- Add bowtie2-test script
- Separate Makefile patches into a static patch for upstream and reinplace
for ports-specifics
- Allow aarch64 per upstream Makefile (untested)
2019-03-15 accessibility/qt4-accessible: Qt4 has been EOL since december 2015
2019-03-15 astro/qlandkartegt: Qt4 has been EOL since december 2015
2019-03-15 astro/stellarium-qt4: Qt4 has been EOL since december 2015
2019-03-15 astro/xglobe: Qt4 has been EOL since december 2015
2019-03-15 audio/acoustid-fingerprinter: Qt4 has been EOL since december 2015
2019-03-15 audio/cueplayer: Qt4 has been EOL since december 2015
2019-03-15 audio/esperanza: Qt4 has been EOL since december 2015
2019-03-15 audio/lastfm-desktop: Qt4 has been EOL since december 2015
2019-03-15 audio/minitunes: Qt4 has been EOL since december 2015
2019-03-15 audio/mixxx20: Qt4 has been EOL since december 2015
2019-03-15 audio/mumble: Qt4 has been EOL since december 2015
2019-03-15 audio/murmur: Qt4 has been EOL since december 2015
2019-03-15 audio/puddletag: Qt4 has been EOL since december 2015
2019-03-15 audio/qmpdclient: Qt4 has been EOL since december 2015
2019-03-15 audio/skype-call-recorder: Qt4 has been EOL since december 2015
2019-03-15 audio/virtual_oss_ctl: Qt4 has been EOL since december 2015
2019-03-15 biology/clustalx: Qt4 has been EOL since december 2015
2019-03-15 cad/klayout: Qt4 has been EOL since december 2015
2019-03-15 cad/layouteditor: Qt4 has been EOL since december 2015
2019-03-15 cad/leocad: Qt4 has been EOL since december 2015
2019-03-15 cad/meshlab: Qt4 has been EOL since december 2015
2019-03-15 cad/qfsm: Qt4 has been EOL since december 2015
2019-03-15 cad/qucs: Qt4 has been EOL since december 2015
2019-03-15 chinese/gcin-qt4: Qt4 has been EOL since december 2015
2019-03-15 chinese/qt4-codecs-cn: Qt4 has been EOL since december 2015
2019-03-15 chinese/qt4-codecs-tw: Qt4 has been EOL since december 2015
2019-03-15 chinese/qterm: Qt4 has been EOL since december 2015
2019-03-15 comms/dabstick-radio: Qt4 has been EOL since december 2015
2019-03-15 comms/hamfax: Qt4 has been EOL since december 2015
2019-03-15 comms/linpsk: Qt4 has been EOL since december 2015
2019-03-15 databases/py-qt4-sql: Qt4 has been EOL since december 2015
2019-03-15 databases/qt4-ibase-plugin: Qt4 has been EOL since december 2015
2019-03-15 databases/qt4-mysql-plugin: Qt4 has been EOL since december 2015
2019-03-15 databases/qt4-odbc-plugin: Qt4 has been EOL since december 2015
2019-03-15 databases/qt4-pgsql-plugin: Qt4 has been EOL since december 2015
2019-03-15 databases/qt4-sql: Qt4 has been EOL since december 2015
2019-03-15 databases/qt4-sqlite-plugin: Qt4 has been EOL since december 2015
2019-03-15 databases/qt4-sqlite3-plugin: Qt4 has been EOL since december 2015
2019-03-15 databases/sqliteman: Qt4 has been EOL since december 2015
2019-03-15 databases/tora: Qt4 has been EOL since december 2015
2019-03-15 deskutils/cdcat: Qt4 has been EOL since december 2015
2019-03-15 deskutils/fbreader: Qt4 has been EOL since december 2015
2019-03-15 deskutils/launchy: Qt4 has been EOL since december 2015
2019-03-15 deskutils/qorganizer: Qt4 has been EOL since december 2015
2019-03-15 deskutils/qrfcview: Qt4 has been EOL since december 2015
2019-03-15 deskutils/qtm: Qt4 has been EOL since december 2015
2019-03-15 deskutils/tuxcards: Qt4 has been EOL since december 2015
2019-03-15 deskutils/vym: Qt4 has been EOL since december 2015
2019-03-15 devel/apiextractor: Qt4 has been EOL since december 2015
2019-03-15 devel/automoc4: Qt4 has been EOL since december 2015
2019-03-15 devel/edb: Qt4 has been EOL since december 2015
2019-03-15 devel/generatorrunner: Qt4 has been EOL since december 2015
2019-03-15 devel/grantlee: Qt4 has been EOL since december 2015
2019-03-15 devel/gwenhywfar-qt4: Qt4 has been EOL since december 2015
2019-03-15 devel/kaptain: Qt4 has been EOL since december 2015
2019-03-15 devel/ninja-ide: Qt4 has been EOL since december 2015
2019-03-12 devel/physfs-devel: is the same as devel/physfs, serving no purpose
2019-03-15 devel/piklab: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-assistant: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-core: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-dbus: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-dbussupport: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-declarative: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-designer: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-designerplugin: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-help: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-qscintilla2: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-script: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-scripttools: Qt4 has been EOL since december 2015
