The current correct link appears to be:
http://upsilon.cc/~zack/talks/2011/20110321-taipei.pdf
--
Michael R. Crusoe
--
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Package: wnpp
Severity: wishlist
Owner: "Michael R. Crusoe"
* Package name: sga
Version : 0.9.35
Upstream Author : Jared Simpson
* URL : https://github.com/jts/sga
* License : GPLv3
Programming Lang: C++
Description : A de novo genome assembler based o
X-Debbugs-Cc: debian-...@lists.debian.org
X-Debbugs-Cc: debian-de...@lists.debian.org
Package: wnpp
Severity: wishlist
Owner: debian-...@lists.debian.org
* Package name: bamtools
Version : 2.2
Upstream Author : Derek Barnett
* URL : https://github.com/pezmaster31/bamto
And here's the package,
https://github.com/mr-c/bamtools/tree/debian
My packaging skills are a bit rusty, so your feedback would be appreciated.
On Tue, Nov 6, 2012 at 1:28 PM, Michael Crusoe wrote:
> X-Debbugs-Cc: debian-...@lists.debian.org
> X-Debbugs-Cc: debian-de...@lists
Thanks Sascha!
Pe 13 mai 2016 11:45 p.m., "Sascha Steinbiss" a
scris:
> Hi all,
>
> I re-introduced the build dependency on bowtie and also did some minor
> housekeeping. Committed the fix in git.
>
> Cheers
> Sascha
>
> > On 19 Mar 2016, at 14:34, Andreas Beckmann wrote:
> >
> > Package: rsem
>
Thank you, Martin for the clarification; and my apologies for the strong
wording.
For your own information, I don't think the Kent code license is at *all*
compatible with the Artistic 2.0 license. It doesn't give anyone the right
to redistribute the code, for example. Let along the other enumerat
If you are looking to ensure that derivative works aren't relicensed, and
you want to use an existing license (which I recommend) then you are
looking for a copyleft license.
I like this interactive guide to software licenses:
http://oss-watch.ac.uk/apps/licdiff/
On Fri, Dec 11, 2015, 10:35 Andre
wrote:
> [ /me is just doing housekeeping of wnpp bugs and removing
> inconsistencies ]
>
> (please keep me in CC if you want to reply to me)
>
> On Wed, Sep 30, 2015 at 03:24:25PM -0700, Michael Crusoe wrote:
> > Oops, I thought I had renamed the source package to libcereal.
Thank you Dhole, I have incorporated this patch into -3.
Note: Transdecoder 2.1.0 is said to have repeatability issues so I'm going
to skip the new release until that is fixed.
https://github.com/TransDecoder/TransDecoder/issues/19
On Fri, Apr 22, 2016 at 8:57 PM, Dhole wrote:
> Source: transd
Thank you Martin for your report. I've contacted upstream who has already
fixed the issue in a soon to be released new version.
Package: wnpp
Severity: wishlist
Owner: Debian Med team
X-Debbugs-CC: debian-...@lists.debian.org
* Package name: python-bz2file
Version : 0.98
Upstream Author : Nadeem Vawda
* URL : https://github.com/nvawda/bz2file
* License : Apache
Programming Lang: Pyt
Package: wnpp
Owner: Debian Med mailing list
Severity: wishlist
X-Debbugs-Cc: debian-...@lists.debian.org
* Package name: khmer
Version : 1.3
Upstream Author : Michael R. Crusoe & C. Titus Brown <
khmer-proj...@idyll.org>
* URL : http://khmer.readthedocs.org/
* Licens
Package: wnpp
Severity: wishlist
Owner: Debian Med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org
* Package name: prokka
Version : 1.10
Upstream Author : Torsten Seemann
* URL : http://www.vicbioinformatics.com/software.prokka.shtml
* Li
Package: wnpp
Severity: wishlist
Owner: Debian Med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org
* Package name: transdecoder
Version : 2.0.1
Upstream Author : Brian Haas
* URL : http://transdecoder.github.io/
* License : BSD-3-
Package: wnpp
Severity: wishlist
Owner: Debian Med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org
* Package name: parafly
Version : 0.0.2013.01.21
