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2602 commits

Author SHA1 Message Date
Jason W. Bacon
e4868fdb92 biology/canu: Upgrade to 1.9 
Numerous bug fixes and enhancements

Reported by:    portscout
 2019-11-08 14:03:15 +00:00
Dmitry Marakasov
d696ac2f3b - Limit python version (does not build with 3.7+) 
Approved by:	portmgr blanket
 2019-11-08 12:12:42 +00:00
Tobias Kortkamp
6a379e2d3a a-b: Add missing USES={gnome,php,sdl,xorg} 2019-11-08 09:27:56 +00:00
Niclas Zeising
ef5d45aaa6 Sprinkle more USES=xorg 2019-11-07 20:19:59 +00:00
Joseph Mingrone
47738adc67 biology/diamond: Update to version 0.9.28 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.28
 2019-11-07 14:12:07 +00:00
Antoine Brodin
cc8ad7de9b Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
Jason W. Bacon
6098bf59b8 biology/kallisto: Upgrade to 0.46.1 
Minor bug fixes and enhancements

Reported by:    portscout
 2019-11-06 00:18:14 +00:00
Niclas Zeising
f01bbf652d Add USES=xorg USES=gl, ports categories b 
Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'.
 2019-11-04 21:08:20 +00:00
Joseph Mingrone
cf2251f192 biology/diamond: Update to version 0.9.27 (plus one fix) 
Since compiling from source no longer performs a native build, remove
-mtune=generic from CLFAGS when package building.

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.27
 2019-11-03 01:34:11 +00:00
Tobias C. Berner
4e896a50f8 math/gsl: update to 2.6 
- math/p5-Math-GSL does not seem to have any upstream activity to make it work with this version -> mark it broken
  - this also breaks the two consumers of this port

- biology/gemma: has a conflict with cblas, and is makred broken.

PR:		241363
Exp-run by:	antoine
 2019-10-25 23:41:34 +00:00
Piotr Kubaj
6cf4d2cdda biology/avida: unbreak on powerpc64 
Builds fine with GCC 9.