2019-03-15 devel/py-qt4-test: Qt4 has been EOL since december 2015
2019-03-15 devel/pyside: Qt4 has been EOL since december 2015
2019-03-15 devel/pyside-tools: Qt4 has been EOL since december 2015
2019-03-15 devel/qbzr: Qt4 has been EOL since december 2015
2019-03-15 devel/qct: Qt4 has been EOL since december 2015
2019-03-15 devel/qdevelop: Qt4 has been EOL since december 2015
2019-03-15 devel/qprog: Qt4 has been EOL since december 2015
2019-03-15 devel/qross: Qt4 has been EOL since december 2015
2019-03-15 devel/qscintilla2: Qt4 has been EOL since december 2015
2019-03-15 devel/qscintilla2-designerplugin: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-assistant: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-assistant-adp: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-corelib: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-dbus: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-designer: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-help-tools: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-libqtassistantclient: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-linguist: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-linguisttools: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-makeqpf: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-moc: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-porting: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qdbusviewer: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qdoc3: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qmake: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qmlviewer: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qt3support: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qtsolutions-singleapplication: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qtsolutions-soap: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-qvfb: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-rcc: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-script: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-scripttools: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-testlib: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-uic: Qt4 has been EOL since december 2015
2019-03-15 devel/qt4-uic3: Qt4 has been EOL since december 2015
2019-03-15 devel/qtscriptgenerator: Qt4 has been EOL since december 2015
2019-03-15 devel/shiboken: Qt4 has been EOL since december 2015
2019-03-15 devel/subcommander2: Qt4 has been EOL since december 2015
2019-03-15 devel/universalindentgui: Qt4 has been EOL since december 2015
2019-03-15 editors/leo: Qt4 has been EOL since december 2015
2019-03-15 editors/lfhex: Qt4 has been EOL since december 2015
2019-03-15 editors/plume-creator-devel: Qt4 has been EOL since december 2015
2019-03-15 editors/textroom: Qt4 has been EOL since december 2015
2019-03-15 editors/yzis: Qt4 has been EOL since december 2015
2019-03-15 emulators/dboxfe: Qt4 has been EOL since december 2015
2019-03-15 emulators/q4wine: Qt4 has been EOL since december 2015
2019-03-15 emulators/qtemu: Qt4 has been EOL since december 2015
2019-03-15 emulators/swine: Qt4 has been EOL since december 2015
2019-03-15 finance/alkimia-qt4: Qt4 has been EOL since december 2015
2019-03-15 finance/bitcoin-armory: Qt4 has been EOL since december 2015
2019-03-15 finance/qhacc: Qt4 has been EOL since december 2015
2019-03-15 ftp/scythia: Qt4 has been EOL since december 2015
2019-03-15 games/bubble-chains: Qt4 has been EOL since december 2015
2019-03-15 games/capicity: Qt4 has been EOL since december 2015
2019-03-15 games/capitalism: Qt4 has been EOL since december 2015
2019-03-15 games/flukz: Qt4 has been EOL since december 2015
2019-03-15 games/goldencheetah: Qt4 has been EOL since december 2015
2019-03-15 games/jag: Qt4 has been EOL since december 2015
2019-03-15 games/kardsgt: Qt4 has been EOL since december 2015
2019-03-15 games/kcheckers: Qt4 has been EOL since december 2015
2019-03-15 games/openpref: Qt4 has been EOL since december 2015
2019-03-15 games/pokerth: Qt4 has been EOL since december 2015
2019-03-15 games/qgo: Qt4 has been EOL since december 2015
2019-03-15 games/qtads: Qt4 has been EOL since december 2015
2019-03-15 games/quackle: Qt4 has been EOL since december 2015
