FreeBSD/ports 1ef6104biology/samtools Makefile distinfo

biology/samtools: Update to 1.24

Numerous fixes and enhancements
Changes: https://github.com/samtools/samtools/releases

Reported by:    portscout
DeltaFile
+3-5biology/samtools/Makefile
+3-3biology/samtools/distinfo
+1-0biology/samtools/pkg-plist
+7-83 files

LLVM/project 0979680llvm/lib/Transforms/Vectorize VPlan.h

[VPlan] Remove dead member functions (NFC) (#208936)

Remove member functions with no remaining callers anywhere in the tree:

 - VPExpressionRecipe::getOperandOfResultType
- VPBlockBase::getSingleHierarchicalSuccessor
 - VPIRFlags::hasNonNegFlag
- VPWidenIntOrFpInductionRecipe::getStartValue, which is an exact
duplicate of the inherited VPWidenInductionRecipe::getStartValue.
DeltaFile
+0-20llvm/lib/Transforms/Vectorize/VPlan.h
+0-201 files

LLVM/project 6e01e73libcxx/utils/ci/images libcxx_runners.txt

[libcxx] Bump runner set (#208929)

This pulls in 6d3cf7f436a01f4622fb660e413a4020209777b8, and
8ece73c9f8b54fea6a98e9e4c55f9a2e6ccc9b3c.
DeltaFile
+1-1libcxx/utils/ci/images/libcxx_runners.txt
+1-11 files

LLVM/project 419cce0libcxx/docs/ReleaseNotes 22.rst 23.rst

[libcxx][NFC] Move release notes for MSVC's implementation of exception_ptr (#208883)

These were accidentally placed in LLVM 22 rather than 23 file.
DeltaFile
+0-6libcxx/docs/ReleaseNotes/22.rst
+6-0libcxx/docs/ReleaseNotes/23.rst
+6-62 files

FreeBSD/ports c688db2biology/bcftools distinfo Makefile

biology/bcftools: Update to 1.24

Numerous fixes and enhancements
Changes: https://github.com/samtools/bcftools/releases

Reported by:    portscout
DeltaFile
+3-3biology/bcftools/distinfo
+2-2biology/bcftools/Makefile
+1-1biology/bcftools/pkg-plist
+6-63 files

FreeBSD/ports b44b3ccbiology/htslib distinfo Makefile, biology/htslib/files patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c patch-htscodecs_htscodecs_rANS__static4x16pr.c

biology/htslib: Update to 1.24

Numerous fixes and enhancements
Changes: https://github.com/samtools/htslib/releases

Reported by:    portscout
DeltaFile
+11-0biology/htslib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c
+11-0biology/htslib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c
+3-3biology/htslib/distinfo
+1-1biology/htslib/Makefile
+1-0biology/htslib/pkg-plist
+27-45 files

FreeBSD/ports 6682793x11-themes/skeuos-gtk-themes Makefile, x11-themes/win98se-icon-theme Makefile

*/*: Update maintainer e-mail address

PR:             296700
MFH:            2026Q3
Approved by:    Alexander Vereeken <Alexander88207 at protonmail.com> (maintainer)
Approved by:    db@, yuri@ (Mentors, implicit)

(cherry picked from commit ba4d25929c804fce4cf29a638504d38560ac1b6f)
DeltaFile
+1-1x11-themes/zorin-icon-themes/Makefile
+1-1x11-themes/zorin-gtk-themes/Makefile
+1-1x11-themes/yaru-icon-theme/Makefile
+1-1x11-themes/yaru-gtk-themes/Makefile
+1-1x11-themes/win98se-icon-theme/Makefile
+1-1x11-themes/skeuos-gtk-themes/Makefile
+6-629 files not shown
+35-3535 files

FreeBSD/ports ba4d259x11-themes/skeuos-gtk-themes Makefile, x11-themes/win98se-icon-theme Makefile

