Hi, team,
I've finished the python-pymummer package. Would someone please upload
to unstable?
git+ssh://git.debian.org/git/debian-med/python-pymummer.git
http://anonscm.debian.org/cgit/debian-med/python-pymummer.git
Many thanks and regards
Afif
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Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team
* Package name: python-pymummer
Version : 0.6.1
Upstream Author : 2015 Martin Hunt and Nishadi De Silva
* URL : https://github.com/sanger-pathogens/pymummer
* License : GPL
Programming Lang:
Hi, team,
I finished preparing the bcftools package:
git+ssh://git.debian.org/git/debian-med/bcftools.git
http://anonscm.debian.org/cgit/debian-med/bcftools.git
Would someone upload to unstable, please?
Many thanks and regards
Afif
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va 7 & 8 and upload as soon as I can.
Thanks and regards
Afif
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ugh.
> We would welcome any pull requests on GitHub which allow for Java 8 support.
>
Thanks for your prompt response. I'll see what we can do.
Thanks and regards
Afif
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regards
Afif
1.
https://github.com/sanger-pathogens/Artemis/commit/9bc9e3bdcebef3e2267e9ff8e4dbfdecf87596c6
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On الأربعاء 4 تشرين الثاني 2015 13:35, Emmanuel Bourg wrote:
> Package: artemis
> Version: 16.0.0+dfsg-1
> Severity: i
anew, would
it be alright if I discard the old repository on Alioth? That attempt
targets a much older upstream release.
Thanks and regards
Afif
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Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team
* Package name: bcftools
Version : 1.2
Upstream Author : Petr Danecek, Shane McCarthy and John Marshall
* URL : http://samtools.github.io/bcftools/
* License : GPL or MIT/X
Programming Lang: C
t here. The executable for
artemis is called "art" even as shipped by upstream, so our artemis
package provides /usr/bin/art and won't really benefit from being called
/usr/bin/artemis.
I can change the desktop file name to be art.desktop, but the name in
the menu will still be Artemis
Hi, team,
I've finished preparing a package for trnascan-se. Would someone please
upload to unstable?
git+ssh://git.debian.org/git/debian-med/trnascan-se.git
http://anonscm.debian.org/cgit/debian-med/trnascan-se.git
Many thanks and regards
Afif
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Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team
* Package name: trnascan-se
Version : 1.3.1
Upstream Author : Todd Lowe and colleagues
* URL : http://lowelab.ucsc.edu/tRNAscan-SE
* License : GPL
Programming Lang: C, Perl
Description :
as, would you mind uploading again? The
corrected version is in git now.
Thanks, apologies, and regards
Afif
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gards
Afif
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o.git
Would someone please upload to unstable?
Many thanks and regards
Afif
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Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team
* Package name: artemis
Version : 16.0.0
Upstream Author : Genome Research Limited
* URL : http://www.sanger.ac.uk/resources/software/artemis
* License : GPL
Programming Lang: Java
Descripti
By the way, we have a patch in
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=734702
related to this transition that touches
source/libs/spool/berkeleydb/sge_bdb.c
I'm not sure if you want to integrate that (or already have) upstream.
Thanks and regards
Afif
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Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team
Control: block 798872 by -1
* Package name: python-avro
Version : 1.7.7
Upstream Author : Apache Software Foundation
* URL : http://avro.apache.org
* License : Apache 2.0
Programming Lang: Pyth
Hi, team,
I finished preparing pbgenomicconsensus. Could someone please upload to
unstable?
http://anonscm.debian.org/cgit/debian-med/pbgenomicconsensus.git/
ssh://git.debian.org/git/debian-med/pbgenomicconsensus.git
Many thanks and regards
Afif
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http
pysam upload.
I will note to check this out.
Thanks and regards
Afif
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Package: fai-server
Version: 4.3.1+deb8u1
Severity: minor
Control: affects -1 debian-lan-config
Dear Maintainer,
The behavior of fai-chboot -d and -e depends on what the default PXE
configuration is.
the man-page fai-chboot(8) currently reads:
-d Disable network booting for HOST. T
fixing
the porting to Hurd. The packaging VCS is at
http://anonscm.debian.org/cgit/users/afif-guest/ori.git
Regards
Afif
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o not have access to a mips machine and
their ticket was still open the last time I checked.
Thanks and regards
Afif
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The reason for the missing build is an issue with its dependency htslib
that needs to be resolved upstream [1].
Thanks and regards
Afif
1. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=749367
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Hi,
Has anyone tested the patch that was applied upstream [1] regarding this
issue? I'm asking because the corresponding upstream ticket is still
open and the commit message on the patch describes it as a "partial fix".