2019-03-15 games/spellathon: Qt4 has been EOL since december 2015
2019-03-15 games/sudoku-sensei: Qt4 has been EOL since december 2015
2019-03-15 games/tbe: Qt4 has been EOL since december 2015
2019-03-15 games/xptools: Qt4 has been EOL since december 2015
2019-03-15 german/tipp10: Qt4 has been EOL since december 2015
2019-03-15 graphics/appleseed: Qt4 has been EOL since december 2015
2019-03-15 graphics/aqsis: Qt4 has been EOL since december 2015
2019-03-15 graphics/autoq3d: Qt4 has been EOL since december 2015
2019-03-15 graphics/burplex: Qt4 has been EOL since december 2015
2019-03-15 graphics/darknock: Qt4 has been EOL since december 2015
2019-03-15 graphics/djview4-qt4: Qt4 has been EOL since december 2015
2019-03-15 graphics/easypaint: Qt4 has been EOL since december 2015
2019-03-15 graphics/eos-movrec: Qt4 has been EOL since december 2015
2019-03-15 graphics/gle-graphics: Qt4 has been EOL since december 2015
2019-03-15 graphics/lprof-devel: Qt4 has been EOL since december 2015
2019-03-15 graphics/luminance: Qt4 has been EOL since december 2015
2019-03-15 graphics/luxrender: Qt4 has been EOL since december 2015
2019-03-15 graphics/luxrender14: Qt4 has been EOL since december 2015
2019-03-15 graphics/meshviewer: Qt4 has been EOL since december 2015
2019-03-15 graphics/natron: Qt4 has been EOL since december 2015
2019-03-15 graphics/oyranos: Qt4 has been EOL since december 2015
2019-03-15 graphics/pencil: Qt4 has been EOL since december 2015
2019-03-15 graphics/prison: Qt4 has been EOL since december 2015
2019-03-15 graphics/py-qt4-svg: Qt4 has been EOL since december 2015
2019-03-15 graphics/qt4-iconengines: Qt4 has been EOL since december 2015
2019-03-15 graphics/qt4-imageformats: Qt4 has been EOL since december 2015
2019-03-15 graphics/qt4-opengl: Qt4 has been EOL since december 2015
2019-03-15 graphics/qt4-pixeltool: Qt4 has been EOL since december 2015
2019-03-15 graphics/qt4-svg: Qt4 has been EOL since december 2015
2019-03-15 graphics/qxv: Qt4 has been EOL since december 2015, qxv is unmaintained
2019-03-15 graphics/scantailor: Qt4 has been EOL since december 2015
2019-03-15 graphics/seexpr: Qt4 has been EOL since december 2015
2019-03-15 graphics/smillaenlarger: Qt4 has been EOL since december 2015
2019-03-15 graphics/structuresynth: Qt4 has been EOL since december 2015
2019-03-15 graphics/yagf: Qt4 has been EOL since december 2015
2019-03-15 japanese/qt4-codecs-jp: Qt4 has been EOL since december 2015
2019-03-15 korean/qt4-codecs-kr: Qt4 has been EOL since december 2015
2019-03-15 mail/qgmailnotifier: Qt4 has been EOL since december 2015
2019-03-15 math/qtiplot: Qt4 has been EOL since december 2015
2019-03-15 math/qtoctave: Qt4 has been EOL since december 2015
2019-03-15 math/qwtplot3d-qt4: Qt4 has been EOL since december 2015
2019-03-15 misc/py-qt4-demo: Qt4 has been EOL since december 2015
2019-03-15 misc/py-qt4-doc: Qt4 has been EOL since december 2015
2019-03-15 misc/qmetro: Qt4 has been EOL since december 2015
2019-03-15 misc/qt4-doc: Qt4 has been EOL since december 2015
2019-03-15 misc/qt4-l10n: Qt4 has been EOL since december 2015
2019-03-15 misc/qt4-qtconfig: Qt4 has been EOL since december 2015
2019-03-15 misc/qt4-qtdemo: Qt4 has been EOL since december 2015
2019-03-15 misc/saaghar: Qt4 has been EOL since december 2015
2019-03-15 multimedia/2mandvd: Qt4 has been EOL since december 2015
2019-03-15 multimedia/abby: Qt4 has been EOL since december 2015
2019-03-15 multimedia/avidemux-qt4: Qt4 has been EOL since december 2015
2019-03-15 multimedia/gstreamer-qt4: Qt4 has been EOL since december 2015
2019-03-15 multimedia/mediadownloader: Qt4 has been EOL since december 2015
2019-03-15 multimedia/mlt-qt4: Qt4 has been EOL since december 2015
2019-03-15 multimedia/phonon-xine: Qt4 has been EOL since december 2015
2019-03-15 multimedia/py-qt4-multimedia: Qt4 has been EOL since december 2015
2019-03-15 multimedia/py-qt4-phonon: Qt4 has been EOL since december 2015
2019-03-15 multimedia/qmmp: Qt4 has been EOL since december 2015
2019-03-15 multimedia/qmmp-plugin-pack: Qt4 has been EOL since december 2015
2019-03-15 multimedia/qt4-mobility: Qt4 has been EOL since december 2015
2019-03-15 multimedia/qt4-multimedia: Qt4 has been EOL since december 2015
2019-03-15 multimedia/umplayer: Qt4 has been EOL since december 2015
2019-03-15 net/avahi-qt4: Qt4 has been EOL since december 2015
2019-03-15 net/cagibi: Qt4 has been EOL since december 2015
2019-03-15 net/hupnp: Qt4 has been EOL since december 2015
2019-03-15 net/ostinato: Qt4 has been EOL since december 2015
