New, more memory-efficient index
Several other new features and enhancements
End of support for bulk RNASeq features
changes: https://github.com/pachterlab/kallisto/releases
Reported by: portscout
Bifrost is a tool and API for parallel construction, indexing and
querying of colored and compacted de Bruijn graphs from FASTA/FASTQ
DNA/RNA sequence files.
With OpenMP not present, the code had a duplicate function definition.
Get rid of one of the two to enable a build on armv7.
Approved by: portmgr (build fix blanket)
The logic in USES=python will automatically convert this to 3.8+ by
itself.
Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.
finance/quickfix: mark BROKEN with PYTHON
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++ -DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable -Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi -Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings -Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x -MT _quickfix_la-QuickfixPython.lo -MD -MP -MF .deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp -fPIC -DPIC -o .libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean '-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
^~~~~~~~~~
1 warning and 1 error generated.
Reviewed by: portmgr, vishwin, yuri
Differential Revision: <https://reviews.freebsd.org/D40568>
Metaport to install tools for typical ChIP-Seq analysis, including QC,
adapter trimming, alignment, and differential analysis.
Presently identical to biology/atac-seq, but may diverge in the future.
This fixes the build on armv7 by picking up our custom fixed libhts
over the bundled unfixed version. The CFLAGS workaround is now no
longer required either.
Approved by: yuri (maintainer)
Differential Revision: https://reviews.freebsd.org/D40251
llvm15 was also merged into 13.2-STABLE effective from OSVERSION
1302505. Fix the ports that failed to build with llvm15.
Approved by: portmgr (blanket)
New feature to output sequences in secondary alignments
Several minor enhancements and fixes
Changes: https://github.com/lh3/minimap2/releases
Reported by: portscout
This project includes some SIMD-enhanced functions for ARM NEON.
Unfortunately the code uses a bunch of intrinsics only available on
aarch64. Disable the use of NEON on armv6 and armv7 to fix the build
on these platforms.
See also: https://github.com/samtools/htslib/issues/1603
Approved by: portmgr (build fix blanket)
- 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)
- 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)
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)
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
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
- 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
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
---
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]
- 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]
A few minor upstream fixes
Unbundle WFA2-lib, which may be useful outside vcflib
Update some submodules to latest commit (no recent releases available)
The wavefront alignment (WFA) algorithm is an exact gap-affine
algorithm that takes advantage of homologous regions between the
sequences to accelerate the alignment process. Unlike traditional
dynamic programming algorithms that run in quadratic time, the WFA runs
in time O(ns+s^2), proportional to the sequence length n and the
alignment score s, using O(s^2) memory (or O(s) using the
ultralow/BiWFA mode). Moreover, the WFA algorithm exhibits simple
computational patterns that the modern compilers can automatically
vectorize for different architectures without adapting the code.
Switch from Mk/bsd.ruby.mk to Mk/Uses/ruby.mk
Notable changes are.
- Mk/bsd.ruby.mk is moved to Mk/Uses/ruby.mk.
- USE_RUBY=yes is replaced with USES=ruby.
- USE_RUBY_EXTCONF is replaced with USES=ruby:extconf.
- USE_RUBY_RDOC is replaced with USES=ruby:rdoc.
- USE_RUBY_SETUP is replaces with USES=ruby:setup.
- RUBY_NO_BUILD_DEPENDS and RUBY_NO_RUN_DEPENDS are replaced with
USES=ruby:{build,none,run}.
- RUBY_REQUIRE isn't used anywhere, so removed.
- USES=gem now implies USES=ruby.
This is mainly the work of yasu@ at https://reviews.freebsd.org/D27863
I have just made some cosmetic changes and ran exp-run to test that the
tree is not in a BROKEN state.
Approved by: portmgr
Differential Revision: https://reviews.freebsd.org/D37925
New plugin variant-distance to annotate records with distance to the
nearest variant
Numerous minor enhancements and bug fixes
Changes: https://github.com/samtools/bcftools/releases
