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* biology/htslib: Upgrade to 1.10.2Jason W. Bacon2020-08-031-1/+1
| | | | | | | | | | | | Numerous bug fixes and enhancements since 1.9: https://github.com/samtools/htslib/tags Bump PORTREVISION on dependents that don't require additional patching PR: 248089 Notes: svn path=/head/; revision=544090
* biology/jellyfish: Patch for clang 10Jason W. Bacon2020-03-073-3/+23
| | | | | | | | | | Add cast to silence implicit conversion error PR: ports/244645 Submitted by: dim Notes: svn path=/head/; revision=527971
* Drop C++11 workaround for GCC < 6 after r449590Jan Beich2019-09-142-36/+1
| | | | | | | | | | | lang/gcc5 will expire in ~1 month. If someone still uses lang/gcc48 they should backport C++11 fix instead. QA on GCC architecuters is currently limited to powerpc64 which uses GCC_DEFAULT. PR: 193528 Notes: svn path=/head/; revision=512079
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2019-07-261-1/+1
| | | | | | | | | | | | | | | | | | as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3 to GCC 9.1 under most circumstances now after revision 507371. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, everything INDEX-11 shows with a dependency on lang/gcc9 now. PR: 238330 Notes: svn path=/head/; revision=507372
* biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64Jason W. Bacon2019-05-138-16/+79
| | | | | | | | PR: 237868 Submitted by: pkubaj Notes: svn path=/head/; revision=501578
* These ports now build on aarch64.Mark Linimon2019-05-031-3/+1
| | | | | | | | | | Where necessary, pet portlint. Approved by: portmgr Obtained from: aarch64 TRYBROKEN run Notes: svn path=/head/; revision=500752
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-12-121-1/+1
| | | | | | | | | | | | | | | | | | defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t GCC 8.2 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, as a double check, everything INDEX-11 showed depending on lang/gcc7. PR: 231590 Notes: svn path=/head/; revision=487272
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-07-291-1/+1
| | | | | | | | | | | | | | | | | in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which has now moved from GCC 6 to GCC 7 by default. This includes ports - featuring USE_GCC=yes or USE_GCC=any, - featuring USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and those - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x, c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib. PR: 222542 Notes: svn path=/head/; revision=475857
* Multiple ports:Jason W. Bacon2018-01-311-2/+1
| | | | | | | | | | | Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org Remove Created by comments for same user Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14128 Notes: svn path=/head/; revision=460452
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2017-09-101-1/+1
| | | | | | | | | | | | | | | | | (via Mk/bsd.default-versions.mk and lang/gcc) which has moved from GCC 5.4 to GCC 6.4 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang, c++14-lang, c++0x, c11, or gcc-c++11-lib. PR: 219275 Notes: svn path=/head/; revision=449591
* Bump PORTREVISIONs for ports depending on the canonical version of GCC andGerald Pfeifer2017-04-011-0/+1
| | | | | | | | | | | | | | | | | lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some circumstances such as versions of FreeBSD or platforms). This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using using Mk/bsd.octave.mk which in turn has USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang, c++11-lang, c++0x, c11, or gcc-c++11-lib. PR: 216707 Notes: svn path=/head/; revision=437439
* Remove BROKEN_FreeBSD_9Sunpoet Po-Chuan Hsieh2017-01-011-1/+0
| | | | | | | Approved by: portmgr (blanket) Notes: svn path=/head/; revision=430235
* biology/jellyfish: Update to version 2.2.6Joseph Mingrone2016-12-193-54/+56
| | | | | | | | | | | | | | Upstream changes since version 2.2.4: - Fix compilation warnings/errors with newer version of gcc (5.3 & 6.1). - Fix bug in parsing function that made it stop on sequences that consist of only empty lines. - New methods in bindings to enumerate the mers of a string. Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8204 Notes: svn path=/head/; revision=428954
* Mark various leaf ports broken on aarch64, and, where appropriate, otherMark Linimon2016-11-111-0/+1
| | | | | | | | | tier-2 archs. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=425879
* Use USES=pathfix where applicable.Mathieu Arnold2016-10-211-7/+1
| | | | | | | | | | | PR: 213195 Submitted by: mat Exp-run by: antoine Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D8093 Notes: svn path=/head/; revision=424427
* Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.Mathieu Arnold2016-04-011-1/+1
| | | | | | | | With hat: portmgr Sponsored by: Absolight Notes: svn path=/head/; revision=412344
* - Use more appropriate BROKEN instead of IGNOREDmitry Marakasov2016-03-291-4/+2
| | | | | | | | | PR: 208367 Submitted by: bacon4000@gmail.com (maintainer) Suggested by: rakuco Notes: svn path=/head/; revision=412137
* Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.Dmitry Marakasov2016-03-245-0/+145
A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. WWW: http://www.genome.umd.edu/jellyfish.html PR: 207929 Submitted by: bacon4000@gmail.com Notes: svn path=/head/; revision=411785
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