thon{version} -p 3.5 returned
> > exit code 13
> > debian/rules:22: recipe for target 'override_dh_auto_test' failed
Upstream has now fixed this issue, and I've cherry-picked the fix into the
package as a patch. I've pushed to git.d.o, so an (urgent) upload would be much
appreciated.
Merry Christmas all!
Cheers
K
---
Kevin Murray
Hi Ghis,
On 11:39 06/12, Ghislain Vaillant wrote:
> On Sun, 4 Dec 2016 11:08:35 +1100 Kevin Murray wrote:
> I can do it if time is limited for you. I am dealing with a different chain of
> package dependencies which would require keepalive being packaged too.
That would be great
Hi Andreas,
On 17:44 04/12, Andreas Tille wrote:
> Kevin Murray added a Closes statement to its latest commits to iqtree.
> This is the according bug report. :-) Kevin, please tell me if you
> consider iqtree ready for Upload.
I was just waiting on the BTS to give me a bug number.
Hi,
I had a look at the build of cwltool, and it appears it depends upon the
`keepalive` python package. I will file an RFS bug for this (and prepare a
package as time permits).
Cheers,
K
---
Kevin Murray
;ve now prepared the package of the latest upstream release, so a review &
upload would be required. Thanks in advance!
Cheers,
K
---
Kevin Murray
> Debian-med-packaging mailing list
> debian-med-packag...@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
---
Kevin Murray
hores when building this
package in pbuider chroots, related to a missing /dev/shm. I have never
experienced the issues you report though.
Cheers,
K
[1]:
https://bitbucket.org/snakemake/snakemake/issues/426/random-test-hangs-during-debian-package
---
Kevin Murray
Hi all,
AFAICT I think I should have fixed the issues in skbio. I've filed an ROM bug,
and updated to latest upstream. Could I please get an upload and see if the
test failure goes away?
Cheers,
Kevin
---
Kevin Murray
Hi Andreas,
On 19:15 15/11, Kevin Murray wrote:
> I will also (but haven't yet) see if I can get it to build against libssw.
Well that turned out to be far easier than I expected. I've pushed a patch that
uses libssw from debian. So let's see if this fixes the build. And we a
re also old binary packages preventing a testing transition,
which I'm not sure how to deal with.
Cheers,
K
---
Kevin Murray
n/listinfo/debian-med-packaging
---
Kevin Murray
Hi Daniel,
I've prepared the update. I'll push as soon as git.debian.org returns to the
internet.
Cheers,
K
---
Kevin Murray
systemd (via /run/systemd/system)
Versions of packages python-falcon depends on:
ii libc6 2.21-9
ii python2.7.11-1
ii python-mimeparse 0.1.4-1
ii python-six1.10.0-2
pn python:any
python-falcon recommends no packages.
python-falcon suggests no
Hi Dmitry,
Thanks for your advice.
On 10:19 23/02, Dmitry Shachnev wrote:
> Hi Kevin,
>
> On Tue, Feb 23, 2016 at 02:34:11PM +1100, Kevin Murray wrote:
> > I have recently needed to use a python3-only sphinx build process on a
> > system with both python-sphinx & py
table'), (300, 'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 4.3.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
---
Kevin Murray
0xA4B4EE6A
Package: wnpp
Severity: wishlist
Owner: Kevin Murray
* Package name: libqcpp
Version : 0.1.9
Upstream Author : Kevin Murray
* URL : https://github.com/kdmurray91/libqcpp
* License : LGPL
Programming Lang: C++
Description : A C++ library for next-gen
Run: 111 Failure total: 3 Failures: 3 Errors: 0
> make[1]: *** [unittests] Error 1
>
> Could you please take a look?
>
> Thanks!
>
---
Kevin Murray
0xA4B4EE6A
. That makes sense, now you mention it.
Cheers,
Kevin
---
Kevin Murray
0xA4B4EE6A
Package: libeigen3-doc
Version: 3.3~beta1-1
Severity: normal
Dear Maintainer,
When viewing the HTML documentation pages, a grey box (which should contain the
navbar) obscures the text of the page. In addition, the version displayed does
not correspond to the package version (documentation says 3.
Package: wnpp
Severity: wishlist
Owner: Kevin Murray
* Package name: hail
Version : 0.1.1
Upstream Author : Kevin Murray
* URL : https://github.com/kdmurray91/hail
* License : GPL
Programming Lang: C
Description : Efficiently extract arbitrary lines
Package: wnpp
Severity: wishlist
Owner: Kevin Murray
* Package name: scrm
Version : 1.6.1
Upstream Author : Paul R. Staab
* URL : https://github.com/scrm/scrm
* License : GPL
Programming Lang: C++
Description : A coalescent simulator for genome-scale
Source: libqes
Version: 0.1.20-1
Severity: important
Tags: upstream
Dear Maintainer,
An upstream bug causes a test failure on systems with char == unsigned char
(e.g. ARM). Importing the new upstream release 0.1.21 should fix this issue.
