bob: Update to 0.99.5.
* Sandbox setup actions and per-package pre/post-build hook `cmd` actions no
longer have any environment applied to them. This allows setting variables
such as `LD_PRELOAD`, which otherwise would be applied directly to the chroot
command and likely lead to failures in the host environment. This is a
breaking change, but is hopefully clearer overall and less surprising for the
common cases.
* Ensure all `bob dev` sandbox commands use `environment.dev` rather than
`environment.build`.
* `bob log <pkg>` falls back to `setup.log` when no failed stage was recorded,
so that failures that happen before any pkgsrc stage runs work as expected.
* Improve error handling and output formatting for pre-build and post-build
scripts and hooks, as well as ensuring that the failure reasons are correctly
propagated to build status results.
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Update devel/objfw to 1.5.2
ObjFW 1.5.1 -> ObjFW 1.5.2, 2026-05-08
* Makes ObjFWConfig.cmake work on MSYS2.
* ObjFWConfig.cmake now also adds the flags for OBJCXX.
* OFFile no longer uses O_EXLOCK for "x" modes.
* Fixes the `OF_AMD64` define on Windows.
* ofhttp now removes the terminal's progress indicator on abort.
py-biopython: update to 1.87.
30 March 2026: Biopython 1.87
=============================
Migrated from ``setup.py`` to ``pyproject.toml`` for packaging configuration.
Addressed security issue CVE-2025-68463 in ``Bio.Entrez.Parser`` if parsing
untrusted files.
Additionally, a number of small bugs and typos have been fixed with additions
to the test suite and type annotations.
28 October 2025: Biopython 1.86
===============================
``Bio.SearchIO`` now supports parsing the tabular and plain text output of
`Infernal <http://eddylab.org/infernal/>` (v1.0.0+) RNA search tool. The
format names are ``infernal-tab`` and ``infernal-text``.
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libgpg-error: updated to 1.61
Noteworthy changes in version 1.61 (2026-05-07)
* Fix possible stack overflow in es_printf for %.100f format.
* Fix out-of-bounds read in vfnameconcat.
* Add cross compile support for wasm*-*-emscripten target.
* Update Japanese and Polish translations.
libksba: updated to 1.7.0
Noteworthy changes in version 1.7.0 (2026-05-07)
* Add support for building AuthEnvelopedData.
* New function ksba_cms_add_attribute.
* Fix silent truncation of 64 bit length fields.
* Fix incorrect overflow guard condition in _ksba_ber_read_tl.
* Interface changes relative to the 1.6.0 release:
ksba_cms_add_attribute NEW.
joker: update to 1.7.2
- Support osc8 in `joker.pprint/print-table`.
- Improve `joker.better-cond` macros to avoid "redundant do" linter
warnings.
- Add SSE support to `joker.http`.
- Add filesystem watch API (`joker.os/watch`).
- Add `joker.time/parse-in-timezone` function.
Add lxqt-clip
See https://github.com/lxqt/lxqt/discussions/2372#discussioncomment-16851376
qlipper is now being integrated into LXQt and has been renamed to lxqt-clip.
There is no release, yet. Makefile can be simplified once there's a release.
Build a package from the latest git-hash for now.