Bug#822701: samtools: FTBFS: UNEXPECTED PASS: Task worked when we expected failure;

Many thanks for the detailed explanation. It's very helpful and informative, but I'll just reply to a couple points here. على الجمعـة 3 حزيران 2016 ‫04:12، كتب John Marshall: > On 1 Jun 2016, at 05:25, Afif Elghraoui <a...@debian.org> wrote: > > Thank you; I am glad to see the sp

Bug#822701: [Debian-med-packaging] Bug#822701: Bug#822701: samtools: FTBFS: UNEXPECTED PASS: Task worked when we expected failure;

I was hoping someone would be able to explain these to me. Should I have been reporting bugs upstream when these happened? I did not press my questions before because I hadn't before got around to digging up the logs. على الثلاثاء 31 أيار 2016 ‫21:25، كتب Afif Elghraoui: > The first vers

Bug#819617: bcftools: FTBFS: test suite fails on several architectures

على الأحد 29 أيار 2016 ‫04:42، كتب Christian Seiler: > Hope that helps. It's very much appreciated! I don't have the chance to try it out myself for a while, but I've notified upstream about your suggestions. We'll see how it goes. Many thanks and regards Afif -- Afif Elghraoui | ع

Bug#825610: Updated Vietnamese translation for adduser

Control: tag -1 + pending على السبت 28 أيار 2016 ‫18:08، كتب Trần Ngọc Quân: > Hi, > > Please help me apply this patch on > <http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=825610> > Many thanks! Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#811411: Maintainer upload is pending

Control: tag -1 + pending I'm planning to adopt this package and a maintainer upload is being prepared, pending translation updates. See the adduser-devel archives for May 2016 for more information. -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#825047: developers-reference: Lintian contradicts suggestion in maintainer scripts best practices

Package: developers-reference Version: 3.4.17 Severity: normal I have a package with a postrm script that has a line like [ -x /usr/bin/ucf ] && ucf --purge /etc/default/gridengine which incurs the following lintian warning: W: gridengine-common: command-with-path-in-maintainer-script

Bug#824982: src:gtk+3.0: unsatisfiable dependency on libgtk-3-common

Package: src:gtk+3.0 Version: 3.20.5-1 Severity: serious Control: affects -1 openjdk-8-jre I ran into a problem while trying to build a package depending on default-jdk in Unstable. In my build, I'd get: The following packages have unmet dependencies: default-jdk : Depends: default-jre (=

Bug#811411: Joining the adduser Alioth team

to publish that as part of the same project. Many thanks and regards Afif - -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name -BEGIN PGP SIGNATURE- Version: GnuPG v2 iQIcBAEBCAAGBQJXQMBOAAoJEFmyMG86+d3BzVgP/3bNXiumne+juAK8/MsBZUFQ

Bug#824752: gridengine-client, qtile: error when trying to install together

Control: notfound -1 gridengine/8.1.8+dfsg-5 Control: reassign -1 qtile على الجمعـة 20 أيار 2016 ‫01:49، كتب Iain R. Learmonth: > > Seems perfectly reasonable to me. Will rename qsh tonight. > > Thanks for the speedy information. (: > Many thanks! Afif -- Afif Elghraoui | عف

Bug#694039: Status? (ddpo - Use a different color for outdated backports)

on DDPO regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#824752: gridengine-client, qtile: error when trying to install together

the qtile package. thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#822701: [Debian-med-packaging] Bug#822701: Bug#822701: samtools: FTBFS: UNEXPECTED PASS: Task worked when we expected failure;

lt;< ${binary,Version}, bcftools (<< ${binary:Version}) samtools/bcftools: Depends: libhts1 (>= ${binary:Version}) What do you think? For bcftools so far, I have only been constraining the build-depends on htslib to be the corresponding upstream version at a minimum. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#822414: et_xmlfile has been accepted - please add dependency to openpyxl

ht. I'd just have to add the indirect build-dependency to get it past the buildds. Unfortunately, et_xmlfile has to pass through NEW again because I botched the binary package names. Thanks for taking a look! Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#822742: why double python- prefix in the pkg name?

