Re: How to interpret the libvcflib & libssw piuparts failures?

; being retried. Anyway, I've seen dozens such errors, so I'm sure nothing > is expected from the maintainers. > > On Sun, 29 Dec 2019, 5:53 pm Michael Crusoe, > wrote: > >> https://piuparts.debian.org/sid/source/libv/libvcflib.html >> >> https://piuparts.debian.org

Re: Bug#946272: ITP: libbio-procedural-perl -- Simple low-dependency procedural interfaces to BioPerl

Dear Andreas, I've fixed the tests for the libbio-db-embl-per and libbio-db-ncbihelper-perl packages. This also allows libbio-variation-perl to build successfully, in addition to libbio-procedural-perl. Therefore it would be appreciate if you could sponsor all four packages: libbio-db-embl-perl

Request for sponsorship / upload rights: reapr delly kallisto qtltools

Hey team, I've updated many packages related to the libhts3 transition and they could use either sponsorship or I can upload them if I'm given the permissions to do so. gbp clone g...@salsa.debian.org:med-team/reapr gbp clone g...@salsa.debian.org:med-team/delly gbp clone

Re: Bug#937606: Droping Python2 support for Biopython

On Fri, Dec 20, 2019 at 12:51 PM Andreas Tille wrote: > On Fri, Dec 20, 2019 at 03:15:49PM +, Peter Cock wrote: > > We (upstream) have just released Biopython 1.76 which should be > > the final release to support Python 2 anyway: > > Cool. Its dropped from the Debian package anyway so we

Re: C++ help for freebayes needed

> > this instruction is okay to use in the particular header, or the C > > code has to be fixed to accomodate for that. > > @Michael Crusoe: Do you have some contact to htslib authors? May > be its the best to forward this upstream. > > I don't know the htslib people well

Re: Request for sponsorship/upload permission: RAxML

Thank you, Andreas Tille! On Mon, Dec 16, 2019 at 3:24 PM Michael Crusoe wrote: > gbo clone g...@salsa.debian.org:med-team/raxml > > I enabled building on all archs, not just x86, via the simde library. > > > https://salsa.debian.org/med

Request for sponsorship/upload permission: RAxML

gbo clone g...@salsa.debian.org:med-team/raxml I enabled building on all archs, not just x86, via the simde library. https://salsa.debian.org/med-team/raxml/commit/d83a944cadabeee33fbc1f672d63ca5cee44f1c6 I also hardened the build

Re: ugene is in the distro, right? Why cannot I upload source-only? Fwd: ugene_33.0+dfsg-1_source.changes REJECTED

Did you change the section from non-free to free? -- Michael R. Crusoe On Sun, Dec 15, 2019, 21:18 Steffen Möller wrote: > Many thanks for your insights > > Steffen > > > > Forwarded Message > Subject:ugene_33.0+dfsg-1_source.changes REJECTED > Date: Sun, 15 Dec

Oops, I broke htslib in Unstable

libhts-private-dev & htslib-test are at 1.10-1 while libhts-dev and libhts2 is at 1.9-12. We are waiting on the corrected source package (1.10-2) to make a (hopefully) fast trip through the NEW queue due to the new libhts3 binary package. https://ftp-master.debian.org/new/htslib_1.10-2.html

Request for sponsorship: htslib_1.10-2 due to libhts2 -> libhts3

gbp clone g...@salsa.debian.org:med-team/htslib.git Thanks! -- Michael R. Crusoe

Request for sponsorship: hopscotch-map a build-dep of VG

gbp clone g...@salsa.debian.org:med-team/hopscotch-map.git Thanks! -- Michael R. Crusoe

Re: Request for feedback: adding additional arch support to libssw using the SIMDE headers

P.S. I tested https://salsa.debian.org/med-team/libssw/tree/simde using i386, could someone sponsor an upload to experimental so I can see the results across all Debian architectures? Thanks! On Thu, Dec 12, 2019 at 1:05 PM Michael Crusoe wrote: > Hello all, > > As an experiment I

Request for feedback: adding additional arch support to libssw using the SIMDE headers

Hello all, As an experiment I've added support for non-SSE2 CPUs to the libssw library at https://salsa.debian.org/med-team/libssw/tree/simde using the SIMDE header only library that provides implementations for many SIMD C/C++ intrinsics using plain source code, or SIMD equivalents on other