2019-03-15 net/py-qt4-network: Qt4 has been EOL since december 2015
2019-03-15 net/qjsonrpc: Qt4 has been EOL since december 2015
2019-03-15 net/qoauth: Qt4 has been EOL since december 2015
2019-03-15 net/qt4-network: Qt4 has been EOL since december 2015
2019-03-15 net/qtweetlib: Qt4 has been EOL since december 2015
2019-03-15 net-im/libjreen: Qt4 has been EOL since december 2015
2019-03-15 net-im/psimedia: Qt4 has been EOL since december 2015
2019-03-15 net-im/ramblercontacts: Qt4 has been EOL since december 2015
2019-03-15 net-im/telepathy-logger-qt4: Qt4 has been EOL since december 2015
2019-03-15 net-im/turpial: Qt4 has been EOL since december 2015
2019-03-15 net-im/vacuum-im: Qt4 has been EOL since december 2015
2019-03-15 net-mgmt/nagiosagent: Qt4 has been EOL since december 2015
2019-03-15 net-mgmt/qkismet: Qt4 has been EOL since december 2015
2019-03-15 net-p2p/bitmessage: Qt4 has been EOL since december 2015
2019-03-15 net-p2p/eiskaltdcpp-qt: Qt4 has been EOL since december 2015
2019-03-15 net-p2p/valknut: Qt4 has been EOL since december 2015
2019-03-15 polish/qfaktury: Qt4 has been EOL since december 2015
2019-03-15 print/kpdftool: Qt4 has been EOL since december 2015
2019-03-15 print/scribus: Qt4 has been EOL since december 2015
2019-03-15 science/MOOSE-neural-simulator: Qt4 has been EOL since december 2015
2019-03-15 science/avogadro: Qt4 has been EOL since december 2015
2019-03-15 science/openstructure: Qt4 has been EOL since december 2015
2019-03-15 science/py-veusz: Qt4 has been EOL since december 2015
2019-03-15 science/qtresistors: Qt4 has been EOL since december 2015
2019-03-15 security/keepassx2: Qt4 has been EOL since december 2015
2019-03-15 security/kqoauth: Qt4 has been EOL since december 2015
2019-03-15 security/tpmmanager: Qt4 has been EOL since december 2015
2019-03-15 sysutils/android-file-transfer-qt4: Qt4 has been EOL since december 2015
2019-03-15 sysutils/bacula9-bat: Qt4 has been EOL since december 2015
2019-03-15 sysutils/bareos-traymonitor: Qt4 has been EOL since december 2015
2019-03-15 sysutils/bareos16-bat: Qt4 has been EOL since december 2015
2019-03-15 sysutils/bareos16-traymonitor: Qt4 has been EOL since december 2015
2019-03-15 sysutils/policykit-qt: Qt4 has been EOL since december 2015
2019-03-15 sysutils/qpxtool: Qt4 has been EOL since december 2015
2019-03-15 sysutils/qsynergy: Qt4 has been EOL since december 2015
2019-03-15 sysutils/qzeitgeist: Qt4 has been EOL since december 2015
2019-03-15 sysutils/searchmonkey: Qt4 has been EOL since december 2015
2019-03-15 sysutils/unetbootin: Qt4 has been EOL since december 2015
2019-03-15 textproc/beediff: Qt4 has been EOL since december 2015
2019-03-15 textproc/dixit: Qt4 has been EOL since december 2015
2019-03-15 textproc/goldendict: Qt4 has been EOL since december 2015
2019-03-15 textproc/ibus-qt: Qt4 has been EOL since december 2015
2019-03-15 textproc/py-qt4-xml: Qt4 has been EOL since december 2015
2019-03-15 textproc/py-qt4-xmlpatterns: Qt4 has been EOL since december 2015
2019-03-15 textproc/qt4-clucene: Qt4 has been EOL since december 2015
2019-03-15 textproc/qt4-xml: Qt4 has been EOL since december 2015
2019-03-15 textproc/qt4-xmlpatterns: Qt4 has been EOL since december 2015
2019-03-15 textproc/qt4-xmlpatterns-tool: Qt4 has been EOL since december 2015
2019-03-15 textproc/scim-bridge-qt4: Qt4 has been EOL since december 2015
2019-03-15 textproc/uim-qt4: Qt4 has been EOL since december 2015
2019-03-15 textproc/xxdiff: Qt4 has been EOL since december 2015
2019-03-15 www/aria2fe: Qt4 has been EOL since december 2015
2019-03-15 www/cutycapt: Qt4 has been EOL since december 2015
2019-03-15 www/py-qt4-webkit: Qt4 has been EOL since december 2015
2019-03-15 www/qt4-webkit: Qt4 has been EOL since december 2015
2019-03-15 www/qupzilla-qt4: Qt4 has been EOL since december 2015
2019-03-15 x11/leechcraft: Qt4 has been EOL since december 2015
2019-03-15 x11/py-qt4-opengl: Qt4 has been EOL since december 2015
2019-03-15 x11/qimageblitz: Qt4 has been EOL since december 2015
2019-03-15 x11/qt4-graphicssystems-opengl: Qt4 has been EOL since december 2015
2019-03-15 x11/qt4-inputmethods: Qt4 has been EOL since december 2015
2019-03-15 x11/qxkb: Qt4 has been EOL since december 2015
2019-03-15 x11-fonts/fontmatrix: Qt4 has been EOL since december 2015
2019-03-15 x11-themes/qt4-style-float: Qt4 has been EOL since december 2015
2019-03-15 x11-themes/qt4-style-phase: Qt4 has been EOL since december 2015
2019-03-15 x11-themes/qt4-style-quantumstyle: Qt4 has been EOL since december 2015
