Adjusted for ports rescued since r534032
2020-05-05 audio/festvox-czech: Broken for more than 6 months
2020-05-05 audio/gkrellmvolume2: Broken for more than 6 months
2020-05-05 audio/mixmos: Broken for more than 6 months
2020-05-05 audio/mma: Broken for more than 6 months
2020-05-05 audio/pd-cyclone: Broken for more than 6 months
2020-05-05 audio/shorten: Broken for more than 6 months
2020-05-05 audio/taglib-sharp: Broken for more than 6 months
2020-05-05 audio/xhippo: Broken for more than 6 months
2020-05-05 biology/consed: Broken for more than 6 months
2020-05-05 biology/plinkseq: Broken for more than 6 months
2020-05-05 biology/seqtools: Broken for more than 6 months
2020-05-05 biology/t_coffee: Broken for more than 6 months
2020-05-05 biology/ugene: Broken for more than 6 months
2020-05-05 comms/ath3k-firmware: Broken for more than 6 months
2020-05-05 comms/geoid: Broken for more than 6 months
2020-05-05 comms/jerm: Broken for more than 6 months
2020-05-05 comms/yaac: Broken for more than 6 months
2020-05-05 converters/dumpasn1: Broken for more than 6 months
2020-05-05 databases/elixir-exredis: Broken for more than 6 months
2020-05-05 databases/hamsterdb: Broken for more than 6 months
2020-05-05 databases/memcacheq: Broken for more than 6 months
2020-05-05 databases/mysql++1: Broken for more than 6 months
2020-05-05 databases/mysql++3: Broken for more than 6 months
2020-05-05 databases/mysql2odbc: Broken for more than 6 months
2020-05-05 databases/mysqlidxchk: Broken for more than 6 months
2020-05-05 databases/p5-DBIx-Ease: Broken for more than 6 months
2020-05-05 databases/p5-DMOZ-ParseRDF: Broken for more than 6 months
2020-05-05 databases/pear-DoctrineORM: Broken for more than 6 months
2020-05-05 databases/pear-MDB2_Driver_mysql: Broken for more than 6 months
2020-05-05 databases/pear-Structures_DataGrid_DataSource_DBQuery: Broken for more than 6 months
2020-05-05 databases/pear-Structures_DataGrid_DataSource_DBTable: Broken for more than 6 months
2020-05-05 databases/pear-Structures_DataGrid_DataSource_DataObject: Broken for more than 6 months
2020-05-05 databases/pear-Structures_DataGrid_DataSource_MDB2: Broken for more than 6 months
2020-05-05 databases/pgagent: Broken for more than 6 months
2020-05-05 databases/useracc: Broken for more than 6 months
2020-05-05 deskutils/devd-notifier: Broken for more than 6 months
2020-05-05 deskutils/sugarcrm: Broken for more than 6 months
2020-05-05 deskutils/tine20: Broken for more than 6 months
2020-05-05 deskutils/tomboy-plugin-latex: Broken for more than 6 months
2020-05-05 deskutils/tomboy-plugin-todo: Broken for more than 6 months
2020-05-05 deskutils/wyrd: Broken for more than 6 months
2020-05-05 deskutils/xrolo: 64-bit unsupported
2020-05-05 devel/autodist: Broken for more than 6 months
2020-05-05 devel/bouml-doc: Broken for more than 6 months
2020-05-05 devel/cobf: Broken for more than 6 months
2020-05-05 devel/djgpp-crx: Broken for more than 6 months
2020-05-05 devel/elfrc: Broken for more than 6 months
2020-05-05 devel/frink: Broken for more than 6 months
2020-05-05 devel/gogland-eap: Broken for more than 6 months
2020-05-05 devel/hive: Broken for more than 6 months
2020-04-01 devel/hs-bytestring-nums: No releases since 2012
2020-05-05 devel/iz: Broken for more than 6 months
2020-05-05 devel/jfrog-cli: Broken for more than 6 months
2020-05-05 devel/libcfg: Broken for more than 6 months
2020-05-05 devel/libdispatch: Broken for more than 6 months
2020-05-05 devel/libjson++: Broken for more than 6 months
2020-05-05 devel/libmonetra: Broken for more than 6 months
2020-05-05 devel/libol: Broken for more than 6 months
2020-05-05 devel/libserver: Broken for more than 6 months
2020-05-05 devel/lua-MessagePack: Broken for more than 6 months
2020-05-05 devel/mercurialeclipse: Broken for more than 6 months
2020-05-05 devel/mime: Broken for more than 6 months
2020-05-05 devel/motor: Broken for more than 6 months
2020-05-05 devel/mq4cpp: Broken for more than 6 months
2020-05-05 devel/myrepos: Broken for more than 6 months
2020-05-05 devel/notify-sharp: Broken for more than 6 months
2020-05-05 devel/oozie: Broken for more than 6 months
2020-05-05 devel/p5-Cdk: Broken for more than 6 months
