Bug#931345: nvchecker: autopkgtest regression in June 2019

tress on our infrastructure until this bug is fixed. > This bug has been fixed for about a week now but nvchecker still appears to be blocked from debci. Does that need to be manually changed? I expected it to be removed automatically once the bug was closed. thanks and regards Afif -- Afif

Bug#985498: marked as pending in gridengine

Control: tag -1 pending Hello, Bug #985498 in gridengine reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at:

Bug#937738: python-et-xmlfile: diff for NMU version 1.0.1-2.1

PMT > I'd have been happy to, but at the time, DPMT was using git-dpm and it didn't seem worth learning to use an unmaintained tool just to package a couple of python modules. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي https://afif.ghraoui.name

Bug#929662: docker.io: CVE-2018-15664 - upstream backport of patch for 18.09

Hello, Is any help needed on this? Upstream has a backport of the patch for the 18.09 series (same as Unstable): https://github.com/docker/engine/pull/253 Hopefully it won't be too much work to incorporate it. thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي https

Bug#903635: docker.io: use of iptables-legacy is incompatible with nftables-based iptables

and it'd be weird to file a bug on release.debian.org asking to apply a tag to another bug. Again, I think it makes more sense to just lower the severity if you don't think it should affect the release. regards Afif -- Afif Elghraoui | عفيف الغراوي https://afif.ghraoui.name

Bug#903635: docker.io: use of iptables-legacy is incompatible with nftables-based iptables

just checking in here as a concerned maintainer of a reverse-dependency threatened with autoremoval. thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي https://afif.ghraoui.name

Bug#929042: singularity-container: CVE-2019-11328)

On May 15, 2019 5:13:24 PM EDT, Salvatore Bonaccorso wrote: >Hi Afif, > >On Wed, May 15, 2019 at 10:57:49PM +0200, Salvatore Bonaccorso wrote: >> Then there is nothing further to be done. > >Oh, actually there is an open point: Is it confirmed that 3.0.3 is not >affected by the CVE? Did you

Bug#929042: closed by Afif Elghraoui (Re: Bug#929042: singularity-container: CVE-2019-11328)

this will hopefully be moot if we can unblock the version now in Unstable. regards Afif -- Afif Elghraoui | عفيف الغراوي https://afif.ghraoui.name

Bug#929042: closed by Afif Elghraoui (Re: Bug#929042: singularity-container: CVE-2019-11328)

eason for making it had nothing to do with this CVE. regards Afif -- Afif Elghraoui | عفيف الغراوي https://afif.ghraoui.name

Bug#921800: nvchecker: FTBFS (failing tests)

On February 8, 2019 7:59:10 PM EST, Santiago Vila wrote: >> It looks like a network access problem. The whole point of this >> package is to check online sources, so it's hard to test it without >> network access. I was able to build it just fine in my schroot, but I >> may have to disable the

Bug#921800: nvchecker: FTBFS (failing tests)

Hello, On February 8, 2019 7:15:55 PM EST, Santiago Vila wrote: >Package: src:nvchecker >Version: 1.3-1 >Severity: serious >Tags: ftbfs > >Dear maintainer: > >I tried to build this package in buster but it failed: >

Bug#875404: src:gridengine - worked around FTBFS by excluding jgdi

/ac79ef75c32e5faf96c5ca8c618955d4c72ffd61 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#875404: gridengine and java

. 1. https://salsa.debian.org/hpc-team/gridengine/tree/java10 2. https://arc.liv.ac.uk/trac/SGE/ticket/1642 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#917867: singularity-container: not supportable for Stable

a stable release. 1. https://bugs.debian.org/898154 2. https://lists.debian.org/debian-hpc/2018/12/msg00029.html 3. https://www.sylabs.io/singularity/ -- Afif Elghraoui

Bug#828481: ori: FTBFS with openssl 1.1.0

على ٣‏/٢‏/١٤٤٠ هـ ‫٤:٣٣ م، كتب Moritz Mühlenhoff: On Fri, Oct 13, 2017 at 12:52:55AM -0400, Afif Elghraoui wrote: What's the status? ori hasn't been uploaded since 21 months, is there any progress? There's been no development activity upstream since then either. I think it's time I

Bug#902132: [Debian-med-packaging] Bug#902132: falcon: FTBFS since python-networkx version 2.1-1; fails in test suite

Hello, On September 12, 2018 5:30:59 AM EDT, Andreas Tille wrote: >Hi Alex, > >On Wed, Sep 12, 2018 at 10:55:20AM +0200, Alex Mestiashvili wrote: >> Well, according upstream, current repository is not active anymore: >> >> >> Oh, sorry. We are no longer mirroring our internal FALCON repo here.