*/*: Update maintainer e-mail address

PR:             296700
MFH:            2026Q3
Approved by:    Alexander Vereeken <Alexander88207 at protonmail.com> (maintainer)
Approved by:    db@, yuri@ (Mentors, implicit)
DeltaFile
+1-1x11-themes/zorin-icon-themes/Makefile
+1-1x11-themes/zorin-gtk-themes/Makefile
+1-1x11-themes/yaru-icon-theme/Makefile
+1-1x11-themes/yaru-gtk-themes/Makefile
+1-1x11-themes/win98se-icon-theme/Makefile
+1-1x11-themes/skeuos-gtk-themes/Makefile
+6-629 files not shown
+35-3535 files

LLVM/project 9a0fd83mlir/test/CAPI rewrite.c

[mlir-c] Fix -Wmissing-field-initializers in rewrite.c test

The new matchAndRewrite1ToN field left three existing
MlirConversionPatternCallbacks initializers under-initialized, which
fails the CI build under -Werror=-Wmissing-field-initializers.
DeltaFile
+4-3mlir/test/CAPI/rewrite.c
+4-31 files

LLVM/project e9577f8mlir/lib/Bindings/Python Rewrite.cpp

[mlir-c] Value-initialize MlirConversionPatternCallbacks in Python bindings

The Python conversion-pattern binding left the struct default-initialized,
so the newly-added optional matchAndRewrite1ToN field held an indeterminate
pointer. The driver's null check then read garbage and jumped into it,
segfaulting mlir/test/python/rewrite.py. Value-initialize the struct so
optional callbacks default to null.
DeltaFile
+3-1mlir/lib/Bindings/Python/Rewrite.cpp
+3-11 files

LLVM/project f847e7bmlir/include/mlir-c Rewrite.h, mlir/lib/CAPI/Transforms Rewrite.cpp

[mlir-c] Add 1:N TypeConverter conversion and materialization bindings

Builds on the source/target materialization C bindings:

- Target materialization callbacks now receive `originalType` (split from the
  previously-shared source/target callback typedef), exposing a documented C++
  capability that was otherwise unreachable from C.
- 1:N type conversion: `mlirTypeConverterAdd1ToNConversion` plus an opaque
  results accumulator (`MlirTypeConverterConversionResults` /
  `mlirTypeConverterConversionResultsAppend`). A declining callback's appended
  types are rolled back so the driver's "try the next conversion" invariant
  holds.
- 1:N target materialization: `mlirTypeConverterAdd1ToNTargetMaterialization`,
  whose callback fills a caller-allocated `outputs` buffer. A success that
  leaves any output null is treated as a decline rather than handing the driver
  a null-containing result.
- `mlirConversionPatternRewriterReplaceOpWithMultiple` for 1:N value
  replacement, which can drive a source materialization with nInputs > 1.
- An optional `matchAndRewrite1ToN` callback on `MlirConversionPatternCallbacks`

    [9 lines not shown]
DeltaFile
+731-2mlir/test/CAPI/rewrite.c
+153-14mlir/lib/CAPI/Transforms/Rewrite.cpp
+103-5mlir/include/mlir-c/Rewrite.h
+987-213 files

LLVM/project 7fb9b32mlir/test/CAPI rewrite.c

[mlir-c] Tighten materialization test CHECKs to pin full module body

Use CHECK-NEXT to match the entire module body (module { ... }) rather
than loose CHECK lines, so the tests also assert the absence of any
stray ops -- e.g. a leftover builtin.unrealized_conversion_cast -- that
a loose CHECK would silently allow.
DeltaFile
+10-6mlir/test/CAPI/rewrite.c
+10-61 files

NetBSD/pkgsrc-wip c804000rust197 Makefile distinfo, rust197/files gcc-wrap

rust197: add a package for rust 1.97.0.

