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* Bump PORTREVISIONs of all users of math/mpc that we just updated toGerald Pfeifer2018-03-111-1/+1
* Remove dependency on the python metaportsAntoine Brodin2018-02-201-2/+4
* Convert Python ports to FLAVORS.Mathieu Arnold2017-11-301-1/+1
* Upgrade - endly! - to Code_Aster 13.4.0-3.Thierry Thomas2017-11-1511-1488/+3179
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2017-09-111-1/+1
* Upgrade science/hdf5-18 to 1.8.19.Thierry Thomas2017-06-171-1/+1
* Bump PORTREVISIONs for ports depending on the canonical version of GCC andGerald Pfeifer2017-04-011-1/+1
* Unbreak after the upgrade of Gcc to 4.9.Thierry Thomas2017-01-233-2/+11
* biology/seaview: Update version 4.6.2=>4.6.3Muhammad Moinur Rahman2018-01-063-7/+8
* New USES=eigenTobias C. Berner2018-01-031-5/+2
* - Update to 3.697Wen Heping2018-01-012-3/+4
* - Update to 5.16.0Wen Heping2018-01-013-4/+9
* biology/iqtree: Fix distinfo after upstream re-released v1.6.1Joseph Mingrone2017-12-302-3/+4
* biology/iqtree: Update to version 1.6.1Joseph Mingrone2017-12-292-9/+8
* Disable the extra flag "-march=native" on arm to fix builds.Mark Linimon2017-12-271-3/+6
* Update to 2.0.1Sunpoet Po-Chuan Hsieh2017-12-273-5/+31
* biology/canu: Replace += with = for dependsJason W. Bacon2017-12-221-2/+2
* - Fix build on 11+Dmitry Marakasov2017-12-222-4/+11
* [new port] biology/canu: Single molecule sequence assemblerJason W. Bacon2017-12-226-0/+167
* Try to bring some consistency to ports that have x86-specific pieces.Mark Linimon2017-12-212-12/+12
* Switch from swig 2.0 to swig 3.0Baptiste Daroussin2017-12-211-2/+4
* Mark more recently failing ports broken on aarch64.Mark Linimon2017-12-191-2/+3
* Back out previous commits by jbeich demand.Mark Linimon2017-12-182-10/+2
* Bah. Remove spare line from cut-and-paste.Mark Linimon2017-12-181-1/+0
* Attempt to fix build on non-x86 archs. Untested, but does no harmMark Linimon2017-12-182-2/+11
* biology/diamond: Update to version 0.9.14Joseph Mingrone2017-12-142-4/+4
* biology/seqtools: re-try on powerpc* after r449590Jan Beich2017-12-121-2/+0
* - Those ports fail to build with python3Antoine Brodin2017-12-121-1/+1
* Mark several ports newly broken on arm.Mark Linimon2017-12-112-3/+9
* biology/py-biom-format: Add required dependency on math/py-pandas and doJoseph Mingrone2017-12-101-3/+7
* [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adap...Jason W. Bacon2017-12-095-0/+47
* These are also broken on aarch64 in the same way as armv6/7.Mark Linimon2017-12-091-0/+1
* Mark more ports broken that fail on both armv6 and armv7.Mark Linimon2017-12-091-0/+3
* Revert previous fat-fingered commit. These are the error messages fromMark Linimon2017-12-081-2/+2
* Update errror message on armvX.Mark Linimon2017-12-081-2/+2
* biology/fasttree: update to version 2.1.10Jason W. Bacon2017-12-054-19/+45
* biology/py-macs2: Restrict to python 2.7.Jason W. Bacon2017-12-051-2/+2
* Add a USES=python:env, that will not add a dependency on Python.Mathieu Arnold2017-12-042-4/+2
* Fix configure options for gnustep-makeDavid Chisnall2017-12-031-1/+1
* [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP)...Jason W. Bacon2017-12-034-0/+41
* [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq ...Jason W. Bacon2017-12-035-0/+91
* Fix packaging with python3Antoine Brodin2017-12-012-14/+14