2020-05-05 devel/p5-Data-Average: Broken for more than 6 months
2020-05-05 devel/p5-Range-String: Broken for more than 6 months
2020-05-05 devel/p5-Shape: Broken for more than 6 months
2020-05-05 devel/pear-PHP_CodeBrowser: Broken for more than 6 months
2020-05-05 devel/pear-PHP_Depend: Broken for more than 6 months
2020-05-05 devel/pear-PHP_PMD: Broken for more than 6 months
2020-05-05 devel/pear-TheSeer_phpDox: Broken for more than 6 months
2020-05-05 devel/picp: Broken for more than 6 months
2020-05-05 devel/pig: Broken for more than 6 months
2020-05-05 devel/pty: Broken for more than 6 months
2020-05-05 devel/py-libiocage: Broken for more than 6 months
2020-05-05 devel/py-lock_file: Broken for more than 6 months
2020-05-05 devel/py-pyev: Broken for more than 6 months
2020-05-05 devel/rpm-spec-mode.el: Broken for more than 6 months
2020-05-05 devel/simple_components: Broken for more than 6 months
2020-05-05 devel/tcloo: Tcl/Tk 8.5 is nearing EOL, please consider porting to Tcl/Tk 8.6
2020-05-05 devel/tkmerge: Broken for more than 6 months
2020-05-05 devel/toh: Broken for more than 6 months
2020-05-05 devel/visualparadigm: Broken for more than 6 months
2020-05-05 dns/autotrust: Broken for more than 6 months
2020-05-05 dns/gdnsd: Broken for more than 6 months
2020-05-05 dns/p5-Stanford-DNSserver: Broken for more than 6 months
2020-05-05 dns/zonecheck: Broken for more than 6 months
2020-05-05 editors/omegaT: Broken for more than 6 months
2020-05-05 finance/cbb: Broken for more than 6 months
2020-05-05 ftp/llnlxdir: Broken for more than 6 months
2020-05-05 ftp/llnlxftp: Broken for more than 6 months
2020-05-05 games/adom: Broken for more than 6 months
2020-05-05 games/bsdrain: Broken for more than 6 months
2020-05-05 games/bunnysay: Broken for more than 6 months
2020-05-05 games/castlevox: Broken for more than 6 months
2020-05-05 games/gnarr: Broken for more than 6 months
2020-05-05 games/hohlin: Broken for more than 6 months
2020-05-05 games/hoichess: Broken for more than 6 months
2020-05-05 games/kajaani-kombat: Broken for more than 6 months
2020-05-05 games/linux-enemyterritory-jaymod-21: Broken for more than 6 months
2020-05-05 games/linux-enemyterritory-omni-bot: Broken for more than 6 months
2020-05-05 games/linux-enemyterritory-omni-bot-0660: Broken for more than 6 months
2020-05-05 games/nadar: Broken for more than 6 months
2020-05-05 games/nxengine: Broken for more than 6 months
2020-05-05 games/oneko: Broken for more than 6 months
2020-05-05 games/seahaven: Broken for more than 6 months
2020-05-05 games/sudoku_solver: Broken for more than 6 months
2020-05-05 games/tetrons: Broken for more than 6 months
2020-05-05 games/xpenguins: Broken for more than 6 months
2020-05-05 games/xvmahjongg: 64-bit unsupported
2020-05-05 games/xvmines: 64-bit unsupported
2020-05-05 graphics/EZWGL: Broken for more than 6 months
2020-05-05 graphics/kix-kmod: Broken for more than 6 months
2020-05-05 graphics/mhgui: Broken for more than 6 months
2020-05-05 graphics/mmrecover: Broken for more than 6 months
2020-05-05 hungarian/hu-phone: Broken for more than 6 months
2020-05-05 hungarian/hu-zipcodes: Broken for more than 6 months
2020-05-05 irc/charybdis: Broken for more than 6 months
2020-05-05 irc/fisg: Broken for more than 6 months
2020-05-05 irc/ircd-ru: Broken for more than 6 months
2020-05-05 irc/ircservices: Broken for more than 6 months
2020-05-05 irc/nethirc: Broken for more than 6 months
2020-05-05 irc/ratbox-services: Broken for more than 6 months
2020-05-05 irc/roxirc: Broken for more than 6 months
2020-05-05 japanese/jstrings: Broken for more than 6 months
2020-05-05 japanese/mg: Broken for more than 6 months
2020-05-05 japanese/ming: Broken for more than 6 months
2020-05-05 japanese/t2ps: Broken for more than 6 months
2020-05-05 java/castor: Broken for more than 6 months
2020-05-05 java/eclipse-windowbuilder: Broken for more than 6 months
2020-05-05 java/jdbcpool: Broken for more than 6 months
2020-05-05 java/jomp: Broken for more than 6 months
2020-05-05 java/langspec: Broken for more than 6 months
2020-05-05 java/xdoclet: Broken for more than 6 months
2020-05-05 korean/xpdf: Broken for more than 6 months
2020-05-05 lang/afnix: Broken for more than 6 months