not really see any > reason > for python-python- prefix... please clarify and/or fix. > No reason for that-- That was left over from my trying py2dsc and I missed it somehow... I'll fix that right now. Thanks for pointing this out. Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#822414: et_xmlfile has been accepted - please add dependency to openpyxl

for it to go through. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#822661: ITP: python-et-xmlfile -- low memory Python library for creating large XML files

Package: wnpp Severity: wishlist Owner: Afif Elghraoui <a...@debian.org> Control: block 822414 by -1 * Package name: python-et-xmlfile Version : 1.0.1 Upstream Author : Charlie Clark <charlie.cl...@clark-consulting.eu> and Elias Rabel * URL : https://b

Bug#822414: Missing dep - ImportError: No module named 'et_xmlfile'

Source: openpyxl Version: 2.3.0-1 Severity: important While trying to update the circlator package, which depends on openpyxl, I get an error while running the test suite. The stack trace indicates a problem with the openpyxl package in Debian: File "/<>/circlator/versions.py", line 3, in

Bug#820874: [Pkg-gridengine-devel] Bug#820874: gridengine-master: doesn't use invoke-rc.d

ainer scripts in the Policy and Developer's reference. I couldn't find anything, but I didn't consider looking at these. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#820851: ITP: sprai -- single-pass sequencing read accuracy improver

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: sprai Version : 0.9.9.12 Upstream Author : Takamasa Imai * URL : http://zombie.cb.k.u-tokyo.ac.jp/sprai/index.html

Bug#820201: nmu python-avro . all . -m "Rebuild with python3.5 as only python3 version"

ds on only python3.4, while the 3.5 transition has apparently finished. The package consequently needs to be rebuilt with the new state of python3 in unstable. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#820170: RM: fitgcp [i386 kfreebsd-i386 mips64el] -- ROM; Dependency has RC bugs with no fixed version available

Package: ftp.debian.org Severity: important Control: tag 818063 - moreinfo fitgcp's dependency of python-pysam had an RC bug that was fixed in its latest upstream release. That release currently does not build on the named architectures, and testing migration is stalled for python-pysam and

Bug#820083: [Pkg-gridengine-devel] Bug#820083: gridengine-drmaa-dev: fails to install: update-alternatives: error: alternative path /usr/lib/gridengine-drmaa/lib/libdrmaa.so doesn't exist

so the names aren't mapping anymore. I'll get to it the next time I sit down to work on the package. Thanks! Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#818063: python-pysam: reduce the RM architecture list and bump severity

testing migration. Autoremovals of its reverse-dependencies are coming up within a week or so. In addition to that, I would like to update the version of pysam in jessie-backports and I cannot do that without it first migrating to testing. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي

Bug#812268: bcftools - bug represents two separate problems

that particular problem while the other one is still being investigated. -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#808851: Artemis: fix for #808851

options as well, though. Thanks and regards Afif - -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name -BEGIN PGP SIGNATURE- Version: GnuPG v2 iQIcBAEBCAAGBQJW9hT+AAoJEM6uatOv6Cb72MgP/2bBiVKGoJVx5ivBrZnP813E P27V6DzMNdvYswGR838IAXTMl8TieON0PePOPYatsOm4xA7Lw3FWJZ1EdoF3tPF

Bug#818958: git-buildpackage: enable dpkg-mergechangelogs when initializing/cloning a repository

Package: git-buildpackage Version: 0.6.22 Severity: wishlist dpkg-mergechangelogs (from the dpkg-dev package) is a very nice tool that allows git to automatically merge debian/changelogs. It is especially useful when updating backports branches, as usually the changelog is the only thing causing

