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* biology/viennarna: Update 2.4.14 -> 2.4.15Yuri Victorovich2020-09-072-5/+4
| | | | Notes: svn path=/head/; revision=547949
* biology/gatk: Update 4.1.8.0 -> 4.1.8.1Yuri Victorovich2020-09-062-6/+6
| | | | Notes: svn path=/head/; revision=547771
* biology/mapm3: Reformat patches.Fernando Apesteguía2020-09-0423-125/+128
| | | | | | | Make them compliant with the expected format. Notes: svn path=/head/; revision=547537
* biology/mapm3: Fix build with llvm11, gcc10Fernando Apesteguía2020-09-041-4/+14
| | | | | | | | | | | | | | | | Another instance of -fno-common issue. While here: * strip executables * add license PR: 249077 Submitted by: tphilipp@potion-studios.com (maintainer) MFH: 2020Q3 (build fix, -fno-common) Notes: svn path=/head/; revision=547530
* biology/hyphy: Update to version 2.5.18 and add AVX optionJoseph Mingrone2020-09-023-6/+29
| | | | | | | | The AVX option is off by default, because hyphy will crash on systems without advanced vector extensions support. Notes: svn path=/head/; revision=547370
* biology/py-ete3: Update 3.1.1 -> 3.1.2Yuri Victorovich2020-09-022-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=547317
* biology/diamond: Update to version 2.0.4Joseph Mingrone2020-08-303-49/+4
| | | | | | | | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v2.0.3 https://github.com/bbuchfink/diamond/releases/tag/v2.0.4 Port changes: Remove a patch that was upstreamed: https://github.com/bbuchfink/diamond/pull/378 Notes: svn path=/head/; revision=547066
* biology/picard-tools: Remove extraneous fileJason W. Bacon2020-08-301-112/+0
| | | | | | | Reported by: Roman Bogorodskiy Notes: svn path=/head/; revision=547056
* Extend expiration of ports broken with -fno-commonNiclas Zeising2020-08-303-7/+9
| | | | | | | | | | | | | | | | | Extend the expiration of unmaintained leaf ports that are broken with -fno-common and previously had a short expiration date. The new date is set to 2021-04-01, meaning the ports will be in the 2021Q2 branch, giving people until 2021-06-30 (10 months from now) to fix issues. Improve the wording of the deprecation message, mentioning both llvm 11 and -fno-common. Bump portrevision to force reinstall. This way the warning message about deprecation will be displayed to users installing or reinstalling the software. MFH: 2020Q3 (maybe) Notes: svn path=/head/; revision=547044
* Chase security/p11-kit updateRoman Bogorodskiy2020-08-302-2/+2
| | | | | | | | | | | | | | After switch to meson libp11-kit.so no longer has symbols in the LIBP11_KIT_1.0 namespace. As a workaround, bump PORTREVISION of consumers to get those rebuilt. See more details in the comments of the linked PR. PR: 248819 Reported by: John Hein Notes: svn path=/head/; revision=546967
* biology/: Fix build with clang11 and deprecate ports@ portsTobias C. Berner2020-08-293-0/+15
| | | | Notes: svn path=/head/; revision=546885
* biology/phyml: fix build on recent currentTobias C. Berner2020-08-294-0/+74
| | | | | | | | | | mostly backport of: https://github.com/stephaneguindon/phyml/commit/3574fb82d54438518d50d5ba8f74423d5395a96a Obtained from: https://github.com/stephaneguindon/phyml/commit/3574fb82d54438518d50d5ba8f74423d5395a96a Notes: svn path=/head/; revision=546884
* biology/cufflinks: fix build on recent currentTobias C. Berner2020-08-281-0/+11
| | | | Notes: svn path=/head/; revision=546790
* biology/bwa: fix build on recent currentTobias C. Berner2020-08-282-1/+6
| | | | | | | Obtained from: https://github.com/lh3/bwa/commit/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284 Notes: svn path=/head/; revision=546721
