Failure to sync Debian-Med packages to Ubuntu

Asked by Tony Travis on 2019-02-15

I work with the Debian-Med team on Bio-Linux, which is an Ubuntu-based Linux distribution for biologists that makes extensive use of packages from the Debian "med-bio" task:

> https://blends.debian.org/med/tasks/bio

We are having problems with two Debian-Med packages that have failed to import automatically into Ubuntu 18.04 LTS:

> https://packages.debian.org/buster/abyss
> https://packages.debian.org/buster/metaphlan2

As I understand it, Ubuntu automatically imports packages from Debian testing, and most packages from Debian-Med have been imported OK into Ubuntu 18.04 LTS. However, the latest versions of these two packages have not been imported.

Would anyone from the MOTU team be interested in attending the next Debian-Med Sprint in Vilnius, Lithuania to explain to us how the automatic import process from Debian testing into Ubuntu works?

> https://wiki.debian.org/Sprints/2019/DebianMed2019

Please forward this email to anyone who might be interested.

Thanks,

  Tony.

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Question information

Language:
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Ubuntu Edit question
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Last query:
2019-02-15
Last reply:
2019-02-16
Manfred Hampl (m-hampl) said : #1

Manfred Hampl suggests this article as an answer to your question:
FAQ #3037: “no rolling release”.

Manfred Hampl (m-hampl) said : #2

abyss version 2.1.5-4 is available in Ubuntu disco (development version, to be published in April).
Similar for metaphlan2 version 2.7.8-1

Versions in older Ubuntu releases are updated to the newest version only in specific cases.
This is somewhat similar to Debian, where packages in jessie and stretch aren't automatically updated either.

Tony Travis (ajtravis) said : #3

On 15/02/2019 15:02, Manfred Hampl wrote:
> Your question #678573 on Ubuntu changed:
> https://answers.launchpad.net/ubuntu/+question/678573
>
> Status: Open => Answered
>
> Related FAQ set to:
> no rolling release
> https://answers.launchpad.net/ubuntu/+faq/3037
>
> Manfred Hampl proposed the following answer:
> Manfred Hampl suggests this article as an answer to your question:
> FAQ #3037: “no rolling release”.

Hi, Manfred.

OK, so would our best option be to back-port the new versions?

Thanks,

   Tony.

--
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548 http://minke-informatics.co.uk
mob. +44(0)7985 078324 mailto:<email address hidden>

Manfred Hampl (m-hampl) said : #4

I assume that a backport would best fit into the Ubuntu development and packaging standards, but I see a problem that the newest abyss version 2.1.5-5 depends on openmpi3 which is not available in Ubuntu 18.04. (I have not looked into the dependencies of metaphlan2.)

Maybe a PPA would also be a feasible option.

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