oid stress 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
--
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:
https://salsa.debian.org/hpc-team/gridengine/-/commit/97af886c1e106fe2161d0a704b
DPMT
>
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
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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
e...@lists.debian.org might get lost
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
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he probably never saw these messages. I'm
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
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
>affe
على ١٠/٩/١٤٤٠ هـ ٥:١٣ م، كتب Salvatore Bonaccorso:
> 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
my reason for making it had nothing to do with this CVE.
regards
Afif
--
Afif Elghraoui | عفيف الغراوي
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creates and keeps archived official build logs for the "all"
> architecture ].
>
I'm with you. I always do so whenever I can, but this was the first upload and
needed to be a binary upload to go through NEW...
regards
Afif
t 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 tests
so the buildds can operate...
regards
Afif
ine/commit/ac79ef75c32e5faf96c5ca8c618955d4c72ffd61
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Afif Elghraoui | عفيف الغراوي
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t [2].
1. https://salsa.debian.org/hpc-team/gridengine/tree/java10
2. https://arc.liv.ac.uk/trac/SGE/ticket/1642
--
Afif Elghraoui | عفيف الغراوي
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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
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 thi
assuming this is what upstream was refereing to).
>We can surely package where those meta.yaml files are pointing to but
>see my comments.
>
>It would be extremely helpful if we would find somebody at PacBio who
>can explain the situation (Afif? I know you said you are not using the
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:
https://salsa.debian.org/hpc-team/gridengine/commit/e2a27bd1ca086a4b20400a6fcf0
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
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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:
https://salsa.debian.org/med-team/sniffles/commit/e7f218e572dcc7f890a0854b2430c75
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
>> > (A
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 sta
taSetIO: ERROR: Invalid file produced:
>/tmp/tmpvYTcX1.subreadset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpiXc1ez.subreadset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpdiSRmI.subreadset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file pr
Control: tag -1 pending
Hello,
Bug #896402 in python-easydev 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:
https://salsa.debian.org/med-team/python-easydev/commit/37df25edf4e95f2d0bd
Control: tag -1 pending
Hello,
Bug #896292 in python-easydev 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:
https://salsa.debian.org/med-team/python-easydev/commit/37df25edf4e95f2d0bd
Control: tag -1 pending
Hello,
Bug #891373 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:
https://salsa.debian.org/hpc-team/gridengine/commit/c90a34ffea682348f28d5871f83
-gridengine.git/commit/?id=79e60e7
---
commit 79e60e7821db901b21e760a5609263e7b2d8f688
Author: Afif Elghraoui
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 100644
--- a/debian/changelog
erious' from 'important'
>Severity set to 'serious' from 'important'
There are patches to resolve this ticket, but I thought I'd wait for the
possibility of a new upstream release that would incorporate them. Since that
hasn't happened, I'll just add the patches the next time I get a chance.
Afif
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.
t the same time either).
Also +1
>
>
>If you find issues getting stuff sponsored, please do point me to it
>privately (I know you are on IRC, that tends to often work best for
>me).
Diane's a DD.
thanks and regards
Afif
On November 9, 2017 2:32:56 AM EST, Diane Trout 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 restoring the bundled
dependency on a specific binary version of libhts?
>
>That should probably probably be documented in a README.Debian for the
>private-dev package.
>
Does this imply a transition for each htslib update?
Many thanks and regards
Afif
gt; if Debian would 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
--
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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 newest
priate for the 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
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yeah, that should be closed. There is a similar bug holding up samtools 1.5
for the same reason that can also be closed. And bcftools 1.5 is held up for
portability regressions on exotic architectures that nobody has time/interest
for...
regards
Afif
. 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
.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
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Afif Elghraoui | عفيف الغراوي
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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/is
ting some of its other dependencies
(htslib/samtools).
regards
Afif
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Afif Elghraoui | عفيف الغراوي
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TP at a later 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
less
of soname changes. I'm currently preparing bcftools 1.5, but there's
still no corresponding pysam release.
Maybe RC bugs are a good idea. They probably should have been uploaded
to experimental to begin with until pysam caught up. I'll upload
bcftools there once I'm done
he past:
>> https://lists.debian.org/debian-med/2017/01/msg00085.html
>>
>> In addition to changing the architecture list, my upload
>> (debdiff attached) uses for #863929 the big hammer of no
>> longer running integration-tests.
>
> Hmmm, we need to discuss th
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
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Afif Elghraoui | عفيف الغراوي
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ekend) and report back.
regards
Afif
--
Afif Elghraoui | عفيف الغراوي
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y set it to "distutils".
Just posting here for the record in case someone else stumbles across a
similar issue.