2019-03-15 x11-themes/qtcurve-qt4: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/attica: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/py-qt4-gui: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/qt4-declarative: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/qt4-gui: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/qt4pas: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/qwt5: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/qwt5-designerplugin: Qt4 has been EOL since december 2015
2019-03-15 x11-toolkits/soqt: Qt4 has been EOL since december 2015
2019-03-15 x11-wm/qlwm: Qt4 has been EOL since december 2015
Approved by: portmgr (implicit)
In file included from FileReader.cpp:1:
In file included from /usr/include/c++/v1/iostream:38:
In file included from /usr/include/c++/v1/ios:216:
In file included from /usr/include/c++/v1/__locale:15:
In file included from /usr/include/c++/v1/string:505:
In file included from /usr/include/c++/v1/string_view:176:
In file included from /usr/include/c++/v1/__string:57:
In file included from /usr/include/c++/v1/algorithm:640:
In file included from /usr/include/c++/v1/initializer_list:47:
In file included from /usr/include/c++/v1/cstddef:38:
../../../utils//gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^
PR: 236192
Approved by: portmgr blanket
Upstream changes as described by the author:
- mcmctree: I have added an option (duplication = 1) for dating a tree with
both speciations and gene duplications, so that some nodes on the tree
share divergence times. Nodes sharing ages are identified using labels in
the tree file: #1, #2, .... I have yet to update the document about
specification of the model.
- mcmctree: The TipDate option was written for one locus or partition and
never worked for more than two loci/partitions. I have edited the code so
that it works for multiple partitions, some of which may be molecular and
the others morphological.
- codeml: The option estFreq = 0 when codonFreq = 6 (FMutSel0) and 7
(FMutSel) is not working in versions 4.9g and 4.9h. This is fixed now. This
option uses the observed codon or amino acid frequencies for the
mutation-selection models of codon usage. Instead the program estimates the
frequencies using maximum likeihood, which is what the option estFreq = 1
does. Look at the README file in the examples/mtCDNAape/ folder.
- codeml clade model D: The bounds for the w (dN/dS) ratios in the first
site classes are set tp (0.0001, 0.5) for w0 and (0.5, 1.5) for w1, in
versions 4.9b,c,d,e,f,g, since I added the BEB calculation for clade model
D in 4.9b. The motivation for the bounds is that site class 0 represents
strong purifying selection with a small w0, while site class 1 should
include sites under weak purifying selection with a larger w1. However the
bounds are arbitrary. In some datasets, the MLEs are found to be at the
bounds, making the interpretation awkward. I have changed the bounds to the
following: w0b[]={0.0001, 1.0}, w1b[]={0.01, 1.5}. This means that the user
should swap the estimates of w0 and w2 if w0 > w1.
Bio::Cluster is the BioPerl cluster modules. Classes and modules here describe
the basic structure for a cluster of BioPerl objects.
WWW: https://metacpan.org/release/Bio-Cluster
* Bump the LLVM revision used for GNUstep to 7, the minimum to support
the new ABI.
* GNUstep-back does not work with lld, so mark it to use Gold (BFD LD
doesn't seem able to link Objective-C things).
* Turn off some annoying debug logs in GNUstep back, which generate
several messages per second when you move the mouse. These should
never have been enabled in a release build anyway.
* Downgrade Cenon to 4.0.2. This was the last version to actually work
with GNUstep (the later ones use XCode >= 5 .xib files, which GNUstep
can't parse).
* Update gorm to git head. The current release doesn't work with the
new Objective-C ABI, but -head has the patches to fix it.
* Update PikoPixel and add it to the gnustep-app meta-package.
* Update the three core GNUstep packages to the latest release.
* Update gnumail and pantomime to the latest release and fix a linking
error with the new ABI.
* Update GNUstep FTP to the latest version.
Reviewed by: bapt (previous version)
a symbol matches multiple clauses the last one takes precedence. If the
catch-all is last it captures everything. In the case of Qt5 libraries
this caused all symbols to have a Qt_5 label while some should have
Qt_5_PRIVATE_API. This only affects lld because GNU ld always gives the
catch-all lowest priority.