* [unbreak] biology/bwa: Remove old patch filesJason W. Bacon2017-12-013-37/+0
* [new port] biology/fastqc: Quality control tool for high throughput sequence ...Jason W. Bacon2017-12-015-0/+260
* biology/py-cutadapt: Remove MASTER_SITE_SUBDIR per mentor commentJason W. Bacon2017-12-011-1/+0
* Convert Python ports to FLAVORS.Mathieu Arnold2017-11-309-17/+15
* For ports that are marked BROKEN on armv6, and also fail to build onMark Linimon2017-11-305-0/+5
* biology/bowtie2: Upgrade to 2.3.3.1Jason W. Bacon2017-11-305-50/+19
* [new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, poJason W. Bacon2017-11-305-0/+74
* biology/bwa: Upgrade to 0.7.17Jason W. Bacon2017-11-282-5/+10
* biology/vcftools: Upgrade to latest release 0.1.15Jason W. Bacon2017-11-282-4/+4
* - Switch to options helpersDmitry Marakasov2017-11-261-1/+5
* biology/diamond: Update to version 0.9.13Joseph Mingrone2017-11-182-4/+4
* - Update to 3.1b2Wen Heping2017-11-115-39/+69
* Fix the context of some patches so that they apply with stricter patch(1)Antoine Brodin2017-11-102-6/+6
* biology/diamond: Update to version 0.9.12Joseph Mingrone2017-11-092-7/+5
* Fix USE_GITHUB usage.Mathieu Arnold2017-11-062-5/+4
* biology/py-pysam: Update to 0.13Yuri Victorovich2017-11-062-6/+8
* biology/diamond: Update to 0.9.11Joseph Mingrone2017-11-033-10/+14
* biology/molden: chase another intransparent upstream distfile upgrade.Johannes M Dieterich2017-11-012-4/+4
* - Fix installing scripts and support binariesWen Heping2017-10-304-8/+39
* Update biology/py-pysam to 0.12.0.1Tobias C. Berner2017-10-262-4/+4
* biology/htslib biology/bcftools biology/samtools: Update to 1.6Luca Pizzamiglio2017-10-2525-897/+171
* biology/iqtree: Add EXAMPLES option and fix mess with installation ofJoseph Mingrone2017-10-221-1/+13
* New port, biology/iqtree: Efficient phylogenomic softwareJoseph Mingrone2017-10-224-0/+43
* Mark as broken ports with no public distfilesBaptiste Daroussin2017-10-136-1/+10
* Remove dead master sitesBaptiste Daroussin2017-10-132-2/+3
* biology/molden: unbreak by chasing latest intransparent distfile update.Johannes M Dieterich2017-09-282-4/+4
* devel/boost-*: update to 1.65.1Jan Beich2017-09-251-1/+1
* devel/boost-*: enable C++11 featuresJan Beich2017-09-251-1/+1
* biology/ssaha: unbreak with gcc7Jan Beich2017-09-251-0/+9
* Remove USES=execinfo.Mathieu Arnold2017-09-222-2/+2
* Update tbb to 2018 and bump dependent ports' revisionsGanael LAPLANCHE2017-09-171-1/+1
* Update to 1.007002Sunpoet Po-Chuan Hsieh2017-09-163-23/+5
* Add p5-Bio-FeatureIO 1.6.905Sunpoet Po-Chuan Hsieh2017-09-165-0/+67
* Fix license information for portgs that use "the same license as Perl".Mathieu Arnold2017-09-1510-10/+10
* - Update to 1.007002Wen Heping2017-09-133-15/+4
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2017-09-1115-15/+15
* Update to 3.3.20170530Sunpoet Po-Chuan Hsieh2017-09-042-3/+5
* Remove expired ports:Rene Ladan2017-08-235-87/+0
* Update GNUstep core libraries.David Chisnall2017-08-211-1/+1
* - update to 1.70Wen Heping2017-08-182-4/+4
* biology/diamond: Update to version 0.9.10Joseph Mingrone2017-08-162-4/+4
* - Update to 1.53Wen Heping2017-07-232-4/+4
* Deprecate ports BROKEN for more than 6 monthsAntoine Brodin2017-07-221-0/+2
* biology/seaview: Update version 4.6.1=>4.6.2Muhammad Moinur Rahman2017-07-222-4/+4