Bug#818584: ImportError: No module named pyyaml2

Package: spades Version: 3.7.1+dfsg-1 Severity: important Control: block 818575 by -1 Tests for the circlator package in progress failed while runnining spades: ~~~ 0:00:47.00892M / 484M INFOGeneral (path_extend_launch.hpp: 247) Traversing tandem repeats

Bug#808552: workaround for jessie-backports (bug exists in Jessie)

-- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#818575: ITP: circlator -- circularize genome assemblies

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: circlator Version : 1.2.0 Upstream Author : Martin Hunt & Nishadi De Silva * URL :

Bug#693722: Set affected versions

Control: found -1 6.2u5-7.1 This bug was closed in the recent upload to experimental, but that was not supposed to trigger immediate testing migration for the old version currently in unstable. This apparently happened because the bug was not associated with any package version. -- Afif

Bug#818584: [Debian-med-packaging] Bug#818584: ImportError: No module named pyyaml2

ny thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#818063: RM: python-pysam [i386 arm64 armel ppc64el] -- ROM; BD-uninstallable

Package: ftp.debian.org Severity: normal The latest version of python-pysam fixes the RC bug #814765, but adds a new build-dependency that is not yet available on the mentioned architectures. Removal of the package from those architectures is needed to allow testing migration and prevent

Bug#814680: RFS: stp/2.1.2+dfsg-1 [ITP] -- Simple theorem prover

-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi, Marko, On الأحد 6 آذار 2016 14:53, Marko Dimjašević wrote: > > On Fri, 2016-02-26 at 17:42 -0800, Afif Elghraoui wrote: >> Something like the following: >> [...] > Thank you Afif for this! > No problem. > I am

Bug#815754: [Pkg-gridengine-devel] Bug#815754: [PATCH] gridengine: proposal to add ppc64el architecture

Though, I'd like to know if SoGE is fully compatible with orginal Sun GE. Based on upstream's notes [1], it should be, but I don't have firsthand experience in making the jump. Thanks and regards Afif 1. http://anonscm.debian.org/cgit/pkg-gridengine/pkg-gridengine.git/tree/source/README.upgra

Bug#807802: pbsuite to move ahead without fringe dependency

://bugs.debian.org/cgi-bin/bugreport.cgi?bug=807804 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#814680: RFS: stp/2.1.2+dfsg-1 [ITP] -- Simple theorem prover

ps://github.com/stp/stp/tags \ (?:.*/)?v?(\d[\d\.]*)\.tar\.gz \ debian opts="dversionmangle=s/\+dfsg\d*$//,component=outputcheck" \ https://github.com/stp/OutputCheck/tags \ (?:.*/)?v?(\d[\d\.]*)\.tar\.gz \ ignore uupdate regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#814680: RFS: stp/2.1.2+dfsg-1 [ITP] -- Simple theorem prover

ttps://debian-handbook.info/browse/stable/sect.source-package-structure.html (see the box "Different source package formats") 2. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=561071 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#815754: [Pkg-gridengine-devel] Bug#815754: [PATCH] gridengine: proposal to add ppc64el architecture

this on ppc64el with the latest gridengine package/upstream version in preparation in git [1]? I see code there that seems to at least intend to handle it. Many thanks and regards Afif 1. http://anonscm.debian.org/cgit/pkg-gridengine/pkg-gridengine.git (master branch) -- Afif Elghraoui | عف

Bug#814680: RFS: stp/2.1.2+dfsg-1 [ITP] -- Simple theorem prover

such problems can be found by running lintian, but we first need the package to build in a minimal environment. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#814867: contacting Debichem regarding inchi ITP

Hi, Have you already contacted the Debichem team about this ITP for inchi? Their mailing list is at <debichem-de...@lists.alioth.debian.org>. You'll probably want to talk to them about joining the team if you haven't already done so. Many thanks and regards Afif -- Afif Elghraoui | عفيف ا

