Minor bug fix release
Also disabled install of test directory, which was not properly
installed under the package subdir and caused a conflict as a result
PR: 262759
- Update sip to 6.5.1
- Update PyQt5 to 5.15.6
- Update PyQtChart, PyQtNetworkAuth and PyQtWebengine to 5.15.5
- Update PyQtSip to 12.9.1
- Update PyQtBuilder to 1.12.2
- Add ${_MAKE_JOBS} for pyqt.mk (reported by Tatsuki Makino)
PR: 261685
Exp-run by: antoine
clang 13 complains about duplicate loop unrolling pragmas for clang and
CGG. According to [1], clang supports #pragma GCC unroll with identical
semantics to #pragma clang loop unroll, so remove instances of #pragma
clang loop unroll and #pragma unroll when they appear with #pragma GCC
unroll for the same loop.
[1]
https://clang.llvm.org/docs/AttributeReference.html#pragma-unroll-pragma-nounroll
Sponsored by: The FreeBSD Foundation
Update the CONFLICTS definitions of ports in the following categories:
- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters
An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.
There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.
Approved by: portmgr (implicit)
DNA Features Viewer is a Python library to visualize DNA features, e.g.
from GenBank or Gff files.
DNA Features Viewer can plot sequence maps linearly or circularly, with
or without nucleotide sequence and amino-acid sequences. The plotter
automatically produces clear plots even for sequences with many
overlapping features and long labels. The library plays well with
Matplotlib and Biopython, and the figures can be saved in different
formats (PNG, JPEG, SVG, PDF), e.g. for report generation or LIMS
interfaces.
SIP:
As mentioned in the update from sip to sip5, this is a transitional version
to remove what is deprecated in sip4.
Sip6 completely removes the deprecated parts.
Unfortunately, some ports — mostly cura things — can not use sip6, so we
reintroduce sip4.
PyQt:
At the same time, we took the opportunity to simplify PyQT and propose only one
package as for devel/pyside2. */py-qt5-* have been merged — excepted chart,
networkauth and webengine — into devel/py-qt5-pyqt.
This allows us to be in adequacy with the packages that the author of these
libraries proposes, namely:
PyQt - devel/py-qt5-pyqt
PyQt-Charts - x11-toolkits/py-qt5-chart
PyQt-NetworkAuth – net/py-qt5-networkauth
PyQt-WebEngine – www/py-qt5-webengine
SIP – devel/py-sip
py-sip - devel/py-qt5-sip
PyQt-builder - devel/py-qtbuilder
Qscintilla - devel/py-qt5-qscintilla2
Reviewed by: diizzy, kde
Tested by: kai, rhurlin, arrowd, madpilot
Approved by: makc, tcberner, kde
Differential Revision: https://reviews.freebsd.org/D33237
Exp-run by: antoine
do-install is removed in favor of project's install target,
Also update 3 other ports to build with cpu_features.
PR: 261252
Approved by: skreuzer@ (maintainer)
Adds the sample, qsegout and tsegout options. It also enables the use of
UDB databases with uchime_ref.
Changes: https://github.com/torognes/vsearch/releases
Reported by: portscout
There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.
This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.
Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port
cannot conflict with itself (due to logic in bsd.port.mk that
supresses the pattern match result in that case).
A few ports that set the conflicts variables depending on complex
conditions (e.g. port options), have been left unmodified, despite
probably containing outdated package names.
These changes should only affect the installation of locally built
ports, not the package building with poudriere. They should give an
early indication of the install conflict in cases where currently
the pkg command aborts an installation when it detects that an
existing file would be overwritten,
Approved by: portmgr (implicit)
FreeBSD port: Add support for aarch64 and powerpc64 using simde
Not yet supported upstream
Several upstream bug fixes and minor enhancements since 2.1
Changes: https://github.com/marbl/canu/tags
Updates for evolving libxtend and biolibc APIs
Add --version flag
Filter out unused SAM fields on input
Numerous other minor fixes and enhancements
Changes: https://github.com/auerlab/ad2vcf/releases/tag/0.1.4
This is an attempt to perform a simple "libraryfication" of the GFF/GTF
parsing code that is used in GFFRead codebase. There are not many
(any?) relatively lightweight GTF/GFF parsers exposing a C++ interface,
and the goal of this library is to provide this functionality without
the necessity of drawing in a heavy-weight dependency like SeqAn. Note:
This library draws directly from the code in GFFRead and GCLib, and
exists primarily to remove functionality (and hence code) that is
unnecessary for our downstream purposes. In the future, it may be
appropriate to just replace this library wholesale with GCLib.
MoChA is a bcftools plugin released under the MIT license for mosaic
chromosomal alteration detection and analysis from DNA microarray or
whole genome sequence data. It can be used both with Illumina and
Affymetrix data. It can also be used for detection of germline copy
number variants. Data can be prepared in usable file formats using the
gtc2vcf plugin.
