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 [email protected] 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 -