Request for sponsorship: libbio-variation-perl

gbp clone g...@salsa.debian.org:med-team/libbio-variation-perl.git Thanks! -- Michael R. Crusoe

Re: Request for sponsorship: libbio-db-refseq-perl

A gentle reminder, libbio-db-refseq-perl still needs sponsorship (thanks!) On Fri, Dec 6, 2019 at 2:52 PM Michael Crusoe wrote: > gbp pull g...@salsa.debian.org:med-team/libbio-db-refseq-perl.git > > Thanks! > > > -- > Michael R. Crusoe > -- Michael R. Crusoe

Request for sponsorship: libbio-cluster-perl

gbp clone g...@salsa.debian.org:med-team/libbio-cluster-perl.git This is a requirement for updating the libbio-asn1-entrezgene-perl package -- Michael R. Crusoe

Re: Accepted python-pbcore 1.7.1+git20191121.7947eb7+dfsg-1 (source all) into unstable, unstable

Yeah, just for testing migration -- Michael R. Crusoe On Fri, Dec 6, 2019, 22:17 Andreas Tille wrote: > On Fri, Dec 06, 2019 at 06:21:57PM +0100, Michael Crusoe wrote: > > Woo-hoo! Though the 'all' binary package got uploaded, so another upload > is > > needed > >

Re: Accepted python-pbcore 1.7.1+git20191121.7947eb7+dfsg-1 (source all) into unstable, unstable

Woo-hoo! Though the 'all' binary package got uploaded, so another upload is needed On Fri, Dec 6, 2019 at 2:01 PM Andreas Tille wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA256 > > Format: 1.8 > Date: Thu, 05 Dec 2019 11:23:55 +0100 > Source: python-pbcore > Binary: python3-pbcore

Request for sponsorship: libbio-db-ncbihelper-perl

gbp pull g...@salsa.debian.org:med-team/libbio-db-ncbihelper-perl Thanks! -- Michael R. Crusoe

Request for sponsorship: libbio-db-refseq-perl

gbp pull g...@salsa.debian.org:med-team/libbio-db-refseq-perl.git Thanks! -- Michael R. Crusoe

Request for sponsorship: libbio-db-swissprot-perl

gbp pull g...@salsa.debian.org:med-team/libbio-db-swissprot-perl.git Thanks! -- Michael R. Crusoe

Tips for compiling LEMON with gcc-9?

Hello, The lemon 1.3.1 source package for Debian no longer builds as Debian has upgraded to GCC 9. Here is the original report: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=925749 Adding '-std=c++2a' to the CXXFLAGS makes the compilation succeed, but then one of the tests fail: 26: Test

Re: [Bioperl-l] Fate of Bio::Perl newbie module?

On Sat, Nov 30, 2019 at 7:32 AM Andreas Tille wrote: > Hi Christopher, > > On Fri, Nov 29, 2019 at 09:11:41PM +, Fields, Christopher J wrote: > > Just a quick update: I have pushed a quick release of > Bio::DB::SwissProt, Bio::DB::RefSeq, and Bio::Procedural (which contains > Bio::Perl) to

Re: Add link to Debian's packages for Infernal?

> > And thanks for the info on the patches, spelling errors and i386 issue. > Re: i386, I think I see the issue and will fix it for the next release. > > Eric > > ---------- > *From:* Michael Crusoe > *Sent:* Sunday, December 1, 2019 5:00 PM > *To:* s

Re: Add link to Debian's packages for Infernal?

/tree/master/debian/patches which you are very welcome to incorporate. Cheers, On Sat, Nov 30, 2019 at 3:40 PM seaneddy wrote: > Hi Michael, > > Thanks! I passed this along to Eric Nawrocki, Infernal's lead developer. > > Sean > > > On Nov 30, 2019, at 5:09 AM,

Re: failed amd64 build of infernal 1.1.3-1

I've fixed this in salsa, if someone wants to submit it (or enable to me upload it myself): dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow infernal On Sat, Nov 30, 2019 at 1:15 AM Debian buildds wrote: > * Source package: infernal > * Version: 1.1.3-1 > * Architecture: amd64

Add link to Debian's packages for Infernal?