Only sra-tools is still non-portable, but it will take some time to
add support for other architectures. In the meantime, allow aarch64
and powerpc64 users to have a biostar-tools package.
Minor patches to utilize simde to emulate SSE (from Debian package)
Add -fsigned-char since clang defaults to unsigned on aarch64
Remove -DPOPCNT_CAPABILITY (not truly safe even on amd64)
The conflict checks compare the patterns first against the package
names without version (as reported by "pkg query "%n"), then - if
there was no match - agsinst the full package names including the
version (as reported by "pkg query "%n-%v").
Approved by: portmgr (blanket)
pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhalign_omp:No such file or directory
pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_ca3m:No such file or directory
pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_omp:No such file or directory
pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhsearch_omp:No such file or directory
powerpc doesn't have LLVM with libomp.
Switch to github submodules for most deps rather than patch build system
Fixes build on powerpc64 and aarch64, possibly others
Changes: https://github.com/vcflib/vcflib/tags
PR: 259622
Reported by: pkubaj
- Cap supported python verions with 3.9. Fails with 3.10:
Traceback (most recent call last):
File "/wrkdirs/usr/ports/biology/py-python-libsbml/work-py310/python-libsbml-5.19.0/libsbml_source/src/bindings/python/doc-converter/rewrite_pydoc.py", line 121, in <module>
from formatter import NullWriter, AbstractFormatter
ModuleNotFoundError: No module named 'formatter'
- Fix library stripping to unbreak port with python != 3.8
Approved by: portmgr blanket
File "/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.19.0/src/bindings/python/doc-converter/rewrite_pydoc.py", line 121, in <module>
from formatter import NullWriter, AbstractFormatter
ModuleNotFoundError: No module named 'formatter'
Approved by: portmgr blanket
The conflict checks compare the patterns first against the package
names without version (as reported by "pkg query "%n"), then - if
there was no match - agsinst the full package names including the
version (as reported by "pkg query "%n-%v").
Many CONFLICTS definitions used patterns like "bash-[0-9]*" to filter
for the bash package in any version. But that pattern is functionally
identical with just "bash".
Approved by: portmgr (blanket)
ONLY_FOR_ARCHS_REASON is used as part of the sentence and thus should
start with lower-case letter and not end with a period which is added
by the framework, similar to other knobs like BROKEN, IGNORE, et al.
While here, remove needless quoting, add missing Oxford comma, expand
contractions and jargonisms, use correct spelling for proper names.
deepTools contains useful modules to process the mapped reads data for
multiple quality checks, creating normalized coverage files in standard
bedGraph and bigWig file formats, that allow comparison between
different files (for example, treatment and control). Finally, using
such normalized and standardized files, deepTools can create many
publication-ready visualizations to identify enrichments and for
functional annotations of the genome.
py-bigwig is a python extension, written in C, for quick access to
bigBed files and access to and creation of bigWig files. This extension
uses libBigWig for local and remote file access.
py2bit is a python extension, written in C, for quick access to 2bit
files for randomly accessible, packed nucleotide sequences. The
extension uses lib2bit for file access.
Utilities for working on SAM/BAM files from The Center for Statistical
Genetics at the University of Michigan School of Public Health. It
includes numerous functions such as splitting, merging, trimming reads,
filtering, validation, diff, etc.
In file included from bit-common.c:63:
In file included from ./bit-choice.h:23:
In file included from ./triangle.h:44:
./openmp.h:19:10: fatal error: 'omp.h' file not found
The option implied a dependency on gcc but clang got openmp support long ago.
Remove compiler:openmp from Mk/Uses/compiler.mk
For ports using USE=compiler:openmp, just remove it and make them build with
clang.
Fix conditionals when necessary
Bump PORTREVISION where appropriate
If problem arises, they can be addressed by using USE_GCC=yes
An update to the Porter's Handbook will follow.
Approved by: portmgr (bapt)
Differential Revision: https://reviews.freebsd.org/D31971
Standard kent userapps commands are installed under ${PREFIX}/userapps
because of multiple conflicts. The kent command turns the standard
commands into subcommands, so no special PATH is needed.
/usr/local/ucsc-userapps/bin/bigWigToBedGraph [args]
can be run as
kent bigWigToBedGraph [args]
Standard emboss commands are installed under a special prefix because
of multiple conflicts. The emboss command turns the standard commands
into subcommands, so no special PATH is needed.
/usr/local/emboss/bin/needle [args]
can be run as
emboss needle [args]
PREFIX is overridden by default in the port Makefile, so PREFIX/bin
is not normally in PATH. The purpose of emboss-shell is to prepend
PREFIX/bin to PATH to give access to emboss tools.
Also fix tcsh detection.
PR: 258316
pywgsim is a modified version of the wgsim short read simulator. The
code for wgsim has been modified to allow visualizing the simulated
mutations as a GFF file.
