samtools and htslib 1.10 and relateds [EXT]

[Martin Pollard]

Hi,


Yes, Focal was what I was looking for. I will have a chat with the Samtools team about fixing the s390x build though it won't be quick. I suspect it's an endianness bug that has crept in again.


In the meantime if s390x could be dropped for as a stopgap it would be appreciated. I just really don't want 1.10 missing the Focal freeze as there were one or two security fixes in it too.


Martin

________________________________
From: Robie Basak <robie.basak at ubuntu.com>
Sent: 29 January 2020 16:39:17
To: Martin Pollard
Cc: ubuntu-motu at lists.ubuntu.com
Subject: Re: samtools and htslib 1.10 and relateds [EXT]

Hi Martin,

On Wed, Jan 29, 2020 at 04:27:39PM +0000, Martin Pollard wrote:
> Please would it be possible to get samtools 1.10, libhts3, bcftools, python2-pysam 0.15.4+ds-1 and python3-pysam 0.15.4+ds-1 ported over from Debian? There is about a year's worth of development since the last samtools release and the samtools team are unlikely to be able to continue to support users on 1.9.

Thank you for reaching out!

If you mean in a previous stable Ubuntu release, see
https://wiki.ubuntu.com/StableReleaseUpdates - Ubuntu users don't expect
versions of most packages to change during the lifetime of a stable
release, which is the point of them, so it's unlikely that 18.04 for
example will be updated with a major new version.

If you mean in the current Ubuntu development release in preparation for
a 20.04 release in April, then it looks like the update is currently
blocked by test failures on the s390x architecture. You can see the
status of this by following these URLs:

https://people.canonical.com/~ubuntu-archive/proposed-migration/update_excuses.html#samtools
https://launchpad.net/ubuntu/+source/htslib
https://launchpad.net/ubuntu/+source/htslib/1.10.2-2
https://launchpad.net/ubuntu/+source/htslib/1.10.2-2/+build/18481041
https://launchpadlibrarian.net/460002929/buildlog_ubuntu-focal-s390x.htslib_1.10.2-2_BUILDING.txt.gz
https://bugs.launchpad.net/ubuntu/+source/htslib/+bug/1860765
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=948092

If the Ubuntu archive administrators remove the s390x build then this
package version and its reverse dependencies should make progress
towards being included in the next Ubuntu release.

However this would be a stopgap; if you could help with a proper fix
then that would be appreciated.

Hope that helps,

Robie



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