Hey Sean, We're updating to Infernal 1.1.3 for the Debian package and I saw that there is a section on http://eddylab.org/infernal/ about package managers. Would you like to add a link to the Debian packages there? https://packages.debian.org/search?keywords=infernal The command would be `sudo

Re: Fate of Bio::Perl newbie module?

On Wed, Nov 27, 2019 at 4:24 PM Andreas Tille wrote: > Hi, > > On Wed, Nov 27, 2019 at 12:08:08PM +, Carnė Draug wrote: > > On Wed, 27 Nov 2019 at 10:52, Andreas Tille wrote: > > > > The Bio::Perl module is on the Bio-Procedural repository [1]. No one > > > > has picked up its maintenance

Fate of Bio::Perl newbie module?

I see that the Bio::Perl newbie module was removed in 1.7.3, but I can't find the successor on CPAN or GitHub. Any hints? This is blocking the acceptance of the 1.7.6 bioperl releases into Debian as this breaks the package "roary". http://sanger-pathogens.github.io/Roary A patch to roary that

request for upload permissions: bioperl and libbio-db-ace-perl

dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow bioperl dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow libbio-db-ace-perl Thanks! -- Michael R. Crusoe

Re: Debian Med Sprint 2020 in Berlin?

Thank you Sascha for organizing this! I have responded to the poll, and I invite others to do so As Soon As Possible :-) Cheers, On Sat, Nov 23, 2019 at 11:12 PM Sascha Steinbiss wrote: > Dear team, > > after some quick discussions with Andreas and Michael, I would be happy to > propose Berlin

Re: Does the bowtie2 2.3.5.1-1 package work for anyone else?

Interestingly using docker I can run the package, so it is some sort of chroot/Ubuntu bug :-( On Tue, Oct 15, 2019 at 10:19 AM Michael Crusoe wrote: > > > On Mon, Oct 14, 2019 at 9:21 PM Alex Mestiashvili < > ames...@rsh2.donotuse.de> wrote: > >> On 10/14/19 7:

Re: Does the bowtie2 2.3.5.1-1 package work for anyone else?

On Mon, Oct 14, 2019 at 9:21 PM Alex Mestiashvili wrote: > On 10/14/19 7:26 PM, Michael Crusoe wrote: > > I can't get it to build from source in a cowbuilder "sid" chroot on my > > laptop, which is currently running Ubuntu Bionic with the > 5.0.0-20-generic &

Does the bowtie2 2.3.5.1-1 package work for anyone else?

I can't get it to build from source in a cowbuilder "sid" chroot on my laptop, which is currently running Ubuntu Bionic with the 5.0.0-20-generic #21~18.04.1-Ubuntu kernel. running bowtie2-build --usage (or anything) results in a segfault [34760.926015] bowtie2-align-s[19983]: segfault at

Re: Bug#941805: [Debian-med-packaging] Bug#941805: hmmer: autopkgtest regression: hmmpgmd_ga] ... FAILED [crash!]

Thanks Olivier. I don't have upload permissions for hmmer, so any DD is welcome to update the changelog and upload my fixes. Cheers, -- Michael R. Crusoe

Re: Please provide source code for Tandem Repeats Finder under a freely redistributable license

gt; > > > > > > > > > > > As for all of your arguments regarding the importance of open > source > > > > > > software, especially in science, please know that I completely > agree > > > > with > > > > > > you on every point. I am per

Request for Sponsorship: seqan3

gbp clone g...@salsa.debian.org:med-team/seqan3.git Cheers! -- Michael R. Crusoe

Re: cnvkit update to 0.9.6 needs Fwd: python-pomegranate_0.11.1-1_amd64.changes is NEW

conditions > > with Andreas - what should I do? > > Please coordinate with Michael. I have no idea what to do, sorry. > > Have a safe travel > > Andreas. > > > Cheers, > > Steffen > > > > > > On 16.09.19 09:33, Andreas Tille wrote: > >

Re: cnvkit update to 0.9.6 needs Fwd: python-pomegranate_0.11.1-1_amd64.changes is NEW

python-pomegranate was accepted on 2019-08-31, but now we need a source only upload Steffen, can you do a source only upload of python-pomegranate so cnvkit can migrate? Thanks! On Wed, Sep 4, 2019 at 4:23 AM Andreas Tille wrote: > Hi Steffen, > > On Tue, Sep 03, 2019 at 10:41:14AM +0200,

