Bug#855600: src:nlopt: Please provide binary package for cxx library

Package: src:nlopt Version: 2.4.2+dfsg-2 Severity: wishlist Control: block 855597 by -1 Hello, I'm looking to package phyx, but it depends on the C++ version of the nlopt library. While libnlopt-dev provides both the C and the C++ headers, the compiled library only works for C++. We need

Bug#855597: ITP: phyx -- phylogenetic analyses on trees and sequences for UNIX

Hi, Andreas, على الإثنين 20 شباط 2017 ‫08:26، كتب Andreas Tille: > Hi Afif > > On Mon, Feb 20, 2017 at 08:14:30AM -0800, Afif Elghraoui wrote: >> Description : phylogenetic analyses on trees and sequences for UNIX > > Please drop " for UNIX" here - sinc

Bug#855597: ITP: phyx -- phylogenetic analyses on trees and sequences for UNIX

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: phyx Version : 0.99 Upstream Author : Joseph W. Brown, Joseph F. Walker, and Stephen A. Smith * URL : https://github.com/FePhyFoFum/phyx *

Bug#852970: RM: pbcopper/0.0.1+20161202-2

على السبت 28 كانون الثاني 2017 ‫07:45، كتب Simon McVittie: > Package: release.debian.org > Severity: normal > User: release.debian@packages.debian.org > Usertags: rm > X-Debbugs-Cc: Afif Elghraoui <a...@debian.org> > > Afif Elghraoui wrote: >> There is not

Bug#852654: src:pbcopper: no point to releasing it without `unanimity`

Package: src:pbcopper Version: 0.0.1+20161202-2 Severity: important There is nothing actually wrong with pbcopper, but there is no sense in releasing this package for stretch since it basically only exists to support unanimity, which did not make the cutoff. -- Afif Elghraoui

Bug#639910: ITP: simple-build-tool -- bootstrapping

apping a compiler is necessary to otherwise avoid doing manual work. The alternative to bootstrapping a build tool is not manual work, but a different, maybe less efficient but still automatic approach. Thanks and regards Afif 1. http://git.savannah.gnu.org/cgit/make.git/tree/build.templ

Bug#849265: user-setup: hardware access groups should not be default

correspondence with pkg-systemd [2]. Thanks and regards Afif 1. http://bugs.debian.org/849265 2. http://lists.alioth.debian.org/pipermail/pkg-systemd-maintainers/2017-January/013684.html -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#849619: python-networkx: agressive use of Recommends

On السبت 7 كانون الثاني 2017 15:17, Sandro Tosi wrote: On Sat, Jan 7, 2017 at 5:34 PM, Afif Elghraoui <a...@debian.org> wrote: I hope what I've said now convinces you sadly you didnt What is it that doesn't make sense to you? Is it that you don't agree that the current sit

Bug#849619: python-networkx: agressive use of Recommends

On الجمعـة 6 كانون الثاني 2017 12:34, Sandro Tosi wrote: On Wed, Dec 28, 2016 at 10:28 PM, Afif Elghraoui <a...@debian.org> wrote: There are many valid use cases of networkx on headless systems or where visualization is done by other, separate programs, possibly written in dif

Bug#850227: singularity-container: homepage URL link is broken

Package: src:singularity-container Version: 2.2-1 Severity: minor Hello, The homepage URL is a dead link. I believe you want . I haven't checked the source URL or d/watch, but that might be bad as well. The source is at

Bug#849265: [Adduser-devel] Bug#849265: adduser: Should not add users to the audio group

o contacting the udev maintainers: http://lists.alioth.debian.org/pipermail/pkg-systemd-maintainers/2017-January/013683.html regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#849498: cme: Please allow "fixing" without restyling

this isn't a one-time fight with cme. Thanks and regards Afif > > [1] http://augeas.net/docs/references/1.4.0/lenses/files/debctrl-aug.html > [2] > http://search.cpan.org/dist/Config-Model-Backend-Augeas/lib/Config/Model/Backend/Augeas.pm > -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#849619: python-networkx: agressive use of Recommends