* Remove expired ports:Rene Ladan2020-08-276-129/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2020-08-26 audio/timidity++-tcltk: Broken for more than 6 months 2020-08-26 biology/pbcopper: Broken for more than 6 months 2020-08-26 devel/ace: Broken for more than 6 months 2020-08-26 devel/bin86: Broken for more than 6 months 2020-08-26 devel/erlang-oserl: Broken for more than 6 months 2020-08-20 emulators/qemu40: Please consider using qemu or qemu41 2020-08-26 games/linux-darwinia-demo: Broken for more than 6 months 2020-08-26 games/linux-defcon: Broken for more than 6 months 2020-08-26 games/linux-uplink-demo: Broken for more than 6 months 2020-08-26 games/xevil: Broken for more than 6 months 2020-08-26 games/xminesweep: Broken for more than 6 months 2020-08-26 graphics/backfract: Broken for more than 6 months 2020-08-26 japanese/kanjipad: Broken for more than 6 months 2020-08-26 japanese/xdtp: Broken for more than 6 months 2020-08-26 korean/hpscat: Broken for more than 6 months 2020-08-26 math/barvinok: Broken for more than 6 months 2020-08-26 math/openmesh: Broken for more than 6 months 2020-08-26 math/rehearse: Broken for more than 6 months 2020-08-26 net/hinfo: Broken for more than 6 months 2020-08-26 science/fleur: Broken for more than 6 months 2020-08-26 science/lm: Broken for more than 6 months 2020-08-26 security/ddos_scan: Broken for more than 6 months 2020-08-26 security/gag: Broken for more than 6 months 2020-08-26 security/py-keystone: Broken for more than 6 months 2020-08-26 sysutils/mono-kmod: mastersite disappeared, unfetchable 2020-08-26 x11-themes/gtk-cleanice-engine: Broken for more than 6 months 2020-08-26 x11-wm/aewm: Broken for more than 6 months Notes: svn path=/head/; revision=546333
* biology/hhsuite: Update 3.2.0 -> 3.3.0Yuri Victorovich2020-08-274-46/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=546314
* biology/paml: fix the build with LLVM 11Kyle Evans2020-08-201-0/+14
| | | | | | | | | | | | | | | | LLVM 11 switched from -fcommon to -fno-common by default. This revealed a slight misposition of names in paml.h, which caused one symbol per enum that's not used anywhere. The fix just moves the names back so that the enums are named that, rather than creating new unused symbols. Reviewed by: zeising Approved by: jrm (maintainer) MFH: 2020Q3 Notes: svn path=/head/; revision=545542
* biology/hyphy: Update to version 2.5.17Joseph Mingrone2020-08-202-4/+4
| | | | | | | | | Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.16 https://github.com/veg/hyphy/releases/tag/2.5.17 Notes: svn path=/head/; revision=545538
* devel/ipython: Update to 7.17.0Danilo G. Baio2020-08-151-1/+1
| | | | | | | | | | | | IPython 7.17+ supports Python 3.7 and above, following NEP 29. Update consumers to use Python >= 3.7 (avoid break bulk -a). Changelog: https://ipython.readthedocs.io/en/latest/whatsnew/version7.html?highlight=7.17#ipython-7-17 Approved by: dbaio (python, maintainer) Notes: svn path=/head/; revision=544938
* Remove deprecated ports:Rene Ladan2020-08-154-65/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2020-08-15 archivers/py-backports.lzma: Uses deprecated version of python 2020-08-15 archivers/py-bup: Uses deprecated version of python 2020-08-15 archivers/py-librtfcomp: Uses deprecated version of python 2020-08-15 audio/blop-lv2: Uses deprecated version of python 2020-08-15 audio/bs2b-lv2: Uses deprecated version of python 2020-08-15 audio/py-gmusicproxy: Uses deprecated version of python 2020-08-15 audio/py-karaoke: Uses deprecated version of python 2020-08-15 audio/py-openal: Uses deprecated version of python 2020-08-15 audio/py-py-jack: Uses deprecated version of python 2020-08-15 audio/py-xmms2: Uses deprecated version of python 2020-08-15 audio/triceratops-lv2: Uses deprecated version of python 2020-08-15 biology/py-biom-format: Uses deprecated version of python 2020-08-15 comms/py-bulksms: Uses deprecated version of python 2020-08-15 comms/py-gammu: Uses deprecated version of python 2020-08-15 databases/py-geoalchemy: Uses deprecated version of python 2020-08-15 databases/py-htsql-mysql: Uses deprecated version of python 2020-08-15 