Cheers,
K
-- System Information:
Debian Release: stretch/
now, thought it's not ready for upload.
Cheers,
Kevin
---
Kevin Murray
0xA4B4EE6A
Hi all,
On 13:22 21/12, Kevin Murray wrote:
> Hi Andreas,
>
> On 09:07 06/12, Andreas Tille wrote:
> > Hi Kevin,
> >
> > any news about building the docs? I have reset the target distribution to
> > UNRELEASED since it does not build in a pbuilder chroot.
>
Package: axe-demultiplexer
Version: 0.3.0+dfsg-2
Severity: important
Tags: upstream
Dear Maintainer,
An upstream bug prevents tests passing on 32-bit systems. Upstream has fixed
this in the latest release.
Cheers,
Kevin
-- System Information:
Debian Release: stretch/sid
APT prefers unstable
d/python-skbio.git
Thanks!
Cheers,
Kevin
---
Kevin Murray
0xA4B4EE6A
Hi all,
I'm working on this bug to find the root of the issue and fix it.
Cheers,
Kevin
---
Kevin Murray
0xA4B4EE6A
Package: wnpp
Severity: wishlist
Owner: Kevin Murray
* Package name: dawg
Version : 1.2.0
Upstream Author : Reed A. Cartwright
* URL : http://scit.us/projects/dawg
* License : GPL-2
Programming Lang: C++
Description : program to simulate the evolution
Hi Tiago and Konstantin
You are both correct, yes. Sorry, and thanks for correcting this (though it's
correct in d/control and d/copyright).
Cheers,
K
On 11:41 01/12, Tiago Ilieve wrote:
> Kevin,
>
> On 1 December 2015 at 00:33, Kevin Murray wrote:
> > Package: wnpp
&g
Package: wnpp
Severity: wishlist
Owner: Kevin Murray
* Package name: libzstd
Version : 0.4.0
Upstream Author : Yann Collet
* URL : https://github.com/Cyan4973
* License : BSD
Programming Lang: C
Description : fast lossless compression algorithm
Zstd
Package: python-skbio
Version: 0.4.0-3
Severity: normal
Tags: patch
Hi all,
I noticed today that scikit-bio (python-skbio in Debian) has no documentation
packaged, despite upstream having quite rich Sphinx documentation. I'm fixing
this, and will push to git soon (patch not so much attached as in
Package: wnpp
Severity: wishlist
Owner: Kevin Murray
* Package name: libqes
Version : 0.1.20
Upstream Author : Kevin Murray
* URL : https://github.com/kdmurray91/libqes
* License : GPL-3+
Programming Lang: C
Description : Next-gen sequencing format
X-Debbugs-CC: Debian Med Packaging
Package: wnpp
Severity: wishlist
Owner: Kevin Murray
* Package name: partitionfinder
Version : 2.0.0
Upstream Author : Brett Calcott and Rob Lanfear
* URL : https://github.com/brettc/partitionfinder
* License : GPL-3
I thought I responded to this already.
I'm fixing this upstream so that the binary name doesn't change; it will now be
`axe-demux` everywhere. I've re-released. I've decided to re-do the entire
packaging too, so that we don't bundle libqes or a cut-down gsl. I have a
coupl
Package: dwgsim
Version: 0.1.11-1
Severity: grave
Justification: renders package unusable
Hi all,
I somehow managed not to add the debian/dwgsim.install file to git. Due to the
upstream makefile not having an install rule, this lead to a Debian package
with no binary. I have fixed this in git.
M
ackage it under DPMT umbrella
>
I think this is just waiting on some of its dependencies I'm packaging. I'll
contact the DPMT about co-maintainership. I think they are all ready for
review, though there are probably issues to address.
Cheers,
Kevin
---
Kevin Murray
GPG pubkey: http
team.
>
OK, sure, I'll contact the DPMT about this and the remainder of the python
modules needed to build seqan's docs.
Cheers,
Kevin
---
Kevin Murray
GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc
FPR: 656C 0632 1EAB 2C3F 3837 9767 17C2 8EB1 A4B4 EE6A
Hi Aaron,
I'm both the Debian packager and upstream, so I'll take this on. It's almost
certainly an upstream issue in the unit tests. I don't test on anything other
than amd64 Debian unfortunately.
Cheers,
K
---
Kevin Murray
GPG pubkey: http://www.kdmurray.id.au/static/A4
ld aid making the switch smoother.
