GSOC] Todo List)

adding test data then it might be helpful to migrate. I will upload the package including the tests soon — thanks Canberk for adding the tests! Cheers Sascha > On 22 Aug 2016, at 12:49, Sascha Steinbiss <sa...@tetrinetsucht.de> wrote: > > Hi Andreas, > > I’ll take a look.

Re: Could somebody please check ncbi-tools6 (Was: [GSOC] Todo List)

Hi Andreas, I’ll take a look. Cheers Sascha > On 22 Aug 2016, at 11:29, Andreas Tille wrote: > > Hi, > > On Sat, Aug 20, 2016 at 10:16:14AM +0300, Canberk Koç wrote: >> I'll commit a test for tools6 but there is a problem ncbi-tools6 not come >> from apt-get install so test

Bug#834940: ITP: lambda-align -- Local Aligner for Massive Biological DatA

Package: wnpp Severity: wishlist Owner: Sascha Steinbiss <sa...@debian.org> * Package name: lambda-align Version : 1.0.0 Upstream Author : Hannes Hauswedell <hannes.hauswed...@fu-berlin.de> * URL : https://seqan.github.io/lambda * License : GPL

Re: RFS: python3-typed-ast, hisat2

Hi Michael, thanks for polishing the packages! > - I would add: > Copyright 1999, N. Jesper Larsson, all rights reserved. >from ls.h to d/copyright > Done > - IMHO d/rules should have a ‘clean' override that removes the man pages > built there > Already taken care of via dh_clean

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