databases/py-htsql-pgsql: Uses deprecated version of python 2020-08-15 databases/py-mysql2pgsql: Uses deprecated version of python 2020-08-15 databases/py-oursql: Uses deprecated version of python 2020-08-15 databases/py-pyPgSQL: Uses deprecated version of python 2020-08-15 databases/py-pyhs: Uses deprecated version of python 2020-08-15 databases/py-pytc: Uses deprecated version of python 2020-08-15 databases/py-riak: Uses deprecated version of python 2020-08-15 databases/py-umemcache: Uses deprecated version of python 2020-08-15 devel/py-Breve: Uses deprecated version of python 2020-08-15 devel/py-PyODE: Uses deprecated version of python 2020-08-15 devel/py-akismet: Uses deprecated version of python 2020-08-15 devel/py-aspects: Uses deprecated version of python 2020-08-15 devel/py-backports.tempfile: Uses deprecated version of python 2020-08-15 devel/py-backports.weakref: Uses deprecated version of python 2020-08-15 devel/py-cfgparse: Uses deprecated version of python 2020-08-15 devel/py-ciphon: Uses deprecated version of python 2020-08-15 devel/py-cjson: Uses deprecated version of python 2020-08-15 devel/py-clonedigger: Uses deprecated version of python 2020-08-15 devel/py-cuisine: Uses deprecated version of python 2020-08-15 devel/py-deliciousapi: Uses deprecated version of python 2020-08-15 devel/py-dialog: Uses deprecated version of python 2020-08-15 devel/py-efl: Uses deprecated version of python 2020-08-15 devel/py-ezpyinline: Uses deprecated version of python 2020-08-15 devel/py-fsm: Uses deprecated version of python 2020-08-15 devel/py-gdbgui: Uses deprecated version of python 2020-08-15 devel/py-gearman: Uses deprecated version of python 2020-08-15 devel/py-generate: Uses deprecated version of python 2020-08-15 devel/py-geotypes: Uses deprecated version of python 2020-08-15 devel/py-gitosis: Uses deprecated version of python 2020-08-15 devel/py-google-apputils: Uses deprecated version of python 2020-08-15 devel/py-hghooks: Uses deprecated version of python 2020-08-15 devel/py-instant: Uses deprecated version of python 2020-08-15 devel/py-jcc: Uses deprecated version of python 2020-08-15 devel/py-json-py: Uses deprecated version of python 2020-08-15 devel/py-json-sempai: Uses deprecated version of python 2020-08-15 devel/py-jsonlib: Uses deprecated version of python 2020-08-15 devel/py-jsonlib2: Uses deprecated version of python 2020-08-15 devel/py-jsonrpclib: Uses deprecated version of python 2020-08-15 devel/py-kayako: Uses deprecated version of python 2020-08-15 devel/py-kid: Uses deprecated version of python 2020-08-15 devel/py-kjbuckets: Uses deprecated version of python 2020-08-15 devel/py-kqueue: Uses deprecated version of python 2020-08-15 devel/py-log4py: Uses deprecated version of python 2020-08-15 devel/py-mwlib.ext: Uses deprecated version of python 2020-08-15 devel/py-mx-experimental: Uses deprecated version of python 2020-08-15 devel/py-option_merge: Uses deprecated version of python 2020-08-15 devel/py-prioritized_methods: Uses deprecated version of python 2020-08-15 devel/py-protocols: Uses deprecated version of python 2020-08-15 devel/py-ptrace: Uses deprecated version of python 2020-08-15 devel/py-pydoop: Uses deprecated version of python 2020-08-15 devel/py-pyke: Uses deprecated version of python 2020-08-15 devel/py-pymtbl: Uses deprecated version of python 2020-08-15 devel/py-pyshapelib: Uses deprecated version of python 2020-08-15 devel/py-pytemplate: Uses deprecated version of python 2020-08-15 devel/py-python2-pythondialog: Uses deprecated version of python 2020-08-15 devel/py-pyutil: Uses deprecated version of python 2020-08-15 devel/py-pyvalid: Uses deprecated version of python 2020-08-15 devel/py-pyxml2obj: Uses deprecated version of python 2020-08-15 devel/py-qpid: Uses deprecated version of python 2020-08-15 devel/py-repoze.what-pylons: Uses deprecated version of python 2020-08-15 