biology/diamond: Update to 2.2.5 and fix deepclust crash
Initialize the seed_only member in the Hsp constructor that takes an
ApproxHsp. deepclust builds Hsps through this constructor for its
approximate alignments, so seed_only was left uninitialized. When it
evaluated to true, the SEED_ONLY flag was set on an otherwise
full-length intermediate output record. The multiblock join later
parsed that record as seed-only, stopped four bytes short, and aborted
with "Unexpected end of file", failing the deepclust-multiblock
regression test.
On Linux, the uninitialized member consistently evaluated to false,
masking the bug. On FreeBSD, it evaluated to true, and triggered the
crash.
Release notes: https://github.com/bbuchfink/diamond/releases/tag/v2.2.5
Sponsored by: The FreeBSD Foundation
x11-fonts/nerd-fonts: Update to 3.5.0
Upstream renamed the D2Coding font to D2Koding due to license reasons.
Consequently, the x11-fonts/nerd-fonts-d2coding subport has moved to
x11-fonts/nerd-fonts-d2koding accompanied by an entry in the MOVED file.
Added subports:
- x11-fonts/nerd-fonts-annotationmono
- x11-fonts/nerd-fonts-googlesanscode
Changed licenses:
- x11-fonts/nerd-fonts-agave (MIT -> OFL11)
- x11-fonts/nerd-fonts-arimo (APACHE20 -> OFL11)
- x11-fonts/nerd-fonts-cousine (APACHE20 -> OFL11)
Changelog:
https://github.com/ryanoasis/nerd-fonts/releases/tag/v3.5.0
PR: 297246
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security/caldera: change RUN_DEP from net/haproxy24 to net/haproxy to unbreak index
- Checked code, it's referenced only by a config and will probably work
with every version of haproxy
devel/llvm23: welcome 23.1.0-rc2
Update to the first usable snapshot of the 23.1.0 release (RC1 lacked
distfiles). Connect to the build.
Sponsored by: DARPA, AFRL
devel/llvm23: bootstrap from devel/llvm22
This is an unmodified copy of llvm22 (except for the removal of the
just added patch files/patch-backport-93a67259cf23 which we won't need).
The next commit will convert this this to llvm23 and attach it to the
tree.
Sponsored by: DARPA, AFRL
irc/unreal: Update 6.1.9.1 => 6.2.6
Port changes:
- Drops LIB_DEPENDS and configure flag for libmaxminddb as there
is a new built-in GeoIP database (mmdb).
- No longer RUN_DEPENDS on geoipupdate as the new database reloads
on start or rehash.
Changelog:
https://github.com/unrealircd/unrealircd/blob/unreal60_dev/doc/RELEASE-NOTES.md#unrealircd-626
PR: 297176
Reported by: Matthew Horan <matt at matthoran.com> (author)
Approved by: tanawts at gmail.com (maintainer)
Approved by: osa, vvd (Mentors, implicit)
MFH: 2026Q3
(cherry picked from commit 0e55a5b8c5945203b0fab7078a3ef1ae5674ed93)
irc/unreal: Update 6.1.9.1 => 6.2.6
Port changes:
- Drops LIB_DEPENDS and configure flag for libmaxminddb as there
is a new built-in GeoIP database (mmdb).
- No longer RUN_DEPENDS on geoipupdate as the new database reloads
on start or rehash.
Changelog:
https://github.com/unrealircd/unrealircd/blob/unreal60_dev/doc/RELEASE-NOTES.md#unrealircd-626
PR: 297176
Reported by: Matthew Horan <matt at matthoran.com> (author)
Approved by: tanawts at gmail.com (maintainer)
Approved by: osa, vvd (Mentors, implicit)
MFH: 2026Q3
security/openssl-oqsprovider: Fix build with liboqs 0.16.0
pending upstream release of new version
PR: 297221
Reported byL Bruno Damour <bruno ruoma net>