Upstream Author : Brian Haas
* URL : http://parafly.sourceforge.net
* License : BS
Just three jars for now (+ an embedded collections15): jung-api.jar,
jung-graph-impl.jar,
and jung-algorithms.jar
Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/libjung-java.git
Vcs-Git: git://anonscm.debian.org/debian-med/libjung-java.git
Patches welcome
Package: wnpp
Severity: wishlist
Owner: Debian Med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org
* Package name: jaligner
Version : 1.0
Upstream Author : Ahmed Moustafa
* URL : http://jaligner.sf.net
* License : GPL
Programmin
Package: wnpp
Severity: wishlist
Owner: Debian Med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org
* Package name: rsem
Version : 1.2.19
Upstream Author : Bo Li
* URL : http://deweylab.biostat.wisc.edu/rsem/
* License : GPL-3
Pr
Package: wnpp
Severity: wishlist
Owner: Debian Med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org
* Package name: r-bioc-ebseq
Version : 1.6.0
Upstream Author : Ning Leng
* URL : https://www.biostat.wisc.edu/~kendzior/EBSEQ/
* License
Package: wnpp
Severity: wishlist
Owner: Debian Med team
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org
* Package name: r-cran-blockmodeling
Version : 0.1.8
Upstream Author : Ales Ziberna
* URL :
http://cran.fhcrc.org/web/packages/blockmodelin
Package: wnpp
Severity: wishlist
Owner: Debian Med team
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* Package name: express
Version : 1.5.1
Upstream Author : Adam Roberts & Lior Pachter
* URL : http://bio.math.berkeley.edu/eXpress/index.ht
Thanks!
On Tue Feb 03 2015 at 4:21:08 AM Debian Bug Tracking System <
ow...@bugs.debian.org> wrote:
> This is an automatic notification regarding your Bug report
> which was filed against the bowtie package:
>
> #776881: bowtie: '-debug' binaries break `bowtie-build`
>
> It has been closed by Cha
Package: trimmomatic
Version: 0.32+dfsg-2
Severity: important
Dear Maintainer,
The files in the adapters directory in upstream's source are an important
part of the Trimmomatic package. They are used to trim contaminants from
sequencing files. Please include them in a future release of the packag
On Thu, Feb 26, 2015 at 3:13 PM Andreas Tille wrote:
> Hi Michael,
>
> thanks a lot for hints like these. Do you think this is severity
> important or even serious (and thus we need to push the fix into
> Jessie)? In the latter case we should stick to 0.32 otherwise I'd go
> with an update to l
On Thu, Feb 26, 2015 at 4:01 PM Andreas Tille wrote:
> Hi Michael,
>
> On Thu, Feb 26, 2015 at 08:40:22PM +, Michael Crusoe wrote:
> > End users will expect adapter files to be installed and available. Please
> > push into Jessie.
>
> OK. I'll bump the
On Thu, Feb 26, 2015 at 4:26 PM Andreas Tille wrote:
> Hi Michael,
>
> On Thu, Feb 26, 2015 at 09:16:07PM +, Michael Crusoe wrote:
> > > Since we are using a wrapper anyway I have set this inside the wrapper
> > > and thus do not see any need for README.De
Control: block 777697 by -1
retitle: ITP: berkeley-express -- Streaming quantification for
high-throughput sequencing
Package is in the NEW queue under new name:
https://ftp-master.debian.org/new/berkeley-express_1.5.1-1.html
Package: wnpp
Owner: "Debian Med Team"
Severity: wishlist
X-Debbugs-CC: debian-...@lists.debian.org
* Package name: cereal
Version : 1.1.2
Upstream Author : Randolph Voorhies, Shane Grant <
cereal...@googlegroups.com>
* URL : https://github.com/USCiLab/cereal
* Licens
Package: wnpp
Owner: "Debian Med Team"
Severity: wishlist
X-Debbugs-CC: debian-...@lists.debian.org
* Package name: libgff-dev
Version : 1.0
Upstream Author : Rob Patro
* URL : http://www.cs.cmu.edu/~robp/files/libgff.tgz
* License : BSL-1.0
Programming Lan
Package: wnpp