devel/py-repoze.who-friendlyform: Uses deprecated version of python 2020-08-15 devel/py-robotframework-ride: Uses deprecated version of python 2020-08-15 devel/py-ruamel.ordereddict: Uses deprecated version of python 2020-08-15 devel/py-sanetime: Uses deprecated version of python 2020-08-15 devel/py-selectors34: Uses deprecated version of python 2020-08-15 devel/py-sqlcc: Uses deprecated version of python 2020-08-15 devel/py-statgrab: Uses deprecated version of python 2020-08-15 devel/py-tconfpy: Uses deprecated version of python 2020-08-15 devel/py-terminable_thread: Uses deprecated version of python 2020-08-15 devel/py-trace2html: Uses deprecated version of python 2020-08-15 devel/py-tvrage: Uses deprecated version of python 2020-08-15 devel/py-tw.forms: Uses deprecated version of python 2020-08-15 devel/py-uncompyle2: Uses deprecated version of python 2020-08-15 devel/py-yum-metadata-parser: Uses deprecated version of python 2020-08-15 devel/rubygem-warden127: No longer needed 2020-08-15 dns/py-dnschain: Uses deprecated version of python 2020-08-15 dns/py-idnkit2: Uses deprecated version of python 2020-08-15 games/colobot: Uses deprecated version of python 2020-08-15 games/endgame-singularity: Uses deprecated version of python 2020-08-15 games/katawa-shoujo: Uses deprecated version of RenPy 2020-08-15 games/pyfa: Uses deprecated version of python 2020-08-15 games/renpy6: Uses deprecated version of python 2020-08-15 games/solarwolf: Uses deprecated version of python 2020-08-15 games/thudboard: Uses deprecated version of python 2020-08-15 graphics/djvusmooth: Uses deprecated version of python 2020-08-15 graphics/py-glewpy: Uses deprecated version of python 2020-08-15 graphics/py-openexr: Uses deprecated version of python 2020-08-15 graphics/py-poppler: Uses deprecated version of python 2020-08-15 graphics/py-pygooglechart: Uses deprecated version of python 2020-08-15 graphics/py-sane: Uses deprecated version of python 2020-08-15 graphics/py-stltools: Uses deprecated version of python 2020-08-15 graphics/sk1: Uses deprecated version of python 2020-08-15 japanese/py-mecab: Uses deprecated version of python 2020-08-15 japanese/py-tegaki-gtk: Uses deprecated version of python 2020-08-15 lang/py-mx-base: Uses deprecated version of python 2020-08-15 mail/mailpile: Uses deprecated version of python 2020-08-15 math/py-ffc: Uses deprecated version of python 2020-08-15 math/py-fiat: Uses deprecated version of python 2020-08-15 math/py-nzmath: Uses deprecated version of python 2020-08-15 math/py-pymc: Uses deprecated version of python 2020-08-15 math/py-ufl: Uses deprecated version of python 2020-08-15 misc/py-socli: Uses deprecated version of python 2020-08-15 misc/py-yolk: Uses deprecated version of python 2020-08-15 multimedia/py-flvlib: Uses deprecated version of python 2020-08-15 net/py-gspreadsheet: Uses deprecated version of python 2020-08-15 net/py-libnet: Uses deprecated version of python 2020-08-15 net/py-netlib: Uses deprecated version of python 2020-08-15 net/py-pynmsg: Uses deprecated version of python 2020-08-15 net/py-rainbowstream: Uses deprecated version of python 2020-08-15 net/py-wolframalpha: Uses deprecated version of python 2020-08-15 net-im/empathy: Uses deprecated version of python 2020-08-15 net-im/farsight2: Uses deprecated version of python 2020-08-15 net-im/py-xmpppy: Uses deprecated version of python 2020-08-15 net-im/telepathy-farsight: Uses deprecated version of python 2020-08-15 net-im/telepathy-python: Uses deprecated version of python 2020-08-15 net-im/telepathy-rakia: Uses deprecated version of python 2020-08-15 net-mgmt/py-pynsca: Uses deprecated version of python 2020-08-15 net-mgmt/py-yapsnmp: Uses deprecated version of python 2020-08-15 net-p2p/py-py2play: Uses deprecated version of python 2020-08-15 news/py-yenc: Uses deprecated version of python 2020-08-15 print/py-pyscript: Uses deprecated version of