* Chase next distfile update. Upstream contacted whether we would be allowed to...Johannes M Dieterich2017-07-142-4/+4
* biology/molden: Unbreak by chasing their latest opaque update to the distribu...Johannes M Dieterich2017-07-122-7/+5
* Update math/gsl to 2.4Tobias C. Berner2017-07-041-1/+1
* biology/diamond: Update to version 0.9.9Joseph Mingrone2017-07-042-4/+4
* Update devel/readline to 7.0 patch 3Sunpoet Po-Chuan Hsieh2017-06-271-1/+1
* Begin deorbit burn of ia64. We have not attempted to build packages forMark Linimon2017-06-251-1/+1
* Mark BROKEN.Mathieu Arnold2017-06-221-0/+2
* biology/diamond: Update to version 0.9.8Joseph Mingrone2017-06-162-4/+4
* - Update WWWDmitry Marakasov2017-06-102-8/+7
* - Update to 0.11.2.2Wen Heping2017-06-102-4/+4
* Previous commit unbroke the port.Mark Linimon2017-06-031-2/+0
* biology/diamond: Update to version 0.9.4Joseph Mingrone2017-06-032-4/+4
* Remove outdated PERL_LEVEL checkSunpoet Po-Chuan Hsieh2017-06-021-8/+2
* Remove outdated PERL_LEVEL checkSunpoet Po-Chuan Hsieh2017-06-021-8/+2
* Update WWWSunpoet Po-Chuan Hsieh2017-05-301-1/+1
* biology/diamond: Update to version 0.9.3Joseph Mingrone2017-05-292-4/+4
* Mark some ports failing on armv6, for errors classified as "clang".Mark Linimon2017-05-271-0/+2
* Mark some ports failing on armv6, for errors classified as "???".Mark Linimon2017-05-272-3/+6
* biology/molden: Chase recent upstream change of molden distfile.Johannes M Dieterich2017-05-242-4/+4
* - Update to 0.11.2.1Jochen Neumeister2017-05-242-5/+5
* biology/diamond: Update to version 0.9.1Joseph Mingrone2017-05-232-6/+6
* Revision bump of all ports with USE_GL after consolidation of mesa-libsMatthew Rezny2017-05-233-3/+3
* It is possible that r441426 will fix the build problem on armv6. GiveMark Linimon2017-05-221-1/+0
* Mark some ports failing on power64. In cases where the error messageMark Linimon2017-05-221-0/+2
* Mark BROKEN: checksum and size mismatchAntoine Brodin2017-05-201-0/+2
* - Update to 5.15.0Wen Heping2017-05-183-3/+14
* Mark some ports failing on power64. In cases where the error messageMark Linimon2017-05-135-3/+6
* - Update to 0.11.1Martin Wilke2017-05-082-4/+4
* - Update to 1.5.1Martin Wilke2017-05-072-6/+4
* bx-python is a python library and associated set of scripts to allow for rapidMartin Wilke2017-05-064-0/+47
* pysam is a lightweight wrapper of the htslib C-API and provides facilities toMartin Wilke2017-05-065-0/+47
* - Update to 1.69Wen Heping2017-05-032-4/+4
* devel/boost-*: update to 1.64.0Jan Beich2017-05-021-1/+1
* Update math/gsl to 2.3Tobias C. Berner2017-05-021-0/+1
* Provide error messages for some ports failing on aarch64, and, in aMark Linimon2017-05-022-0/+5
* 2017-04-30 devel/stormlib-ghost++: Unfetchable for more than six months (goog...Larry Rosenman2017-04-305-79/+0
* biology/py-biom-format: Update to version 2.1.6Joseph Mingrone2017-04-292-4/+5
* - Fix shebangsMartin Wilke2017-04-221-2/+3
* - Fix shebangsMartin Wilke2017-04-221-3/+4
* - Fix shebangsDmitry Marakasov2017-04-221-3/+7
* biology/diamond: Update to version 0.8.38Joseph Mingrone2017-04-212-6/+5
* biology/seaview: Update version 4.6=>4.6.1Muhammad Moinur Rahman2017-04-122-4/+5
* biology/diamond: Update to version 0.8.37Joseph Mingrone2017-04-022-5/+5
* Bump PORTREVISIONs for ports depending on the canonical version of GCC andGerald Pfeifer2017-04-0116-11/+16