Owner: "Debian Med Team"
Severity: wishlist
X-Debbugs-CC: debian-...@lists.debian.org
* Package name: libspdlog-dev
Version : 1.4
Upstream Author : Gabi Melman
* URL : https://github.com/COMBINE-lab/spdlog
* License : MIT
Programming Lang: C++
Package: wnpp
Owner: "Debian Med Team"
Severity: wishlist
X-Debbugs-CC: debian-...@lists.debian.org
* Package name: salmon
Version : 0.4.2
Upstream Author : Rob Patro, Carl Kingsford and Steve Mount
* URL : https://github.com/COMBINE-lab/salmon
* License : GPL
Package: wnpp
Owner: "Debian Med Team"
Severity: wishlist
X-Debbugs-CC: debian-...@lists.debian.org
* Package name: snap-aligner
Version : 0.18~1.0~beta.18
Upstream Author : The SNAP Team
* URL : http://snap.cs.berkeley.edu/
* License : Apache-2.0
Programmin
Package: wnpp
Owner: "Debian Ruby Team"
Severity: wishlist
X-Debbugs-CC: debian-r...@lists.debian.org
* Package name: ruby-facade
Version : 1.0.7
Upstream Author : Daniel J. Berger
* URL : https://github.com/djberg96/facade
* License : Artistic-2.0
Programmin
Package: wnpp
Owner: "Debian Ruby Team"
Severity: wishlist
X-Debbugs-CC: debian-r...@lists.debian.org
* Package name: ruby-fix-trinity-output
Version : 1.0.0
Upstream Author : Chris Boursnell
* URL : http://rubygems.org/gems/fix-trinity-output
* License : MIT
Package: wnpp
Owner: "Debian Ruby Team"
Severity: wishlist
X-Debbugs-CC: debian-r...@lists.debian.org
* Package name: ruby-yell
Version : 2.0.5
Upstream Author : Rudolf Schmidt
* URL : https://github.com/rudionrails/yell
* License : MIT
Programming Lang: Ruby
Oops, I thought I had renamed the source package to libcereal.
What's the best way to correct this situation? The package is already in
the NEW queue: http://ftp-master.debian.org/new/cereal_1.1.2-1.html
Package: wnpp
Owner: "Debian Ruby Team"
Severity: wishlist
X-Debbugs-CC: debian-r...@lists.debian.org
* Package name: transrate
Version : 1.0.1
Upstream Author : - Richard Smith-Unna, Chris Boursnell, Rob Patro,
Julian Hibberd, Steven Kelly
* URL : http://hibberdlab.co
Package: wnpp
Owner: "Debian Ruby Team"
Severity: wishlist
X-Debbugs-CC: debian-r...@lists.debian.org
* Package name: ruby-threach
Version : 0.2.0
Upstream Author : Bill Dueber
* URL : http://github.com/billdueber/threach
* License : MIT
Programming Lang: Ru
Package: wnpp
Owner: "Debian Ruby Team"
Severity: wishlist
X-Debbugs-CC: debian-r...@lists.debian.org
* Package name: ruby-crb-blast
Version : 0.6.4
Upstream Author : Chris Boursnell & Richard Smith-Unna
* URL : https://github.com/cboursnell/crb-blast
* License
Package: wnpp
Owner: "Debian Ruby Team"
Severity: wishlist
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* Package name: ruby-pathname2
Version : 1.7.4
Upstream Author : Daniel J. Berger
* URL : https://github.com/djberg96/pathname2
* License : MIT
Programming
Package: wnpp
Owner: "Debian Ruby Team"
Severity: wishlist
X-Debbugs-CC: debian-r...@lists.debian.org
* Package name: ruby-fixwhich
Version : 1.0.2
Upstream Author : Erik Hollensbe & Richard Smith-Unna
* URL : http://github.com/Blahah/which
* License : MIT
P
Package: wnpp
Owner: "Debian Med Team"
Severity: wishlist
X-Debbugs-CC: debian-...@lists.debian.org
* Package name: macs2
Version : 2.1.0.20150731
Upstream Author : Tao Liu
* URL : http://github.com/taoliu/MACS/
* License : BSD-3-clause, Expat
Programming L
Whoops, totally missed that macs2 was already packaged as `macs` (I only
search for macs2 as that was the name in PyPI).
FYI: upstream has stopped updating the GitHub tags & releases and switched
to PyPI.
Differences between macs 2.0.9 and macs2 version 2.1.0 in my package
- Upstream's license is
I've attached a patch
You'll need to make use of the `jvm_includes` variable that /usr/share/java/
java_defaults.mk defines.