--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
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 we can
Hi, Andreas,
على السبت 24 كانون الأول 2016 01:30، كتب Andreas Tille:
> Hi Afif,
>
> pbhoney is marked for autoremoval due to this bug. I'm guessing from
> the description of the problem that it should be easy to fix (without
> having checked). Do you intend to upload soo
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
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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
&
-gridengine.git/commit/?id=b20bd7f
---
commit b20bd7f1ac4ad26686c2797eac5520c0bf0ec441
Author: Afif Elghraoui
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 100644
--- a/debian/changelog
lm -lpthread
-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
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packaged before
removing this one.
Thanks and regards
Afif
--
Afif Elghraoui | عفيف الغراوي
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;s source integration builder:
<https://github.com/PacificBiosciences/pitchfork>
Thanks and regards
Afif
--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
using that
for the orig tarball here. We will likely run into fhe same or worse problems
trying to package everything from one unanimity source package.
I can elaborate when I get off work, but please do not remove this source
package.
Afif
Sent from my T-Mobile 4G LTE Device Original messa
i.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
>
> About the archive rebuild: The rebuild was done on EC2 VM instances from
> Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
> failed build was retried once to eliminate random failures.
ther packaged pytest module on Python 2,
python-pytest-django, and I see that it's detected properly. The problem
does not therefore seem to be with the Python 2 version of pytest.
Many thanks and regards
Afif
://lists.debian.org/debian-release/2016/11/msg00573.html
--
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/2016/11/msg00573.html
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just been monitoring the
transition 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
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
ore2 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
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fac9f5db03b2a0b3272d10bffb4b14e12fab29db
Author: Afif Elghraoui
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 +1,17 @@
+gridengine (8.1.9
the failed-build log:
>
[...]
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
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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
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amd64
and i386 in sbuild before uploading the current version of the package
and it built fine in both cases for me, so I thought this problem would
not be coming up again. I'm not sure what's going on, so I'm filing this
bug to prevent the package from being released in this condition.
regards
Afif
"-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
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yet.
Thanks and regards
Afif
--
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terested.
Thanks and regards
Afif
--
Afif Elghraoui | عفيف الغراوي
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s,
so 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
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version adds
much more functionality and runs a test suite that wasn't run before.
--
Afif Elghraoui | عفيف الغراوي
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ich can sometimes 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
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restrict this to the architectures where it is available or
> request decrufting of the outdated binary packages on the architectures
> where it is missing/failing.
>
Maybe removal on just armhf, mips, powerpc, and s390x if the armel build
can be fixed. Those are what are h
.. here
[...]
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 r
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 ال
your 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 regard
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 wrote:
>
> Thank you; I am glad to see the specific conte
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 ve
Hi, John,
على الثلاثاء 31 أيار 2016 03:01، كتب John Marshall:
> On Mon, 2 May 2016 21:54:49 -0700 Afif Elghraoui wrote:
>> This seems to happen with every htslib upgrade in the past few releases.
>> bcftools builds have also been breaking as a result and I was a little
>
3-examples
E: Package 'libgtk-3-common' has no installation candidate
Coulud someone take a look, please?
Many thanks and regards
Afif
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
his within the qtile package.
thanks and regards
Afif
--
Afif Elghraoui | عفيف الغراوي
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ks: samtools (<< ${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
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tainer 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
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Afif Elghraoui | عفيف الغراوي
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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
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Afif Elghraoui | عفيف الغراوي
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o it, 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
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Afif Elghraoui | عفيف الغراوي
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ss along the command line options as well, though.
Thanks and regards
Afif
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-BEGIN PGP SIGNATURE-
Version: GnuPG v2
iQIcBAEBCAAGBQJW9hT+AAoJEM6uatOv6Cb72MgP/2bBiVKGoJVx5ivBrZnP813E
P27V6DzMNdvYswGR838IAXTMl8TieON0PePOPY
Control: found -1 1.2
Hi,
I ran into this bug while trying to backport a package to jessie.
Following the hint given in the bug log, I was able to work around the
problem by adding the following line to debian/rules:
export DZIL_GLOBAL_CONFIG_ROOT=/sbuild-nonexistent
Thanks and regards
Afif
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
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
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tries to overwrite other packages 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
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Afif Elghraoui | عفيف الغراوي
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ard and 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
ality. Any help would
be appreciated. I'm going to push my latest work and also plan to
revisit this.
regards
Afif
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Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
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.
>&
f the 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
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Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
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.
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Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
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
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Afif
ed in 0.8.1. Are you sure 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
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Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
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 for
ds. This has limitations
>> 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
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Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
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
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