Bulk RFS Re: Packages needed for the bioperl restructuring

gbp clone g...@salsa.debian.org:med-team/libbio-db-biofetch-perl.git and 5 more below: On Sat, Sep 14, 2019 at 7:25 PM Michael Crusoe wrote: > > > On Sat, Sep 14, 2019 at 12:58 AM Andreas Tille wrote: > > BTW, we should care for bioperl more seriosly to reflect th

Packages needed for the bioperl restructuring

On Sat, Sep 14, 2019 at 12:58 AM Andreas Tille wrote: BTW, we should care for bioperl more seriosly to reflect the restructuring > of the upstream code. > Checking their changelog, here are some other modules that have their own packages since the Buster bioperl release 1.7.2: as of bioperl

RFS: libbio-searchio-hmmer-perl

Recent releases of libbio-perl-perl have decoupled a few modules to their own packages, libbio-searchio-hmmer-perl is one of them: gbp clone g...@salsa.debian.org:med-team/libbio-searchio-hmmer-perl.git This module is needed by prokka (even the currently packaged version) I just pushed updates

Request for review: vg initial packaging

https://salsa.debian.org/med-team/vg I know the debian/copyright file needs updating Many code copies in deps/, I removed all that are in Debian except 4 which are still required due to forking by upstream. The hardening patch is currently disabled, but being worked on actively here at the

Re: Bug#933527: snakemake: fails to install: SyntaxError: duplicate argument 'stay_on_remote' in function definition

The current packaging builds and installs fine for me; shall I upload? On Thu, Sep 5, 2019 at 4:51 PM Andreas Tille wrote: > Hi folks, > > this issue is urgent since if snakemake is not installable several of > our packages where snakemake is in (Build-)Depends are broken. Is > anybody working

Re: Please give back abyss on all archs

Hey Cyril, Thanks for the give back of amd64; it built just fine: https://buildd.debian.org/status/package.php?p=abyss Can we get the give backs for the rest of the archs? Cheers, On Mon, Aug 19, 2019 at 10:28 AM Cyril Brulebois wrote: > Hi, > > Michael Crusoe (2019-08-19): >

Re: Fwd: failed amd64 build of abyss 2.2.2-1

Thank you Graham and Andreas for the sanity check. I've requested a rebuild -- Michael R. Crusoe On Sun, Aug 18, 2019, 09:48 Graham Inggs wrote: > On Sun, 18 Aug 2019 at 07:16, Andreas Tille wrote: > > Builds here with pbuilder as well. I only know that the build daemons > > are not using

Please give back abyss on all archs

Hello, No one can replicate the build failure for abyss, not even Ubuntu, so hopefully it was just a transient error. Please give back abyss on all architectures gb abyss_2.2.2-1 . ANY Thanks, -- Michael R. Crusoe -- Forwarded message - From: Graham Inggs Date: Sun, Aug 18,

Fwd: failed amd64 build of abyss 2.2.2-1

*sigh* It builds fine for me; any ideas? -- Forwarded message - From: Debian buildds Date: Sat, Aug 17, 2019 at 1:30 PM Subject: failed amd64 build of abyss 2.2.2-1 To: * Source package: abyss * Version: 2.2.2-1 * Architecture: amd64 * State: failed * Suite: sid *

Re: Any clue about python3-typed-ast migration?

On Mon, Aug 5, 2019 at 9:24 PM Mattia Rizzolo wrote: > On Mon, Aug 05, 2019 at 05:47:03PM +0200, Michael Crusoe wrote: > > python3-mypy 0.670-2 in testing has a dependency on python3-typed-ast (<< > > 1.4.0) > > > > But autopkgtests is combining python3-ty

Any clue about python3-typed-ast migration?

python3-mypy 0.670-2 in testing has a dependency on python3-typed-ast (<< 1.4.0) But autopkgtests is combining python3-typed-ast 1.4.0-1 with python3-mypy 0.670-2 and predictably that fails :-( https://qa.debian.org/excuses.php?package=python3-typed-ast Is the "<<" comparator inclusive or

Re: Source uploads not processing?