Bug#814765: [Debian-med-packaging] Bug#814765: python-pysam: FTBFS: samtools index: "ex2_truncated.bam" is corrupted or unsorted

sts.alioth.debian.org > > Dear Maintainer, > > python-pysam fails to build from source in unstable/amd64: > > [..] > This will likely be resolved by the imminent release of 0.8.5, which will match the htslib release we have in Debian. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#812175: RFS: qsopt-ex

://anonscm.debian.org/cgit/debian-med/qsopt-ex.git Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#803542: trnascan-se_1.3.1+dfsg-1_amd64.changes REJECTED

Hello, على الأربعاء 3 شباط 2016 ‫23:40، كتب Andreas Tille: > Hi, > > On Wed, Feb 03, 2016 at 09:27:07PM -0800, Afif Elghraoui wrote: >>> there seems to be something wrong with this package. >>> A DFSG package should not be in non-free. >>> >> >

Bug#811154: poretools_0.5.1-1_amd64.changes REJECTED

ards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#803542: trnascan-se_1.3.1+dfsg-1_amd64.changes REJECTED

have a more appropriate alternative to +dfsg for the repack suffix? Thanks and regards Afif 1. https://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-November/036574.html -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#811460: [Debian-med-packaging] Bug#811460: ITP: fast5 -- library for reading Oxford Nanopore Fast5 files

preciated :) I myself have mostly just been working with Pacific Biosciences data, but I thought Debian could get ahead and be prepared with software for analysis of nanopore data. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#812328: [Debian-med-packaging] Bug#812328: bcftools: fails to upgrade from 'jessie' - trying to overwrite /usr/share/man/man1/bcftools.1.gz

ages files without declaring a > Breaks+Replaces relation. > Thanks for reporting this. I had forgotten that bcftools used to be part of samtools in older versions, so this breaks/replaces relation is in order. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#812175: ITP: qsopt-ex -- exact linear and integer programming solver

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: qsopt-ex Version : 2.5.10.3 Upstream Author : Daniel Espinoza and others; currently maintained by Jon Lund Steffenson * URL

Bug#812268: [Debian-med-packaging] Bug#812268: bcftools: FTBFS: test suite fails on several architectures

> Hmm. Well, a new upstream release has been made while the package froze in the NEW queue. We'll have to see whether this issue still exists there. But that will also require packaging the latest htslib release. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#812175: ITP: qsopt-ex -- exact linear and integer programming solver

of it, though. I generally like to copy the developers of the software on these messages to notify that the packaging is ongoing. Thanks for providing it under a free license. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name على الخميس 21 كانون الثاني 2016 ‫05:19، كتب

Bug#811458: RFS: nanopolish

Hello, Since fast5 was accepted (Thanks for uploading it, Andreas), nanopolish is now ready to go in. Could someone please upload this one? git+ssh://git.debian.org/git/debian-med/nanopolish.git http://anonscm.debian.org/debian-med/nanopolish.git Many thanks and regards Afif -- Afif Elghraoui

Bug#811911: kmer-tools: FTBFS with GCC 6: declared in this scope

://lists.debian.org/debian-med/2015/05/msg00075.html -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#811460: ITP: fast5 -- library for reading Oxford Nanopore Fast5 files

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 811458 by -1 * Package name: fast5 Version : 0~20150918 Upstream Author : Matei David * URL : https://github.com/mateidavid/fast5 * License

Bug#811460: RFS: fast5

Hello, I finished the fast5 package, which is needed for nanopolish. Could someone please upload to unstable? git+ssh://git.debian.org/git/debian-med/fast5.git http://anonscm.debian.org/cgit/debian-med/fast5.git Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http

Bug#808851: [Debian-med-packaging] Bug#808851: artemis REMOVED from testing

I think htsjdk is now a dependency. I could use some help with this bug (which is why I tagged it "help"), especially if the maintainers who triggered the transition could offer some insight. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#811509: [Pkg-gridengine-devel] Bug#811509: gridengine: [INTL:pt_BR] Brazilian Portuguese debconf templates translation

