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2022-11-08clisp: fix module linking with X11_TYPE = native on NetBSDnros2-7/+10
X11 pkg-config files on NetBSD includes -Wl,-rpath,/usr/X11R7/lib that can't be understood by the ld command, so use the compiler that can understand this for linking instead. Fixes build of x11/clisp-gtk2 with X11_TYPE = native and cwrappers. Concerns PR pkg/57077 .
2022-11-08slony1: updated to 2.2.11adam2-6/+6
2.2.11 - Add support for PG 15 - Remove standard_conforming_strings autoconf check - Fix typo in admin guide
2022-11-08orc: add upstream bug report URLwiz3-5/+9
2022-11-08doc: Updated devel/orc to 0.4.33wiz2-3/+3
2022-11-08orc: update to 0.4.33.wiz4-9/+24
0.4.33 ====== - Add support for aarch64 (64-bit ARM) architecture (not yet enabled on Windows though) (Marek Vasut, Dongju Chae, Gaetan Bahl) - aarch32: Implement loadupdb instruction used e.g. for video pixel format packing/unpacking/conversions (Marek Vasut, Gaetan Bahl) - neon: Fix unsigned only implementation of loadoffb, loadoffw and loadoffl (Daniel Knobe) - neon: Fix testsuite not passing on arm CPUs (Gaetan Bahl) - orccodemem: Fix use-after-free in error paths (Bastien Nocera) - orccpu-powerpc: Fix build with kernel < 4.11 (Fabrice Fontaine) - Add support for macOS Hardened Runtime (Doug Nazar) - Enable only SSE and MMX backends for Windows (Seungha Yang) - Fix ORC_RESTRICT definition for MSVC (Tim-Philipp Müller) - pkgconfig: add -DORC_STATIC_COMPILATION flag to .pc file for static-only builds (Steve Lhomme)
2022-11-08Updated biology/py-pydicom, devel/py-pipadam1-1/+3
2022-11-08py-pip: updated to 22.3.1adam2-6/+6
22.3.1 (2022-11-05) =================== Bug Fixes --------- - Fix entry point generation of ``pip.X``, ``pipX.Y``, and ``easy_install-X.Y`` to correctly account for multi-digit Python version segments (e.g. the "11" part of 3.11).
2022-11-08py-pydicom: updated to 2.3.0adam3-66/+60
Version 2.3.0 ================================= Changes ------- * :meth:`DataElement.description<pydicom.dataelem.DataElement.description>` is deprecated and will be removed in v3.0, use :attr:`DataElement.name<pydicom.dataelem.DataElement.name>` instead * Updated the private dictionary * :attr:`~pydicom.config.enforce_valid_values` is deprecated in favor of :attr:`~pydicom.config.settings.reading_validation_mode` * Added `download` parameter to :func:`~pydicom.data.get_testdata_file` to allow skipping downloading the file if missed locally (:pr:`1617`) Enhancements ------------ * Values are now validated for valid length, allowed character set and format on reading and writing. Depending on the value of :attr:`~pydicom.config.settings.reading_validation_mode` and :attr:`~pydicom.config.settings.writing_validation_mode` a warning is logged, an exception is raised, or the validation is skipped. * Added :class:`~pydicom.valuerep.VR` enum (:pr:`1500`) * UIDs for all Storage SOP Classes have been added to the ``uid`` module (:issue:`1498`) * Use rle_handler as last resort handler for decoding RLE encoded data as it is the slowest handler (:issue:`1487`) * Added, enhanced, or removed a number of Mitra private dictionary entries (:pr:`1588`) * Added support for