On Wed, Feb 17, 2016 at 10:03 PM Andreas Tille wrote:
> Sorry, but do you have a better hint for me since my attempt below did
> not change anything?
>
> Kind regards
>
>
On Wed, 9 Dec 2015 16:47:56 +0100 Andreas Tille wrote:
> Hi,
>
> could you please verify whether this issue remains also for version 1.2.1?
According to the buildd, it does
https://buildd.debian.org/status/package.php?p=htslib&suite=sid#problem-6
--
Michael R. Crusoe CWL Community Engineer
Thanks for the update; I've alerted upstream.
On Thu, Mar 3, 2016 at 4:17 AM, Martin Michlmayr wrote:
> * Martin Michlmayr [2016-03-02 17:18]:
> > The package builds fine with GCC 6 6-20160228-1. Since the package
> > itself didn't change, I guess that either a bug in GCC 6 got fixed or
> > po
Hello Andreas Beckmann,
Thank you for the report!
I've uploaded a new version though I was unable to replicate the piuparts
test to verify it. Any guidance on what command I should add to my
checklist would be appreciated.
On Tue, Mar 8, 2016 at 9:34 PM, Andreas Beckmann wrote:
> Package: libb
Thanks Charles!
Lun, 28 dec. 2015, 04:57, Charles Plessy a scris:
> Control: tak -1 pending
>
> Le Mon, Dec 28, 2015 at 02:18:47AM +, Chris Lamb a écrit :
> >
> > Whilst working on the "reproducible builds" effort [0], we noticed that
> transdecoder could not be built reproducibly.
> >
> > P
Control: forwarded 811841 https://github.com/seqan/seqan/issues/1342
thankyou
I've alerted upstream about this issue.
--
Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu
Common Workflow Language projectUniversity of California, Davis
https://impactstory.org/MichaelRCruso
Control: forwarded 809058 https://github.com/seqan/seqan/issues/1344
I've reported this upstream; though I haven't checked to see if this issue
is present in their current release (v2.0.1)
--
Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu
Common Workflow Language project
Control: tags upstream, wontfix
Upstream is no longer updating the 1.4.x series. They tested their
development branch using GCC 6 and found no errors.
On Wed, Jan 20, 2016 at 11:36 AM Michael Crusoe
wrote:
> Control: forwarded 811841 https://github.com/seqan/seqan/issues/1342
>
>
Control: forwarded -1 https://github.com/arq5x/bedtools2/issues/352
I have alerted upstream to the issue.
--
Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu
Common Workflow Language projectUniversity of California, Davis
https://impactstory.org/MichaelRCrusoe http://twitt
Additional support from Steffen Möller
https://lists.debian.org/debian-newmaint/2016/01/msg00013.html
--
Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu
Common Workflow Language projectUniversity of California, Davis
https://impactstory.org/MichaelRCrusoe http://twitter.
Control: forwarded https://github.com/amplab/snap/issues/68
Thank you Aaron for your reports.
x32 is out of my league; and I suspect outside of upstream's interest
though I have still reported it there for completeness.
I made the suggested change but it wasn't sufficient:
g++ -g -O2 -fstack-pr
Upstream points out that the sort of data one would use with this program
basically means that running it on 32bit platforms won't work out due to
the 4GB limitation.
https://github.com/amplab/snap/issues/68#issuecomment-174326529
Seems about right to me, so I'm not going to put further effort in
Control: tags -1 wontfix
Control: severity -1 wishlist
Sounds like a plan!
Lun, 25 ian. 2016, 01:24, Aaron M. Ucko a scris:
> Michael Crusoe writes:
>
> > Upstream points out that the sort of data one would use with this program
> > basically means that running it on 32b
The khmer package latest upstream version now uses this theme. I would be
happy to take over maintenance.
On Thu, 5 May 2016 09:29:14 -0400 David =?iso-8859-1?Q?Pr=E9vot?= <
taf...@debian.org> wrote:
> Package: python-guzzle-sphinx-theme
> Version: 0.7.10-1
> Severity: serious
>
> [ Filled as an R
I have a fix checked in as part of the 2.1-1 release, but it is blocked on
me uploading a python3 version of sphinx-guzzle
Pe 4 iul. 2017 23:12, "Sascha Steinbiss" a scris:
> Hi all,
>
> >> I've applied this patch to get the build working now that Python 3.6 is
> a
> >> supported version in Ubun
You are welcome!
git+ssh://git.debian.org/git/debian-med/easel.git is ready for review
2017-04-19 20:11 GMT+03:00 Andreas Tille :
> Very sensible! Thanks for working on this
> Andreas.