Thanks. I'll plan to include this while preparing the new gridengine package. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#811458: ITP: nanopolish -- consensus caller for nanopore sequencing data

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: nanopolish Version : 0.4.0 Upstream Author : Jared Simpson * URL : https://github.com/jts/nanopolish * License

Bug#811255: config-package-dev: support for debconf seeding

(charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) -- no debconf information >From a8ed0e6b21dc3e9250930949678d24f62e50eb2d Mon Sep 17 00:00:00 2001 From: Afif Elghraoui <a...@ghraoui.name> Date: Sun, 17 Jan 2016 01:30:57 -0800 Subject: [PATCH] Ad

Bug#811154: RFS: poretools

Hi, team, I've completed the poretools package after forgetting about it for some time. Could someone please upload to unstable? git+ssh://git.debian.org/git/debian-med/poretools.git http://anonscm.debian.org/cgit/debian-med/poretools.git Many thanks and regards Afif -- Afif Elghraoui | عفيف

Bug#811154: ITP: poretools -- toolkit for nanopore nucleotide sequencing data

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: poretools Version : 0.5.1 Upstream Author : Aaron Quinlan & Nick Loman * URL : http://poretools.readthedocs.org *

Bug#395843: wgs-assembler is now canu

hedocs.org/en/latest/ -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#810576: ITP: hail -- Efficiently extract arbitrary lines from a file or stream

Hi, Kevin, على السبت 9 كانون الثاني 2016 ‫15:17، كتب Kevin Murray: > Package: wnpp > Severity: wishlist > Owner: Kevin Murray > > * Package name: hail > Version : 0.1.1 > Upstream Author : Kevin Murray > * URL :

Bug#808851: Artemis FTBFS due to picard API changes

. Any help would be appreciated. I'm going to push my latest work and also plan to revisit this. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#703256: [Pkg-gridengine-devel] moving the gridengine team repository to collab-maint

t;> > Are you a Debian Maintainer and/or do you need sponsoring for uploads? > He said he would need sponsors, but I've offered to do so as well (in > case you want this off your hands). I am a DM, but the package in preparation adds new binary packages. Wouter kindly offered to sponsor

Bug#808895: ITP: lofreq -- sensitive variant calling from sequencing data

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: lofreq Version : 2.1.2 Upstream Author : Andreas Wilm and Niranjan Nagarajan * URL :

Bug#703256: moving the gridengine team repository to collab-maint

l/2015-October/000774.html 4. https://lists.alioth.debian.org/pipermail/pkg-gridengine-devel/2015-October/000779.html -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name signature.asc Description: OpenPGP digital signature

Bug#734702: [Pkg-gridengine-devel] libdb dependency in v8.1.8

Control: tag -1 pending على الجمعـة 11 كانون الأول 2015 ‫14:08، كتب Dave Love: > Afif Elghraoui <a...@ghraoui.name> writes: > >>> * Replace dependency on db-5.1 with unversioned package >>> >>> The db tools need to be consistent with the

Bug#808708: ITP: falconkit -- genome assembly toolkit

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 395843 by -1 * Package name: falconkit Version : 0.4.0 Upstream Author : Jason Chin * URL :

Bug#808708: RFS: falconkit (blocker for wgs-assembler)

://git.debian.org/git/debian-med/falconkit.git and it's browsable at the following link, in case anyone would like to review: http://anonscm.debian.org/cgit/debian-med/falconkit.git Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#807804: status of packaging intervaltree

I'm waiting for the Python 3.5 compatibility issue [1] to be resolved before finalizing this package. 1. https://github.com/chaimleib/intervaltree/issues/35 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#808202: RFS: pbbarcode

needs to be revised for acceptance to unstable, I would just delete/update the tag. Otherwise, I will surely forget until the next time I have to work on the package. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#808202: ITP: pbbarcode -- annotate PacBio sequencing reads with barcode information

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 787977 by -1 * Package name: pbbarcode Version : 0.8.0 Upstream Author : Pacific Biosciences * URL :

