I just discovered that biology/htslib and biology/samtools were upgraded without my knowledge immediately before the freeze.
revision 1.29
date: 2022-12-13 04:27:03 -0600; author: adam; state: Exp; lines: +8 -10; co
mmitid: CV8O1zaNSHQ7Qn5E;
htslib: updated to 1.16
1.16
In addition, biology/bcftools was *not* upgraded along with them and is now out of sync with htslib in the quarterly packages.
https://github.com/samtools/bcftools/releases/tag/1.16
biology/kallisto also depends on htslib. I see no discussion about this on the mailing lists, and I had no opportunity to test the v1.16 packages before they were committed, or retest kallisto with htslib 1.16.
Please consult with package maintainers before upgrading their packages.
I was planning to upgrade these packages shortly after the freeze to allow ample time for testing before they end up in a quarterly branch.