On Wed, Jul 24, 2019 at 2:53 PM Mattia Rizzolo wrote: > On Wed, Jul 24, 2019 at 02:48:35PM +0200, Michael Crusoe wrote: > > On Wed, Jul 24, 2019 at 1:14 PM Mattia Rizzolo > wrote: > > > That's the clear sign of a gpg problem > > > > No error message →

Re: Source uploads not processing?

On Wed, Jul 24, 2019 at 2:56 PM Mattia Rizzolo wrote: > On Wed, Jul 24, 2019 at 02:41:45PM +0200, Michael Crusoe wrote: > > There were no errors in the dput output: > > > > Trying to upload package to ftp-master (ftp.upload.debian.org) > > Checking signature on .cha

Re: Source uploads not processing?

On Wed, Jul 24, 2019 at 1:14 PM Mattia Rizzolo wrote: > On Wed, Jul 24, 2019 at 09:03:12AM +0200, Michael Crusoe wrote: > > Hello friends, > > > > My new laptop is running Ubuntu Bionic (for now) and I thought I had > > recreated my packaging environment successfully.

Re: Source uploads not processing?

-1_source.buildinfo: done. Uploading hhsuite_3.2.0-1_source.changes: done. Successfully uploaded packages. I've attached hhsuite_3.2.0-1_source.changes ­— Maybe I'm using the wrong key? On Wed, Jul 24, 2019 at 1:14 PM Mattia Rizzolo wrote: > On Wed, Jul 24, 2019 at 09:03:12AM +0200, Michael Cru

Re: Source uploads not processing?

On Wed, Jul 24, 2019, 11:27 Olivier Sallou wrote: > > On 7/24/19 9:03 AM, Michael Crusoe wrote: > > Hello friends, > > My new laptop is running Ubuntu Bionic (for now) and I thought I had > recreated my packaging environment successfully. Alas, none of my uploaded > sou

Source uploads not processing?

Hello friends, My new laptop is running Ubuntu Bionic (for now) and I thought I had recreated my packaging environment successfully. Alas, none of my uploaded source package updates seem to have shown up in the unstable distribution:

Source of bio* test data: Galaxy IUC

Example: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools/test-data -- Michael R. Crusoe

Re: Co-mentors for Outreachy / GSoC urgently needed

I also volunteer On Mon, May 6, 2019 at 4:48 PM Andreas Tille wrote: > Hi folks, > > as you might have noticed I have registered > > >

Bug#928333: RM: htslib [i386 hurd-i386 kfreebsd-i386] -- ANAIS; ROM; *i386 no longer supported upstream

Package: ftp.debian.org Severity: normal Owner: Debian Med team Hello, this request is a repeat of https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=914991 The *i386 packages have somehow crept back in for all the reverse-(build-)deps of htslib binary packages. Could the removal of *i386

"Season of Docs" & Debian-Med

Google's new "Season of Docs" is an experiment to connect technical writers with open source projects to improve their documentation. It is unpaid, unlike Outreachy or the Google Summer of Code. However, maybe the Debian-Med process documentation could be updated and moved to readthedocs.org ?

Debian Med at the EU Biohackathon

Deadline for application in April 7th -- Forwarded message - From: Jennifer Harrow HI All, Just to let you know that the Biohackathon2019 website ( https://biohackathon-europe.org/) has been launched and the Call for Hacking projects is officially open. So please submit the

Re: Sprint preparation

În mar., 5 mar. 2019 la 11:56, a scris: > On Tuesday, March 05, 2019 01:57:24 AM Andrius Merkys wrote: > > I've forgot to mention that luggage with dimensions exceeding 120 cm > > require additional ticket... > > Does that mean the total of the 3 dimensions? > Yes, one will have to pay for an

Re: Sprint preparation

În lun., 4 mar. 2019 la 15:29, Andrius Merkys a scris: > Hi Andreas, > hi all, > > On 2019-03-04 14:38, Andreas Tille wrote: > > our sprint is coming soon - I'm delighted to see you again. I wonder > > whether there are recommendations how to reach the sprint location / > > appartments on

Re: Sprint preparation

În lun., 4 mar. 2019 la 15:29, Andrius Merkys a scris: > . Michael offers > everyone €6 discount for Taxify [2]. > Are you a Taxify user? I don't use them so much, so maybe you should generate your own referral link and update the site? Thanks again for the organizing! -- Michael R. Crusoe

