math/R: on NetBSD, disable the ntohl / htonl dance.
These are already declared at the point in the code it's used,
and on macppc it causes build failure, and probably also on other
big-endian targets.
There still appears to be rpath issues, libR.so is installed in
${PREFIX}/lib/R/lib/, but that directory is not in rpath of other
libs or executables, so this does not install, at least not on
macppc at the moment.
Bump PKGREVISION.
biology/subread: Alignment, quantification, SNPs
The Subread package comprises a suite of software programs for
processing next-gen sequencing read data including:
Subread: a general-purpose read aligner which can align both
genomic DNA-seq and RNA-seq reads. It can also be used to
discover genomic mutations including short indels and structural
variants.
Subjunc: a read aligner developed for aligning RNA-seq reads
and for the detection of exon-exon junctions. Gene fusion events
can be detected as well.
featureCounts: a software program developed for counting
reads to genomic features such as genes, exons, promoters and
genomic bins.
Sublong: a long-read aligner that is designed based on
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py-minio: updated to 7.2.15
7.2.15
MinioAdmin: conditionally decrypt response in {attach,detach}_policy APIs
xml: prepend namespace for each path in findall()
Fix ExcludedPrefixes in set/get bucket versioning config
doxygen: updated to 1.13.2
Release 1.13.2
Bug fixes
* Template class with the same name as existing class gets in the same output file,
* SVG dot graphs have added padding
* Markdown blockquotes with lists do not render as expected
* Template class specializations are ignored, which leads to invalid links
* "Copy to clipboard" button broken with XHTML
* Documentation fails to build (it freezes, no crash)
* C++ 20 Modules: Links to global functions, links to modules
* Missing description for a class member of a using-declared class
* Snippet trimleft option does not handle newlines well,
* rebuilding fedora ignition-transport causes abort in isExplicitPage with doxygen 1.13.1
String representation at "show configuration" in doxywizard
Support for Plus sign code fence directives - GitHub flavor
Improved user feedback and documentation
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ckmame: update to 3.0.
3.0 (2025-01-20)
================
* Keep results of last runs, use `ckstatus` to query state of ROM
set. The `ckmame` command line options duplicating this functionality
(`--complete-list`, `--missing-list`, and `--report-changes`) are
deprecated.
* Add support for SHA256 and mia flag for ROMs and disks.
* Don't match any files for ROMs or disks with no hashes.
* When only keeping complete games, minimize searching when a ROM is missing.
lang/llvm: Fix Python dependency.
This ships a script llvm-lit with a Python interpreter baked into it
now, so Python is no longer tool-only. Hack around the #! line for
cross-builds when PYTHONBIN != TOOL_PYTHONBIN.
If the intent is to ship llvm without a runtime Python dependency, we
either need to nix llvm-lit or split it into a separate package.
converters/aklomp-base64: import aklomp-base64-0.5.2
Fast Base64 stream encoder/decoder
This is an implementation of a base64 stream encoding/decoding
library in C99 with SIMD (AVX2, AVX512, NEON, AArch64/NEON, SSSE3,
SSE4.1, SSE4.2, AVX) and OpenMP acceleration. It also contains
wrapper functions to encode/decode simple length-delimited strings.
This library aims to be:
- fast
- easy to use
- elegant
py-parsel: updated to 1.10.0
1.10.0 (2024-12-16)
* Removed support for Python 3.8.
* Added support for Python 3.13.
* Changed the default encoding name from ``"utf8"`` to ``"utf-8"`` everywhere.
The former name is not supported in certain environments.
* CI fixes and improvements.
py-cpplint: updated to 2.0.0
2.0.0
Python 2 and 3.7 are no longer supported. Python 3.12 support was added along with fixed CI for 3.8, courtesy of @jayvdb
As a result of all this, setup.py's lint subcommand was removed. Please run the commands directly instead.
Lots of refactoring , bug fixes, and updates to be more in line with latest C++ and Google style standards.
py-prompt_toolkit: updated to 3.0.49
3.0.49: 2025-01-20
New features:
- On Windows, use virtual terminal input when available.
- Support for multiline suggestions.
Fixes:
- Handle `InvalidStateError` during termination when using
`run_in_terminal`/`patch_stdout`. This can happen in some cases during
cancellation, probably when using anyio.
- Fix cursor that remains in hidden state when the application exits. This can
happen when the application doesn't show the cursor and `erase_when_done` is
being used.
Breaking changes:
- Drop support for Python 3.7:
libzip: update to 1.11.3.
# 1.11.3 [2025-01-20]
* Report read error for corrupted encrypted file data.
* Avoid unnecessary seeks when writing archive.
* Don't hardcode `_Nullable` support in `zip.h` to allow it to be used with different compilers.
* Improve check for GetSecurityInformation availability on Windows.
