| Commit message (Collapse) | Author | Age | Files | Lines |
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PR: 254218
Exp-run by: antoine
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svn path=/head/; revision=568547
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Generate random genomic data in FASTA/FASTQ, SAM, or VCF format, suitable for
small academic examples or test inputs of arbitrary size. Output can be piped
directly to programs or redirected to a file and edited to taste.
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svn path=/head/; revision=568501
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svn path=/head/; revision=568329
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Project was renamed and reimplemented.
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svn path=/head/; revision=568296
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Reported by: fallout
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svn path=/head/; revision=568271
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svn path=/head/; revision=568141
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https://github.com/bbuchfink/diamond/releases/tag/v2.0.8
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svn path=/head/; revision=568088
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Altivec/VSX code in this port works only on big-endian POWER.
powerpcspe has neither SSE2 nor Altivec.
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svn path=/head/; revision=568013
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GCC is also necessary on powerpc64:
In file included from skbio/alignment/_ssw_wrapper.c:626:
In file included from skbio/alignment/_lib/ssw.h:17:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
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svn path=/head/; revision=567918
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Use GCC:
In file included from skbio/alignment/_ssw_wrapper.c:626:
In file included from skbio/alignment/_lib/ssw.h:17:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
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svn path=/head/; revision=567882
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* PyQt5: update to 5.15.3
This is a minor feature and bug-fix release. There are corresponding releases of the other PyQt5-related packages.
- Added the missing QImage.setAlphaChannel().
- Support for the QtNetworkAuth library has been moved to a separate PyQtNetworkAuth package.
- Wheels no longer bundle the corresponding Qt libraries and instead automatically install them from an external wheel.
* QScintilla2: update to 2.12.0
This adds support for Qt6 and removes support for Qt4.
- Change the new distname (again)i due to a conflict
- Use the new sip-build system
* devel/py-qtbuilder: update to 1.9.0
* devel/py-sip: fix flavor for sip-distinfo
PR: 253865
Exp-run by: antoine
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svn path=/head/; revision=567825
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svn path=/head/; revision=567519
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Numerous small bug fixes and enhancements, code refactoring
py-xopen: Update to 1.1.0
Required by cutadapt 3.3
Drop python 3.5 support
Add isal support (not yet utilized in FreeBSD port)
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svn path=/head/; revision=567503
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svn path=/head/; revision=567439
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In file included from /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/dispatcher.cpp:7:
/usr/local/include/cpuinfo_x86.h:228:2: error: "Including cpuinfo_x86.h from a non-x86 target."
#error "Including cpuinfo_x86.h from a non-x86 target."
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svn path=/head/; revision=567333
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Use GCC's SSE->Altivec translation:
In file included from ksw.c:29:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
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svn path=/head/; revision=566960
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svn path=/head/; revision=566662
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https://github.com/veg/hyphy/releases/tag/2.5.29
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svn path=/head/; revision=566516
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https://github.com/veg/hyphy/releases/tag/2.5.28
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svn path=/head/; revision=566423
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Intel oneAPI tbb 2021.1 (onetbb) has been released[1][2] and has deprecated
several interfaces over tbb 2020, breaking most dependent ports.
Old tbb 2020 will be kept for a certain time to allow transition but will be
removed in a near future as it CONFLICTS with devel/onetbb. New ports should
now use devel/onetbb instead of devel/tbb.
We tried to move a maximum number of dependent ports to devel/onetbb (or
disable dependency when not possible), but some of them still remain stuck
to devel/tbb. Remaining ones have not been identified as major dependencies
themselves and will be fixed as soon as updates are available from upstream.
PR: 252648, 252688 [3], 252683 [4], 252651 [5], 252690 [3], 252693 [3],
252695 [3], 252696 [3], 252786 [3], 252649, 252868 [6], 252870 [5],
252684 [7], 252785 [7]
Approved by: yuri [3], jwb [4], thierry [5], FreeBSD@Shaneware.biz [6],
maintainer timeout [7]
[1] https://software.intel.com/content/www/us/en/develop/articles/intel-oneapi-threading-building-blocks-release-notes.html
[2] https://software.intel.com/content/www/us/en/develop/articles/tbb-revamp.html
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svn path=/head/; revision=566074
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Reported by: fallout
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svn path=/head/; revision=566037
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svn path=/head/; revision=565807
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https://github.com/bbuchfink/diamond/releases/tag/v2.0.7
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svn path=/head/; revision=565520
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* devel/gnustep-make: Update to 2.8.0
* lang/gnustep-base: Update to 1.27.0
* x11-toolkits/gnustep-back: update to 0.28.0
* x11-toolkits/gnustep-gui: update to 0.28.0
Also bump PORTREVISION on dependent ports.
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svn path=/head/; revision=565273
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Fix runtime error due to incompatibility of 1.8 with latest matplotlib
Drop python2 support
Numerous new features and bug fixes
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svn path=/head/; revision=564072
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Minor bug fixes since 0.11.8
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svn path=/head/; revision=564040
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Install target is added.
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svn path=/head/; revision=563906
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biology/py-dnaio: Update to 0.5.0
archivers/py-xopen: Update to 1.0.0
Numerous bug fixes and enhancements since cutadapt 3.2
Document cutadapt dependency versions dnaio~=0.5.0 xopen~=1.0.0
Bump python dependency to 3.6+ to restrict package builds
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svn path=/head/; revision=563844
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Mistakenly believed onetbb was already committed
PR: 252683
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svn path=/head/; revision=563428
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PR: 252683
Submitted by: martymac
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svn path=/head/; revision=563427
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Code clean up and modernization
Reported by: portscout
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svn path=/head/; revision=563418
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PR: 250103
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svn path=/head/; revision=563407
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https://github.com/veg/hyphy/releases/tag/2.5.27
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svn path=/head/; revision=563045
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PR: 252965
Submitted by: thierry
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svn path=/head/; revision=562627
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Several bug fixes and performance enhancements
Reported by: portscout
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svn path=/head/; revision=562501
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Also clean up plist
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svn path=/head/; revision=562414
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svn path=/head/; revision=562312
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svn path=/head/; revision=562270
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svn path=/head/; revision=562258
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CMake Error in CMakeLists.txt:
Target "runTests" requires the language dialect "CXX14" , but CMake does
not know the compile flags to use to enable it.
Approved by: portmgr (tier-2 blanket)
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svn path=/head/; revision=562108
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CMake Error in CMakeLists.txt:
Target "rampler" requires the language dialect "CXX11" , but CMake does not
know the compile flags to use to enable it.
Approved by: portmgr (tier-2 blanket)
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svn path=/head/; revision=562107
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svn path=/head/; revision=562040
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svn path=/head/; revision=562039
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distance
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svn path=/head/; revision=562038
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(POA) algorithm
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svn path=/head/; revision=562036
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bioinformatics
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svn path=/head/; revision=562035
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formats in bioinformatics
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svn path=/head/; revision=562033
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While here, pet portlint (Makevar order).
Approved by: portmgr (tier-2 blanket)
Obtained from: lonesome.com build testing
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svn path=/head/; revision=562006
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# make[2]: cannot open makefile..
Note the filname reported is "Makefile." (e.g. probably empty suffix).
Approved by: portmgr (tier-2 blanket)
Obtained from: lonesome.com build testing
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svn path=/head/; revision=562005
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Notes:
svn path=/head/; revision=561748
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