python 2020-08-15 print/py-stapler: Uses deprecated version of python 2020-08-15 print/py-trml2pdf: Uses deprecated version of python 2020-08-15 science/py-PyQuante: Uses deprecated version of python 2020-08-15 science/py-mlpy: Uses deprecated version of python 2020-08-15 science/py-ws2300: Uses deprecated version of python 2020-08-15 security/py-PF: Uses deprecated version of python 2020-08-15 security/py-cracklib: Uses deprecated version of python 2020-08-15 security/py-fteproxy: Uses deprecated version of python 2020-08-15 security/py-onetime: Uses deprecated version of python 2020-08-15 security/py-pydeep: Uses deprecated version of python 2020-08-15 security/py-slowaes: Uses deprecated version of python 2020-08-15 security/py-sslstrip: Uses deprecated version of python 2020-08-15 security/py-volatility: Uses deprecated version of python 2020-08-15 sysutils/py-analyzemft: Uses deprecated version of python 2020-08-15 sysutils/py-cdmi: Uses deprecated version of python 2020-08-15 sysutils/py-ezjailremote: Uses deprecated version of python 2020-08-15 sysutils/py-gmailfs-fuse: Uses deprecated version of python 2020-08-15 sysutils/py-ploy_ec2: Uses deprecated version of python 2020-08-15 sysutils/py-ploy_fabric: Uses deprecated version of python 2020-08-15 sysutils/py-scriptine: Uses deprecated version of python 2020-08-15 sysutils/py-superlance: Uses deprecated version of python 2020-08-15 textproc/py-bugzillatools: Uses deprecated version of python 2020-08-15 textproc/py-elib.intl: Uses deprecated version of python 2020-08-15 textproc/py-errorhandler: Uses deprecated version of python 2020-08-15 textproc/py-hyperestraier-python: Uses deprecated version of python 2020-08-15 textproc/py-pyes: Uses deprecated version of python 2020-08-15 textproc/py-pyhwp: Uses deprecated version of python 2020-08-15 textproc/py-sphinx_numfig: Uses deprecated version of python 2020-08-15 www/py-HTMLgen: Uses deprecated version of python 2020-08-15 www/py-albatross: Uses deprecated version of python 2020-08-15 www/py-amf: Uses deprecated version of python 2020-08-15 www/py-apachelog: Uses deprecated version of python 2020-08-15 www/py-aws-requests-auth: Uses deprecated version of python 2020-08-15 www/py-clientform: Uses deprecated version of python 2020-08-15 www/py-django-appmedia: Uses deprecated version of python 2020-08-15 www/py-django-evolution: Uses deprecated version of python 2020-08-15 www/py-fedex: Uses deprecated version of python 2020-08-15 www/py-formalchemy: Uses deprecated version of python 2020-08-15 www/py-frappe-bench: Uses deprecated version of python 2020-08-15 www/py-funkload: Uses deprecated version of python 2020-08-15 www/py-goobook: Uses deprecated version of python 2020-08-15 www/py-poster: Uses deprecated version of python 2020-08-15 www/py-pyquery: Uses deprecated version of python 2020-08-15 www/py-pysearch: Uses deprecated version of python 2020-08-15 www/py-pywebdav: Uses deprecated version of python 2020-08-15 www/py-slimmer: Uses deprecated version of python 2020-08-15 www/py-surl: Uses deprecated version of python 2020-08-15 www/py-tmdb3: Uses deprecated version of python 2020-08-15 www/py-trello: Uses deprecated version of python 2020-08-15 www/py-uliweb: Uses deprecated version of python 2020-08-15 www/py-wsgiauth: Uses deprecated version of python 2020-08-15 x11-toolkits/py-wax: Uses deprecated version of python 2020-08-15 x11-toolkits/py-wxPython-common: Uses deprecated version of python 2020-08-15 x11-toolkits/py-wxPython28-common: Uses deprecated version of python Notes: svn path=/head/; revision=544927
* biology/graphlan: Remove the 2.7 limitation on python because it's no longer ↵Yuri Victorovich2020-08-141-4/+2
| | | | | | | needed Notes: svn path=/head/; revision=544867
* biology/groopm: Remove python's 2.7 restriction placed here by mistakeYuri Victorovich2020-08-131-5/+2
| | | | Notes: svn path=/head/; revision=544832
