Re: Please add hint to remove q2-feature-classifier from testing to enable scikit-learn migrating

Hi Andreas, Étienne On Sun, 5 Feb 2023 at 19:31, Andreas Tille wrote: > we need to check why q2-feature-classifier does not work with > scikit-learn. But for the moment it would help if scikit-learn could > migrate to testing to free lots of its rdepends from testing removal > warnings. I

Re: Packages in non-free can be autobuilt

Hi I was reminded of this thread now that cluster3 needs another rebuild for Python 3.11 (#1028186). On Wed, 30 Mar 2022 at 06:48, tony mancill wrote: > Thanks for the reminder. It's unfortunate, but the link to the full > license that causes the package to be non-free is broken and I don't

Re: Packages in non-free can be autobuilt

Hi Another reminder about this: On Sun, 20 Dec 2020 at 01:33, Adrian Bunk wrote: > Looking at the cluster3 discussion, just a reminder that many packages > in non-free can be autobuilt just like packages in main: >

Re: Why is isal limited to just three archs?

Hi On Sat, 16 Oct 2021 at 10:42, Thomas Goirand wrote: > > On 10/16/21 9:09 AM, Nilesh Patra wrote: > > Hi Ondřej, > > > > I see that isal package is limited to amd64, arm64 and kfreebsd-amd64. > > Is there a particular reason for this? -- Is it possible to extend > > support to other archs? > >

Re: Failed build for seqan2 on i386

On Sun, 14 Feb 2021 at 10:56, Andreas Tille wrote: > Since it would to "experimental" to me I have not choosen this option > since I wanted to be quick. The fact that my upload had successfully > built on i386 meanwhile makes me optimistic, that we can ask for a > migration to testing hint. I

Re: [RFS] vsearch 2.25.2-3 arm64 port (Was: Some q2 friends are still not in testing)

Hi Étienne On Sat, 13 Feb 2021 at 01:24, Étienne Mollier wrote: > > 2. port vsearch on arm64. > > Good news, this option turns out to work out of the box! :) Thanks for testing this! > Assuming this kind of change is welcome in Soft Freeze, would it > be possible to do a sponsored upload to

Re: Plan for Soft Freeze?

Hi Nilesh On Sat, 6 Feb 2021 at 09:46, Nilesh Patra wrote: > - I had been seeing a few bug reports and messages on IRC for different > (binary-all)packages whose source-only upload hasn't been done post first > binary upload, and are hence being stalled from migrating to testing - are > there

Status of MRIcron package

Hi Debian Med, NeuroDebian I noticed that the maintainer address for MRIcron [1] is NeuroDebian Team yet the VCS is under med-team on Salsa [2]. Which is correct? I'd like to make some changes to this package which are not suitable for a non-maintainer upload. Shall I adopt the package on

Re: Should the pandas 1.x transition be forced (breaking python-biom-format and q2-demux/q2-types) or keep waiting?

Hi Rebecca On Mon, 24 Aug 2020 at 01:03, Rebecca N. Palmer wrote: > pandas 1.0 has been in experimental for 6+ months, because it breaks > some of its reverse dependencies: ... > Ubuntu freezes this Thursday, but I suspect I may have left this too > late for that. We can sync 1.0.4+dfsg-1 from

Re: Missing dependancies for streamlit

On Tue, 7 Apr 2020 at 12:46, Andreas Tille wrote: > > On Tue, Apr 07, 2020 at 11:15:17AM +0100, Rebecca N. Palmer wrote: > > A potential workaround for testing: while package builds (including > > build-time tests) are not allowed to use the network, autopkgtests *are* > > allowed to => skip the

Re: Bug#937606: Droping Python2 support for Biopython

On Sat, 21 Dec 2019 at 08:59, Andreas Tille wrote: > The versions in unstable are depending python3-biopython. The packages are > not migrating due to > >seqsero/i386 unsatisfiable Depends: sra-toolkit [1] See #947098. Hopefully the hint solves it.

Re: racon - missing dep

Hi Olivier On 2019/11/04 12:34, Olivier Sallou wrote: Was looking at racon FTBS and I saw that you started a new upstream release 1.4.7. It now depends on liblogger-dev, I cannot however find this lib in debian (not even in NEW). Is it a pending issue? An error? See discussion in #940564.

