Commit graph

3589 commits

Author SHA1 Message Date
Po-Chuan Hsieh
02db5c97dd
biology/libsbml: Update WWW and clean up pkg-descr 2023-04-06 01:29:43 +08:00
Antoine Brodin
1730e97e04 USE_PYTHON=pep517: bump PORTREVISION 2023-04-04 18:29:11 +00:00
Muhammad Moinur Rahman
4cda17ab14 */*: Refactor java/openjdk7 removal
- java/openjdk7* has been removed from the tree since 2022-09-03 however
  the relevant codebases in bsd.java.mk has not been removed and the
  consumers has also not been updated to use the next jdk version. This
  commit updates all relevant consumers to use JAVA_VERSION=8 instead of
  JAVA_VERSION=1.7
- Since the introduction of jdk version 18 it looks like similar with
  jdk version 8(java version string 1.8). This is prone to error as it
  looks similar and is only seperated by a '.'. Remove using
  JAVA_VERSION with dotted fomat of java version string and update all
  consumers to utilize version 8 instead of 1.8.

Approved by:	portmgr (blanket)
2023-04-04 13:10:53 -05:00
Jason W. Bacon
13d6c974c4 biology/py-pybigwig: Update to 0.3.21
No relevant changes, just an upstream wheel fix.

Reported by:    portscout
2023-04-01 16:10:15 -05:00
Muhammad Moinur Rahman
56932296b7 */*: Sunset 12.3-RELEASE from ports tree
- Mk/bsd.port.mk: mark FreeBSD 12.3 as unsupported.
- Mk/Uses/cabal.mk: Remove the text-2 workaround for 12.3-RELEASE
- biology/wfa2-lib: remove obsolete patch
- databases/mongodb60: remove IGNORE for EOL FreeBSD 12.3
- devel/concurrencpp: remove workaround for EOL FreeBSD 12.3
- devel/electron22: remove IGNORE for EOL FreeBSD 12.3
- devel/malloy: this should build fine on 12.4-RELEASE
- devel/qcoro: remove BROKEN for EOL FreeBSD 12.3
- devel/root: remove workaround for EOL FreeBSD 12.3
- editors/imhex: remove IGNORE for EOL FreeBSD 12.3
- emulators/ppsspp: remove workaround for EOL FreeBSD 12.3
- emulators/rpcs3: remove workaround for EOL FreeBSD 12.3
- emulators/yuzu: remove workaround for EOL 12.3-RELEASE
- games/aquaria: remove support for EOL FreeBSD 12.3
- games/punchy: remove workaround for EOL FreeBSD 12.3
- graphics/cxxplot: remove support for EOL FreeBSD 12.3
- lang/gcc11*: bump a __FreeBSD_version in libphobos to 1204000
- lang/rust: untangle OSVERSION logic a bit
- misc/mbuffer: remove workaround for EOL FreeBSD 12.3 for aarch64
- sysutils/libdisplay-info: remove workaround for EOL FreeBSD 12.3
- www/*chromium: remove IGNORE for EOL FreeBSD 12.3
- x11/hyprpaper: remove workaround for expired FreeBSD 12.3
- x11-wm/labwc: remove workaround for EOL FreeBSD 12.3
- x11-wm/kwinft: remove workaround for EOL FreeBSD 12.3
- www/iridium: remove IGNORE for EOL FreeBSD 12.3

Differential Revision: https://reviews.freebsd.org/D38664
2023-03-30 18:59:51 -05:00
Robert Clausecker
7227c569bd biology/kmcp: fix build on i386 and riscv64
- fix an issue with wrong copy-editing in a fork of one
   of my Go packages
 - fix an issue with wrong build constraints

Sponsored by:	Berliner Linux User Group e.V.
Approved by:	portmgr (build fix blanket)
2023-03-24 21:54:47 +01:00
Joseph Mingrone
68b8e0027d
biology/hyphy: Update to 2.5.49
Sponsored by:	The FreeBSD Foundation
2023-03-24 12:54:30 -03:00
Robert Clausecker
175e8e7ae3 biology/unikmer: fix build on riscv64
Bump golang.org/x/sys dependency to a version new enough
to support riscv64-freebsd.