Re: Bug#923637: ffindex FTCBFS: uses mpicc

Thank you Helmut for your testing and your patch. I've applied it at https://salsa.debian.org/med-team/ffindex/commit/5a7eeb53972e97ee264eb67d9df2f6c7089e4e14 However I'm just a Debian Maintainer, so I'll need a DD to grant me upload permission: dcut dm --uid

Re: [COMBINE-lab/RapMap] rapmap v0.6.0

Hey Rob, We packaged rapmap for Debian because we were packaging salmon as well. Looks like we adopted the numbering of the salmon-v* release of rapmap (recently 0.12) so this 0.6.0 release will currently be ignored as it is numerically smaller. Is that okay with you? What would you like done in

making picard-tools and downstream packages amd64 only due to GKL

Hello, I propose that we mark picard-tools/libpicard-java and all dependent packages amd64 only due to its dependency on gkl (which is itself amd64 only). This will unstick many package migrations. Shall I proceed? -- Michael R. Crusoe

another request for sponsorship: librcsb-core-wrapper

This package is 436 days old (!) https://salsa.debian.org/med-team/librcsb-core-wrapper/commit/004daf33a7d49c1abf4167ca69d51a0cca1a8313 Highlights from the changelog: * Adapt patches for latest boost version dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow librcsb-core-wrapper

Fwd: hinge_0.5.0-4_source.changes REJECTED

Another request for upload permissions: dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow hinge * Added libspdlog-dev 1:1.3.0 compatibility, Closes: #909763 This package has been out of "testing" since October and the new version has been waiting almost a year to clear the queue!

fix for biojava4-live pending testing removal, requesting upload permissions

Looks like icedtea-netx isn't migrating to testing anytime soon, so to avoid the pending removal of biojava4-live from "testing" I switched to another netx implementation and did more package cleanup work: https://salsa.debian.org/med-team/biojava4-live/commits/master dcut dm --uid

Re: bcbio - kind of ready, but dependencies gffutils and pybedtools are no longer distributed

Glad to hear about the BCBIO progress! I removed those packages, they were only removed due to lack of use, so it is not problem if you bring them back. În joi, 17 ian. 2019 la 17:53, Steffen Möller a scris: > Hello, > > I just finished what started at 2018 Sprint, i.e. the packaging of >

Request for sponsorship: python-mypy-extensions

https://salsa.debian.org/med-team/python-mypy-extensions This Python module has split off from the mypy sources upstream, so now it needs splitting out of python3-mypy into its own package. This package is required for the latest version of mypy, v0.660 gbp clone

Re: how to make https://salsa.debian.org/med-team/libdeflate public?

În mar., 15 ian. 2019 la 20:40, Andreas Tille a scris: > On Tue, Jan 15, 2019 at 07:02:34PM +0200, Michael Crusoe wrote: > > I think I lack the permissions > > if you used the inject-into-salsa-git script and the result was not > public that script is most probably broken.

how to make https://salsa.debian.org/med-team/libdeflate public?

I think I lack the permissions -- Michael R. Crusoe Co-founder & Lead, Common Workflow Language project Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania https://orcid.org/-0002-2961-9670 m...@commonwl.org

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

[Keeping Hannes on the CC in case he isn't subscribed] Thanks for the responses, all. În lun., 14 ian. 2019 la 17:48, Sascha Steinbiss a scris: > 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

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

Currently we package v 1.0.3, last stable release of Debian had v1.0.1 , https://github.com/seqan/lambda/releases/tag/lambda-v2.0.0 https://github.com/seqan/lambda/wiki/LAMBDA-%E2%86%92-lambda2-guide The CLI has significant

Re: Bug#914814: spades: FTBFS with jemalloc/experimental

On Sat, 5 Jan 2019 11:05:38 +0200 Faidon Liambotis wrote: > Therefore attached is a patch that addresses this using the je_rallocx > API. It also deals with the deprecation of the stats.cactive statistic > (as of jemalloc 4.0), using the stats.active instead. > > The patch should be

request for sponsorship: Toil is ready!