Package updates relative to rust196:
 * Version & checksum changes
 * Applied patches to updated vendored crates

Upstream changes:

Version 1.97.0 (2026-07-09)
==========================

Language
--------
- [Consider `Result<T, Uninhabited>` and `ControlFlow<Uninhabited,
  T>` to be equivalent to `T` for must use lint]
  (https://github.com/rust-lang/rust/pull/148214)
- [Add allow-by-default `dead_code_pub_in_binary` lint for unused
  pub items in binary crates] (https://github.com/rust-lang/rust/pull/149509)
- [Stabilize the `div32`, `lam-bh`, `lamcas`, `ld-seq-sa` and `scq`

    [125 lines not shown]
DeltaFile
+808-0rust197/Makefile
+215-0rust197/files/gcc-wrap
+195-0rust197/distinfo
+140-0rust197/cargo.mk
+128-0rust197/patches/patch-vendor_memchr-2.7.4_src_memchr.rs
+125-0rust197/options.mk
+1,611-088 files not shown
+4,327-094 files

FreeBSD/ports dfbc248devel/freebsd-git-mfc distinfo Makefile

devel/freebsd-git-mfc: Update to 0.20260710
DeltaFile
+5-5devel/freebsd-git-mfc/distinfo
+2-2devel/freebsd-git-mfc/Makefile
+7-72 files

OpenBSD/src oMmHkS0usr.sbin/vmd vioqcow2.c

   vmd(8): fix qcow2 refcounts on lazy allocated refcnt blocks.

   Lazy-allocated refcount blocks, such as those created when growing the
   disk past 2 GiB, should have refcount initialized to 1. While the disk
   is functional, operations on the metadata (such as resizing) fail as
   the reference counting is corrupt.

   From Chris Cunningham.

   "looks right to me" from @ori (original author of vioqcow2.c)
VersionDeltaFile
1.28+2-1usr.sbin/vmd/vioqcow2.c
+2-11 files

FreeBSD/src 4d37c2etests/sys/net/routing test_routing.sh

routing: Add test for nexthop subscription

Make sure we have reachability when one of our nexthops
gets down without deleting the route.

Differential Revision: https://reviews.freebsd.org/D57552
DeltaFile
+84-6tests/sys/net/routing/test_routing.sh
+84-61 files

FreeBSD/src be42ac4sys/net/route nhgrp_ctl.c nhop_ctl.c

routing: Replace unreachable nhops in nhgrp

If a nhop gets an interface event, revalidate the nhops and
immediately try to recompile existing nexthop groups by
replacing unreachable nexthops with reachable ones.
If none are available, recompile them back to
their normal position in nexthop group slots.

Reviewed by:    glebius
Discussed with: markj
Relnotes:       yes
Differential Revision: https://reviews.freebsd.org/D57389
DeltaFile
+60-6sys/net/route/nhgrp_ctl.c
+13-2sys/net/route/nhop_ctl.c
+1-0sys/net/route/route_var.h
+74-83 files

OpenBSD/ports OkiUHOVdevel/kf6/frameworkintegration Makefile, devel/kf6/kauth distinfo

   Update KDE Frameworks to 6.28.0

   https://kde.org/announcements/frameworks/6/6.28.0/
VersionDeltaFile
1.4+11-3devel/kf6/frameworkintegration/Makefile
1.11+5-3devel/kf6/kfilemetadata/Makefile
1.5+6-0devel/kf6/kconfig/pkg/PLIST
1.7+6-0devel/kf6/kcoreaddons/pkg/PLIST
1.4+4-1devel/kf6/kded/Makefile
1.26+2-2devel/kf6/kauth/distinfo
+34-986 files not shown
+200-15492 files

FreeBSD/src d05d1f2sys/net route.h, sys/net/route nhop_ctl.c nhop.h

routing: Subscribe nhops to ifnet link events

Update nexthop flags with interface link status events and
instead of checking link status of interface for every packet
only check the reachability flag of the final nexthop.