Approved by:	mentors (implicit approval)
 2019-10-23 16:25:10 +00:00
Rene Ladan
13d4527a34 Remove expired ports: 
2019-10-16 archivers/freetar: Unfetchable, unmaintained
2019-10-16 archivers/hffzip: Unfetchable, unmaintained
2019-10-16 archivers/hpack.non-usa.only: Unfetchable, unmaintained
2019-10-16 archivers/untar: Unfetchable, unmaintained
2019-10-16 astro/gpsdrive: Unfetchable, unmaintained
2019-10-16 astro/planets: Unfetchable, unmaintained
2019-10-16 audio/ascd: Unfetchable, unmaintained
2019-10-16 audio/audiotag: Unfetchable, unmaintained
2019-10-16 audio/gmidimonitor: Unfetchable, unmaintained
2019-10-16 audio/gmpc-lyricwiki: Unfetchable, unmaintained
2019-10-16 audio/jack_mixer: Unfetchable, unmaintained
2019-10-16 audio/jmusic: Unfetchable, unmaintained
2019-10-16 audio/maplay: Unfetchable, unmaintained
2019-10-16 audio/mbox: Unfetchable, unmaintained
2019-10-16 audio/nuvolaplayer: Unfetchable, unmaintained
2019-10-16 audio/vagalume: Unfetchable, unmaintained
2019-10-16 audio/wmsmixer: Unfetchable, unmaintained
2019-10-16 audio/xmms2-scrobbler: Unfetchable, unmaintained
2019-10-16 benchmarks/filebench: Unfetchable, unmaintained
2019-10-16 biology/chemeq: Unfetchable, unmaintained
2019-10-16 biology/linux-foldingathome: Unfetchable, unmaintained
2019-10-16 cad/dxf2fig: Unfetchable, unmaintained
2019-10-16 cad/gerbv: Unfetchable, unmaintained
2019-10-16 cad/ghdl: Unfetchable, unmaintained
2019-10-16 comms/gsmlib: Unfetchable, unmaintained
2019-10-16 comms/nokryptia: Unfetchable, unmaintained
2019-10-16 databases/mrtg-mysql-load: Unfetchable, unmaintained
2019-10-16 databases/postgres-xl: Unfetchable, unmaintained
2019-10-16 databases/wmjsql: Unfetchable, unmaintained
2019-10-16 deskutils/dlume: Unfetchable, unmaintained
2019-10-16 deskutils/gkrellm-reminder2: Unfetchable, unmaintained
2019-10-16 deskutils/ljit: Unfetchable, unmaintained
2019-10-16 deskutils/mdh: Unfetchable, unmaintained
2019-10-16 devel/atlassian-plugin-sdk: Unfetchable, unmaintained
2019-10-15 devel/bingo: Abandoned upstream
2019-10-16 devel/dprog: Unfetchable, unmaintained
2019-10-16 devel/eblob: Unfetchable, unmaintained
2019-10-16 devel/elftoaout: Unfetchable, unmaintained
2019-10-16 devel/fga: Unfetchable, unmaintained
2019-10-16 devel/fib: Unfetchable, unmaintained
2019-10-16 devel/flickrnet: Unfetchable, unmaintained
2019-10-16 devel/fujaba: Unfetchable, unmaintained
2019-10-16 devel/funnelweb: Unfetchable, unmaintained
2019-10-16 devel/genproto: Unfetchable, unmaintained
2019-10-16 devel/gitphp: Unfetchable, unmaintained
2019-10-16 devel/gnatcoll: Unfetchable, unmaintained
2019-10-16 devel/kimwitu: Unfetchable, unmaintained
2019-10-16 devel/libghthash: Unfetchable, unmaintained
2019-10-16 devel/lua-alien: Unfetchable, unmaintained
2019-10-16 devel/monotone-viz: Unfetchable, unmaintained
2019-10-16 devel/noweb: Unfetchable, unmaintained
2019-10-16 devel/p65: Unfetchable, unmaintained
2019-10-16 devel/py-fileutils: Unfetchable, unmaintained
2019-10-16 devel/py-mercurialserver: Unfetchable, unmaintained
2019-10-16 devel/py-pqueue: Unfetchable, unmaintained
2019-10-16 devel/pypersrc: Unfetchable, unmaintained
2019-10-16 devel/root-doc: Unfetchable, unmaintained
2019-10-16 devel/sfio: Unfetchable, unmaintained
2019-10-16 devel/styx: Unfetchable, unmaintained
2019-10-16 devel/tclmore: Unfetchable, unmaintained
2019-10-16 devel/umem: Unfetchable, unmaintained
2019-10-16 dns/ez-ipupdate: Unfetchable, unmaintained
2019-10-16 editors/zoinks: Unfetchable, unmaintained
2019-10-16 emulators/aftp: Unfetchable, unmaintained
2019-10-16 emulators/ia64sim: Unfetchable, unmaintained
2019-10-16 emulators/loemu: Unfetchable, unmaintained
2019-10-16 emulators/pipelight: Unfetchable, unmaintained
2019-10-16 finance/ledgersmb: Unfetchable, unmaintained
2019-10-16 ftp/atftp: Unfetchable, unmaintained
2019-10-16 ftp/cftp: Unfetchable, unmaintained
2019-10-16 games/arkanoidsb: Unfetchable, unmaintained
2019-10-16 games/balazar: Unfetchable, unmaintained
2019-10-16 games/blockade: Unfetchable, unmaintained
2019-10-16 games/cleanq3: Unfetchable, unmaintained
2019-10-16 games/conquest: Unfetchable, unmaintained
2019-10-16 games/crafty-tablebase-no-pawn: Unfetchable, unmaintained
2019-10-16 games/epiar: Unfetchable, unmaintained
2019-10-16 games/exmars: Unfetchable, unmaintained
2019-10-16 games/fteqw: Unfetchable, unmaintained
2019-10-16 games/gnake: Unfetchable, unmaintained
2019-10-16 games/gru: Unfetchable, unmaintained
2019-10-16 games/gtkpool: Unfetchable, unmaintained