* biology/diamond: Update to version 2.0.2Joseph Mingrone2020-08-073-4/+49
| | | | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v2.0.1 https://github.com/bbuchfink/diamond/releases/tag/v2.0.2 Notes: svn path=/head/; revision=544321
* biology/py-gtfparse: Update 1.2.0 -> 1.2.1Yuri Victorovich2020-08-072-5/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=544312
* biology/samtools: Upgrade to 1.10Jason W. Bacon2020-08-035-22/+68
| | | | | | | | | | | | Numerous bug fixes and enhancements: https://github.com/samtools/samtools/releases/tag/1.10 Take maintainership per ports/248089 PR: ports/248089 Notes: svn path=/head/; revision=544098
* biology/bcftools: Upgrade to 1.10.2Jason W. Bacon2020-08-036-78/+69
| | | | | | | | | | | | Numerous bug fixes and enhancements since 1.9: https://github.com/samtools/bcftools/tags Take maintainership per ports/248089. PR: ports/248089 Notes: svn path=/head/; revision=544096
* biology/vt: Patch to work with htslib 1.10.2Jason W. Bacon2020-08-035-1/+62
| | | | | | | Minor API changes requiring type casts Notes: svn path=/head/; revision=544091
* biology/htslib: Upgrade to 1.10.2Jason W. Bacon2020-08-0312-43/+113
| | | | | | | | | | | | 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/kallisto: Revert to 0.46.1Jason W. Bacon2020-08-035-60/+32
| | | | | | | | | | | 0.46.2 has long-standing regressions that are not being addressed, including a seg fault when using --genomebam. Also revert to bundled htslib in preparation for biology/htslib upgrade to 1.10. Kallisto source contains modified bits of htslib 1.4.1 that are incompatible with htslib > 1.9. Notes: svn path=/head/; revision=544077
* biology/diamond: Update to version 2.0.0Joseph Mingrone2020-07-283-14/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v2.0.0 Notes: svn path=/head/; revision=543567
* Deprecate ports broken for more than 6 monthsAntoine Brodin2020-07-261-0/+2
| | | | Notes: svn path=/head/; revision=543440
* Update to 2.0.1Sunpoet Po-Chuan Hsieh2020-07-242-10/+4
| | | | | | | Changes: https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc Notes: svn path=/head/; revision=543176
* Add rubygem-bio-shell 1.0.0Sunpoet Po-Chuan Hsieh2020-07-244-0/+38
| | | | | | | | | | | | | | bio-shell, providing BioRuby Shell, is a command-line interface for BioRuby, an open source bioinformatics library for Ruby. This code has historically been part of the BioRuby gem, but has been split into its own gem as part of an effort to modularize BioRuby. bio-shell and many more plugins are available at biogems.info. WWW: https://github.com/bioruby/bioruby-shell Notes: svn path=/head/; revision=543012
* Add rubygem-bio-old-biofetch-emulator 1.0.0Sunpoet Po-Chuan Hsieh2020-07-244-0/+33
| | | | | | | | | | | | | bio-old-biofetch-emulator emulates Bio::Fetch object in BioRuby as if discontinued BioRuby BioFetch server were still alive. It overrides methods and objects in Bio::Fetch, and if the old BioRuby BioFetch server's URL is given, it intercepts all requests and converts them into existing web services such as TogoWS, KEGG REST API, NCBI E-Utilities, and GenomeNet(genome.jp). WWW: https://github.com/ngoto/bioruby-old-biofetch-emulator Notes: svn path=/head/; revision=543011
* Add rubygem-bio-executables 1.0.0Sunpoet Po-Chuan Hsieh2020-07-244-0/+43
| | | | | | | | | | | | | | | bio-executables is a collection of miscellaneous utilities for bioinformatics that were formerly part of the BioRuby core ("bio" gem). Because of reducing complexity, they were moved to this gem. This code has historically been part of the BioRuby gem, but has been split into its own gem as part of an effort to modularize BioRuby. bio-executables and many more plugins are available at biogems.info. WWW: https://github.com/bioruby/bioruby-executables Notes: svn path=/head/; revision=543010
* Update devel/tbb to 2020.3 and bump dependent ports' revisionsGanael LAPLANCHE2020-07-171-1/+1