>
> On Wed, Apr 19, 2017 at 10:06:57AM -0700, Michael R. Crusoe wrote:
> > Package: wnpp
> > Severity: wis
2016-12-09 12:19 GMT+00:00 Andreas Tille :
> Hi Michael,
>
> I assumed simply adding the now available python-keepalive would easily
> fix the bug would be a simple task. However, I stumbled about several
> issues which prevented me from conituning here since I have no idea
> about the internals.
11, 2016 at 05:31:28PM +0100, Andreas Tille wrote:
> > On Fri, Dec 09, 2016 at 01:18:04PM +, Michael Crusoe wrote:
> > > > 1. Patch to not use python-typing.
> > > > Why this? Adding the package to Build-Depends would be cheap
> > >
> > > A
forwarded 852819 https://github.com/python/mypy/issues/2769
tags 852819 confirmed
thanks
Hello Leonhard,
My apologies for not testing the package. Clearly a test needs to be added!
Package: lintian
Version: 2.5.50
Severity: normal
Dear Maintainer,
Please, add cwl-runner to the list of acceptable interpeters. It is found in
cwltool package, a reference implementation for Common Worklflow Language
standard.
-- System Information:
Debian Release: stretch/sid
APT prefers
Package: wnpp
Severity: wishlist
Owner: anton.kho...@ukr.net
* Package name: python-galaxyxml
Version : 0.1
Upstream Author : Eric Rasche
* URL : https://github.com/erasche/galaxyxml
* License : Apache-2.0
Programming Lang: Python
Description : XML Gene
On Sat, Sep 3, 2016 at 11:21 AM, Axel Beckert wrote:
> Hi Antonio,
>
> Antonio Terceiro wrote:
> > On Tue, Aug 18, 2015 at 06:26:06PM +0200, Christian Hofstaedtler wrote:
> > - something else can replace ruby-ronn and we manage to make reverse
> > (build) dependencies switch to it.
>
> Before s
control: forwarded -1 https://github.com/seqan/needle/issues/128
They are different programs, with different interfaces, alas.
So a workaround will be needed: probably we should rename the binary
`seqan-needle` and provide a directory with a regular `needle` that can be
added to a user's `PATH`.
On Tue, 06 Mar 2018 18:08:48 -0500 "Aaron M. Ucko" wrote:
> Source: seqan2
> Version: 2.4.0+dfsg-8
> Severity: normal
> Tags: upstream
> User: debian-sp...@lists.debian.org
> Usertags: sparc64
>
> Builds of seqan2 for sparc64 (admittedly not a release architecture)
> have been failing lately, per
Andreas Tille, et al. I propose that we drop *-i386 for htslib, as it is
blocking a lot of packages.
On Sat, 04 Aug 2018 16:45:42 +0200 Andreas Beckmann wrote:
> Source: htslib
> Version: 1.9-1
> Severity: serious
> Tags: ftbfs
> Justification: fails to build from source (but built successfully i
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 :
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 724D609337113C710550D7473C26763F6C67
Dear maintainers,
I have a fix for this bug (by copying in the relevant files from OpenJDK 9)
at https://salsa.debian.org/java-team/icedtea-web/merge_requests/5
It is a hack, but from my testing it works.
I hope this is helpful; I would like to see this package stay in Debian
Buster.
Cheers,
-
Attached is a fix , also available at
https://salsa.debian.org/multimedia-team/obs-studio/-/merge_requests/3 for
the convenience of the maintainers
On Fri, May 29, 2020 at 7:51 AM Adrian Bunk wrote:
> Source: obs-studio
> Version: 25.0.8+dfsg1-1
> Severity: serious
> Tags: ftbfs
>
> https://bui
Sure, I'll add this to my queue
On Sun, May 31, 2020 at 7:54 AM Andreas Tille wrote:
> Hi Michael,
>
> On Sat, May 23, 2020 at 11:10:37PM +0300, Adrian Bunk wrote:
> > Source: hyphy
> > Version: 2.2.7+dfsg-1
> > Severity: serious
> >
> > https://buildd.debian.org/status/package.php?p=hyphy
> >
>
bowtie2 segfaults for me if eatmydata and/or cowbuilder are being used, so
try with clearing out LD_PRELOAD first
On Fri, 15 Jan 2021 at 11:22, Andreas Tille wrote:
> On Fri, Jan 15, 2021 at 11:16:48AM +0100, Michael Crusoe wrote:
> > bowtie2 segfaults for me if eatmydata and/or cowbuilder are being used,
> so
> > try with clearing out LD_PRELOAD first
>
> Ahhh, this makes perfectly
I pushed a commit that works around the _mm_malloc / xmmintrin.h issue ,
but there is usage of the rdtsc assembly operand that I don't have an arm64
analogue for.