2019-10-16 games/imaze: Unfetchable, unmaintained
2019-10-16 games/inform: Unfetchable, unmaintained
2019-10-16 games/iourbanterror: Unfetchable, unmaintained
2019-10-16 games/iourbanterror-server: Unfetchable, unmaintained
2019-10-16 games/jools: Unfetchable, unmaintained
2019-10-16 games/legends: Unfetchable, unmaintained
2019-10-16 games/linux-enemyterritory-etpro: Unfetchable, unmaintained
2019-10-16 games/linux-worldofgoo-demo: Unfetchable, unmaintained
2019-10-16 games/noegnud-data: Unfetchable, unmaintained
2019-10-16 games/poker-engine: Unfetchable, unmaintained
2019-10-16 games/ptools: Unfetchable, unmaintained
2019-10-16 games/pyawale: Unfetchable, unmaintained
2019-10-16 games/pysycache-lang: Unfetchable, unmaintained
2019-10-16 games/qmars: Unfetchable, unmaintained
2019-10-16 games/quake-reaper: Unfetchable, unmaintained
2019-10-16 games/quake3-ra3: Unfetchable, unmaintained
2019-10-16 games/sdlCC: Unfetchable, unmaintained
2019-10-16 games/speyes: Unfetchable, unmaintained
2019-10-16 games/vodovod: Unfetchable, unmaintained
2019-10-16 games/wmeyes: Unfetchable, unmaintained
2019-10-16 games/wmshuffle: Unfetchable, unmaintained
2019-10-16 games/xabacus: Unfetchable, unmaintained
2019-10-16 games/xpacman: Unfetchable, unmaintained
2019-10-16 games/xscorch: Unfetchable, unmaintained
2019-10-16 graphics/aeskulap: Unfetchable, unmaintained
2019-10-16 graphics/agave: Unfetchable, unmaintained
2019-10-16 graphics/cbview: Unfetchable, unmaintained
2019-10-16 graphics/copperspice: Unfetchable, unmaintained
2019-10-16 graphics/cthumb: Unfetchable, unmaintained
2019-10-16 graphics/fujiplay: Unfetchable, unmaintained
2019-10-16 graphics/gimp-ez-perspective-plugin: Unfetchable, unmaintained
2019-10-16 graphics/gimp-focusblur-plugin: Unfetchable, unmaintained
2019-10-16 graphics/gimp-jagged-border-script: Unfetchable, unmaintained
2019-10-16 graphics/gimp-manual-html: Unfetchable, unmaintained
2019-10-16 graphics/gimp-save-for-web: Unfetchable, unmaintained
2019-10-16 graphics/gimp-wavelet-denoise-plugin: Unfetchable, unmaintained
2019-10-16 graphics/gimp-wavelet-sharpen-plugin: Unfetchable, unmaintained
2019-10-16 graphics/giram: Unfetchable, unmaintained
2019-10-16 graphics/inventor: Unfetchable, unmaintained, Depends on expiring graphics/libGLw
2019-10-16 graphics/jpg2pdf: Unfetchable, unmaintained
2019-10-16 graphics/jpgraph2: Unfetchable, unmaintained
2019-10-16 graphics/makehuman: Unfetchable, unmaintained
2019-10-16 graphics/pstoepsi: Unfetchable, unmaintained
2019-10-16 graphics/xmandel: Unfetchable, unmaintained
2019-10-16 irc/minbif: Unfetchable, unmaintained
2019-10-16 japanese/VTPSfont: Unfetchable, unmaintained
2019-10-16 japanese/asterisk-sounds: Unfetchable, unmaintained
2019-10-16 japanese/cannadic: Unfetchable, unmaintained
2019-10-16 japanese/edict-utf-8: Unfetchable, unmaintained
2019-10-16 japanese/kpcal: Unfetchable, unmaintained
2019-10-16 japanese/multiskkserv: Unfetchable, unmaintained
2019-10-16 japanese/skkfep: Unfetchable, unmaintained
2019-10-16 java/eclipse-log4e: Unfetchable, unmaintained
2019-10-16 java/eclipse-lomboz: Unfetchable, unmaintained
2019-10-16 java/java-checkstyle: Unfetchable, unmaintained
2019-10-16 korean/baekmukfonts-ttf: Unfetchable, unmaintained
2019-10-16 korean/gtkcomm: Unfetchable, unmaintained
2019-10-16 lang/arena: Unfetchable, unmaintained
2019-10-16 lang/diveintopython: Unfetchable, unmaintained
2019-10-16 lang/modula3: Unfetchable, unmaintained
2019-10-16 lang/p2c: Unfetchable, unmaintained
2019-10-16 lang/quack: Unfetchable, unmaintained
2019-10-16 lang/stldoc: Unfetchable, unmaintained
2019-10-16 mail/altermime: Unfetchable, unmaintained
2019-10-16 mail/autosig: Unfetchable, unmaintained
2019-10-16 mail/gkrellmmailwatch2: Unfetchable, unmaintained
2019-10-16 mail/mboxcheck-applet: Unfetchable, unmaintained
2019-10-16 mail/nmzmail: Unfetchable, unmaintained
2019-10-16 mail/poppy: Unfetchable, unmaintained
2019-10-16 mail/prom-wl: Unfetchable, unmaintained
2019-10-16 mail/py-apolicy: Unfetchable, unmaintained
2019-10-16 mail/spamdb-curses: Unfetchable, unmaintained
2019-10-16 mail/xlbiff: Unfetchable, unmaintained
2019-10-16 math/algotutor: Unfetchable, unmaintained
2019-10-16 math/nyh-hoc: Unfetchable, unmaintained
2019-10-16 math/superlu_mt: Unfetchable, unmaintained
2019-10-16 math/testu01: Unfetchable, unmaintained
2019-10-16 misc/astrolog: Unfetchable, unmaintained
2019-10-16 misc/chord2html: Unfetchable, unmaintained