Package: python-networkx Version: 1.11-2 Severity: normal Hello, I maintain and use some genomics packages that depend on this library, but do not need some of the packages it Recommends. I think some of the Recommends of this package should instead be Suggests. I would say that at least

Bug#849500: libconfig-model-dpkg-perl: improper handling of comments

; >> or they should be removed >> altogether. > > I can certainly add an option to cme to remove comments. Would that be > helpful? Well, not to me. I'm of the opinion that if the debian/control format supports comments, other tools shouldn't consider them illegal. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#832391: consensuscore2: figured out the resolution

o "distutils". Just posting here for the record in case someone else stumbles across a similar issue. -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#849500: libconfig-model-dpkg-perl: improper handling of comments

Package: libconfig-model-dpkg-perl Version: 2.087 Severity: normal Hello, I'm not a cme user, but I've seen as part of team uploads in my packages before that comments in debian/control are moved away from the lines they refer to in the process of reorganization (and inadvertently committed

Bug#849498: cme: Please allow "fixing" without restyling

Package: cme Version: 1.016-1 Severity: wishlist Hello, For the case of team uploads (and maybe NMU's) where people like to use cme to fix certain issues in debian/control, it would be helpful if calling cme fix would *only* fix issues and not restyle it. If the primary maintainer is not using

Bug#849265: [Adduser-devel] Bug#849265: adduser: Should not add users to the audio group

up. > I'd like to get in touch with the udev maintainers about this. There may be other groups in this set of extra_groups that are in a similar situation. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#849431: [Debian-med-packaging] Bug#849431: daligner: FTBFS with ld --as-needed

). That was my ignorance. Thanks for correcting it. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#844034: Any intend to fix this soon

Hi, Andreas, على السبت 24 كانون الأول 2016 ‫11:34، كتب Andreas Tille: > On Sat, Dec 24, 2016 at 07:24:22AM -0800, Afif Elghraoui wrote: >> I'm really sad to see the duplication of effort when I was so >> particular to make sure my work was pushed :(. Is there a way

Bug#844034: Any intend to fix this soon

nonscm.debian.org/git/debian-med/pbsuite.git/log/?h=topic/blasr5 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#849187: RM: kmer-tools -- ROM; superceded by kmer

Package: ftp.debian.org Severity: normal The source package has been renamed, so this old source package should be removed. I noticed that this doesn't happen automatically if the source package is renamed without a change in the upstream version, which is the case here. Many thanks and regards

Bug#849186: RM: pbseqlib [i386 armel mipsel] -- ROM; new build-dependency not available

Package: ftp.debian.org Severity: normal Control: block -1 with 849183 849184 pbseqlib is now built with pbbam, which is not available on 32-bit architectures. I've also filed for removal of the reverse-dependencies on these architectures for the same reason (see blocking bugs). Many thanks and

Bug#849184: RM: pbdagcon [i386 armel mipsel] -- ROM; new build-dependency not available

Package: ftp.debian.org Severity: normal pbdagcon (like blasr) has a new build-dependency on pbbam, which is not available on 32-bit architectures. Many thanks and regards Afif

Bug#849183: RM: blasr [i386 armel mipsel] -- ROM; new build-dependency not available

Package: ftp.debian.org Severity: normal blasr has a new build-dependency (pbbam) that is not available on 32-bit architectures. Many thanks and regards Afif

Bug#832391: consensuscore2: Any news?

على الخميس 22 كانون الأول 2016 ‫00:55، كتب Afif Elghraoui: > > I think it's > a good time to have this package removed. > FTR, I've just filed for its removal. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#849057: RM: consensuscore2 -- ROM; superceded by unanimity

Package: ftp.debian.org Severity: normal consensuscore2 has been moved to part of a larger project called unanimity (#847310). I kept consensuscore2 around in the meantime since unanimity hasn't been packaged yet, but the older version from there has been found to be too buggy to pursue

Bug#832391: consensuscore2: Any news?