* Update devel/tbb to 2017.5Ganael LAPLANCHE2017-03-071-0/+1
* Mark the remaining ports depending on Google Code as DEPRECATED, with anMathieu Arnold2017-03-041-0/+2
* - Update to 1.42Wen Heping2017-03-012-4/+4
* Fix USE_GITHUB's GH_TAGNAME usage.Mathieu Arnold2017-02-282-5/+5
* biology/plinkseq: unbreak with clang 4.0Jan Beich2017-02-272-0/+12
* biology/bowtie2: update to 2.3.0Jan Beich2017-02-274-6/+48
* Mark a few more ports that create large logfiles broken on armv6.Mark Linimon2017-02-261-0/+2
* Mark various ports as broken on armv6: invokes x86 asm.Mark Linimon2017-02-262-0/+2
* - Update to 1.14.9Danilo Egea Gondolfo2017-02-253-6/+12
* Move -fPIC to where Linux puts it so it is limited to a single library.Tijl Coosemans2017-02-142-4/+2
* biology/diamond: Update to version 0.8.36.Joseph Mingrone2017-02-122-4/+4
* biology/molden: Unbreak port, regenerate checksums, increment PORTREVISION.Johannes M Dieterich2017-02-112-7/+5
* Add -fPIC to various ports to enable them to build on armv6.Mark Linimon2017-02-101-8/+3
* - Mark BROKEN: does not fetch, size/checksum mismatchDmitry Marakasov2017-02-071-0/+2
* Update to 1.5.1Sunpoet Po-Chuan Hsieh2017-02-072-9/+8
* biology/diamond: Update to version 0.8.35.Joseph Mingrone2017-02-062-5/+5
* Move devel/rubygem-bio to biology/rubygem-bioSunpoet Po-Chuan Hsieh2017-02-054-0/+36
* Bump PORTREVISION for ports affected by the fix the last commit.Mathieu Arnold2017-02-013-1/+3
* Mark various ports broken on aarch64 and armv6.Mark Linimon2017-01-311-0/+2
* biology/diamond: Update to version 0.8.34.Joseph Mingrone2017-01-232-4/+4
* Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/Sunpoet Po-Chuan Hsieh2017-01-213-3/+3
* biology/diamond: Update to version 0.8.32.Joseph Mingrone2017-01-162-4/+4
* biology/diamond: Update to version 0.8.31.Joseph Mingrone2017-01-132-4/+4
* - Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOLDmitry Marakasov2017-01-092-15/+3
* devel/boost-*: update to 1.63.0Jan Beich2017-01-061-1/+1
* Never set WRKSRC when using USE_GITHUB.Mathieu Arnold2017-01-042-4/+0
* Assume "pkg-config zlib" works after 9.x reached EOLJan Beich2017-01-041-3/+0
* Remove BROKEN_FreeBSD_9Sunpoet Po-Chuan Hsieh2017-01-012-3/+0
* biology/diamond: Update to version 0.8.30Joseph Mingrone2016-12-312-4/+4
* biology/ncbi-blast+: Add MAKE_JOBS_UNSAFEJoseph Mingrone2016-12-231-0/+2
* - Update to 1.007001Sunpoet Po-Chuan Hsieh2016-12-212-4/+4
* biology/bowtie2: Update to version 2.2.9Joseph Mingrone2016-12-212-14/+18
* biology/cd-hit: Update to bug-fix release 4.6.6Joseph Mingrone2016-12-212-5/+4
* biology/jellyfish: Update to version 2.2.6Joseph Mingrone2016-12-203-54/+56
* - Update *_DEPENDS: Bio::Coordinate family has been moved from biology/p5-Bio...Sunpoet Po-Chuan Hsieh2016-12-191-2/+4
* - Add p5-Bio-Coordinate 1.007001Sunpoet Po-Chuan Hsieh2016-12-195-0/+58
* - Update to 1.007000Sunpoet Po-Chuan Hsieh2016-12-194-20/+29
* - Update to 1.007001Sunpoet Po-Chuan Hsieh2016-12-196-383/+180
* - Update to 2.5.0Wen Heping2016-12-195-68/+190
* - Update to 2.40Sunpoet Po-Chuan Hsieh2016-12-183-10/+22
* - Move biology/p5-bioperl-run to biology/p5-BioPerl-RunSunpoet Po-Chuan Hsieh2016-12-186-8/+10
* - Add LICENSE_FILESunpoet Po-Chuan Hsieh2016-12-181-2/+5
* - Add LICENSESunpoet Po-Chuan Hsieh2016-12-181-4/+8