Older versions of Qt5Webengine exported some memory allocation symbols from
the bundled Chromium. Version 5.9 stopped exporting these [1] but the
symbols were kept as weak wrappers for the standard allocation functions to
maintain binary compatibility. [2][3] The problem is that the call to the
standard function in these weak wrappers is only resolved to the standard
function if there's a call to this standard function in other parts of
Qt5Webengine, because only then is there a non-weak symbol that takes
precedence over the weak one. If there's no such non-weak symbol the call
in the weak wrapper resolves to the weak wrapper itself creating an infinite
call loop that overflows the stack and causes a crash. Some of the
allocation functions are variants of C++ new and delete and it probably
depends on the compiler whether these variants are used in other parts of
Qt5Webengine.
Remove the weak wrappers (make them Linux specific). This isn't binary
compatible but we are already breaking that with the changes to the symbol
versions.
[1] 5c2cbfccf9
[2] 2ed5054e3a
[3] 009f5ebb4b
Bump all ports that depend on Qt5.
PR: 234070
Exp-run by: antoine
Approved by: kde (adridg)
Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".
I tried to only set insource where explictely needed.
PR: 232038
Exp-run by: antoine
Also:
- update license since upstream changed to GPLv3
- only build/package for amd64, since it is untested on other architectures
and currently does not build on i386
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.23
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
While here, chase some KDE4 ports and functionality, these are scheduled for
removal on 2018-12-31. Change the default option/flavor to QT5 where applicable
or use alternative toolkits like GTK.
Submitted by: tcberner
Reviewed by: adridg, jhale, rene, tcberner
Approved by: portmgr (implicit, flavor hook)
Differential Revision: https://reviews.freebsd.org/D17741
Port changes:
* Take maintainership
* Add to LIB_DEPENDS and USExx
* Remove lists of executables and manpages, use file listing instead (*)
* Update WWW
Port changes:
* Take maintainership
* Implement the 'benchmarks' target, and stop installing benchmarks
* Add USES=gmake
* Update license
* Change MASTER_SITES and WWW to https
* Silence some commands
Report.cpp:208:12: error: invalid operands to binary expression ('std::ostream' (aka 'basic_ostream<char>') and 'const std::__1::ostream' (aka 'const basic_ostream<char>'))
*myStream << a;
~~~~~~~~~ ^ ~
/usr/include/c++/v1/ostream:218:20: note: candidate function not viable: no known conversion from 'const std::__1::ostream' (aka 'const basic_ostream<char>') to 'const void *' for 1st argument; take the address of the argument with &
basic_ostream& operator<<(const void* __p);
^
... and so on ...
http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/protomol-2.0.3_13.log
In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp:41:
In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLDocument.h:298:
In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLTransforms.h:48:
In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/FunctionDefinition.h:129:
In file included from /wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBO.h:207:
/usr/include/c++/v1/map:629:15: error: object of type 'std::__1::pair<std::__1::pair<const std::__1::basic_string<char>, int>, FormulaUnitsData *>' cannot be assigned because its copy assignment operator is implicitly deleted
{__nc = __v.__cc; return *this;}
^
http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/libsbml-5.17.0.log
avida-core/source/main/cPopulation.cc:2916:20: error: no matching member function for call to 'push_back'
track_founders.push_back(make_pair(organism->GetBioGroup("genotype")->GetID(), new_genome.AsString()));
~~~~~~~~~~~~~~~^~~~~~~~~
/usr/include/c++/v1/vector:688:36: note: candidate function not viable: no known conversion from 'pair<[...], typename __make_pair_return<cString>::type>' to 'const pair<[...], std::__1::basic_string<char>>' for 1st argument
_LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
^
/usr/include/c++/v1/vector:691:36: note: candidate function not viable: no known conversion from 'pair<[...], typename __make_pair_return<cString>::type>' to 'pair<[...], std::__1::basic_string<char>>' for 1st argument
_LIBCPP_INLINE_VISIBILITY void push_back(value_type&& __x);
^
http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/avida-2.12.4.log
libs/tcmalloc-1.4/src/sysinfo.cc:832:88: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
"%08"PRIx64"-%08"PRIx64" %c%c%c%c %08"PRIx64" %02x:%02x %-11"PRId64" %s\n",
^
src/tools/mathx.cpp:781:12: error: no matching function for call to 'make_pair'
return std::make_pair<DoubleVec1d, DoubleVec2d>(eigvals, eigvecs);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/v1/utility:639:1: note: candidate function not viable: no known conversion from 'DoubleVec1d' (aka 'vector<double>') to 'std::__1::vector<double, std::__1::allocator<double> > &&' for 1st argument
make_pair(_T1&& __t1, _T2&& __t2)
^
http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/lamarc-2.1.8_1,1.log
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
Jonatan lacks the time to maintain the port. Thank you for your help so
far, and you're welcome back any time.
