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 <[email protected]> Sent: 29 January 2020 16:39:17 To: Martin Pollard Cc: [email protected] 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 -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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