Reviewed by:    glebius
Discussed with: markj
Differential Revision: https://reviews.freebsd.org/D57375
DeltaFile
+66-2sys/net/route/nhop_ctl.c
+1-7sys/net/route/nhop.h
+3-3sys/netinet/in_fib.c
+3-3sys/netinet6/in6_fib.c
+1-3sys/net/route.h
+1-0sys/net/route/route_ctl.h
+75-186 files

OpenBSD/ports nSdt7Qjtextproc/xan distinfo Makefile

   Update to xan 0.60.0.
VersionDeltaFile
1.8+2-2textproc/xan/distinfo
1.9+1-1textproc/xan/Makefile
1.8+2-0textproc/xan/crates.inc
+5-33 files

FreeBSD/ports 631b5deaudio/lame distinfo Makefile

audio/lame: Update to 4.0.
DeltaFile
+3-3audio/lame/distinfo
+2-2audio/lame/Makefile
+5-52 files

NetBSD/pkgsrc-wip cb27a45crush COMMIT_MSG distinfo

crush: Update to 0.84.1

Changelog
5a7899e chore(deps): bump fantasy (0.35.2 -> 0.36.0) (@coloryourlife)
DeltaFile
+2-17crush/COMMIT_MSG
+9-9crush/distinfo
+2-2crush/go-modules.mk
+1-1crush/Makefile
+14-294 files

LLVM/project 4329818mlir-summer-school outline.md, mlir-summer-school/slides lecture1-passes.html lecture1-passes.md

update
DeltaFile
+2,608-0mlir-summer-school/slides/lecture1-passes.html
+997-77mlir-summer-school/slides/lecture1-passes.md
+182-3mlir-summer-school/slides/lecture3-canonicalization.md
+130-1mlir-summer-school/slides/lecture2-patterns.md
+98-0mlir-summer-school/slides/cheat-sheet.md
+37-4mlir-summer-school/outline.md
+4,052-851 files not shown
+4,052-857 files

FreeBSD/ports 3957ae2. GIDs UIDs, security/dogtag-pki Makefile

security/dogtag-pki: Add pkiuser account

Create the pkiuser system account required by Dogtag PKI.
DeltaFile
+4-1security/dogtag-pki/Makefile
+1-1GIDs
+1-1UIDs
+6-33 files

OpenZFS/src b8a8c7etests/zfs-tests/tests/functional/cli_root/zpool_initialize zpool_initialize_multiple_pools.ksh

ZTS: fix zpool_initialize_multiple_pools suspend race

zpool_initialize_multiple_pools verifies that "zpool initialize -a -s"
suspends initializing on all four pools. It starts initializing and,
without slowing it down, expects every pool to still be initializing
when the suspend runs.

On fast storage a pool can finish initializing before the suspend, so
"zpool initialize -a -s" reports "there is no active initialization"
and the pool's status is "completed" rather than "suspended". The
suspend command then fails the test intermittently.

Throttle zfs_initialize_chunk_size before the suspend phase, the same
way the zpool_wait_initialize_* tests do, so initializing stays active
through the suspend and cancel checks. The earlier phases that wait for
initializing to finish ("zpool wait" and "-w -a") are left at the
default chunk size so they still complete promptly.

The chunk size is saved and restored, and the pools are destroyed

    [5 lines not shown]
DeltaFile
+19-1tests/zfs-tests/tests/functional/cli_root/zpool_initialize/zpool_initialize_multiple_pools.ksh
+19-11 files

NetBSD/pkgsrc kR8htKGlang/nodejs24 distinfo Makefile

   Pullup ticket #7154 - requested by taca
   lang/nodejs24: Security fix

   Revisions pulled up:
   - lang/nodejs24/Makefile                                        1.11
   - lang/nodejs24/distinfo                                        1.11

   ---
      Module Name:      pkgsrc
      Committed By:     adam
      Date:             Mon Jun 22 08:55:52 UTC 2026

      Modified Files:
        pkgsrc/lang/nodejs24: Makefile distinfo

      Log Message:
      nodejs24: updated to 24.17.0

      24.17.0 'Krypton' (LTS)

    [14 lines not shown]
VersionDeltaFile
1.10.2.1+4-4lang/nodejs24/distinfo
1.10.2.1+2-2lang/nodejs24/Makefile
+6-62 files

FreeBSD/ports ff5a731www/freenginx-devel distinfo Makefile.extmod, www/freenginx-devel/files extra-patch-passenger-disable-telemetry extra-patch-passenger-build-nginx.rb

www/freenginx-devel: third-party modules management (+)

- update lua
- update luastream
- update passenger

to their recent releases/snapshots.