على الأربعاء 21 كانون الأول 2016 ‫08:01، كتب Adrian Bunk: > On Tue, Dec 06, 2016 at 11:19:02PM -0800, Afif Elghraoui wrote: >> ... >> I'd like to just be a little conservative with this. Indeed, if >> everything goes well with unanimity, we will need to file for this >&g

Bug#848542: src:kineticstools: new upstream version 0.6.1

know. The BTS didn't send any notification. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#848542: src:kineticstools: new upstream version 0.6.1

Package: src:kineticstools Version: 0.5.2+dfsg-2 Severity: normal Control: block -1 by 846663 kineticstools can be updated, but it has a new dependency on pybigwig. Afif

Bug#848541: src:blasr: build with pbbam

Package: src:blasr Version: 5.3-1 Severity: normal Control: block 844034 by -1 I can't find a link for this right now, but I understand that the `--sam` option to blasr cannot be used unless blasr is compiled with pbbam. pbsuite makes use of this `--sam` option, so in order for it to work with

Bug#848122: ITP: pbcopper -- data structures, algorithms, and utilities for C++ applications

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team Control: block 847310 by -1 * Package name: pbcopper Version : 0.0.1 Upstream Author : Pacific Biosciences * URL :

Bug#846770: gridengine: FTBFS: cc: error: libsched.a: No such file or directory

pthread -ljemalloc -lmunge cc: error: libsched.a: No such file or directory ../daemons/common/Makefile:94: recipe for target 'pdc' failed make[2]: *** [pdc] Error 1 so yes, libsched.a needs to be declared as a prerequisite of pdc. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#832391: consensuscore2: Any news?

before removing this one. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#847310: RFP: unanimity -- generate and process accurate genomic consensus sequences from single-molecule sequencing data

Package: wnpp Severity: wishlist * Package name: unanimity Version : 2.0.4 Upstream Author : Pacific Biosciences * URL : https://github.com/PacificBiosciences/unanimity * License : BSD Programming Lang: C++, Python Description :

Bug#832391: consensuscore2: Any news?

https://github.com/PacificBiosciences/pitchfork> Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#832391: consensuscore2: Any news?

Whoa, wait a minute. Consensuscore2 hasn't been deprecated yet--it's just been bundled with other things in the unanimity suite. The reason I don't support removal of this source package is that we might find the best solution to be extracting consensuscore2 from unanimity and using that for

Bug#847013: src:libsbml: build python3 bindings

Package: src:libsbml Version: 5.12.0+dfsg-3 Severity: wishlist The package currently builds only python2 bindings, but it would be nice to build them for both python2 and python3. I briefly looked into this, but it looks like it will not be quick to do. regards Afif

Bug#846770: gridengine: FTBFS: cc: error: libsched.a: No such file or directory

ust tried a parallel build on an up-to-date unstable chroot on amd64 and it builds just fine for me. Can you confirm? Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#846045: python-pytest-benchmark: fixture is not detected by pytest

Package: python-pytest-benchmark Version: 3.0.0-1 Severity: serious Hello, I am trying to run build-time tests for one of my packages where upstream just switched to pytest. The benchmark module does not get loaded (as verified by running `python2 -m pytest --traceconfig` after installing

Bug#845791: [Adduser-devel] Bug#845791: adduser: /bin/false vs /usr/sbin/nologin

ones created by base-passwd are the ones using /usr/sbin/nologin. > adduser --system defaults to /bin/false.. wouldn't it be nicer to default to > /usr/sbin/nologin? > Yes. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#708073: adduser: Recreating a system user fails when its UID is out of range

fferent range to determine what a system user is. I'd appreciate any suggestions to make this more clear so this confusion can be avoided in the future. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#521883: adduser: Please accept underscore prefixed system names

ign for making it the resolution of #248809 is another matter. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#521883: adduser: Please accept underscore prefixed system names

patibility with BSDs. I don't see that any of the breakage concerns originally raised in #432562 apply to this suggestion. I am also in favor of reducing unnecessary incompatibilities that can cause confusion. People of #432562, do you have any comments? regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#828329: gridengine: staying with libssl1.0

://lists.debian.org/debian-release/2016/11/msg00573.html -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#828481: ori: staying with libssl1.0