Bug#808270: RM: blasr [armhf mips powerpc s390x] -- ROM; build-dependencies not available

Package: ftp.debian.org Severity: important Control: block 808185 by -1 blasr has a new build-dependency (pbseqlib), which is not available on these architectures. blasr is affected by a grave bug in testing and stable-backports [1], and the absence of the package on some architectures is one of

Bug#808185: [Debian-med-packaging] Bug#808185: blasr: outdated binaries on several architectures

e package for those architectures, but just hadn't got around to it yet. The testing migration would have been delayed anyway because pbseqlib is not in testing currently and there appears to be an ongoing hdf5 transition. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#808185: [Debian-med-packaging] Bug#808185: blasr: outdated binaries on several architectures

على الأربعاء 16 كانون الأول 2015 ‫19:18، كتب Afif Elghraoui: > على الأربعاء 16 كانون الأول 2015 ‫14:15، كتب Emilio Pozuelo Monfort: >> Your package no longer builds on armhf, mips, mipsel, powerpc and s390x, >> where it built in the past. That prevents testing migration. &g

Bug#807979: [Debian-med-packaging] Bug#807979: bamtools cannot open bam files on big endian systems

big endian systems (mips, powerpc, ...) . It is not > possible to handle bam files. > I'm reducing the severity because it does not appear to affect *all* users (only users on a subset of architectures) based on your description. Many thanks for your bug report regards Afif -- Afif Elghr

Bug#807985: blasr: /usr/bin/blasr - No such file or directory

or directory $ which sawriter /usr/bin/sawriter $ sawriter bash: /usr/bin/sawriter: No such file or directory I am preparing an upload to resolve this problem, but I think this should be documented in the BTS. -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#807804: ITP: python-intervaltree -- mutable, self-balancing interval tree

Package: wnpp Severity: wishlist Owner: Afif Elghraoui <a...@ghraoui.name> Control: block 807803 by -1 * Package name: python-intervaltree Version : 2.1.0 Upstream Author : Chaim-Leib Halbert <chaim.leib.halb...@gmail.com> * URL : https://github.c

Bug#807802: ITP: pbsuite -- software for Pacific Biosciences sequencing data

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block -1 by 796644 * Package name: pbsuite Version : 15.8.24 Upstream Author : Adam English * URL :

Bug#807803: ITP: python-intervaltree-bio -- interval tree convenience classes for genomic data

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 807802 by -1 * Package name: python-intervaltree-bio Version : 1.0.1 Upstream Author : Konstantin Tretyakov * URL :

Bug#796644: RFS: pbdagcon (unstable NEW)

Hi, team, I've completed the pbdagcon package. Could someone upload to unstable, please? The repository is at: git+ssh://git.debian.org/git/debian-med/pbdagcon.git http://anonscm.debian.org/cgit/debian-med/pbdagcon.git Many thanks for all your support! regards Afif -- Afif Elghraoui | عفيف

Bug#798066: Multiarch-renamed python extensions not found during autopkgtest testing

*.${gnutype}.so ; do sudo ln -sf $so `basename $so .${gnutype}.so`.so ; done http://anonscm.debian.org/cgit/debian-med/python-pysam.git/tree/debian/tests/run-nose-tests regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#797676: RFS: kineticstools (unstable NEW)

Hi, team, I have the kineticstools package ready. Could someone upload to Unstable, please? The repository is at: git+ssh://git.debian.org/git/debian-med/kineticstools.git http://anonscm.debian.org/cgit/debian-med/kineticstools.git Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي

Bug#798066: Multiarch-renamed python extensions not found during autopkgtest testing

is currently not very helpful because there are many spurious failures due to this issue. There are more details in my original bug report [1]. Many thanks and regards Afif 1. http://bugs.debian.org/798066 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#798218: pbseqlib_0~20151014+gitbe5d1bf-1_amd64.changes is NEW

is in turn blocking still another package). I'm waiting for this one to be accepted before I can move on with that work. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name على الأربعاء 18 تشرين الثاني 2015 ‫22:58، كتب Afif Elghraoui: > > The package ha