I am not particularly interested in mips/mipsel, but this build failure
is pre
Afif
1.
https://github.com/samtools/htslib/commit/e8806c71f3408d2cbff8caa8df17eef848d33a02
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a renamed version of samtools.pl
The fixed package is now in git and awaits upload.
Thanks and regards
Afif
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hon3-packaging), but obviously, Python2 packaging needs to be
working first.
Many thanks and regards
Afif
1. http://bugs.debian.org/795619
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Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team
* Package name: dazzdb
Version : 1.0
Upstream Author : Eugene W. Myers, Jr.
* URL : https://github.com/thegenemyers/DAZZ_DB
* License : BSD
Programming Lang: C
Description : database lib
Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team
Control: block 797676 by -1
* Package name: pbcommand
Version : 0.2.8
Upstream Author : Pacific Biosciences
* URL : https://github.com/PacificBiosciences/pbcommand
* License : BSD
Programming
Hello,
I've made the requested changes to pbalign. Could someone please sponsor?
Thanks and regards
Afif
On الأحد 6 أيلول 2015 10:15, Afif Elghraoui wrote:
> Hi, Andreas,
>
> On الأحد 6 أيلول 2015 06:27, Andreas Tille wrote:
>> On Sun, Sep 06, 2015 at 02:13:12AM -0700,
Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team
* Package name: pbbam
Version : 0.1.0
Upstream Author : Pacific Biosciences
* URL : https://github.com/PacificBiosciences/pbbam
* License : BSD
Programming Lang: C++
Description : Pacifi
Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging
Control: affects -1 blasr
* Package name: pbseqlib
Version : 0~20150702+git98a302a
Upstream Author : Pacific Biosciences
* URL : https://github.com/PacificBiosciences/blasr_libcpp
* License : BSD
P
h has also been renamed:
git+ssh://git.debian.org/git/debian-med/pbalign.git
Could someone sponsor this, please?
Many thanks and regards
Afif
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Package: autopkgtest
Version: 3.6jessie1
Severity: normal
Tests fail on Python packages that have Cython-compiled modules. See,
for example, the test log for python-cobra on DebCI [1]. The tests there
fail with the error "solver not found", where the solver is the Cython-compiled
module that has b
Hi, all,
I've completed preparation of the python-pbconsensuscore package. Could
someone sponsor this upload, please?
The repository is at
git+ssh://git.debian.org/git/debian-med/python-pbconsensuscore.git
Thanks and regards
Afif
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Package: wnpp
Severity: wishlist
Control: affects -1 blasr python-pbh5tools
* Package name: python-cram
Version : 0.6
Upstream Author : Brodie Rao
* URL : https://github.com/brodie/cram
* License : GPL
Programming Lang: Python
Description : simple testi
e for this effort.
Thanks and regards
Afif
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Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team
* Package name: daligner
Version : 1.0
Upstream Author : Eugene W. Myers, Jr.
* URL : http://github.com/thegenemyers/DALIGNER
* License : BSD
Programming Lang: C
Description : local alig
;t continue working on mhap until its build-dependency
jaligner enters the archive.
regards
Afif
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Upstream has accepted to support GNU/kFreeBSD and GNU/Hurd [1] and I
have created some patches to hopefully make Ori work on these platforms [2].
1.
https://mailman.stanford.edu/pipermail/orifs-devel/2015-August/000182.html
2. https://bitbucket.org/aelghraoui/ori/branch/compatibility
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Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team
Control: block 787977 by -1
* Package name: pbdagcon
Version : git1d12e13
Upstream Author : Pacific Biosciences
* URL : https://github.com/PacificBiosciences/pbdagcon
* License : BSD**
Program
Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team
Control: block 395843 by -1
* Package name: libuncommons-maths-java
Version : 1.2.3
Upstream Author : Daniel W. Dyer
* URL : http://maths.uncommons.org
* License : Apache
Programming Lang: Java
Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team
Control: block 395843 by -1
* Package name: mhap
Version : 1.6
Upstream Author : Sergey Koren , Konstantin Berlin
* URL : https://github.com/marbl/MHAP
* License : Apache
Programming Lang: Ja
This bug still affects the current stable release. Can the solution
please be put through stable-updates as well?
I hate to imagine if a user finally figures out how to file an RFP and
then has reportbug crash in this way.
Thanks and regards
Afif
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http
x27;d suggest substituting __unix__, as every vaguely-modern Unixlike
> system should support pthreads. (Certainly, all Debian architectures
> do.)
>
> Could you please take a look?
>
Will do.