| | | | | | | Changelog: https://github.com/oneapi-src/oneTBB/blob/v2020.3/CHANGES Notes: svn path=/head/; revision=542423
* Unbreak bulk -aAntoine Brodin2020-07-141-1/+1
| | | | Notes: svn path=/head/; revision=542200
* biology/phyml: update to 3.3.20200621Fernando Apesteguía2020-07-102-6/+5
| | | | | | | | | | | | | From ChangeLog: https://github.com/stephaneguindon/phyml/releases/tag/v3.3.20200621 This release fixes a few minor bugs (see recent commits). The manual also gives extra XML configuration information in order to apply fancy substitution models (e.g., CAT-like) on single- or multiple-gene data sets Reported by: portscout Notes: svn path=/head/; revision=541852
* biology/gatk: Update 4.1.7.0 -> 4.1.8.0Yuri Victorovich2020-07-092-6/+6
| | | | Notes: svn path=/head/; revision=541723
* biology/cufflinks: fix build on GCC architecturesPiotr Kubaj2020-07-081-1/+1
| | | | | | | | | Using Boost requires modern compiler. MFH: 2020Q3 (fix build blanket) Notes: svn path=/head/; revision=541482
* Chanse update of devel/libffiNiclas Zeising2020-07-041-0/+1
| | | | | | | | | | | | | Chase the devel/libffi update Bump portrevision of all dependent ports to chace shard library version bump in libffi. Update LIB_DEPENDS lines where needed to not require a specific version of libffi.so. PR: 247028 (for tracking) Notes: svn path=/head/; revision=541232
* biology/psi88: Unbreak build with GCC 10Tobias Kortkamp2020-07-041-0/+1
| | | | | | | | | | | | | | | ctplot.f:69:29: 69 | CALL SYMBOL (XA,YA,.15,STRING,ANGLE,K) | 1 Error: Rank mismatch in argument 'string' at (1) (scalar and rank-1) http://package18.nyi.freebsd.org/data/121amd64-default-PR244494/2020-06-10_18h04m44s/logs/errors/psi88-1.0_16.log PR: 246700 Notes: svn path=/head/; revision=541204
* biology/bowtie: Unbreak build with GCC 10Tobias Kortkamp2020-07-041-0/+11
| | | | | | | | | | | | | | | | | | In file included from ebwt.h:43, from ebwt_build.cpp:11: processor_support.h:52:22: error: extended character “ is not valid in an identifier 52 | std::cerr << “ERROR: please define __cpuid() for this build.\n”; | ^ processor_support.h:52:72: error: extended character ” is not valid in an identifier 52 | std::cerr << “ERROR: please define __cpuid() for this build.\n”; | ^ http://package18.nyi.freebsd.org/data/121amd64-default-PR244494/2020-06-10_18h04m44s/logs/errors/bowtie-1.1.2_9.log PR: 246700 Notes: svn path=/head/; revision=541191
* biology/diamond: Update to version 0.9.36Joseph Mingrone2020-07-033-4/+14
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.36 Notes: svn path=/head/; revision=541097
* Bump devel/jsoncpp consumers after r540853.Tobias C. Berner2020-06-301-1/+1
| | | | | | | Reported by: Kevin Oberman <rkoberman@gmail.com> Notes: svn path=/head/; revision=540909
* biology/hyphy: Update to version 2.5.15Joseph Mingrone2020-06-282-4/+4
| | | | | | | Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.15 Notes: svn path=/head/; revision=540728
* biology/diamond: Update to version 0.9.35Joseph Mingrone2020-06-272-4/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.35 Notes: svn path=/head/; revision=540624
* Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113Sunpoet Po-Chuan Hsieh2020-06-261-1/+2
| | | | | | | | | | | | - Fix LICENSE_FILE - Update pkg-descr - Update WWW - Bump PORTREVISION of dependent ports for dependency change Changes: https://metacpan.org/changes/distribution/IO-Stringy Notes: svn path=/head/; revision=540492
* biology/py-bx-python: Update 0.8.8 -> 0.8.9Yuri Victorovich2020-06-262-4/+5
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=540420
* biology/seaview: Update version 5.0.3=>5.0.4Muhammad Moinur Rahman2020-06-222-4/+4
| | | | | | | Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES Notes: svn path=/head/; revision=539893
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