2019-10-16 misc/crosspad: Unfetchable, unmaintained
2019-10-16 misc/detachtty: Unfetchable, unmaintained
2019-10-16 misc/dphys-config: Unfetchable, unmaintained
2019-10-16 misc/dvorakng: Unfetchable, unmaintained
2019-10-16 misc/gctpc: Unfetchable, unmaintained
2019-10-16 misc/gkrellm-helium: Unfetchable, unmaintained
2019-10-16 misc/gkrellweather2: Unfetchable, unmaintained
2019-10-16 misc/linm: Unfetchable, unmaintained
2019-10-16 misc/mc-light: Unfetchable, unmaintained
2019-10-16 misc/newer: Unfetchable, unmaintained
2019-10-16 misc/telbook: Unfetchable, unmaintained
2019-10-16 misc/valspeak: Unfetchable, unmaintained
2019-10-16 misc/xd: Unfetchable, unmaintained
2019-10-16 multimedia/audiopreview: Unfetchable, unmaintained
2019-10-16 multimedia/dvts: Unfetchable, unmaintained
2019-10-16 multimedia/gcfilms: Unfetchable, unmaintained
2019-10-16 multimedia/kissdx: Unfetchable, unmaintained
2019-10-16 multimedia/playd: Unfetchable, unmaintained
2019-10-16 multimedia/subtitleeditor: Unfetchable, unmaintained
2019-10-16 multimedia/umr: Unfetchable, unmaintained
2019-10-16 net/bluemix-cli: Unfetchable, unmaintained
2019-10-16 net/boclient: Unfetchable, unmaintained
2019-10-16 net/csync2: Unfetchable, unmaintained
2019-10-16 net/dictd-database: Unfetchable, unmaintained
2019-10-16 net/gtic: Unfetchable, unmaintained
2019-10-16 net/hidentd: Unfetchable, unmaintained
2019-10-16 net/ldap2dns: Unfetchable, unmaintained
2019-10-16 net/libmxp: Unfetchable, unmaintained
2019-10-16 net/librouteros: Unfetchable, unmaintained
2019-10-16 net/nettest: Unfetchable, unmaintained
2019-10-16 net/py-netstring: Unfetchable, unmaintained
2019-10-16 net/radiusd-cistron: Unfetchable, unmaintained
2019-10-16 net/rtptools: Unfetchable, unmaintained
2019-10-16 net/smbldap-tools: Unfetchable, unmaintained
2019-10-16 net/tcptrace: Unfetchable, unmaintained
2019-10-16 net/wackford-squeers: Unfetchable, unmaintained
2019-10-16 net/wmnet2: Unfetchable, unmaintained
2019-10-16 net-im/pidgin-birthday-reminder: Unfetchable, unmaintained
2019-10-16 net-im/pidgin-pidgimpd: Unfetchable, unmaintained
2019-10-16 net-im/poezio: Unfetchable, unmaintained
2019-10-16 net-mgmt/bsnmp-jails: Unfetchable, unmaintained
2019-10-16 net-mgmt/iog: Unfetchable, unmaintained
2019-10-16 net-mgmt/lanmap: Unfetchable, unmaintained
2019-10-16 net-mgmt/nagios-spamd-plugin: Unfetchable, unmaintained
2019-10-16 net-mgmt/nefu: Unfetchable, unmaintained
2019-10-16 net-mgmt/pixilate: Unfetchable, unmaintained
2019-10-16 net-mgmt/slate: Unfetchable, unmaintained
2019-10-16 net-mgmt/weplab: Unfetchable, unmaintained
2019-10-16 net-p2p/bnbt: Unfetchable, unmaintained
2019-10-16 net-p2p/btpd: Unfetchable, unmaintained
2019-10-16 net-p2p/gkremldk: Unfetchable, unmaintained
2019-10-16 news/newscache: Unfetchable, unmaintained
2019-10-16 news/nntpbtr: Unfetchable, unmaintained
2019-10-16 news/slrnconf: Unfetchable, unmaintained
2019-10-16 news/xpn: Unfetchable, unmaintained
2019-10-16 polish/ekg: Unfetchable, unmaintained
2019-10-16 polish/ekg2: Unfetchable, unmaintained
2019-10-16 ports-mgmt/fastest_sites: Unfetchable, unmaintained
2019-10-16 ports-mgmt/pkg-plist: Unfetchable, unmaintained
2019-10-16 ports-mgmt/symports: Unfetchable, unmaintained
2019-10-16 print/poster: Unfetchable, unmaintained
2019-10-16 russian/d1489: Unfetchable, unmaintained
2019-10-16 science/metaf2xml: Unfetchable, unmaintained
2019-10-16 security/authforce: Unfetchable, unmaintained
2019-10-16 security/avcheck: Unfetchable, unmaintained
2019-10-16 security/digest: Unfetchable, unmaintained
2019-10-16 security/fpm2: Unfetchable, unmaintained
2019-10-16 security/fwipe: Unfetchable, unmaintained
2019-10-16 security/gnome-password-generator: Unfetchable, unmaintained
2019-10-16 security/httprint: Unfetchable, unmaintained
2019-10-16 security/ike-scan: Unfetchable, unmaintained
2019-10-16 security/ipfwcount: Unfetchable, unmaintained
2019-10-16 security/libsparkcrypto: Unfetchable, unmaintained
2019-10-16 security/md4coll: Unfetchable, unmaintained
2019-10-16 security/md5coll: Unfetchable, unmaintained
2019-10-16 security/osiris: Unfetchable, unmaintained
2019-10-16 security/ranpwd: Unfetchable, unmaintained
2019-10-16 security/rdigest: Unfetchable, unmaintained
2019-10-16 security/smap: Unfetchable, unmaintained
2019-10-16 security/sshblock: Unfetchable, unmaintained
2019-10-16 shells/bashc: Unfetchable, unmaintained
2019-10-16 shells/flash: Unfetchable, unmaintained
2019-10-16 sysutils/cotty: Unfetchable, unmaintained