Approved by: onatan@gmail.com (maintainer)
From now on, ports that depend on Qt4 will have to set
USES= qt:4
USE_QT= foo bar
ports depending on Qt5 will use
USES= qt:5
USE_QT= foo bar
PR: 229225
Exp-run by: antoine
Reviewed by: mat
Approved by: portmgr (antoine)
Differential Revision: →https://reviews.freebsd.org/D15540
Port changes:
* Take maintainership
* Change to github
* Change to DISTVERSION
* Add LICENSE
* Depends on bash
* Add USES=gmake
* Remove NO_BUILD: needs to build jars from java files
* Update the post-extract target
* Change do-install to do minimal installation
* Update WWW
2018-06-06 biology/ssaha: Broken for more than 6 months
2018-06-06 biology/crux: Broken for more than 6 months
2018-06-06 biology/ariadne: Broken for more than 6 months
2018-06-06 cad/sceptre: Broken for more than 6 months
2018-06-06 cad/cider: Broken for more than 6 months
2018-06-06 chinese/scim-array: Broken for more than 6 months
2018-06-06 chinese/xpdf: Broken for more than 6 months
2018-06-06 chinese/telnet: Broken for more than 6 months
2018-06-06 comms/java-commapi-freebsd: Depends on BROKEN and expiring comms/java-commapi
2018-06-06 comms/soundmodem: Broken for more than 6 months
2018-06-06 comms/jsdr: Broken for more than 6 months
2018-06-06 comms/java-commapi: Broken for more than 6 months
2018-06-06 converters/pdf2djvu: Broken for more than 6 months
2018-06-06 databases/rdb: Broken for more than 6 months
2018-06-06 databases/animenfo-client: Broken for more than 6 months
2018-06-06 databases/ruby-mysql: Broken for more than 6 months
2018-06-06 databases/riak: Broken for more than 6 months
2018-06-06 databases/animenfo-client-gtk: Broken for more than 6 months
2018-06-06 databases/rdfdb: Broken for more than 6 months
2018-06-06 databases/riak2: Broken for more than 6 months
2018-06-06 devel/subversion-static: Broken for more than 6 months
2018-06-06 japanese/xgate: Broken for more than 6 months
2018-06-06 textproc/opengrm-ngram: Broken for more than 6 months
2018-06-06 textproc/ocaml-tyxml: Depends on BROKEN and expiring www/ocaml-net
2018-06-06 www/ocaml-net: Broken for more than 6 months
2018-06-06 audio/linux-genpuid: Broken for more than 6 months
2018-06-06 x11/enventor: Broken for more than 6 months
2018-06-06 audio/xmms-timidity: Broken for more than 6 months
2018-06-06 audio/kaudiocreator: Broken for more than 6 months
2018-06-06 audio/jxm: Depends on BROKEN and expiring comms/java-commapi
2018-06-06 audio/deforaos-mixer: Broken for more than 6 months
2018-06-06 audio/gkrellmss2: Broken for more than 6 months
2018-06-06 audio/ogg2mp3: Broken for more than 6 months
2018-06-06 audio/abcmidi: Broken for more than 6 months
2018-06-06 benchmarks/netpipe: Broken for more than 6 months
2018-06-06 biology/plink: Broken for more than 6 months
Infernal is a tool for searching DNA sequence database for RNA
structure and sequence similarities. The Rfam database of RNA
families is based on Infernal, and we can search DNA sequences for
structural homologs of Rfam families.
WWW: http://eddylab.org/infernal/
PR: 228776
Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp>
On the clang architectures, these changes have no effect: the baser
compiler already includes the needed features.
While here, remove now-redundant CXXFLAGS statements and pet portlint
(no other content change).
Tested on both powerpc64 and amd64.
Approved by: portmgr (tier-2 blanket)
_tmp/ui/ui_Bowtie2Settings.h:189:35: error: no viable conversion from 'QLatin1String' to 'const QKeySequence'
gbarCheckBox->setShortcut(QLatin1String(""));
^~~~~~~~~~~~~~~~~
PR: 228213
Two items prevented python3 compatibility:
* Breakage of ASCII codec due to non-ascii characters in README: https://github.com/biopython/biopython/issues/1649
* The outdated dependency: print/py-reportlab1 instead of the modern version 3.X print/py-reportlab
Port changes:
* USES=python:2.7 -> USES=python
* Add pre-configure that clears the README file
* Add LICENSE/LICENSE_FILE
Testing:
* Ran the tutorial testcase http://biopython.org/DIST/docs/tutorial/Tutorial.html,
particularly pdf writing through print/py-reportlab worked fine.
Asked the upstream to clarify the acceptable dependency version: https://github.com/biopython/biopython/issues/1650
Approved by: portmgr blanket (unbreak for python3; add license)
Port Changes:
- Add EXAMPLES option and install most files under EXAMPLESDIR
- Add USES=dos2unix to fix DOS line endings
Upstream Changes:
Version 4.9h, March 2018
(*) mcmctree: gamma-Dirichlet versus conditional i.i.d. priors for
rates for loci. Since 4.9d, the program and the documentation are
inconsistent about the two priors, and which value (0 or 1) means
which prior. I have now checked the program and the documentation to
make sure that they are consistent:
prior = 0: gamma-Dirichlet (dos Reis 2014). This is the default.
prior = 1: conditional i.i.d. prior (Zhu et al. 2015).