Bug#903406: Bug #903406 in gridengine marked as pending

Control: tag -1 pending Hello, Bug #903406 in gridengine reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below, and you can check the diff of the fix at:

Bug#903192: [Debian-med-packaging] Bug#903192: sniffles: FTBFS in buster/sid (dh_installman: Cannot find "debian/sniffles.1")

npage is defined in debian/manpages, but is created during the package build. I've worked around that, but it's still curious why the error is not consistent without `-B`. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#903192: Bug #903192 in sniffles marked as pending

Control: tag -1 pending Hello, Bug #903192 in sniffles reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below, and you can check the diff of the fix at:

Bug#900485: [Debian-med-packaging] Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14

On June 26, 2018 3:45:49 AM EDT, Andreas Tille wrote: >On Mon, Jun 25, 2018 at 09:52:50AM -0400, Afif Elghraoui wrote: >> I think we can give 1.5.0 a try, but it might have the same problem. > >Since it builds successfully I've just uploaded. > Ok >> > (And wh

Bug#900485: [Debian-med-packaging] Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14

On June 25, 2018 5:07:48 AM EDT, Andreas Tille wrote: >Hi Afif, > >On Mon, Jun 25, 2018 at 03:41:11AM -0400, Afif Elghraoui wrote: >> >pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced: >> >/tmp/tmpveTAsa.subreadset.xml >> > >> >Before I

Bug#900485: [Debian-med-packaging] Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14

Hi, Andreas On June 25, 2018 3:32:00 AM EDT, Andreas Tille wrote: >Hi Graham, > >On Sun, Jun 24, 2018 at 08:48:32PM +0200, Graham Inggs wrote: >> Control: tags -1 + patch > >thanks for the patch. Since we are targeting in Git at version 1.4.2 I >adapted the patch to this version and it works

Bug#827076: in package pkg-gridengine marked as pending

-gridengine.git/commit/?id=79e60e7 --- commit 79e60e7821db901b21e760a5609263e7b2d8f688 Author: Afif Elghraoui <a...@debian.org> Date: Sun Nov 19 00:19:43 2017 -0500 releasing package gridengine version 8.1.9+dfsg-6 diff --git a/debian/changelog b/debian/changelog index d7dbfa8..1c4218c

Bug#827076: Processed: raise severity of openssl-1.1-trans blockers

On November 13, 2017 2:43:16 PM EST, ow...@bugs.debian.org wrote: >Processing commands for cont...@bugs.debian.org: > >> # Raising the severity of bugs which are blocking the removal of >> # libssl1.0.2 which we want gone for Buster. >> #

Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

On November 9, 2017 6:20:03 PM EST, Diane Trout wrote: > [...] > >Anyone want to review? or should I go ahead and release? > I think you can release. However, it appears the changelog wasn't updated in git since the last upload [1] you'll need to go for a 1.5-3. regards

Bug#879886: libhts2: libhts2 needs to handle ABI changes

On November 9, 2017 3:06:32 AM EST, Mattia Rizzolo wrote: >On Wed, Nov 08, 2017 at 04:58:49PM -0800, Diane Trout wrote: >> > > I was wondering if we should split the cram headers into a >> > > libhts-private-dev so we can at least track what is depending on >> > > the >> > >

Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

On November 9, 2017 2:32:56 AM EST, Diane Trout <di...@ghic.org> wrote: >On Thu, 2017-11-09 at 02:03 -0500, Afif Elghraoui wrote: >> > - TODO Split private cram headers off into a new libhts-private-dev >> > package >> >> I'd rather be in favor of

Bug#879886: [Debian-med-packaging] Bug#879886: libhts2: libhts2 needs to handle ABI changes

Hi, Diane, Thanks for working on this. On November 8, 2017 7:58:49 PM EST, Diane Trout wrote: >One of the htslib developers filed a new bug, > >https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881170 > >asking us to not make their private libraries public. His suggestions >are

Bug#879886: [Debian-med-packaging] libhts2: libhts2 needs to handle ABI changes

ould start by running "git log -S symbolname" which will > usually provide an explanation, rather than assuming that something > terrible has happened. regards Afif 1. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=822701#56 -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#879886: [Debian-med-packaging] libhts2: libhts2 needs to handle ABI changes

على الجمعـة 27 تشرين الأول 2017 ‫09:55، كتب Mattia Rizzolo: > On Fri, Oct 27, 2017 at 12:52:31AM -0400, Afif Elghraoui wrote: [...] > > What would have been good to prevent the current breakage that has been > brought to my attention (samtools), what happened is that the newe

