- USES=compiler:openmp still forces building with GCC. This is no longer
necessary on tier 1 platforms, which have openmp in base.
- Mark broken on i386, because base clang doesn't have 64 bit atomic
functions for i386 (see bug 230888).
PR: 247753, 252379
Submitted by: cmt (based on)
USES=compiler:openmp still forces building with GCC. This is no longer
necessary on tier 1 platforms, which have openmp in the base system.
PR: 247753, 252379
Replace compiler:openmp with compiler:c++11-lang and localbase
Set USE_GCC for i386 to work around limitations in clang atomic (PR 230888)
PR: port/247753, ports/252379
Replace compiler:openmp with compiler:c++14-lang
Clang build also requires localbase:ldflags and a source patch to explicitly
set variables to shared
GCC-based platforms still require -latomic
PR: port/247753, ports/252379
Replace compiler:openmp with compiler:c++11-lang
Clang build also requires localbase:ldflags
Build tested on amd64, i386 and powerpc64 12.x-RELEASE
PR: port/247753, ports/252379
- Add some dependencies which might be detected by Find_Package but not registered;
- Bump PORTREVISION of consumers.
PR: 250833
Submitted by: /me
Approved by: tcberner@ (KDE / maintainer) + exp-run
This commit combines several updates.
- Update Qt to 5.12.2
- Update PyQt to 5.15.1
- Since PySide 5.15.1 is broken with Qt 5.15.2, so PySide and Shiboken are also updated to 5.15.2.
- Update sip to 5.4.0
SIP is a collection of tools to create Python bindings for C and C++ libraries and used by PyQt and wxPython. There are some changes with sip5 [1]:
- python 3.5+ is required
- sip drops support of old deprecated methods as sipdistutils & cie.
- this version breaks also PyQt5 extension ABI. SIP files will be installed in ${PYTHON_SITELIBDIR}/PyQt${_PYQT_VERSION}/bindings
- some ports will use the new pyqtbuilder package with the pyproject.toml setup. Instead if the project have a setup.py, you should use sip-build to build it.
- if a port needs sip, it should also needs pysip. BTW, py-qt5-core requires pysip, so that should be enough for PyQt packages.
List of ports impacted by this change. Most of the patches have been integrated or are in the process of being integrated upstream:
- devel/libsavitar
- graphics/py-python-poppler-qt5
- net-im/scudcloud
- net/libarcus
- print/py-frescobaldi
- science/py-veusz
- graphics/qgis and graphics/qgis-ltr
- deskutils/calibre
A special note regarding calibre. New versions require sip>=5, we update it to the latest version (thanks to madpilot@)
science/scidavis will remove the PyQt binding soon and there is no patch planned, so we remove the python option (ok makc@)
While here, convert some ports to USE_PYQT (cad/cura, cad/uranium, devel/eric6, ...)
Thanks to tcberner and adridg!
[1] https://www.riverbankcomputing.com/static/Docs/sip/
PR: 250853
Exp-run by: antoine
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -c tabix.cpp -Ihtslib
In file included from /usr/local/include/htslib/hts.h:37,
from /usr/local/include/htslib/tbx.h:30,
from tabix.hpp:5,
from tabix.cpp:1:
/usr/local/include/htslib/kstring.h: In function 'int ks_resize(kstring_t*, size_t)':
/usr/local/include/htslib/kstring.h:149: error: 'SIZE_MAX' was not declared in this scope
tabix.cpp: In constructor 'Tabix::Tabix(std::string&)':
tabix.cpp:15: warning: 'bgzf_is_bgzf' is deprecated (declared at /usr/local/include/htslib/bgzf.h:263)
tabix.cpp:15: warning: 'bgzf_is_bgzf' is deprecated (declared at /usr/local/include/htslib/bgzf.h:263)
Optimise combinations of primers and minimise the formation of dimers in
multiplexed PCR.
Primer Pooler can:
* Check through each proposed pool for combinations that are likely to form
dimers
* Automatically move prospective amplicons between proposed pools to reduce
dimer formation
* Automatically search the genome sequence to find which amplicons overlap, and
place their corresponding primers in separate pools
* Optionally keep pool sizes within a specified range
* Handle thousands of primers without being slow (useful for high-throughput
sequencing applications)
* Do all of the above with degenerate primers too.
WWW: http://ssb22.user.srcf.net/pooler/
PR: ports/251065
Submitted by: Silas S. Brown <silas-freebsd@flatline.org.uk>