On Sat, 5 Dec 2020 at 21:07, Andreas Tille wrote:
> Hi Steve,
>
> On Sat, Dec 05, 2020 at 04:18:53PM +, Steve McIntyre wrote:
> >
Hey Nilesh,
No problem for me when you ask for help!
I suspect that
https://salsa.debian.org/med-team/scrappie/-/commit/a00691d910110a460ef5e61a6c74cc2cb0e1a626#5dc91bdd30262777c0556235b73413cd5865a144_0_31
is the issue
You should add the regular simde includes here, so that v4sf typedef works
d
On Mon, 7 Dec 2020 at 11:49, Nilesh Patra wrote:
> Hi Michael
>
> Thanks for the hint, I did this (not yet pushed):
>
> -#include
> -
> /* yes I know, the top of this file is quite ugly */
>
> +define SIMDE_ENABLE_NATIVE_ALIASES
> +#include
>
> But I end up with the same error that I pasted ea
On Mon, 7 Dec 2020 at 12:44, Nilesh Patra wrote:
> Hi again,
>
> Since that didn't work, I manually added a typedef definition for it, and
> it works now on both am64 machine and arm64 porter box - with passing
> build-time tests.
> I've pushed to salsa.
>
Ah, good thing I used a different branc
Dear Nilesh,
Thanks again for doing this.
Don't forget step 8 of https://wiki.debian.org/SIMDEverywhere#Approach ;
I've updated the sample scripts for multi-compiling x86 at different SIMD
levels
Please also update https://wiki.debian.org/SIMDEverywhere#Packages_Status &
https://wiki.debian.org/
Thank Berhard for this patch.
Also the autopkgtests do not yet patch with i386 (at least):
Testing bedtools shuffle:
shuffle.t1...1,10c1,10
< chr2 34697611 34698079 trf 789
< chr4 97373990 97374163 trf 346
< chr1 211569500 211569740 trf 434
< chr15 100895645 100895867 trf 273
< chr10 79193410
Fine by me. Looks like it isn't needed by trinityrnaseq anymore, so that
build-depends can be dropped.
Unfortunately it is a dependency on the recently packaged bio-tradis, as I
think you are aware.
2017-11-10 10:16 GMT+02:00 Andreas Tille :
> Package: ftp.debian.org
> Severity: normal
>
> Hi,
On Sun, 19 Nov 2017 21:26:34 +0100 Andreas Beckmann wrote:
> Source: seqan2
> Version: 2.3.2.000platform-issues6-9cf5a69+dfsg-3
> Severity: serious
> Justification: fails to build from source (but built successfully in the
past)
>
> Hi,
>
> seqan2 FTBFS during the indep-only build of the arch:all
On Sat, 16 Dec 2017 16:40:11 +0100 Andreas Beckmann wrote:
> Source: seqan2
> Version: 2.3.2.000platform-issues8-6f85721+dfsg-2
> Severity: serious
> Justification: fails to build from source (but built successfully in the
past)
>
> Hi,
>
> seqan2 FTBFS on most platforms with failing unittests:
>
Thank you Chris for your response.
I only recently added the `cwl-runner` virtual package to cwltool as we are
about to introduce another CWL runner, toil, to the archive soon.
Here's a Lintian error from the latest seqan-apps package:
E: seqan-apps: missing-dep-for-interpreter cwl-runner => cwl
Package: libnxt
Version: 0.3-8
Severity: normal
Dear Maintainers,
I have no NXT devices installed on my system, but I get an alert that I
should
install libnxt due to the following modalias match in
/usr/share/appdata/libnxt.metainfo.xml:
usb:v03EBp*
(While I am running Debian Stable, I confirm
On Thu, 29 Dec 2016 06:59:50 +0100 Matthias Klose wrote:
> Control: tags -1 + moreinfo
>
> please recheck with 0.168 available in experimental, and provide an
updated
> patch if necessary.