gbp clone g...@salsa.debian.org:med-team/toil.git https://salsa.debian.org/med-team/toil The "toil-cwl-runner" build from this passes all 197 CWL conformance tests! It would be nice to get this in the NEW queue ASAP, thanks! -- Michael R. Crusoe Co-founder & Lead, Common Workflow Language

Re: Odil : getting back into testing

I'm increasingly of the opinion that we should not stretch our limited resources even thinner by spending so much time on architectures used for network routers where it is unlikely that anyone will want to view medical image files. În vin., 4 ian. 2019 la 18:40, Julien Lamy a scris: > Hi all,

Re: What ffindex do we want to package

I think 0.9.9.7+sog+git20160415.14274c9-1 is the source of the recent FTBFS of hhsuite: https://bugs.debian.org/917495 as our packaged version is missing the "ffsort_index" function. The hh-suite github repo contains a submodule pointing at their fork of ffindex at ~ 2017-06-01:

request for uploader rights: staden-io-lib & rapmap

I've pushed my changes to fix the builds for these packages to salsa: https://salsa.debian.org/med-team/staden-io-lib https://salsa.debian.org/med-team/rapmap Could a Debian Developer please grant me upload privileges? dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow staden-io-lib

Re: Help requested for htslib build failure on ppc64el

În joi, 27 dec. 2018 la 22:14, Gustavo Romero a scris: > Hi Michael, > > On 12/27/2018 04:35 PM, Gustavo Romero wrote: > > On 12/27/2018 12:41 PM, Michael Crusoe wrote: > >> > https://buildd.debian.org/status/fetch.php?pkg=htslib=ppc64el=1.9-7=1545236716=0 > >

Help requested for htslib build failure on ppc64el

https://buildd.debian.org/status/fetch.php?pkg=htslib=ppc64el=1.9-7=1545236716=0 Can I get some assistance here? Rebuilding using Qemu and the earlier source packages produces the same error, so maybe this is a regression in the compiler? -- Michael R. Crusoe Co-founder & Lead, Common Workflow

Re: python-typing-extensions_3.6.6-2_source.changes REJECTED

:-D Thanks! În mar., 18 dec. 2018 la 13:45, Andreas Tille a scris: > On Tue, Dec 18, 2018 at 01:21:36PM +0200, Michael Crusoe wrote: > > I hereby promise to finish my DD application during the upcoming sprint. > > Promise accepted. ;-) > > -- > http://fam-tille.de >

Re: python-typing-extensions_3.6.6-2_source.changes REJECTED

Dear Debian Developer friends, I hereby promise to finish my DD application during the upcoming sprint. In the meantime, could a DD run the following command so I may upload updates to this package? dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow python-typing-extensions Thanks!

Re: Renamed repository gcsa to gcsa2 - general recommendation for creating repositories

Oops! Thank you Andreas for catching my mistake. I'm now using inject-into-salsa-git as documented in my personal checklist: https://github.com/mr-c/misc/wiki/Debian-Packaging-Checklist În joi, 13 dec. 2018 la 21:16, Andreas Tille a scris: > Hi Michael, > > by chance I realised that you have

Re: patch: Mark CVE-2018-1384{3,4,5} as fixed in htslib 1.9-1

a scris: > Hi Michael, > > it is not clear to me what this means: Do you intend to upload a fixed > package or do you expect somebody else to take action (and if the latter > what action exactly). > > Kind regards > >Andreas. > > On Sun, Dec 09, 2018 at 11:29

Re: patch: Mark CVE-2018-1384{3,4,5} as fixed in htslib 1.9-1

[adding the Debian Med Project List in CC] În dum., 9 dec. 2018 la 11:28, Michael Crusoe a scris: > Dear colleagues, > > Attached is a patch to mark CVE-2018-1384{3,4,5} as fixed in htslib 1.9-1. > > I also submitted a pull request > https://salsa.debian.org/security-tra

Re: Processed: ITP: arcp -- (Archive and Package) URI parser and generator

Hello, Is it not still Debian Med policy to set the owner of ITP bugs to the group? https://med-team.pages.debian.net/policy/#itp În vin., 7 dec. 2018 la 19:21, Debian Bug Tracking System < ow...@bugs.debian.org> a scris: > Processing commands for cont...@bugs.debian.org: > > > owner 915829

Bug#914928: ITP: python-typing-extensions -- Backported and Experimental Type Hints for Python