2019-10-16 sysutils/dt: Unfetchable, unmaintained
2019-10-16 sysutils/gkrellfire: Unfetchable, unmaintained
2019-10-16 sysutils/log_analysis: Unfetchable, unmaintained
2019-10-16 sysutils/mksunbootcd: Unfetchable, unmaintained
2019-10-16 sysutils/rfstool: Unfetchable, unmaintained
2019-10-16 sysutils/skill: Unfetchable, unmaintained
2019-10-16 sysutils/sloth: Unfetchable, unmaintained
2019-10-16 sysutils/snowlog: Unfetchable, unmaintained
2019-10-16 sysutils/wmfire: Unfetchable, unmaintained
2019-10-16 sysutils/xbattbar: Unfetchable, unmaintained
2019-10-16 textproc/bedic-data: Unfetchable, unmaintained
2019-10-16 textproc/clit: Unfetchable, unmaintained
2019-10-16 textproc/docbook-tdg: Unfetchable, unmaintained
2019-10-16 textproc/emacs-wiki: Depends on expiring ports
2019-10-16 textproc/htmlize.el: Unfetchable, unmaintained
2019-10-16 textproc/libflate: Unfetchable, unmaintained
2019-10-16 textproc/mguesser: Unfetchable, unmaintained
2019-10-16 textproc/opensched: Unfetchable, unmaintained
2019-10-16 textproc/opentoken: Unfetchable, unmaintained
2019-10-16 textproc/rot: Unfetchable, unmaintained
2019-10-16 textproc/rtfx: Unfetchable, unmaintained
2019-10-16 textproc/supercat: Unfetchable, unmaintained
2019-10-16 textproc/xml_ez_out: Unfetchable, unmaintained
2019-10-16 textproc/xmldiff: Unfetchable, unmaintained
2019-10-16 textproc/xqilla: Unfetchable, unmaintained
2019-10-16 www/WebMagick: Unfetchable, unmaintained
2019-10-16 www/bins: Unfetchable, unmaintained
2019-10-16 www/blogsum: Unfetchable, unmaintained
2019-10-16 www/boa: Unfetchable, unmaintained
2019-10-16 www/cgihtml: Unfetchable, unmaintained
2019-10-16 www/cgiparse: Unfetchable, unmaintained
2019-10-16 www/flot: Unfetchable, unmaintained
2019-10-16 www/ftasv: Unfetchable, unmaintained
2019-10-16 www/hastymail2-devel: Unfetchable, unmaintained
2019-10-16 www/htmlpp: Unfetchable, unmaintained
2019-10-16 www/http-analyze: Unfetchable, unmaintained
2019-10-16 www/junkbuster: Unfetchable, unmaintained
2019-10-16 www/links-hacked: Unfetchable, unmaintained
2019-10-16 www/llgal: Unfetchable, unmaintained
2019-10-16 www/mgstat: Unfetchable, unmaintained
2019-10-16 www/php-screw: Unfetchable, unmaintained
2019-10-16 www/phproxy: Unfetchable, unmaintained
2019-10-16 www/py-prewikka: Unfetchable, unmaintained
2019-10-16 www/redmine-backlogs: Unfetchable, unmaintained
2019-10-16 www/swfdec-plugin: Unfetchable, unmaintained
2019-10-16 www/swish-e: Unfetchable, unmaintained
2019-10-16 x11/blast: Unfetchable, unmaintained
2019-10-16 x11/dynamag: Unfetchable, unmaintained
2019-10-16 x11/xcurs: Unfetchable, unmaintained
2019-10-16 x11/xscreensaver-gnome: Unfetchable, unmaintained
2019-10-16 x11/xscreensaver-gnome-hacks: Unfetchable, unmaintained
2019-10-16 x11-clocks/cairo-clock: Unfetchable, unmaintained
2019-10-16 x11-clocks/pclock: Unfetchable, unmaintained
2019-10-16 x11-clocks/stopwatch: Unfetchable, unmaintained
2019-10-16 x11-clocks/wmfuzzy: Unfetchable, unmaintained
2019-10-16 x11-fm/emelfm2: Unfetchable, unmaintained
2019-10-16 x11-fm/ezfm: Unfetchable, unmaintained
2019-10-16 x11-fm/ultracopier: Unfetchable, unmaintained
2019-10-16 x11-fm/xplore: Unfetchable, unmaintained
2019-10-16 x11-fonts/indic-ttf: Unfetchable, unmaintained
2019-10-16 x11-fonts/pingwi: Unfetchable, unmaintained
2019-10-16 x11-themes/cursor-ecliz: Unfetchable, unmaintained
2019-10-16 x11-themes/cursor-grounation-theme: Unfetchable, unmaintained
2019-10-16 x11-themes/cursor-neutral-theme: Unfetchable, unmaintained
2019-10-16 x11-themes/cursor-polar-theme: Unfetchable, unmaintained
2019-10-16 x11-themes/gtk-envy-theme: Unfetchable, unmaintained
2019-10-16 x11-themes/gtk-equinox-engine: Unfetchable, unmaintained
2019-10-16 x11-themes/gtk-qnxtheme: Unfetchable, unmaintained
2019-10-16 x11-themes/plank-theme-moka: Unfetchable, unmaintained
2019-10-15 x11-toolkits/swt-devel: Obsolete. Superseded by x11-toolkits/swt
2019-10-16 x11-wm/genmenu: Unfetchable, unmaintained
2019-10-16 x11-wm/musca: Unfetchable, unmaintained
2019-10-16 x11-wm/weewm: Unfetchable, unmaintained
2019-10-16 x11-wm/windowlab: Unfetchable, unmaintained
2019-10-16 x11-wm/wmfs: Unfetchable, unmaintained
 2019-10-16 15:29:32 +00:00
Yuri Victorovich
2182a49d0e biology/prodigal: Eliminate a very old version from the portscout discovery process 2019-10-12 15:40:21 +00:00
Yuri Victorovich
179ca4e700 biology/prodigal: Update 2.6.3-2 -> 2.6.3-7 2019-10-12 15:36:47 +00:00
Jason W. Bacon
c904df3468 biology/star: Upgrade to 2.7.2d 
Fix chimeric output bug.