Bug#797793: samtools update seems to breaks even more tests

you're not accidentally building with a Jessie chroot (where pysam is at version 0.7.7) rather than an Unstable one? [...] > > > Strange that you can not reproduce this. > I just made sure my working directory was clean and tried building again. It still works for me... regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#797793: samtools update seems to breaks even more tests

mitations >> because I use Stable and can't get an up-to-date report without changing >> my sources.list > > You could create an unstable chroot and login via dchroot. At least > that's my way to have an unstable system at hand. > Thanks for the tip. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#797793: samtools update seems to breaks even more tests

على الأحد 6 كانون الأول 2015 ‫11:35، كتب Afif Elghraoui: > The recent pysam release dropped support for some deprecated interfaces > and this package appears to have been affected. I can prepare a patch > for those pysam issues as I did for pbcore That patch is now in git. The tests ar

Bug#797793: samtools update seems to breaks even more tests

o look out for packages that may have problems later on due to the change, but the only way I know how to do that is using apt-cache rdepends. This has limitations because I use Stable and can't get an up-to-date report without changing my sources.list regards Afif 1. http://anonscm.debian.org/cgi

Bug#797793: samtools update seems to breaks even more tests

على الأحد 6 كانون الأول 2015 ‫13:21، كتب Afif Elghraoui: >>> The recent pysam release dropped support for some deprecated interfaces >>> >> and this package appears to have been affected. I can prepare a patch >>> >> for those pysam issues as I did

Bug#803542: trnascan-se_1.3.1+dfsg-1_amd64.changes REJECTED

to do anything about it. May I suggest that we upload the package to non-free in the meantime? Thanks and regards Afif 1. https://github.com/groleo/mpatrol/blob/master/tools/dbmalloc.h 2. https://packages.qa.debian.org/m/mpatrol.html 3. http://c-faq.com/resources/mallocdbg.html -- Afif Elghraoui

Bug#806271: RM: python-pbconsensuscore [hurd-i386] -- ROM; Current version does not build on hurd

Package: ftp.debian.org Severity: normal The build for this version of the package fails on hurd and it's going to hold back testing migration.

Bug#798872: python-pbcommand_0.2.16-1_amd64.changes REJECTED

Hi, Charles, I've addressed the below issue in git. Would you be able to upload this again, please? Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name On الأحد 22 تشرين الثاني 2015 08:00, Thorsten Alteholz wrote: > > Hi Afif, > > please add the

Bug#805754: ITP: ensembl-tools -- Ensembl tools for genomic data processing

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: ensembl-tools Version : 82 Upstream Author : European Bioinformatics Institute & Wellcome Trust Sanger Institute * URL :

Bug#805743: ITP: pyconfigure -- automatic configure script builder for Python software

Package: wnpp Severity: wishlist Owner: Afif Elghraoui <a...@ghraoui.name> * Package name: pyconfigure Version : 0.2.2 Upstream Author : Brandon Invergo <bran...@invergo.net> * URL : https://www.gnu.org/software/pyconfigure/ * License : GPL Prog

Bug#805687: [Debian-med-packaging] Bug#805687: python-pbcore: FTBFS: AttributeError: 'pysam.csamfile.Samfile' object has no attribute '_hasIndex'

upstream since about a week ago. -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#805607: ITP: piler -- genomic repeat analysis

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: piler Version : 0~20140707 Upstream Author : Robert Edgar * URL : http://www.drive5.com/piler/ * License : Public Domain

Bug#805607: RFS: piler - genomic repeat discovery

-- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#798218: RFS: pbseqlib (unstable)

Since these libraries are for internal use by other programs, upstream has not put versions in the library sonames, but this should be alright given its intended use. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#805230: ITP: python-pymummer -- Python interface to MUMmer

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 :

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