* - Add LICENSESunpoet Po-Chuan Hsieh2016-12-181-1/+7
* - Move biology/p5-bioperl to biology/p5-BioPerlSunpoet Po-Chuan Hsieh2016-12-187-9/+7
* biology/diamond: Update to version 0.8.29Joseph Mingrone2016-12-182-4/+4
* biology/protomol: Support build with C++11 (taken from dports)John Marino2016-12-185-0/+48
* biology/blat: Fix build on DF (taken from dports)John Marino2016-12-181-0/+14
* biology/lamarc: Fix build on DF (taken from dports)John Marino2016-12-181-0/+11
* biology/chemeq: fix build on GCC (taken from dports)John Marino2016-12-181-0/+11
* Remove libintl.so.9 compatibility link that was added in r374303 toTijl Coosemans2016-12-093-2/+3
* Remove libjpeg.so.11 compatibility link that was added in r374303 toTijl Coosemans2016-12-091-0/+1
* Bump PORTREVISIONS for ports depending on the canonical version of GCC andGerald Pfeifer2016-12-077-5/+7
* biology/molden: distfile was updated in xwin.cKurt Jaeger2016-12-042-4/+4
* Do not use post-stage. Use post-install instead.Mathieu Arnold2016-12-021-1/+1
* biology/njplot: Add site in MASTER_SITES because package builders areJoseph Mingrone2016-11-281-2/+4
* biology/diamond: Update to version 0.8.28Joseph Mingrone2016-11-282-5/+6
* Fixup USE_GITHUB usage.Mathieu Arnold2016-11-262-3/+3
* Replace USE_GCC=4.9+ by USE_GCC=yes, now that lang/gcc and the defaultGerald Pfeifer2016-11-261-1/+1
* devel/boost-*: update to 1.62.0Jan Beich2016-11-231-0/+1
* - Remove unnecessary USES=shebangfixSunpoet Po-Chuan Hsieh2016-11-211-4/+8
* Bump PORTREVISIONS for ports depending on the canonical version of GCC andGerald Pfeifer2016-11-205-2/+5
* biology/avida: Fix ncurses from ports supportJohn Marino2016-11-191-1/+3
* biology/njplot: Revive and update to version 2.4Joseph Mingrone2016-11-165-0/+109
* Mark various leaf ports broken on aarch64, and, where appropriate, otherMark Linimon2016-11-114-2/+8
* Attempt to fix build on non-x86 archs.Mark Linimon2016-11-111-3/+5
* biology/seqtools: update 4.43.0 -> 4.44.1Kurt Jaeger2016-11-113-4/+14
* biology/molden: add missing LICENSE_NAMEKurt Jaeger2016-11-101-1/+2
* biology/molden: fix distinfo, set LICENSEKurt Jaeger2016-11-102-7/+11
* The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.Mark Linimon2016-11-093-3/+3
* Mark as broken on arm64.Mark Linimon2016-11-081-0/+2
* Mark broken on all tier-2 archs.Mark Linimon2016-11-081-0/+3
* Mark broken on the rest of the tier-2 archs: invokes x86 asm.Mark Linimon2016-11-081-1/+4
* biology/diamond: Update to version 0.8.26Joseph Mingrone2016-11-062-4/+4
* Cleanup no longer needed CHMOD usage after r424898.Mathieu Arnold2016-11-034-12/+5
* - Mark it BROKENWen Heping2016-10-281-1/+3
* Use USES=pathfix where applicable.Mathieu Arnold2016-10-214-21/+11
* ${RM} already has -f.Mathieu Arnold2016-10-213-3/+3
* biology/diamond: update to version 0.8.24Joseph Mingrone2016-10-172-4/+4
* biology/diamond: update to version 0.8.23Joseph Mingrone2016-10-102-4/+4
* Mark BROKEN: unfetchable, size mismatchAntoine Brodin2016-10-011-0/+1
* biology/blat: Fix build with non-base SSLJohn Marino2016-10-011-4/+4
* Update PORTREVISION and dinstinfo due to upstream tarball changeJoseph Mingrone2016-09-302-3/+4
* biology/paml: update to version 4.9c and various improvementsJoseph Mingrone2016-09-284-33/+48
* Update email address to jrm@FreeBSD.org for ports that I maintainJoseph Mingrone2016-09-243-5/+3