unpacking bit-packed data without using NumPy to :func:`~pydicom.pixel_data_handlers.utils.unpack_bits`(:pr:`1594`) * Added :func:`~pydicom.pixel_data_handlers.util.expand_ybr422` for expanding uncompressed ``YBR_FULL_422`` data to ``YBR_FULL`` (:pr:`1593`) * Replacement of ``UN`` VR with ``SQ`` VR for undefined length data elements (introduced in 2.2.2), can now be configured via :attr:`~pydicom.config.settings.infer_sq_for_un_vr` * Updated dictionaries to DICOM 2022a Fixes ----- * Fixed odd-length **OB** values not being padded during write (:issue:`1511`) * Fixed Hologic private dictionary entry (0019xx43) * Fixed Mitra global patient ID private dictionary entry (:pr:`1588`) * Fixed :meth:`~pydicom.dataset.Dataset.compress` not setting the correct encoding for the rest of the dataset (:issue:`1565`) * Fixed `AttributeError` on deep copy of :class:`~pydicom.dataset.FileDataset` (:issue:`1571`) * Fixed an exception during pixel decoding if using GDCM < 2.8.8 on Windows (:issue:`1581`) * Fixed crashes on Windows and MacOS when using the GDCM plugin to compress into *RLE Lossless* (:issue:`1581`) * Fixed ``dir(Dataset())`` not returning class attributes (:issue:`1599`) * Fixed bad DICOMDIR offsets when using :meth:`FileSet.write() <pydicom.fileset.FileSet.write>` with a *Directory Record Sequence* using undefined length items (:issue:`1596`) * Assigning a list of length one as tag value is now correctly handled as assigning the single value (:issue:`1606`) * Fixed an exception with multiple deferred reads with file-like objects (:issue:`1609`)
2022-11-08Updated devel/py-xopen, databases/py-asyncpgadam1-1/+3
2022-11-08py-asyncpg: updated to 0.27.0adam2-12/+6
v0.27.0 Support Python 3.11 and PostgreSQL 15. This release also drops support for Python 3.6. Changes Add arm64 mac and linux wheels Add Python 3.11 to the test matrix Exclude .venv from flake8 Upgrade to flake8 5.0.4 (from 3.9.2) Show an example of a custom Record class Use the exact type name in Record.repr Drop Python 3.6 support Test on Python 3.11 and PostgreSQL 15, fix workflow deprecations
2022-11-08py-xopen: updated to 1.7.0adam2-6/+6
1.7.0: Unknown changes
2022-11-08Removed devel/py-typed-ast; comms/py-enrichadam1-1/+3
2022-11-08py-enrich: removed; not needed anymore for ansible-lintadam5-53/+1
2022-11-08py-typed-ast: removed; included in Python 3.8 - ast moduleadam6-78/+1
2022-11-08py-astroid: no need to depend on py-typed-ast anymoreadam1-2/+1
2022-11-08py-black: no need to depend on py-typed-ast anymoreadam1-5/+1
2022-11-08Updated sysutils/py-psutil, devel/py-immutabledict, lang/py-mypy, devel/py-fakeradam1-1/+5
2022-11-08py-faker: updated to 15.3.1adam3-14/+14
v15.3.1 * Update the `word_list` for `pl_PL`. v15.3.0 * Add color provider for `id_ID`. v15.2.0 * Add banks for `en_IN` locale. v15.1.5 * Fix type variable inside the `ElementsType`. v15.1.4 * Remove test dependency on `random2`. v15.1.3 * Fix pyfloat causing ValueError. v15.1.2 * Fix missing return in `en_US` `state_abbr`. v15.1.1 * Fix ImportError on python <3.7.2. v15.1.0 * Add enum provider. v15.0.0 * Add support for Python 3.10. * Drop support for Python 3.6. v14.2.1 * Fix misspelled first name in `da_DK` locale.
