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Groups > linux.debian.devel.release > #145727

Bug#1134352: Bioconductor and HDF5 transition clash

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Hi Graham,

most of the Bioconductor transition went smoothly, but unfortunately it clashed
with the HDF5 transition.

When Bioconductor was released, it contained core packages shipping a vendored
version 1.14 of HDF5, which was very close to the one in Testing.  Unvendoring
was very easy.  After the Bioconductor transition started, the HDF5 transition
took place and now we have version 2.1 in testing, and I simply do not have the
skill to unvendor HDF5 in Bioconductor and do the major upgrade instead of
upstream themselves.  I am CCing debian-r@ and debian-med@lists.debian.org to
see if somebody else wants to pick the ball, but I am pessimistic about this.

The next Bioconductor release might solve the problem, or might not.  The
next-next release will be in April.

I think that our possibilities are:

 0 Someone unvendors HDF5 in Bioconductor and ports the dependencies to be
   compatible with the major upgrade to1 version 2.1.  I tried with Claude 4.8 in
   OpenCode and failed after spending 20$ of OpenRouter tokens, but my AI skills
   are still beginner level…

 1 Ship the r-bioc-* packages with their vendored HDF5 library and trust that
   they will handle major security issues well.  The Bioconductor project has good
   programmers, more than a decade of acheivements, and a full commitment to
   security.  Also, they might migrate before the Freeze.

 2 Leave the r-bioc-* packages depending on r-bioc-rhdf5lib in Sid, migrate the
   rest and call the transition done.  The next one is next month.  Revisit the
   issue before the Freeze.

 3 Remove r-bioc-rhdf5lib and its dependencies from Debian until we can
   unvendor HDF5.  The NEW queue is very efficient those days.

 4 Give up and remove all r-bioc-* packages from Debian.  There are excellent
   third-party repositories shipping them.  In that case we may need to move some
   non-R dependencies to contrib, or remove them too.

My favorite is option 1.

What shall we do?

-- 
Charles Plessy                         Nagahama, Yomitan, Okinawa, Japan
Debian Med packaging team         http://www.debian.org/devel/debian-med
Tooting from home                  https://framapiaf.org/@charles_plessy
- You  do not have  my permission  to use  this email  to train  an AI -

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Bug#1134352: transition: Bioconductor 3.23 Charles Plessy <plessy@debian.org> - 2026-04-19 01:50 +0200
  Bug#1134352: transition: Bioconductor 3.23 Graham Inggs <ginggs@debian.org> - 2026-04-21 21:10 +0200
  Processed: Re: Bug#1134352: transition: Bioconductor 3.23 "Debian Bug Tracking System" <owner@bugs.debian.org> - 2026-04-21 21:10 +0200
  Processed: Ready for Bioconductor transition? "Debian Bug Tracking System" <owner@bugs.debian.org> - 2026-07-10 01:50 +0200
  Bug#1134352: Ready for Bioconductor transition? Charles Plessy <plessy@debian.org> - 2026-07-10 01:50 +0200
    Bug#1134352: Ready for Bioconductor transition? Graham Inggs <ginggs@debian.org> - 2026-07-10 12:40 +0200
      Bug#1134352: Ready for Bioconductor transition? Graham Inggs <ginggs@debian.org> - 2026-07-11 13:40 +0200
        Bug#1134352: Ready for Bioconductor transition? Charles Plessy <plessy@debian.org> - 2026-07-15 04:20 +0200
  Processed: Re: Bug#1134352: Ready for Bioconductor transition? "Debian Bug Tracking System" <owner@bugs.debian.org> - 2026-07-10 12:40 +0200
  Bug#1134352: Bioconductor and HDF5 transition clash Charles Plessy <plessy@debian.org> - 2026-09-03 02:30 +0200
    Bug#1134352: Bioconductor and HDF5 transition clash Andreas Tille <tille@debian.org> - 2026-09-03 10:50 +0200
    Bug#1134352: Bioconductor and HDF5 transition clash Graham Inggs <ginggs@debian.org> - 2026-09-03 17:00 +0200
      Bug#1134352: Bioconductor and HDF5 transition clash Charles Plessy <plessy@debian.org> - 2026-09-04 01:50 +0200
        Bug#1134352: Bioconductor and HDF5 transition clash Charles Plessy <plessy@debian.org> - 2026-09-09 02:30 +0200
          Bug#1134352: Bioconductor and HDF5 transition clash Graham Inggs <ginggs@debian.org> - 2026-10-07 18:10 +0200
            Bug#1134352: Bioconductor and HDF5 transition clash Charles Plessy <plessy@debian.org> - 2026-10-08 13:40 +0200
  Bug#1134352: marked as done (transition: Bioconductor 3.23) "Debian Bug Tracking System" <owner@bugs.debian.org> - 2026-10-08 14:30 +0200

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