Numerous other minor fixes and enhancements since 2.7.0.

Reported by:    portscout
 2019-10-06 22:18:31 +00:00
Jason W. Bacon
899d6cc0cd biology/fastahack: Upgrade to 1.0.0 
Very few changes, upstream just finally got around to cutting a release.

Reported by:    portscout
 2019-10-06 21:34:32 +00:00
Yuri Victorovich
d844b03004 biology/mothur: Update 1.42.3 -> 1.43.0 
Reported by:	portscout
 2019-10-05 17:04:42 +00:00
Niclas Zeising
dcb57b7643 biologi/ncbi-toolkit: Remove dependency on libXp 
Remove the dependency on libXp from ncbi-toolkit, since libXp is deprecated
and it isn't needed.
Remove deprecation from ncbi-toolkit.
 2019-09-28 10:52:57 +00:00
Niclas Zeising
45ce25247b Deprecate x11/libXp, it is deprecated upstream 
Deprecate x11/libXp, since it is about to be deprecated upstream.  Do *not*
yet set a removal date for x11/libXp, this will be decided later, once most
dependencies are fixed.
Deprecate all ports depending on x11/libXp.
* astro/xephem
* audio/xmcd
* audio/xmmix
* biology/ncbi-toolkit
* deskutils/xmdiary
* ftp/llnlxdir
* ftp/llnlxftp
* graphics/SciPlot
* misc/xtar
* multimedia/mpeg2play
* science/afni
* textproc/mgdiff