>
> Thanks,
>
> Scott K
I've applied the patch and added a (Closes: ) in d/changelog. Can a DD upload
please?
Cheers,
Kevin
---
Kevin Murray
GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc
FPR: 656C 0632 1EAB 2C3F 3837 9767 17C2 8EB1 A4B4 EE6A
e is that no-one in such teams has packaged it yet, and I am only
packaging it as a build-depend of SeqAn, which is very much a Debian Med
package.
Though I understand if the team would rather this be maintained elsewhere.
Cheers,
K
---
Kevin Murray
GPG pubkey: http://www.kdmurray.id.au/stati
Package: wnpp
Severity: wishlist
Owner: Kevin Murray
* Package name: python-latexcodec
Version : 1.0.1
Upstream Author : Matthias C. M. Troffaes
* URL : https://github.com/mcmtroffaes/pybtex-docutils
* License : Expat
Programming Lang: Python
Description
Package: wnpp
Severity: wishlist
Owner: Kevin Murray
* Package name: pybtex-docutils
Version : 0.2.1
Upstream Author : Matthias C. M. Troffaes
* URL : https://github.com/mcmtroffaes/pybtex-docutils
* License : Expat
Programming Lang: Python
Description
Package: wnpp
Severity: wishlist
Owner: Kevin Murray
* Package name: python-oset
Version : 0.1.3
Upstream Author : Carlos Martin, Raymond Hettinger
* URL : https://gitorious.com/sleipnir/python-oset
* License : BSD
Programming Lang: Python
Description
Package: wnpp
Severity: wishlist
Owner: Kevin Murray
* Package name: python-sphinxcontrib.bibtex
Version : 0.3.2
Upstream Author : Matthias C. M. Troffaes
* URL :
https://github.com/mcmtroffaes/sphinxcontrib-bibtex/blob/develop/LICENSE.rst
* License : BSD
Package: wnpp
Severity: wishlist
Owner: Kevin Murray
* Package name: dwgsim
Version : 0.1.11
Upstream Author : Nils Homer
* URL : https://github.com/nh13/DWGSIM
* License : GPLv2, MIT/X
Programming Lang: C
Description : DWGSIM: an improved short read
Package: wnpp
Severity: wishlist
Owner: Kevin Murray
* Package name: snakemake
Version : 3.4
Upstream Author : Johannes Köster
* URL : https://bitbucket.org/johanneskoester/snakemake
* License : MIT
Programming Lang: Python
Description : Snakemake
Package: wnpp
Severity: wishlist
Owner: Kevin Murray
* Package name: axe-demultiplexer
Version : 0.2.8
Upstream Author : Kevin Murray
* URL : https://github.com/kdmurray91/axe
* License : GPL3+
Programming Lang: C
Description : Axe demultiplexes DNA
Package: sphinxcontrib-autoprogram
Version: 0.1.1-1
Severity: important
Hi all,
The python3 packaging of khmer will need a python3 version of
sphinxcontrib.autoprogram. This is a bug to let you know that I'm
working on this.
Cheers,
Kevin
-- System Information:
Debian Release: stretch/sid
AP
Charles,
On 09:23 10/07, Charles Plessy wrote:
> Le Thu, Jul 09, 2015 at 04:15:35PM +1000, Kevin Murray a écrit :
> > Package: wgsim
> > Severity: serious
> > Justification: Policy 7.6.1
> >
> > Hi all,
> >
> > I have inadvertently packaged wgsim for
inary) package and offer my apologies for not having inspected samtools
throughly.
Kevin Murray
-- System Information:
Debian Release: stretch/sid
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'testing'), (500, 'stable'), (500,
'oldstable'), (1
package: wnpp
Severity: wishlist
Owner: 'Kevin Murray'
*Package Name : wgsim
Version : 0.3.1-r13
Upstream Author : Heng Li
*URL : https://github.com/lh3/wgsim
*License : MIT
*Description : wgsim simulates sequencing reads from a reference genome.
Wgsim is a small tool for simulatin
ve I am
sufficiently familiar with its development and code base to maintain
this package.
I've made the package, and uploaded it to mentors.debian.net (see above
dget/webpage links).
Please let me know how I can improve!
Thanks,
Kevin Murray
s...@kdmurray.id.au
I'm an FSF member -- He
package: wnpp
Severity: wishlist
Owner: 'Kevin Murray'
*Package Name : scythe
Version : 0.994-1
Upstream Author : Vince Buffalo
*URL : https://github.com/vsbuffalo/scythe
*License : MIT
*Description : Bayesian adaptor trimmer for sequencing reads
I am packaging as it is a frequ
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