Thank you for the information. I'm already using this for schema_salad. I'll patch out the need for it and request removal of this package when Py3.6 is retired. -- Michael R. Crusoe În vin., 7 dec. 2018, 01:57 Piotr Ożarowski [Michael Crusoe, 2018-12-06] > > How soon is soon? >

Bug#914928: ITP: python-typing-extensions -- Backported and Experimental Type Hints for Python

How soon is soon? -- Michael R. Crusoe Co-founder & Lead, Common Workflow Language project https://impactstory.org/u/-0002-2961-9670 m...@commonwl.org În joi, 6 dec. 2018, 19:27 Piotr Ożarowski > The typing module was added to the standard library in Python 3.5 on a > > provisional basis

Re: htslib: FTBFS on i386: 2 tests fail

I uploaded htslib 1.9-3 but now the "missing builds" are blocking its migration. Can someone remind me how to fix the situation when architectures are removed from a package? Thanks, În dum., 14 oct. 2018 la 00:05, Andreas Tille a scris: > On Sat, Oct 13, 2018 at 04:47:14PM +

Re: htslib: FTBFS on i386: 2 tests fail

În lun., 15 oct. 2018 la 01:56, Sascha Steinbiss a scris: > 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

Re: Request for sponsorship: Bug#914928: ITP: python-typing-extensions -- Backported and Experimental Type Hints for Python

În mie., 28 nov. 2018 la 23:33, Andreas Tille a scris: > On Wed, Nov 28, 2018 at 09:49:08PM +0200, Michael Crusoe wrote: > > https://salsa.debian.org/med-team/python-typing-extensions > > a.k.a > > gbp clone g...@salsa.debian.org:med-team/python-typing-extensions.git &g

Request for sponsorship: Bug#914928: ITP: python-typing-extensions -- Backported and Experimental Type Hints for Python

https://salsa.debian.org/med-team/python-typing-extensions a.k.a gbp clone g...@salsa.debian.org:med-team/python-typing-extensions.git Thanks! -- Forwarded message - From: Michael R. Crusoe Date: mie., 28 nov. 2018 la 21:21 Subject: Bug#914928: ITP: python-typing-extensions --

Status of rsat?

Hello from the EU Biohackathon http://bh2018paris.info/ The rsat team is here, working on packaging for bioconda. I found https://salsa.debian.org/med-team/rsat/ and I was wondering what blockers that might be to finishing this. Their chat room for the event is at

Re: 2019 DebianMed Sprint in Vilnius: 2019-03-09 - 2019-03-11

eimbursement [0] > > > [0] https://wiki.debian.org/Sprints/HowTo > > > Olivier > > On 10/17/2018 10:00 AM, Michael Crusoe wrote: > > By popular acclaim, the 2019 Debian Med Sprint will be in March from > Saturday, March 9th until Monday, March 11th, 2019 in Vilnius

2019 DebianMed Sprint in Vilnius: 2019-03-09 - 2019-03-11

By popular acclaim, the 2019 Debian Med Sprint will be in March from Saturday, March 9th until Monday, March 11th, 2019 in Vilnius, Lithuania: https://wiki.debian.org/Sprints/2019/DebianMed2019 Thanks to NVO Avilys for donating a nice working space! -- Michael R. Crusoe Co-founder & Lead,

Re: Bug#911076: Request for sponsorship: libdeflate -- fast, whole-buffer DEFLATE-based compression and decompression)

Thank you Steffen În mar., 16 oct. 2018 la 20:52, Steffen Möller a scris: > Done > > On 15.10.18 13:15, Michael Crusoe wrote: > > g...@salsa.debian.org:med-team/libdeflate.git > > > > Thanks! > > > > În lun., 15 oct. 2018 la 14:12, Michael R. Crusoe > &

Bug#911076: Request for sponsorship: libdeflate -- fast, whole-buffer DEFLATE-based compression and decompression)

g...@salsa.debian.org:med-team/libdeflate.git Thanks! În lun., 15 oct. 2018 la 14:12, Michael R. Crusoe a scris: > Package: wnpp > Severity: wishlist > Owner: Debian Med team > > * Package name: libdeflate > Version : 1.0 > Upstream Author : Eric Biggers > * URL :

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