/11/msg00573.html -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#795890: ori: limiting architectures to linux-any

Control: severity -1 wishlist I'm lowering the severity of this bug since I'm removing kfreebsd and hurd from the architecture list of the package. If anyone would like to help upstream add support for them, that would fulfill this ticket and I'd change ori back to architecture:any. -- Afif

Bug#634262: arpwatch-ng status

-lived, so I don't expect to be working on it. Your update might spark someone else's interest, though, and it's good that it's now documented here. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#827061: transition: openssl - will both 1.0.x and 1.1.x be in Stretch?

bug to important, and unblock the transition by it? Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#829645: src:gtest: Cannot build against libgtest-dev with std=c++11

-BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Hi, Steve, على السبت 19 تشرين الثاني 2016 ‫20:36، كتب Steve M. Robbins: > On Mon, Jul 04, 2016 at 05:51:20PM -0700, Afif Elghraoui wrote: The > googletest package has recently been updated to 1.8.0 and built > with gcc 6. So I expect t

Bug#828329: [Pkg-gridengine-devel] Bug#828329: forwarded to https://arc.liv.ac.uk/trac/SGE/ticket/1572

ansition hubbub on -devel to see what's going to happen. > I'm happy to prepare/upload a version with either fix in, depending on > preference. I can take care of it. I think there were a couple other simple bugs that need to be fixed and now's a good time for that. Thanks and regards Afif --

Bug#634262: arpwatch-ng status

project again. Anyway, I'm not sure if anyone is interested in pursuing this, but I thought I should post the research I've just done in case it turns out to be useful. 1. http://freecode.com/about -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#844377: fai-client: Please allow installing packages with apt's -t option

users to specify them for a certain set of packages? Many thanks and regards Afif -- Afif Elghraoui Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence San Diego State University Alvarado Medical Center 6367 Alvarado Court, Suite 206 San Diego, CA 92120 p. 858-222-0454 http

Bug#844034: pbhoney: incompatible with blasr 5.x

Package: pbhoney Version: 15.8.24+dfsg-1 Severity: serious Control: forwarded -1 https://sourceforge.net/p/pb-jelly/tickets/5/ As blasr has been updated to 5.x in Unstable/Testing, pbhoney no longer works due to the interface change there. blasr options in 5.x have been changed from single dashes

Bug#832391: consensuscore2: Any news?

e2 be one of its binary packages. I'll have to see whether this problem will come up again after that. regards Afif 1. https://github.com/PacificBiosciences/unanimity -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#819617: [Debian-med-packaging] Bug#819617: Bug#819617: bcftools: FTBFS: test suite fails on several architectures

على الجمعـة 28 تشرين الأول 2016 ‫00:51، كتب Afif Elghraoui: > Hi, Andreas, > > على الجمعـة 28 تشرين الأول 2016 ‫00:18، كتب Andreas Tille: >> >> Any other volunteer? I think if the problem persists until our advent >> bug squashing party I'll ask for removal of the p

Bug#819617: [Debian-med-packaging] Bug#819617: bcftools: FTBFS: test suite fails on several architectures

w binary package for the pysam source code. I think you can expect for this bug not to be resolved soon, so I see that it is either the pysam source-package copy or the removal of rdeps on i386. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#819617: [Debian-med-packaging] Bug#819617: bcftools: FTBFS: test suite fails on several architectures

Hi, Andreas, على الخميس 27 تشرين الأول 2016 ‫23:39، كتب Andreas Tille: > On Sun, 26 Jun 2016 16:10:02 -0700, Afif Elghraoui wrote: >> For the record here, building with -msse2 doesn't help on i386 (build >> log attached). According to upstream discussion, the problem has to

Bug#842006: RM: src:python-pbh5tools -- ROM; source package renamed to "pbh5tools"

Package: ftp.debian.org Severity: normal Several months ago, the python-pbh5tools package was renamed to simply pbh5tools. The old source package (and the older versions of binary packages it built) were not automatically removed--apparently because the renaming upload was not part of a new

Bug#841671: [Debian-med-packaging] Bug#841671: pbbam: Fix for building with -Wl, --as-needed

e -Wl,--as-needed by default and this is > not a build issue in Debian, applying this patch will make your package more > portable in general. Please consider applying it. > Thanks for your report and patch. I definitely have no problem applying it. I'll upload after testing the build.