Bump PORTREVISION.

Sponsored by:   tipi.work
DeltaFile
+9-9www/freenginx-devel/distinfo
+5-5www/freenginx-devel/Makefile.extmod
+2-2www/freenginx-devel/files/extra-patch-passenger-disable-telemetry
+2-2www/freenginx-devel/files/extra-patch-passenger-build-nginx.rb
+2-2www/freenginx-devel/files/extra-patch-passenger-Configuration.c
+1-1www/freenginx-devel/Makefile
+21-216 files

Linux/linux cab9e33arch/x86/events/amd core.c brs.c, kernel/events core.c

Merge tag 'perf-urgent-2026-07-11' of git://git.kernel.org/pub/scm/linux/kernel/git/tip/tip

Pull perf events fixes from Ingo Molnar:

 - Fix SVM #GP on AMD CPUs that LBR but not BRS (Sandipan Das)

 - Fix UAF bug in the perf AUX code (Lee Jia Jie)

 - Fix address leakage in the AMD LBR code (Sandipan Das)

 - Fix address leakage in the AMD BRS code (Sandipan Das)

* tag 'perf-urgent-2026-07-11' of git://git.kernel.org/pub/scm/linux/kernel/git/tip/tip:
  perf/x86/amd/brs: Fix kernel address leakage
  perf/x86/amd/lbr: Fix kernel address leakage
  perf/aux: Fix page UAF in map_range()
  perf/x86/amd/core: Avoid enabling BRS from the SVM reload path
DeltaFile
+8-4arch/x86/events/amd/core.c
+5-5arch/x86/events/amd/brs.c
+2-1arch/x86/events/amd/lbr.c
+2-0kernel/events/core.c
+17-104 files

Linux/linux b37fa0darch/x86/video video-common.c, arch/x86/virt/svm sev.c

Merge tag 'x86-urgent-2026-07-11' of git://git.kernel.org/pub/scm/linux/kernel/git/tip/tip

Pull x86 fixes from Ingo Molnar:

 - Fix resctrl resource leak (Tony Luck)

 - Fix resctrl umount race (Tony Luck)

 - Fix resctrl double-free (Reinette Chatre)

 - Fix x86 VGA display fallback logic during bootup on
   certain multi-GPU systems (Mario Limonciello)

 - Re-add a WBINVD call to the SNP bootstrap path to
   fix an SNP regression (Tycho Andersen)

* tag 'x86-urgent-2026-07-11' of git://git.kernel.org/pub/scm/linux/kernel/git/tip/tip:
  x86/virt/sev: Revert "Drop WBINVD before setting MSR_AMD64_SYSCFG_SNP_EN"
  x86/video: Only fall back to vga_default_device() without screen info

    [3 lines not shown]
DeltaFile
+26-7fs/resctrl/rdtgroup.c
+14-9arch/x86/video/video-common.c
+2-0arch/x86/virt/svm/sev.c
+42-163 files

FreeBSD/ports 35dfcb9www/waterfox distinfo Makefile, www/waterfox/files patch-bug2046162 patch-gfx_skia_skia_src_core_SkCpu.cpp

www/waterfox: Update 6.6.15 => 6.6.16

Release Notes:
https://www.waterfox.com/releases/6.6.16/

PR:             296677
Sponsored by:   UNIS Labs
MFH:            2026Q3

(cherry picked from commit 71743838563eff87812f4ea702bcd228551ee39f)
DeltaFile
+0-31www/waterfox/files/patch-bug2046162
+0-29www/waterfox/files/patch-gfx_skia_skia_src_core_SkCpu.cpp
+3-3www/waterfox/distinfo
+2-2www/waterfox/Makefile
+5-654 files