- 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)