Sponsored by:	Berliner Linux User Group e.V.
Approved by:	portmgr (build fix blanket)
2023-03-22 21:15:16 +01:00
Po-Chuan Hsieh
68b8a1ddaa
devel/grpc: Update to 1.52.1
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/grpc/grpc/releases
2023-03-22 03:20:03 +08:00
Robert Clausecker
bd71c9d3c6 biology/seqkit: fix build on riscv64
Bump golang.org/x/sys dependency to a version new enough
to support riscv64-freebsd.

Sponsored by:	Berliner Linux User Group e.V.
Approved by:	yuri (maintainer)
Differential Revision: https://reviews.freebsd.org/D39154
2023-03-21 13:53:48 +01:00
Yuri Victorovich
179798616f biology/py-scikit-bio: Update 0.5.7 → 0.5.8
Reported by:	portscout
2023-03-20 08:30:16 -07:00
Yuri Victorovich
9f5d0a66dd biology/py-scikit-bio: Update 0.5.7 → 0.5.7
Reported by:	portscout
2023-03-19 23:05:44 -07:00
Yuri Victorovich
9d07cf3ba2 biology/py-pyrodigal: Update 2.0.3 → 2.1.0
Reported by:	portscout
2023-03-19 09:42:53 -07:00
Joseph Mingrone
43743a89d4
biology/diamond: Update to 2.1.6
Changes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.5
		https://github.com/bbuchfink/diamond/releases/tag/v2.1.6
Sponsored by:	The FreeBSD Foundation
2023-03-18 12:49:03 -03:00
Yuri Victorovich
bf997b76d8 biology/seqkit: Update 2.3.1 → 2.4.0
Reported by:	portscout
2023-03-17 15:54:48 -07:00
Jason W. Bacon
276f662b76 biology/py-dna-features-viewer: Update to 3.1.2
Fixes compatibility with biophython 1.80
2023-03-17 12:55:54 -05:00
Jason W. Bacon
efaa7cc98f biology/py-bcbio-gff: Update to 0.7.0
Fix compatibility with biopython 1.81

Changes: https://github.com/chapmanb/bcbb/commits/master

Reported by:    portscout
2023-03-16 17:32:06 -05:00
Yuri Victorovich
fed178dc88 biology/py-gtfparse: Update 1.2.1 → 1.3.0
Reported by:	portscout
2023-03-12 01:02:32 -08:00
Yuri Victorovich
f3ac5fd5e5 biology/py-gffutils: Update 0.11.0 → 0.11.1
Reported by:	portscout
2023-03-12 01:02:31 -08:00
Robert Clausecker
8ede8da5f1 biology/ncbi-entrez-direct: fix build on riscv64
Bump golang.org/x/sys dependency to a version new
enough to build on riscv64-freebsd.

Sponsored by:	Berliner Linux User Group e.V.
Approved by:	portmgr (build fix blanket)
Differential Revision: https://reviews.freebsd.org/D38996
2023-03-11 09:34:45 +01:00
Wen Heping
191db1b73f biology/py-biopython: Update to 1.81
PR:		269995
Reported by:	wen@
Approved by:	maintainer
2023-03-10 06:13:08 +08:00
Dmitri Goutnik
09079730e9 all: Bump PORTREVISION after Go ports update 2023-03-09 14:18:07 -05:00
Loïc Bartoletti
486ea1d293 graphics/proj: Update to 9.2.0 2023-03-09 13:42:31 +01:00
Loïc Bartoletti
6d3a647cc0 PyQt: Update to latest versions
- PyQt5: update to 5.15.9
- PyQt6: upate to 6.4.2
- PyQt6-sip: update to 13.4.1
- PyQt5-sip: update to 12.11.1
- PyQt-builder: update to 1.14.1
- sip: upate to 6.7.7

PR:		269751
Exp-run by:	antoine
2023-03-09 12:15:07 +01:00
Jason W. Bacon
fbe7ee56d5 biology/py-pybigwig: Update to 0.3.20
Build system fixes

Reported by:    portscout
2023-03-08 07:50:30 -06:00
Jason W. Bacon
d892482728 biology/fastx-toolkit: Unbreak build on 14-CURRENT
Remove developer warning flags, including -Werror causing build failure
2023-03-07 11:28:13 -06:00
Joseph Mingrone
99d4dc3c2b
biology/hyphy: Update to 2.5.48
Changes:	https://github.com/veg/hyphy/releases/tag/2.5.48
Sponsored by:	The FreeBSD Foundation
2023-03-05 11:51:37 -04:00
Joseph Mingrone
d363e4b4eb
biology/diamond: Update to 2.1.4
Changes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.4
Sponsored by:	The FreeBSD Foundation
2023-03-05 11:33:44 -04:00
Jason W. Bacon
a5b1448e8e biology/fastqc: Update to 0.12.1
Several feature enhancements and a few bug fixes
Changes: https://github.com/s-andrews/FastQC/releases