Bug#841396: ITP: dascrubber -- alignment-based scrubbing pipeline for DNA sequencing reads

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: dascrubber Version : 0~20160601 Upstream Author : Eugene W. Myers, Jr. * URL :

Bug#837871: no need for addgroup: The group `input' already exists as a system group. Exiting. messages

oing to say that this would be fixed sooner than you think, but I'm planning to travel soon, so it could be about a month or so. :) Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#828873: openjdk-8-jre-headless: inconsistent library installation paths - workaround applied in gridengine

Control: affects -1 - src:gridengine I've patched in special cases for arm64 and sparc64. gridengine can now build there, so this bug doesn't affect it anymore. -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#828874: hppa still FTBFS - [javac] Base64 cannot be resolved

hppa (and hurd) does not have Java 8. It might need a dependency on libcommons-codec-java to provide Base64 on this architecture. -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#836553: [Debian-med-packaging] Bug#836553: Bug#836553: poretools: short gpg key used in script

poretools is concerned, all R-related packages have been dropped as dependencies in the latest release. It seems the Dockerfile was contributed by a third party and has not kept up. I've simply excluded it from the tarball in the next release. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#836553: [Debian-med-packaging] Bug#836553: poretools: short gpg key used in script

re in the package > Yes, this file is not used at all during the build process or distributed in the binary package. I believe it's just used by upstream. I can repack the tarball and exclude this file if that will alleviate concerns. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#833995: [Pkg-gridengine-devel] Bug#833995: gridengine: embedded tcsh copy uses deprecated BSD union wait type

ears that upstream has applied this patch as well as some similar changes elsewhere in other affected areas of the codebase [1]. Many thanks and regards Afif 1. https://gitlab.com/loveshack/sge/commit/538640ffe09a44a14d9f0047708f9c87d90c29ac -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#834965: virtualbox-guest-utils: should not recommend virtualbox-guest-x11

Package: virtualbox-guest-utils Version: 5.0.24-dfsg-1 Severity: normal Hello, The description of virtualbox-guest-utils perfectly fits the expectation of what someone would want on text-only VM. Unfortunately, it recommends the virtualbox-guest-x11 package, which pulls in a ton of graphics

Bug#834856: [Debian-med-packaging] Bug#834856: python-pysam fails to build on mips64el arch.: failed test

: > [...] I'd be happy to apply any patch that resolves this problem, but porting work is beyond what I can commit to do for this package. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#770187: Fwd: debcommit: Please merge patch to to standardize git tag version mangle

Please merge patch to to standardize git tag version mangle Date: Sat, 16 Jul 2016 14:19:25 -0700 From: Afif Elghraoui <a...@debian.org> To: 770187-submit...@bugs.debian.org Control: tag -1 + patch Hello, I've implemented the changes proposed by Ian Jackson in this bug report. As an affected u

Bug#776131: gridengine available in jessie-backports

Just to drop a note here; although gridengine did not make it into jessie proper, it has been made available to systems running jessie via the jessie-backports repository. -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#832391: src:consensuscore2: python module packages come out empty on some architectures

Package: src:consensuscore2 Version: 0.12.0-1 Severity: serious The package build is apparently unpredictable. On the various package pages (like https://packages.debian.org/sid/python3-consensuscore2), the built binary packages are empty. For the example below, those that are 2.6 kB only contain

Bug#832311: ITP: pbtestdata -- small Pacific Biosciences datasets for testing

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: pbtestdata Version : 0.0.13 Upstream Author : Pacific Biosciences * URL :

Bug#831105: pbdagcon: FTBFS with GCC 6: cstdlib:75:25: fatal error: stdlib.h: No such file or directory

be resolved by replacing all "-isystem" flags with "-I" in the build system. I haven't implemented this change here yet because I was planning to update the packages to a new upstream revision (upstream doesn't label releases...). regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#826042: Spyder crashes on start

