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 ahead
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. Use "Team upload" in
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 favouri
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
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!
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]
2. Once you have a bu
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
> even build properly on my
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 impossible to use pys
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 either unset the paramet
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 objections,
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 don't know any good
w
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
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 n
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.
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 of date. We have
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 pro
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 >= 1.29.14
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 it is not me who wil
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
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 mailingli
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 c
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 spo
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 $AUTOPKGT
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] https://wiki.ubuntu.com/StableR
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
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 Ca
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, ab
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 succe
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.
R
On Fri, 20 Dec 2019 at 23:19, Andreas Tille wrote:
> On Fri, Dec 20, 2019 at 12:54:02PM -0800, Michael Crusoe wrote:
> > python-biopython 1.76-1 is already pushed to salsa.debian.org
>
> Cool!
>
> > and will be
> > uploaded to the archive once the current release has migrated to testing
> > :-)
>
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.
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 t
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 e
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 beha
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
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 e
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 do
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?
> >
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:
> https://www.debian.org/doc/manuals/developers-reference/pkgs.en.html#marking-non-
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 see
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 don't
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