I believe these two are similar especially if the number of loci
(partitions) is large, but no serious comparisons between the two
priors have been published.
Thanks to Adnan Moussalli for pointing out the errors.
(*) codeml. It was discovered that the mechanistic amino acid
substitution model implemented in Yang et al. (1998; see table 3),
specified by seqtype = 2 model = 6, has been broken for a long time,
since version 3.0 (2000) at least. Version 2.0 (1999) seems to be
correct. This means that the model become broken soon since it was
published. I have now fixed this.
This model of amino acid substitution starts from a Markov chain for
codons and then aggregate the states and merge the synonymous codons
into one state (the coded amino acid). This is an approximate
formulation since the process after state aggregation is not Markovian
anymore.
I have now added another codon-based amino acid substitution model
that treats amino acids as ambiguities codons. The model is specified
by seqtype = 2 model = 5. This is an exact formulation.
(*) codeml. The number of categories in the BEB calculation under M2
and M8 is unintentionally set to 4 rather than 10. I have changed
this back to 10. The details of this calculation are in Yang et
al. 2005 MBE.
Version 4.9g, December 2017
(*) codeml. A bug caused the BEB calculation under the site model M8
(NSsites = 8) to be incorrect, with the program printing out warming
messages like "strange: f[ 5] = -0.0587063 very small." This bug was
introduced in version 4.9b and affects versions 4.9b-f. A different
bug was introduced in version 4.9f that causes the log likelihood
function under the site model M8 (NSsites = 8) to be calculated
incorrectly. These are now fixed.
Version 4.9f, October 2017
(*) baseml, nonhomogeneous models (nhomo & fix_kappa). Those models
allow different branches on the tree to have different Q matrices.
Roughly nhomo controls the base frequency parameters while gix_kappa
controls kappa or the exchangeability parameters (a b c d e in
GTR/REV, for example). I added the option (nhomo = 5, fix_kappa = 2),
which lets the user to define branch types, so that branches of the
same type have the same exchangeability parameters (a b c d e for GTR)
and base composition parameters, while branches of different types
have different parameters. Branch types are labeled (using # and $),
0, 1, 2, .... The labels should be consecutive positive integers.
The old options nhomo = 3 or 4 work for some models like GTR, but not
some other models which also have base composition parameters. In
this update, I think those options should work with all those models.
I have also edited the documentation (look for option variable nhomo
for baseml).
(*) baseml & codeml. i added an option fix_blength = 3
(proportional), which means that branch lengths will be proporational
to those given in the tree file, and the proportionality factor is
estimated by ML.
(*) codeml. The program does not count the parameters correctly for
model M0 when fix_kappa = 1. The bug was introduced in version 4.9c
and affects versions 4.9c-e. This is now fixed.
(*) codeml (seqtype = 2 model = 2). If you are analyzing multiple
protein data sets (ndata > 1) under the empirical models such as wag,
jtt, dayhoff. The results for the first data set are correct, but all
later data sets are analyzed incorrectly under the corresponding +F
models, that is, wag+F, jtt+F, dayhoff+F, etc. A bug in the program
means that for the second and later data sets, the equilibrium amino
acid frequencies are taken from the real data and not correctly set to
those specified by the empirical models. I note that this bug was
recorded in the update Version 3.14b, April 2005, but it was somehow
not fixed, even in that version. This is now fixed. Thanks to Nick
Goldman for reporting this again.
(*) evolver (options 5, 6, 7 for simulating nucleotide, codon and
amino acid alignments). If you choose the option of printing out the
site pattern counts instead of the sequences (specified at the
beginning of the control file such as MCbase.dat), and if you are
simulating two or more alignments, the program crashes after finishing
the first alignment. This is now fixed.
(*) mcmctree. The program crashes if you have a mixture of
morphological loci and molecular loci, if not all the morphological
loci are before the molecular loci. I have now fixed this.
I think this was never described anyway.
Version 4.9e, March 2017
(*) Edited the readme files to change the license to GPL.
(*) mcmctree. A bug was introduced in version 4.9b which causes the
program to read the fossil calibration information in the tree file
incorrectly, if joint (minimum and maximum) bounds are specified using
the symbol '<' and '>'. If you use the notation "B()", "L()", and
'U()', the information is read correctly. This bug was introduced in
version 4.9b and exists in 4.9c and 4.9d. Versions 4.9a and earlier
were correct.
Version 4.9d, February 2017
(*) mcmctree. Changed the default prior for rates for loci to
gamma-Dirichlet (dos Reis 2014), and updated the documentation as
well. It was set to the conditional i.i.d. prior (Zhu et al. 2015).
(*) mcmctree. Added Bayes factor calculation. A program called
BFdriver is included in the release, as well as a pdf document in the
folder examples/DatingSoftBound/BFdriverDOC.pdf. We suggest that you
use the exact likelihood calculation when you use this option, since the
normal approximation is unreliable when the power posterior is close to
the prior (when beta is small).