Thanks for your report
Afif
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x27;d suggest substituting __unix__, as every vaguely-modern Unixlike
> system should support pthreads. (Certainly, all Debian architectures
> do.)
>
> Could you please take a look?
>
Will do.
Thanks for your report
Afif
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Hi, all,
I've finished preparing the first version of the pbh5tools package.
Could someone upload to unstable please?
Many thanks and regards
Afif
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Package: wnpp
Severity: wishlist
* Package name: python-cylp
Version : 0.7.2
Upstream Author : Mehdi Towhidi
* URL : https://github.com/coin-or/CyLP
* License : CPL
Programming Lang: Python
Description : Python interface to COIN-OR linear and mixed-inte
Package: python-cobra
Severity: normal
Control: block -1 by 794511
Packaging of 0.4.0b2 is delayed until cython again becomes installable
in unstable.
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with a
Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team
Control: block 794447 by -1
* Package name: pb-consensuscore
Version : 1.0.0
Upstream Author : Pacific Biosciences
* URL : https://github.com/PacificBiosciences/ConsensusCore
* License : BSD
P
Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team
Control: block 787977 by !
* Package name: pb-genomicconsensus
Version : 1.0.0
Upstream Author : Pacific Biosciences
* URL : https://github.com/PacificBiosciences/GenomicConsensus
* License : BS
/package.php?p=samtools&suite=sid
3.
https://buildd.debian.org/status/logs.php?pkg=htslib&ver=1.2.1-1&arch=mips
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ières.
Replication, History, and Grafting in the Ori File System. In
Proceedings of the 24th Symposium on Operating Systems Principles,
November 2013.
http://dl.acm.org/ft_gateway.cfm?id=2522721&ftid=1403940&dwn=1
Please consider sponsoring my package.
Many thanks and regards
Afif
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A
ding a sponsor will greatly increase if you use a
> VCS for the Debian packaging. You can then reference this using the
> Vcs-Browser/Vcs-Git sections in d/control.
>
That's a good tip. I'll publish my repository on launchpad or something
with the necessary changes and report
using this command:
dget -x
http://mentors.debian.net/debian/pool/main/o/ori/ori_0.8.1+ds1-1.dsc
Many thanks and regards,
Afif
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_0~20150520%2B2004-1.html
4. https://wiki.debian.org/Python/StretchRoadmap
5. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=783833#10
6.
http://anonscm.debian.org/cgit/debian-med/python-pbcore.git/tree/debian/patches/modernize-python.patch
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current failures look like
python2/python3 transition issues, I think any new failures should stand
out, so I will review these pysam patches.
Thanks for all your support
Regards
Afif
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Package: debian-maintainers
Severity: normal
Tags: patch
Please add my key to the Debian maintainers keyring. The jetring
changeset is attached.
Many thanks and regards
Afif
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Comment: Add Afif Elghraoui as a Debian Maintainer
Date: Wed
I would very much like to have orifs on my android phone.
>
It looks like this is a direction the developers intend to go [2].
1. https://mailman.stanford.edu/pipermail/orifs-devel/2015-June/000171.html
2. https://mailman.stanford.edu/pipermail/orifs-devel/2015-April/000163.html
Reg
Package: wnpp
Severity: wishlist
Owner: Afif Elghraoui
X-Debbugs-Cc: debian-de...@lists.debian.org
* Package name: ori
Version : 0.8.1
Upstream Author : Stanford University
* URL : http://ori.scs.stanford.edu/
* License : ori (MIT-like)
Programming Lang: C
the python3-package. The *_java.py files are intended to provide jython
support according to upstream, and jython is not available for python3.
These files aren't relevant for this package, so I will make sure that
they are removed from python3-cobra.
Thanks and regards
Afif
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false);
Many thanks and regards
Afif
1.
https://github.com/zotero/zotero-standalone-build/issues/35#issuecomment-83163124
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Description: Fix issue of empty preferences window
Origin: upstream, https://github.com/zotero/zotero-sta
Hello,
I have updated this package for python3 and it is lintian clean.
Would someone be able to upload to experimental? Its dependency
python-pysam currently resides there.
Many thanks and regards
Afif
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* This package build-depends on python-pbcore (#787981)
* This package is python2-only and must be modified to support both
python2 and python3.
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Hi, team,
I have finished preparing the first version of python-cobra. Could
someone please review and upload it?
Many thanks and regards
Afif
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Vcs-Git: git://anonscm.debian.org/debian-med/python-cobra.git
Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/python-cobra.git
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Hello,
I believe my python-pbcore package is ready for uploading. It depends on
a newer version of python-pysam than is currently in unstable, but it's
not a build-dependency. If that's ok, I'd like to request a review and
upload of python-pbcore.
