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Groups > linux.debian.bugs.dist > #1307650

Bug#1134352: Bioconductor and HDF5 transition clash

Cross-posted to 2 groups.

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Hi Charles

On Thu, 3 Sept 2026 at 00:21, Charles Plessy <plessy@debian.org> wrote:
>  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.

...

> My favorite is option 1.

The release team is fine with option 1.  Please see the packaging
notes about embedded code copies [1], and please register the affected
packages with the security team.  Previously, you could add them
yourself in the wiki, but now you can do it in salsa [2].

Regards
Graham


[1] https://wiki.debian.org/Packaging/EmbeddedCopies
[2] https://salsa.debian.org/security-tracker-team/security-tracker/raw/master/data/embedded-code-copies

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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

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