Sprinkle USES=xorg as needed.

Discussed with:	bapt
 2019-09-27 16:18:58 +00:00
Jason W. Bacon
a0498a53b5 biology/tophat: Fast splice junction mapper for RNA-Seq reads 
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq
reads to mammalian-sized genomes using the ultra high-throughput short read
aligner Bowtie, and then analyzes the mapping results to identify splice
junctions between exons.

Note:

TopHat has been Superseded by HISAT2 and is no longer maintained upstream.
This port is provided mainly for revisiting old studies where TopHat was used.
 2019-09-27 00:49:48 +00:00
Ganael LAPLANCHE
03166a4b36 Update devel/tbb to 2019.8 and bump dependent ports' revisions 
Changelog: https://github.com/intel/tbb/blob/tbb_2019/CHANGES
 2019-09-25 10:03:49 +00:00
Jason W. Bacon
490aa151f9 biology/py-multiqc: Aggregate bioinformatics analysis reports 
MultiQC searches a given directory for analysis logs and compiles an HTML
report. It's a general use tool, perfect for summarising the output from
numerous bioinformatics tools.
 2019-09-23 16:09:30 +00:00
Jan Beich
b03c67869c devel/openmp: update to 9.0.0 
- Connect tests to the framework to help QA remaining patches
- Force rebuild all consumers after https://reviews.llvm.org/D59783

Changes:	http://llvm.org/viewvc/llvm-project/openmp/tags/RELEASE_900/final/?view=log
ABI:		https://abi-laboratory.pro/tracker/timeline/llvm_openmp/
 2019-09-21 18:59:57 +00:00
Jason W. Bacon
2eee6a30e8 biology/p5-TrimGalore: Upgrade to 0.6.4 
Improved adapter autodetection, minor bug fixes.
 2019-09-21 02:51:26 +00:00
Jason W. Bacon
8a83d3eb39 biology/fastqc: Upgrade to 0.11.8 
Minor bug fixes and edge case handling.

Minor Makefile clean up.
 2019-09-21 02:44:54 +00:00
Joseph Mingrone
1aeb4149fc biology/diamond: Update to version 0.9.26 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.26
 2019-09-18 18:45:09 +00:00
Tobias Kortkamp
c8b9433fc5 Fix some misspelled or duplicated LICENSE_* 2019-09-17 19:21:45 +00:00
Jason W. Bacon
6ee3cbecfe biology/haplohseq: Identify regions of allelic imbalance 
Haplohseq identifies regions of allelic imbalance (AI) in sequencing data
obtained from impure samples where AI events exist in a potentially low
proportion of cells in the sample.  Input to the software includes a VCF file
of genotypes and estimated phased genotypes.
 2019-09-16 01:07:31 +00:00
Antoine Brodin
637b3d75f3 Deprecate a few ports 2019-09-15 17:28:08 +00:00
Jan Beich
e5688543b0 Drop C++11 workaround for GCC < 6 after r449590 
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
 2019-09-14 22:01:13 +00:00
Jason W. Bacon
848c6ffeb5 biology/trimmomatic: Upgrade to 0.39 
Add convenience script to run without knowing the location of the Java jar
 2019-09-14 14:45:49 +00:00
Jason W. Bacon
6e04e12944 biology/bedtools: Upgrade to 2.29.0 
Add test target to run test scripts in dist

Reported by:    portscout
 2019-09-13 13:21:59 +00:00
Jason W. Bacon
95b394ac5a biology/py-cutadapt: Upgrade to 2.5 
Add pigz run depend for parallel gzip/gunzip
 2019-09-13 13:17:26 +00:00
Fernando Apesteguía
fc8669c808 biology/phyml: update to 3.3.20190909 
While here, add license.