Thanks and regards
Afif
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Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/python-pbcore.git
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all the components of
SMRTAnalysis, which are managed in separate SCM repositories at
<https://github.com/PacificBiosciences>. It will be maintained by
the Debian Med team at
http://anonscm.debian.org/cgit/debian-med/smrtanalysis.git
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and regards
Afif
1. https://ftp-master.debian.org/new/kmer-tools_0~20150520+2004-1.html
2. http://anonscm.debian.org/cgit/debian-med/kmer-tools.git/tree/debian
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Hi, Andreas,
On الإثنين 25 أيار 2015 00:13, Andreas Tille wrote:
Hi Afif,
On Sun, May 24, 2015 at 11:12:00PM -0700, Afif Elghraoui wrote:
Hi, Andreas,
I tried to go ahead with packaging shared libraries, but it looks like I
have to read three to five more manuals before I can proceed and know
don't get
this warning for them. Otherwise, the package is lintian clean.
How does this look to you?
Thanks and regards
Afif
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1. https://www.debian.org/doc/debian-policy/ch-sharedlibs.html
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l, we have the Debian Med list and the packaging
log for kmer in Debian.
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See <https://bugs.debian.org/784863> for its status.
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Package: wnpp
Severity: wishlist
Owner: Debian Med Team
* Package name: kmer-tools
Version : 20141114+1994
Upstream Author : Brian Walenz
* URL : http://kmer.sourceforge.net
* License : GPL
Programming Lang: C
Description : suite of tools for DNA sequ
I made a proposal for this issue on FreedomSponsors [1] in case anyone
is interested in putting a bounty on it. I'd like to package this, but I
doubt it will be anytime soon. Maybe this will become more interesting
for someone else to take on and it will get done faster.
Regards,
Afif
1.
https://
Hello,
On الأربعاء 4 شباط 2015 13:16, Gene Cooperman wrote:
> Hi Afif,
> Sorry for the delay in writing back. We talked about your request.
No problem. Thanks for considering
> We're hesitant to package the plugins in the _ contrib/ _ directory,
> because those are contributed by various p
Package: dmtcp
Version: 2.3.1-6
Severity: normal
Dear Maintainer,
Many thanks for your package. I (privately backported and) installed
this version from testing to use dmtcp with the plugins and didn't find
them.
It looks like the plugins in the source archive's contrib/ directory are
not buil
On الثلاثاء 13 كانون الثاني 2015 22:34, Russ Allbery wrote:
Yes, you're entirely right -- this is weird and kind of contradictory and
it's hard to figure out just what this was supposed to mean. What I
spelled out is what we arrived at in previous discussion, but there may be
other possible int
Forgot to reply-all and include the bug address...
رسالة ممرّرة
الموضوع: Re: Bug#775318: debian-policy: Using /srv instead of /var/lib
for served user-level data
التاريخ:Tue, 13 Jan 2015 22:21:30 -0800
مِن:Afif Elghraoui
إلى:Russ Allbery
On الثلاثاء 13
Hello,
On الثلاثاء 13 كانون الثاني 2015 19:50, Russ Allbery wrote:
I'm afraid that you're misreading the FHS. It actually*prohibits* the
distribution from doing what you want and using /srv by default.
This is the important part of the /srv description for this purpose:
The methodology
Package: debian-policy
Severity: wishlist
Dear Maintainer,
I wanted to separate user-level data (for special RAID, backups,
encryption and
such) from system data on my machine, so I targeted /home and /srv. I
found out
that data managed by system services are being stored in
/var/lib/
when I
It appears that the only modification upsteam made to pdfinfo is to
redirect its output to a file. As suggested in the mentioned thread [1],
a shell script wrapper might be used to call poppler's pdfinfo and do
this output redirection as zotero requires.
I appreciate your work on this package.
Package: xorg
Version: 1:7.7+7
Severity: serious
Dear Maintainer,
* What led up to the situation?
After executing dist-upgrade to move from Wheezy to Jessie, I am
faced with the text login prompt
rather than kdm.
* What exactly did you do (or not do) that was effective (or
in
oblem. It is a severe problem since the machine is no longer
practically usable without the graphical interface and I have not been
able to find a workaround on Jessie.
--
Afif Elghraoui
System Administrator, Biological & Medical Informatics Research Center
San Diego State Universit
Package: xorg
Version: 1:7.7+7
Followup-For: Bug #653079
Dear Maintainer,
* What led up to the situation?
I was running Wheezy; upon dist-upgrade to
testing, I am faced with the console login prompt rather than kdm.
* What exactly did you do (or not do) that was effective (or
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