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

Hi Michael On Mon, 14 Oct 2019 at 19:27, 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 > #21~18.04.1-Ubuntu kernel. According to reproducible builds [1], it built

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

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 pbuilder but sbuild and may be that might make some > difference. Any volunteer to build abyss using sbuild and report > whether this works or not? FWIW,

Re: FW: Bio linux download

On Wed, 24 Apr 2019 at 23:42, Tony Travis wrote: > I reported the bug and provided a patch - What else should I have done? Subscribing the 'ubuntu-sponsors' team to the bug would have made it visible to someone who could have done the upload for you. It's mostly only the packages supported by

Re: FW: Bio linux download

Hi On Wed, 24 Apr 2019 at 21:30, Dylan Aïssi wrote: > I am preparing the fix [1], I will ping you when it is ready. Uploaded, thanks! For future reference, the general procedure to get a fix into Ubuntu is to attach a patch and subscribe 'ubuntu-sponsors' to the bug. Regards Graham

Re: FW: Bio linux download

Hi Tony On Wed, 24 Apr 2019 at 16:32, Tony Travis wrote: > [Note: There is a problem installing "metaphlan2" under Ubuntu 18.04] Is this LP: #1777165 [1]? Let's get this fixed, I'm happy to sponsor a SRU [2] upload. Regards Graham [1] https://pad.lv/1777165 [2]

Re: [Help] Re: pbgenomicconsensus: autopkgtest regression

Hi Andeas On Sun, 7 Apr 2019 at 07:50, Andreas Tille wrote: > I have no idea why command1 is failing. Anybody who can reproduce > this test result and can fix this test? The output of command1 is the following: autopkgtest [15:39:43]: test command1: unset GZIP && cp -r Makefile tests

Re: Figtree on Ubuntu

Hi Fabian On 2018/10/18 13:26, Graham Inggs wrote: I've uploaded with a workaround, hopefully this can still make it into the release. It is in! Would you be able to complete steps 3 and 4 of the SRU procedure [1]? No need to subscribe 'ubuntu-sponsors' to the bug, I can sponsor an upload

Re: Figtree on Ubuntu

Hi Fabian On 2018/10/17 16:02, Fabian Klötzl wrote: That's weird. Building works fine on my Ubuntu 18.04. Unfortunately, I am not a Java person so I have no clue what to do. Apparently this was due to the recent switch to openjdk-11 for 18.10. I've uploaded with a workaround, hopefully this

Re: Figtree on Ubuntu

Hi Fabian On 2018/10/17 13:33, Fabian Klötzl wrote: Currently, figtree crashes on Ubuntu due to a simple bug [1]. I have opened a bug on launchpad some time ago but nobody has yet volunteered to integrate the debian version into ubuntu (and backport it to 18.04). Does someone on this

can we disable the bounce kicker? Re: confirm

Hi List Maintainers As per: https://lists.debian.org/debian-python/2018/06/msg00045.html Would you consider disabling the bounce kicker for debian-science and debian-med please? Although, I am more affected by the debian-med-packaging and debian-science-maintainers lists. Regards Graham

Re: Updating Build-Depends for R packages

On 10 November 2017 at 09:59, Andreas Tille wrote: > Just go ahead. :-) OK, pushed but not uploaded. I don't think these changes are worth uploads on their own. > We do not *yet* have a tool but I think dh-make-R could / should be > tweaked to enable updating a package (but

Updating Build-Depends for R packages

Hi! I noticed the following build failures in Ubuntu recently: r-bioc-genomicfeatures 1.30.0+dfsg-1 Error : package ‘GenomicRanges’ 1.28.6 was found, but >= 1.29.14 is required by ‘GenomicFeatures’ r-bioc-genomicalignments 1.14.0-1 Error : package ‘GenomicRanges’ 1.28.6 was found, but >=

convert_svn_2_git (was: Bug#877288: r-base: Rebuilding r-bioc-biocgenerics with new R changes behaviour)

Hi I wanted to upload the new upstream versions of r-bioc-s4vectors and r-bioc-iranges, but figured I should convert from svn to git first. I tried 'convert_svn_2_git' on both, but after a long while, I ended up with an empty git repo and no 'debian' directory. Looking again now, I think the