Reported by:	portscout
 2019-09-10 21:04:16 +00:00
Sunpoet Po-Chuan Hsieh
20b6ec5afb Update to 1.007006 (1.7.6) 
- Remove PGTEST and SQLITETEST options: DBD::Pg and DBD::SQLite have been removed from BioPerl by upstream for the move of modules and programs into separate distributions

Changes:	https://metacpan.org/changes/distribution/BioPerl
 2019-09-07 22:44:02 +00:00
Cy Schubert
4b8362f61d Fix after gets(3) retirement using gets_s(3). 
Bump PORTREVISION as this is a security issue too.

PR:		222796
MFH:		2019Q3
 2019-09-02 05:00:43 +00:00
Li-Wen Hsu
5bf9108d86 Add a patch to remove use of gets(3) 
PR:		238685
Submitted by:	Walter Schwarzenfeld <w.schwarzenfeld@utanet.at>
Reported by:	emaste
Sponsored by:	The FreeBSD Foundation
 2019-09-01 16:40:06 +00:00
Yuri Victorovich
e6c3d1ddd9 biology/py-pysam: Update 0.15.2 -> 0.15.3 
Reported by:	portscout
 2019-08-31 15:49:18 +00:00
Yuri Victorovich
c90779610e biology/ngs-sdk: Update 2.9.6 -> 2.10.0 
Reported by:	portscout
 2019-08-31 15:09:47 +00:00
Joseph Mingrone
e4f4ed9cec biology/iqtree: Update to version 1.6.12 
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.12
 2019-08-27 01:19:11 +00:00
Kurt Jaeger
bc7e4c2f4a biology/gperiodic: fix NLS and other rough edges 
PR:		239642
Submitted by:	Walter Schwarzenfeld <w.schwarzenfeld@utanet.at>
Reported by:	bapt
 2019-08-23 15:26:55 +00:00
Jan Beich
befa71e0f3 devel/boost-*: update to 1.71.0 
Changes:	http://www.boost.org/users/history/version_1_71_0.html
PR:		238827
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20774
 2019-08-19 15:35:27 +00:00
Yuri Victorovich
ba3c2338e8 biology/checkm: Update 1.0.17 -> 1.0.18 
Reported by:	portscout
 2019-08-19 08:25:29 +00:00
Mathieu Arnold
a6c40a689b Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
Jason W. Bacon
cdd2c0e9b9 biology/bolt-lmm: Upgrade to 2.3.4 
Remove previously upstreamed patches
New Makefile patch that preserves default behavior and should be palatable
to upstream
 2019-08-13 15:30:21 +00:00
Yuri Victorovich
d9c09cd680 biology/checkm: Update 1.0.16 -> 1.0.17 
Reported by:	portscout
 2019-08-11 19:16:49 +00:00
Kurt Jaeger
ad26c38bf6 biology/gperiodic: upgrade 2.0.10 -> 3.0.3 
- new mastersite

PR:		239642
Submitted by:	Walter Schwarzenfeld <w.schwarzenfeld@utanet.at>
Relnotes:	https://sourceforge.net/p/gperiodic/code/HEAD/tree/branches/3.0.3/ChangeLog
 2019-08-11 17:29:10 +00:00
Sunpoet Po-Chuan Hsieh
b470f47c18 Update to 1.007005 (1.7.5) 
- Fix DISTNAME
- Bump PORTREVISION for package change

Changes:	https://metacpan.org/changes/distribution/BioPerl
 2019-08-11 16:49:24 +00:00
Sunpoet Po-Chuan Hsieh
303b9c7e48 Update WWW 2019-08-11 11:28:16 +00:00
Yuri Victorovich
d5c0a71815 biology/checkm: Update 1.0.13 -> 1.0.16 
Reported by:	portscout
 2019-08-09 07:22:48 +00:00