0.175-2 was tested on 2019-01-09 and now gets a configure time error of
checking for gcc with GNU99 support
All of those have been submitted, but were rejected due to my lack of
uploader privileges.
Any DD can allow me to upload the fixed packages via the following command
dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow ${srcpackage}
--
Michael R. Crusoe
On Wed, Oct 30, 2019, 19:09 A
Maybe this isn't worth our time. libgtextutils is only needed for fastx
toolkit.
Both are officially abandoned by upstream since 2017.
>From the fastx toolkit readme:
https://github.com/agordon/fastx_toolkit/blob/master/README#L7
* FASTX TOOLKIT is unmaintained software.
This is a bug in the libpython3.8-stdlib package. See my similar request to
fix libpython3.7-stdlib:
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=922285
On Thu, 4 Apr 2019 07:21:25 +0200 Andreas Tille
wrote:
> Hi,
>
> I stumbled again about this package:
>
> $ runPmv
> Run PMV from /usr/lib/python2.7/dist-packages/Pmv
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/Pmv/__init__.py", line 378, in
runPmv
> from P
Control: forwarded -1 https://github.com/bxlab/bx-python/issues/48
On Sat, 9 Nov 2019 13:53:25 +0100 Matthias Klose wrote:
> see https://buildd.debian.org/status/package.php?p=python-bx
> Exception: 2147483648 is larger than the maximum possible size
(2147483647)
Thanks, I had already reported t
Control: block -1 by 944041
On Fri, 18 Oct 2019 16:07:51 +0200 =?UTF-8?B?RnLDqWTDqXJpYw==?= Bonnard <
fre...@debian.org> wrote:
> Dear maintainer,
> is there any reason that cnvkit isn't built on ppc64el ?
> Looks like it builds out of the box.
Thanks, I didn't see that python-pysam was building
pbcopper's latest release has slipped in a code copy of libssw which uses
x86 SIMD intrinsics. I've pushed up a fix along the lines I made to libssw
to enable cross architecture compilation at
https://salsa.debian.org/med-team/pbcopper/commit/f9678ed29590b57fe30638eed3d6819577b4ace1
and it awaits s
On Mon, 9 Dec 2019 12:14:02 +0100 Matthias Klose wrote:
> On 09.12.19 11:46, Andreas Tille wrote:
> > Hi,
> >
> > I have upgraded python-datrie in Git[1] to latest upstream version
> > (0.8). It shows the same issue - so I admit I have no better clue than
> > reporting the issue upstream which I'
Control: forwarded -1
https://github.com/sanger-pathogens/Bio-Tradis/issues/116
On Fri, 27 Dec 2019 11:42:05 +0100 Paul Gevers wrote:
> Dear maintainers,
>
> With a recent upload of bio-tradis the autopkgtest of bio-tradis fails
> in testing when that autopkgtest is run with the binary packages
Dear all,
I have finished the Python3 conversion based off of Andreas's work:
https://salsa.debian.org/med-team/smalt/blob/master/debian/patches/2to3.patch
Andreas: feel free to sponsor the upload, or to give me upload permissions:
dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow sm
Hello,
I've fixed this at https://salsa.debian.org/med-team/gatb-core and it is
available for sponsoring by any Debian Developer.
gbp clone g...@salsa.debian.org:med-team/gatb-core
Or I can be given permission to upload the fixed package
dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --
Control: severity -1 important
Control: forwarded -1
https://github.com/samtools/htslib/issues/355#issuecomment-566058829
Dear Graham,
Thank you for your report. This issues is already known by upstream. So as
to not hold up multiple transitions, the s390x builds of htslib (and its
reverse-depend
[whoops, forgot to CC everyone]
On Mon, 9 Dec 2019 12:14:02 +0100 Matthias Klose wrote:
> On 09.12.19 11:46, Andreas Tille wrote:
> > Hi,
> >
> > I have upgraded python-datrie in Git[1] to latest upstream version
> > (0.8). It shows the same issue - so I admit I have no better clue than
> > repo
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