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

Bug#831523: RM: python-kineticstools [armel mipsel] -- ROM; not installable

Package: ftp.debian.org Severity: normal This package is not installable on the named architectures because of the absence of python-pysam there. Many thanks and regards Afif

Bug#831522: RM: pbh5tools [armel mipsel] -- ROM; not installable

Package: ftp.debian.org Severity: normal This package is not installable on the named architectures because of the absence of python-pysam there. Thanks and regards Afif

Bug#831520: RM: pbbarcode [armel mipsel i386 kfreebsd-i386] -- ROM; not installable

Package: ftp.debian.org Severity: normal This package is not installable on the named architectures because of its eventual dependency python-pysam not being available there. Thanks and regards Afif

Bug#831516: RM: pbbam [i386 armel mipsel] -- ROM; Antiquated and prevents testing migration

Package: ftp.debian.org Severity: normal The latest upload of the pbbam package has major changes, a new binary package, and also runs a test suite. This test suite fails on 32-bit platforms, where the original (very old version) used to be able to build. The presence of the outdated binaries on

Bug#829741: pbbam: severity is important

version adds much more functionality and runs a test suite that wasn't run before. -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#828199: RM: python-pysam [armel mipsel] -- ROM; FTBFS (test suite failures)

n: python-pbalign > pbsuite: pbhoney > python-pbsuite-utils > python-pbcore: python-pbcore > All of these packages are arch:all. The arch-dependent rdeps have all been taken care of already. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#829645: src:gtest: Cannot build against libgtest-dev with std=c++11

Package: src:gtest Version: 1.7.0-4 Severity: important Hello, I'm trying to enable tests for the pbbam package, but there is a compilation error that is triggered by simply including gtest.h: tests/CMakeFiles/test_pbbam.dir/build.make:65: recipe for target

Bug#829622: [Debian-med-packaging] Bug#829622: consensuscore2: FTBFS on hurd-i386: 'dict' object has no attribute 'iteritems'

quot; > --destdir="/«PKGBUILDDIR»/debian/python3-consensuscore2" -- > dh_install -a -O--buildsystem=pybuild > > I'm not sure offhand why not. Could you please take a look? > It looks like the linux i386 python module packages come out empty. Thanks for pointing this out. I'll have a look. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#829395: [Debian-med-packaging] Bug#829395: python-cobra: FTBFS on hurd-i386: This platform lacks a functioning sem_open implementation

> Ran 129 tests in 6.040s > > FAILED (errors=1, skipped=11) > > > If this is not trivially fixable, please request decrufting of the > outdated binary packages: > > Control: reassign -1 ftp.debian.org > Control: severity -1 normal > Control: retitle -1 RM: python-cobra [hurd-i386] -- RoM; FTBFS; platform lacks a functioning sem_open implementation > -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#829515: [Debian-med-packaging] Bug#829515: htseq: B-D python-pysam not available on all architectures where htseq previously built

testing migration [2]. regards Afif 1. https://buildd.debian.org/status/fetch.php?pkg=htseq=armel=0.6.1p1-4=1449681506 2. https://release.debian.org/migration/testing.pl?package=htseq -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#829519: RM: kineticstools [i386 kfreebsd-i386 hurd-i386] -- ROM; not installable

Package: ftp.debian.org Severity: normal This package indirectly depends on python-pysam, which is no longer available for any-i386. Testing migration of the new kineticstools upload is currently blocked by the lack of an i386 build. Many thanks and regards Afif

Bug#829510: ITP: consensuscore2 -- generate consensus sequences for PacBio sequencing data

Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team * Package name: consensuscore2 Version : 0.12.0 Upstream Author : Pacific Biosciences * URL :

Bug#829506: ITP: flask-multistatic -- A simple flask plugin for overriding static files

على الأحد 3 تـمـوز 2016 ‫15:15، كتب Sergio Durigan Junior: [...] > > This package is a dependency necessary for pagure. > Many thanks for working towards a pagure package! It looks like a very nice thing to have in Debian. regards Afif -- Afif Elghraoui | عفيف الغ