Re: Bug#877288: r-base: Rebuilding r-bioc-biocgenerics with new R changes behaviour

Control: reassign -1 src:r-bioc-s4vectors 0.14.3-1 Control: affects -1 = r-bioc-iranges r-bioc-variantannotation Control: tags -1 + fixed-upstream Control: clone -1 -2 Control: reassign -2 src:r-bioc-iranges 2.10.2-1 On 30 September 2017 at 14:30, Dirk Eddelbuettel wrote: > Out

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

On 07/08/2017 17:49, Andreas Tille wrote: Do you think it would be sensible to file some RC bug against it to not enter testing? I cloned #871083 against python-pysam to #871314 and #871315 against htslib and samtools respectively.

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

On 24/07/2017 06:12, Afif Elghraoui wrote: I was under the impression that htslib 1.5, required for bcftools 1.5, has a soname bump. There is no pysam release yet to wrap htslib 1.5, so I think upgrading bcftools/samtools/htslib right now to 1.5 will just make it impossible to use pysam until a

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

On 29/07/2017 10:36, Sascha Steinbiss wrote: 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

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

On 28 July 2017 at 16:30, Sascha Steinbiss wrote: > Once I'm at it I can also take a shot at bcftools. Never worked on that > before though, let's see how it goes. Please take note you'll need to backtract in git until version 1.4.1-2, add the patches, and upload 1.4.1-3. I

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

On 25/07/2017 11:20, Andreas Tille wrote: So how will we deal with #865006 and issues in python-pysam? I made a few minor changes to python-pysam 0.11.2.2 (which builds against bcftools 1.4.1) as it stands in git, and managed to get it to build and pass its tests. If there are no

Re: CI for ray

Hi Nadiya On 28 July 2017 at 05:35, Nadiya Sitdykova wrote: > -- > The value of the MCA parameter "plm_rsh_agent" was set to a path > that could not be found: > > plm_rsh_agent: ssh : rsh > > Please

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

On 24 July 2017 at 06:12, Afif Elghraoui wrote: > I was under the impression that htslib 1.5, required for bcftools 1.5, > has a soname bump. There is no pysam release yet to wrap htslib 1.5, so > I think upgrading bcftools/samtools/htslib right now to 1.5 will just > make it

Re: Please fix bugs

On 13 July 2017 at 09:52, Fabian Klötzl wrote: > I tried to do my part and applied an available patch to trimmomatic. Not > sure if you want to upload a new version for such a tiny change, though. > I also had a look at the jellyfish issues with PIE [1]. But it doesn't >

Re: Trimmomatic bug

Hi Redmar On 4 July 2017 at 09:56, Redmar wrote: > I have found the code on the debian-med git [2] and fixed the issue, > but I don't have access to push it, and I'm not sure where to go from > here. Here's one way to do it: 1. Report a bug against trimmomatic in Debian [1]

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

On 28/06/2017 23:44, Nadiya Sitdykova wrote: I added autopkgtest test-suite to fasttree package. As Andreas is travelling, I hope someone else would step in. Uploaded, thanks!

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

Hi Nadiya On 28/06/2017 23:44, Nadiya Sitdykova wrote: I added autopkgtest test-suite to fasttree package. As Andreas is travelling, I hope someone else would step in. I'll review this for you. Regards Graham

Re: New versions of some Bioconductor packages for R 3.4.0

On 14/05/2017 12:08, Andreas Tille wrote: I have created a dependency graph of most of the bioc packages here: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-000-dependency-scheme/3.3/ The makefile created a PNG but the ditaa file is perfectly readable in your

Re: New versions of some Bioconductor packages for R 3.4.0

On 12 May 2017 at 02:18, Charles Plessy wrote: > as R 3.4.0 is in Unstable and as the current Bioconductor packages in Unstable > are from a release that does not support R 3.4.0, I think that you can upload > to unstable directly. > > And yes, please commit directly to SVN.

New versions of some Bioconductor packages for R 3.4.0

Hi I've like to package some new versions of existing Bioconductor packages for compatibility with R 3.4.0. I'm looking at, at least: r-bioc-annotationhub r-bioc-aroma.light r-bioc-biocparallel r-bioc-s4vectors I see these are all maintained by Debian Med Packaging Team in SVN. May I go