2022-11-08py-mypy: updated to 0.990adam3-10/+18
v0.990 Remove +dev from version
2022-11-08py-immutabledict: updated to 2.2.3adam2-7/+6
Version 2.2.3 Fix TypeError message when using |=. Update docstring for ImmutableOrderedDict to indicate that is not needed anymore for Python >= 3.7 but kept for compatibility purposes Use postponed evaluation of annotations (PEP 563) for the typing Version 2.2.2 Update classifiers, Github Actions... for Python 3.11 (no code changes)
2022-11-08py-psutil: updated to 5.9.4adam4-9/+28
5.9.4 ===== 2022-11-07 **Enhancements** - 2102_: use Limited API when building wheels with CPython 3.6+ on Linux, macOS and Windows. This allows to use pre-built wheels in all future versions of cPython 3. (patch by Matthieu Darbois) **Bug fixes** - 2077_, [Windows]: Use system-level values for `virtual_memory()`_. (patch by Daniel Widdis) - 2156_, [Linux]: compilation may fail on very old gcc compilers due to missing ``SPEED_UNKNOWN`` definition. (patch by Amir Rossert) - 2010_, [macOS]: on MacOS, arm64 ``IFM_1000_TX`` and ``IFM_1000_T`` are the same value, causing a build failure. (patch by Lawrence D'Anna)
2022-11-08doc: Updated net/unison to 2.53.0gdt1-1/+2
2022-11-08net/unison: Update to 2.53.0gdt5-53/+15
Change to lablgkt3. Drop MAKE_JOBS_SAFE because the issue was fixed upstream. ## Changes in 2.53.0 Released 2022-11-07 * OCaml >= 4.08 is required to build unison. * unison can be built with (unreleased) OCaml 5. * Change GUI to use GTK3 (via lablgtk3) instead of GTK2 (via lablgtk2) * Add support for syncing extended attributes. * Add support for syncing ACLs. * On Windows, add the ability to build unison as a hybrid application (GUI application attached to a text console) by defining UI_WINOS=hybrid (see src/Makefile). Add this to CI. (Doing this for non-Windows is unnecessary as all applications, both GUI and non-GUI, are always executed with a connection to stdout/stderr. GUI-only applications (ie, no stdout/stderr) is a Windows-only concept.) * Notable bugfixes - Merge results are stored in archive more accurately. - Windows `\\?\` paths now work correctly (including `\\?\Volume{GUID}\` paths). * CI changes - The macOS binaries are properly signed. - Add workaround for bugs in the github CI Windows builds, one of which resulted in the 2.52.1 GUI version failing, in the Windows CI build artifacts. (This does not affect platforms other than Windows, and may not affect other Windows builds.) * Changes that should not affect behavior - Clean up a variety of unmaintained and unused bits, mainly build-related. - OCaml's Unix library is now extensively used also on Windows. This allowed removal of large amount of Windows-specific OCaml and mainly C code.
2022-11-08seamonkey: update Python 3 tool dependencygutteridge1-3/+3
2022-11-08thunderbird68: update Python 3 tool dependencygutteridge1-5/+5
2022-11-07doc: Updated devel/patchelf to 0.17.0fcambus1-1/+2
2022-11-07patchelf: update to 0.17.0.fcambus2-6/+6
- fix pagesize on ia64 - write out replace sections in original order - patchelf: correct page size for sparc64/sparc32 - update vendored elf file - add workaround for readelf from binutils 2.30 - make objdump/objcopy/readelf configurable and respect cross-compiling
2022-11-07doc: Updated security/sudo to 1.9.12p1taca1-1/+2
2022-11-07security/sudo: update to 1.9.12p1taca3-48/+6
1.9.12p1 (2022-11-07) What's new in Sudo 1.9.12p1 * Sudo's configure script now does a better job of detecting when the -fstack-clash-protection compiler option does not work. GitHub issue #191. * Fixed CVE-2022-43995, a potential out-of-bounds write for passwords smaller than 8 characters when passwd authentication is enabled. This does not affect configurations that use other authentication methods such as PAM, AIX authentication or BSD authentication. * Fixed a build error with some configurations compiling host_port.c.
2022-11-07Updated textproc/utf8-cpp, devel/py-jaraco.collectionsadam1-1/+3
2022-11-07py-jaraco.collections: updated to 3.8.0adam2-6/+6
v3.8.0 ====== Made ``DictStack`` mutable.
2022-11-07utf8-cpp: updated to 3.2.2adam3-10/+10
v3.2.2 Minor changes that eliminate some conversion warnings in some cases.