Bug#829393: RM: pbh5tools [i386 kfreebsd-i386] -- ROM; not installable

Package: ftp.debian.org Severity: normal pbh5tools depends on pysam, which is not built for {kfreebsd-,}i386 anymore and has already been removed from those architectures. Many thanks and regards Afif

Bug#828837: [Debian-med-packaging] Bug#828837: python-pbconsensuscore: please also build a C++ library

able with ConsensusCore anyway. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#829040: pandoc-citeproc: Should declare relationship with ca-certificates

Package: pandoc-citeproc Version: 0.9-1 Severity: normal While creating a Stretch chroot to work around #765091 in jessie, I was still missing a dependency when trying to run pandoc-citeproc (via pandoc): pandoc paper.tex -s --bibliography=references.bib --csl=style.csl -o paper.html

Bug#826113: [Pkg-gridengine-devel] Bug#826113: bugfix

Anyway, thanks for taking a look! I uploaded the package earlier today with the corrected patch. The latest changes should already be in git, but the package itself needs ftpmaster approval before it can enter the archive because I added a new binary package (gridengine-dev). Thanks and regards Afif --

Bug#819617: bcftools i386 - update on compiling with -msse2

For the record here, building with -msse2 doesn't help on i386 (build log attached). According to upstream discussion, the problem has to do with NaNs. -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name bcftools_1.3.1-2_i386.build.gz Description: application/gzip

Bug#828202: RM: fitgcp [armel mipsel] -- ROM; unsatisfiable dependency

Package: ftp.debian.org Severity: normal Control: block 828199 by -1 This package depends on python-pysam, which does not successfully build on the architectures in question. It will cease to be installable there once python-pysam is removed, so this one should be removed first. Thanks and

Bug#828200: RM: sga [armhf mips powerpc s390x armel mipsel i386] -- ROM; unsatisfiable dependencies

Package: ftp.debian.org Severity: normal This package has been blocked from testing migration for a long time. The testing excuses page mentions armhf, mips, powerpc, and s390x [1]. However, python-pysam is additionally not available for i386, (and (recently) armel and mipsel. Many thanks and

Bug#828199: RM: python-pysam [armel mipsel] -- ROM; FTBFS (test suite failures)

Package: ftp.debian.org Severity: normal Up until the 0.9.1 upstream release, the test suite had spurious failures, so they were being ignored. Now that the exit status is not ignored, we notice real test failures on armel and mipsel, so even though the 0.9.0 package successfully compiled

Bug#826113: Found in all prior releases

Control: found -1 6.2~beta-1 Looks like this problem was introduced in commit 50d1580b5b91f65e9a33a205a90a7c6925d45e8d (2008), which was part of the package's initial release. I'm not sure if this was a policy violation back then, though. -- Afif Elghraoui | عفيف الغراوي http

Bug#826113: [Pkg-gridengine-devel] Bug#826113: bugfix

ur patch did). The debian/*examples and debian/*install files are used by dh_installexamples(1) and dh_install(1), respectively, during the package build. debhelper(7) has a list of similar commands. Does this look good to you? I haven't tested it, but it looks ok to me. Many thanks and regards Afif -- Af

Bug#827638: ITP: sniffles -- structural variation caller using third-generation sequencing

Package: wnpp Severity: wishlist Owner: Afif Elghraoui <a...@debian.org> * Package name: sniffles Version : 0.0.1 Upstream Author : Fritz Sedlazeck <fritz.sedlaz...@gmail.com> * URL : https://github.com/fritzsedlazeck/Sniffles * License : MIT Prog

Bug#827076: src:gridengine: FTBFS with openssl 1.1.0

Package: src:gridengine Version: 8.1.8+dfsg-6 Severity: important As posted by Kurt Roeckx to debian-devel [1]: ~~~ The release of OpenSSL 1.1.0 is getting nearer. Some packages will no longer build with the new version without changes. Most of those changes should be trivial, like you can't

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