Bug#879886: [Debian-med-packaging] Bug#879886: Bug#879886: libhts2: libhts2 needs to handle ABI changes

1.4 release if I remember correctly. That's all I can say about this; I don't actually work on the htslib packaging myself. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#871314: [Debian-med-packaging] Bug#871314: pysam 0.12 depends on libhts2 1.5

Hi, Diane, On October 26, 2017 1:41:30 PM EDT, "Trout, Diane E." wrote: >The new version of pysam 0.12 requires libhts2 1.5. > >Unfortunately pysam 0.12 just migrated to testing, and libhts2 was >blocked from migrating by this bug because it breaks pysam 0.11 > > Oh, yeah,

Bug#868958: [Debian-med-packaging] bcftools FTBFS on 32bit: test failures

oing to add it back in. It'd also be extremely helpful if you could forward your patch upstream. Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#871083: [Debian-med-packaging] Bug#871083: python-pysam: FTBFS: Test failures

.7 > package. Your package is on said list. > > So for the new python2.7 to migrate to testing the FTBFS in python-pysam > needs to be fixed. Okay, I've just skipped that one failing test and uploaded the new version in order to move things along. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#871083: [Debian-med-packaging] Bug#871083: python-pysam: FTBFS: Test failures

على السبت 30 أيلول 2017 ‫16:43، كتب Afif Elghraoui: > I'll see if I can do it today, I see Andreas Tille is on top of this. The current issue right now is this upstream bug we encounter when trying to build the latest upstream version: https://github.com/pysam-developers/pysam/issues/

Bug#871083: [Debian-med-packaging] Bug#871083: python-pysam: FTBFS: Test failures

er dependencies (htslib/samtools). regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#823379: Found Maintainer for Elmer

ter time) > The last I heard, he had joined the Debian Science alioth group, but I didn't follow-up either. Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#871083: [Help] Failed to upgrade bcftools to version 1.5

n. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#863929: falcon: FTBFS: Test failures ("Task Node(0-rawreads/job_0001) failed with exit-code=256")

e on the weekends, but I don't think this will mean much for falcon. >> I'll open a new (non-RC) bug to make it visible that this is >> an issue that should be investigated properly. > > Thanks a lot for your last minute rescue action. I'll commit your > changes to Git (however, if you used

Bug#863929: [Debian-med-packaging] Bug#863929: falcon: FTBFS: Test failures ("Task Node(0-rawreads/job_0001) failed with exit-code=256")

any actual use (de novo genome assembly), it will require more memory than would be addressable on a 32-bit system. It's not really worth the time and effort to debug that. I don't know of an alias like !32bit for the Architecture field in debian/control to exclude that. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

Bug#859660: [Debian-med-packaging] Bug#859660: artemis running issue

) and report back. 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#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#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#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#846770: in package pkg-gridengine marked as pending

-gridengine.git/commit/?id=b20bd7f --- commit b20bd7f1ac4ad26686c2797eac5520c0bf0ec441 Author: Afif Elghraoui <a...@debian.org> Date: Sat Dec 10 13:21:45 2016 -0800 releasing package gridengine version 8.1.9+dfsg-4 diff --git a/debian/changelog b/debian/changelog index c7689a4..be34ce1

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#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#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#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#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#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#833995: marked as pending

fac9f5db03b2a0b3272d10bffb4b14e12fab29db Author: Afif Elghraoui <a...@debian.org> Date: Sat Sep 10 23:48:37 2016 -0700 releasing package gridengine version 8.1.9+dfsg-2 diff --git a/debian/changelog b/debian/changelog index fd4d9a1..a2e646f 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3

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#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#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#823379: Found Maintainer for Elmer

yet. Thanks and 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#823379: Maintaining elmer packaging officially within Debian

the package is in bad shape and about to be removed from the archive. Would you be interested in getting involved with Debian to make this a usable, official package? Many thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name

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#823379: Elmer version

metimes provide newer packages than Ubuntu. Many thanks and regards Afif 1. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=823379 -- 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#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#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#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#822701: [Debian-med-packaging] Bug#822701: Bug#822701: samtools: FTBFS: UNEXPECTED PASS: Task worked when we expected failure;

Hi, John, على الثلاثاء 31 أيار 2016 ‫03:01، كتب John Marshall: > On Mon, 2 May 2016 21:54:49 -0700 Afif Elghraoui <a...@debian.org> wrote: >> This seems to happen with every htslib upgrade in the past few releases. >> bcftools builds have also been breaking as a resu

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

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

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#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#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#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#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#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#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#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#803945: horae, artemis: error when trying to install together

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. Will that be

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