2022-11-07firefox52: adjust outdated commentsgutteridge1-3/+2
2022-11-07thunderbird: remove 37 from PYTHON_VERSIONS_ACCEPTEDgutteridge1-2/+2
2022-11-06devel/backports.cached-property-1.0.1: Drop 37gdt1-2/+2
as this depends on things that no longer exist. It should be removed, but this should fix the bulk scan failure.
2022-11-06devel/Makefile: comment out py-backports.cached-propertywiz1-2/+2
python 3.7 only and the packages it depends upon by default do not build 3.7 versions any longer
2022-11-06biology/Makefile: Add gffreadbacon1-1/+2
2022-11-06doc: Added biology/gffread version 0.12.7bacon1-1/+2
2022-11-06biology/gffread: GFF/GTF format conversions, filtering, etcbacon5-0/+110
GFF/GTF utility providing format conversions, filtering, FASTA sequence extraction and more. The program gffread can be used to validate, filter, convert and perform various other operations on GFF files. Because the program shares the same GFF parser code with Cufflinks, Stringtie, and gffcompare, it could be used to verify that a GFF file from a certain annotation source is correctly "understood" by these programs.
2022-11-06biology/Makefile: Add fastq-trimbacon1-1/+2
2022-11-06doc: Added biology/fastq-trim version 0.1.1.16bacon1-1/+2
2022-11-06biology/fastq-trim: Lightening fast sequence read trimmerbacon4-0/+107
Fastq-trim is a lightening fast read trimming tool for QA of DNA and RNA reads prior to analyses such as RNA-Seq. it runs in a fraction of the time required by popular trimmers and uses only a few megabytes of RAM, so it will run almost entirely in cache. The design supports adding any number of alignment functions, so it can be easily adapted to any trimming needs.
2022-11-06doc: Updated emulators/dosbox-x to 0.84.3triaxx1-1/+2
2022-11-06dosbox-x: Update to 0.84.3triaxx6-19/+40
pkgsrc changes: --------------- * Fix building of FreeBSD by adding -lpthread to LDFLAGS and by disabling call to X11_ErrorHandlerInstall. upstream changes: ----------------- * 0.84.3: https://dosbox-x.com/release-0.84.3.html * 0.84.2: https://dosbox-x.com/release-0.84.2.html * 0.84.1: https://dosbox-x.com/release-0.84.1.html * 0.84.0: https://dosbox-x.com/release-0.84.0.html
2022-11-06doc: Updated shells/zsh to 5.9nb2wiz2-3/+4
2022-11-06zsh: add candidate upstream patch for bg/fg issue with shell functionswiz3-3/+74
Bump PKGREVISION.
2022-11-06Updated devel/py-jaraco.itertools, www/py-websocketsadam1-1/+3
2022-11-06py-websockets: updated to 10.4adam2-6/+6
10.4 New features Validated compatibility with Python 3.11. Added the latency property to protocols. Changed ping to return the latency of the connection. Supported overriding or removing the User-Agent header in clients and the Server header in servers. Added deployment guides for more Platform as a Service providers. Improvements Improved FAQ.
2022-11-06py-jaraco.itertools: updated to 6.2.1adam3-23/+18
v6.2.1 ====== Fixed broken test in ``ensure_unique``. v6.2.0 ====== Added ``accumulate`` function. v6.1.1 ====== Fixed typo in ``ensure_unique`` doctest. v6.1.0 ====== Add ``ensure_unique`` function. v6.0.3 ====== Fixed doc build errors. v6.0.2 ====== Minor fixes. v6.0.1 ====== Switch to PEP 420 for namespace package. v6.0.0 ====== Remove ``Counter.GetCount``. Remove ``flatten`` and ``iflatten``.
2022-11-06Added devel/py-jaraco.collections; Updated time/py-tempora, net/py-portend, ↵adam2-3/+8
www/py-cheroot, www/py-cherrypy, www/py-webpy
generated by cgit v1.2.3 (git 2.39.1) at 2025-02-23 18:06:45 +0000