Reported by:    portscout
2023-03-04 18:17:20 -06:00
Tobias C. Berner
fa81a4f5f8 accessibility/at-spi2-core: update to 2.46.0
What's new in at-spi2-core 2.46.0:
* Fix GetInterfaces documentation on org.a11y.atspi.Accessible
  interface.

What's new in at-spi2-core 2.45.91:
* Send device event controller events using the same signature as other
  events.
* Document the Accessible, Action, and Cache dbus interfaces.
* Fix license of atspi-gmain.c (#87).

What's new in at-spi2-core 2.45.90:
* xml: Add some documentation.
* xml: Fix event arguments.
* xml: Add some missing DeviceEventController methods.
* Bind the AT-SPI bus to the graphical session.
* Mark bus service as belonging to the session slice.
* Add ATSPI_ROLE_PUSH_BUTTON_MENU.
* Add an "announcement" event/signal to allow objects to send
  notifications (!63).
* Various code clean-ups and test improvements.

What's new in at-spi2-core 2.45.1:
* Atk and at-spi2-atk are now merged into this project.
* Now requires meson 0.56.2 and glib 2.67.4.
* at-spi2-atk: Expose the accessible hierarchy via dbus introspection.
* Properly escape the AT-SPI bus address; fixes warnings about the address
  not containing a colon (!55).
* Add a text value to AtspiValue, so that a value can expose a textual
  description, as in the new Atk value API.
* Add atspi_event_listener_register_with_app, to allow an event listener
  to be registered only for a given application (!52).

- accessibility/atk and accessibility/at-spi2-atk have been merged into
  accessibility/at-spi2-core

- accessibility/at-spi2-core: bump consumers of removed ports atk and at-spi2-atk

PR:		269704
Exp-run by:	antoine
---
2023-03-02 06:23:10 +01:00
Jason W. Bacon
68c12d4ad4 biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics
Score is a set of tools in the form of a bcftools plugin, for handling
and converting summary statistics files following the GWAS-VCF
specification.
2023-02-25 08:27:46 -06:00
Jason W. Bacon
65b8ab9349 biology/bcftools: Update to 1.17
Numerous enhancements and bug fixes

Changes: https://github.com/samtools/bcftools/releases

Reported by:    portscout
2023-02-24 17:30:58 -06:00
Jason W. Bacon
1993bfc7cf biology/samtools: Update to 1.17
Numerous enhancements and bug fixes

Changes: https://github.com/samtools/samtools/releases

Reported by:    portscout
2023-02-24 17:27:21 -06:00
Jason W. Bacon
5ce4151480 biology/htslib: Update to 1.17
Numerous enhancements and fixes

Changes:    https://github.com/samtools/htslib/releases

Reported by:    portscout
2023-02-24 17:23:25 -06:00
Joseph Mingrone
85920ea2cc
biology/diamond: Update to 2.1.3
Changes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.3
Sponsored by:	The FreeBSD Foundation
2023-02-22 07:48:44 -04:00
Joseph Mingrone
89f956fe5f
biology/diamond: Update to 2.1.2
Changes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.2
Sponsored by:	The FreeBSD Foundation
2023-02-20 10:35:05 -04:00
Yuri Victorovich
b021237b2d biology/igv: Update 2.9.4 → 2.16.0
PR:		269690
Reported by:	jwb@
2023-02-19 23:20:49 -08:00
Jason W. Bacon
ada9b15851 biology/atac-seq: Drop biology/igv dep
Non-essential and currently broken
2023-02-19 12:11:12 -06:00
Jason W. Bacon
d91c1fae70 biology/rna-seq: Drop biology/igv dep
Non-essential and currently broken
2023-02-19 12:10:17 -06:00
Dmitri Goutnik
56b5ec772f all: Bump PORTREVISION after lang/go{119,120} update 2023-02-15 14:06:01 -05:00
Joseph Mingrone
056255445e
biology/diamond: Update to 2.1.1
Changes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.0
		https://github.com/bbuchfink/diamond/releases/tag/v2.1.1
Sponsored by:	The FreeBSD Foundation
2023-02-10 13:36:10 -04:00
Dmitri Goutnik
2297efc51b all: Bump PORTREVISION after GO_DEFAULT update. 2023-02-09 16:55:23 -05:00
Jason W. Bacon
5fee60fc3c biology/vcflib: Update to 1.0.7
Fixes regression in 1.0.6

Made Zig language support a default off option
Zig is experimental and problematic

Reported by:    portscout
2023-02-09 09:35:32 -06:00
Charlie Li
f5890bd3cb
Revert "Mk/Uses/python.mk: Fix USE_PYTHON=pep517: always compile and install bytecode"
Despite installer's default behaviour to compile and install bytecode,
we are not doing so going forward at stage/package time. [0] During
initial development and qualification of PEP-517 framework support,
compiling and installing bytecode at stage/package time was considered,
but was found problematic, fragile and ultimately unreliable, both
currently and historically (with USE_PYTHON=distutils), due to our
fixed plist requirement. While the living binary distribution format
(wheel) specification [1] says to compile bytecode, that is in the
pure Python package management context (pip, etc); nuance always
exists when interacting with "system" package management.

Additionally, "bytecode is an implementation detail of the CPython
interpreter. No guarantees are made that bytecode will not be added,
removed, or changed between versions of Python," thus "should not
be considered to work across Python VMs or Python releases." [2]
This is important to ensuring correctness for those ports specifying
NO_ARCH.

Instead of compiling and installing bytecode at stage/package time,
there is a WIP, review D34739, that compiles and installs bytecode
at install time instead, using triggers.

The aforementioned build_fs_violations will be investigated.

This reverts commit de6965254c.

With hat:	python
Approved by:	tcberner (mentor, portmgr)
Reference:	https://wiki.freebsd.org/Python/PEP-517 [0]
		https://packaging.python.org/en/latest/specifications/binary-distribution-format/ [1]
		https://docs.python.org/3/library/dis.html [2]
2023-02-05 14:05:02 -05:00
Po-Chuan Hsieh
de6965254c
Mk/Uses/python.mk: Fix USE_PYTHON=pep517: always compile and install bytecode
- While I'm here, use long options for easier reading [1][2]
- Bump PORTREVISION of dependent ports (USE_PYTHON=pep517) for package change

It fixes build_fs_violation of dependent ports in poudriere (with -t flag).
It is also the default behavior of installer [2].

from py-sphinx log:
=>> Checking for staging violations... done
=>> Error: Filesystem touched during stage (files must install to ${STAGEDIR}):
extra: usr/local/lib/python3.9/site-packages/importlib_metadata/__pycache__
=>> Cleaning up wrkdir

from installer documentation:
--compile-bytecode
    Possible choices: 0, 1, 2
    generate bytecode for the specified optimization level(s) (default=0, 1)
--no-compile-bytecode
    don’t generate bytecode for installed modules
    Default: False

With hat:	python
Reference:	https://pypa-build.readthedocs.io/en/stable/ [1]
		https://installer.pypa.io/en/stable/cli/installer/ [2]
2023-02-06 02:16:47 +08:00
Joseph Mingrone
048831ec57
biology/hyphy: Update to 2.5.47
Changes:	https://github.com/veg/hyphy/releases/tag/2.5.47
Sponsored by:	The FreeBSD Foundation
2023-02-03 23:36:47 -04:00
Muhammad Moinur Rahman
6db7a8c38e biology/emboss: Ignore with mysql 8.0
PR:		269203
Reported by:	exp-run
2023-02-01 04:39:38 -06:00
Jason W. Bacon
0d9ff1bcab biology/vcflib: Unbreak build on aarch64, probably others
Patch out hard-coded -march=native, not supported by clang aarch64
2023-01-31 10:25:33 -06:00
Jason W. Bacon
eb340a643e biology/wfa2-lib: Unbreak build on aarch64, probably others
Patch out hard-coded -march=native, not supported by clang aarch64

Reported by:    pkg-fallout
2023-01-31 09:17:52 -06:00
Jason W. Bacon
8aad5af0de biology/p5-transdecoder: Update to 5.7.0
Numerous small fixes and enhancements since 5.4.0
Changes: https://github.com/TransDecoder/TransDecoder/tags

Reported by:    portscout
2023-01-30 16:30:54 -06:00