2020-05-05 lang/elan: Broken for more than 6 months
2020-05-05 lang/gnatcross-aarch64: Broken for more than 6 months
2020-05-05 lang/hope: Broken for more than 6 months
2020-05-05 lang/hugs: Broken for more than 6 months
2020-05-05 lang/ici: Broken for more than 6 months
2020-05-05 lang/icon: Broken for more than 6 months
2020-05-05 lang/newlisp-devel: Broken for more than 6 months
2020-05-05 lang/ohugs: Broken for more than 6 months
2020-05-05 lang/opendylan: Broken for more than 6 months
2020-05-05 lang/phc: Broken for more than 6 months
2020-05-05 lang/starlogo: Broken for more than 6 months
2020-05-05 lang/yap: Broken for more than 6 months
2020-05-05 lang/yap-devel: Broken for more than 6 months
2020-05-05 mail/chk4mail: Broken for more than 6 months
2020-05-05 mail/librfc822: Broken for more than 6 months
2020-05-05 mail/mailmgr: Broken for more than 6 months
2020-05-05 mail/mreport: Broken for more than 6 months
2020-05-05 mail/msgconvert: Broken for more than 6 months
2020-05-05 mail/nullpop: Broken for more than 6 months
2020-05-05 mail/p5-Mail-MailStats: Broken for more than 6 months
2020-05-05 mail/poppassd: Broken for more than 6 months
2020-05-05 mail/prayer: Broken for more than 6 months
2020-05-05 mail/py-cyruslib: Broken for more than 6 months
2020-05-05 mail/qmail-auditor: Broken for more than 6 months
2020-05-05 mail/qmailmrtg7: Broken for more than 6 months
2020-05-05 mail/qmqtool: Broken for more than 6 months
2020-05-05 mail/relaydb: Broken for more than 6 months
2020-05-05 mail/rftp: Broken for more than 6 months
2020-05-05 mail/smtp-gated: Broken for more than 6 months
2020-05-05 mail/spamoracle: Broken for more than 6 months
2020-05-05 math/calctool: 64-bit unsupported
2020-05-05 math/diehard: Broken for more than 6 months
2020-05-05 math/e: Broken for more than 6 months
2020-05-05 math/entropy: Broken for more than 6 months
2020-05-05 math/liblbfgs: Broken for more than 6 months
2020-05-05 math/libtsnnls: Broken for more than 6 months
2020-05-05 math/ltl: Broken for more than 6 months
2020-05-05 math/naturalmath: Broken for more than 6 months
2020-05-05 math/proofgeneral: Broken for more than 6 months
2020-05-05 math/py-basemap-data: Broken for more than 6 months
2020-05-05 math/py-igakit: Broken for more than 6 months
2020-05-05 math/py-rapi: Broken for more than 6 months
2020-05-05 math/sfst: Broken for more than 6 months
2020-05-05 math/truthtable: Broken for more than 6 months
2020-05-05 math/wingz3: Broken for more than 6 months
2020-05-05 math/x12arima: Broken for more than 6 months
2020-05-05 math/xppaut: Broken for more than 6 months
2020-05-05 misc/achievo: Broken for more than 6 months
2020-05-05 misc/auto-multiple-choice: Broken for more than 6 months
2020-05-05 misc/display: Broken for more than 6 months
2020-05-05 misc/esniper: Broken for more than 6 months
2020-05-05 misc/free42-skins: Broken for more than 6 months
2020-05-05 misc/libisocodes: Broken for more than 6 months
2020-05-05 misc/loop: Broken for more than 6 months
2020-05-05 misc/p5-Norge: Broken for more than 6 months
2020-05-05 misc/pantry: Broken for more than 6 months
2020-05-05 misc/phraze: Broken for more than 6 months
2020-05-05 misc/podsleuth: Broken for more than 6 months
2020-05-05 misc/py-osd: Broken for more than 6 months
2020-05-05 misc/rfc: Broken for more than 6 months
2020-05-05 misc/spamcalc: Broken for more than 6 months
2020-05-05 misc/us-zipcodes: Broken for more than 6 months
2020-05-05 misc/xtypo: Broken for more than 6 months
2020-05-05 misc/yaunc: Broken for more than 6 months
2020-05-05 multimedia/clipgrab: Broken for more than 6 months
2020-05-05 multimedia/libsmacker: Broken for more than 6 months
2020-05-05 multimedia/lxdvdrip: Broken for more than 6 months
2020-05-05 multimedia/mjpg-streamer: Broken for more than 6 months
2020-05-05 multimedia/vcdpad: Broken for more than 6 months
2020-05-05 net/erlang-xmlrpc: Broken for more than 6 months
2020-05-05 net/etrace: Broken for more than 6 months
2020-05-05 net/fonulator: Broken for more than 6 months
2020-05-05 net/gkrellmwireless2: Broken for more than 6 months
2020-05-05 net/howl: Broken for more than 6 months
2020-05-05 net/libp0f: Broken for more than 6 months
2020-05-05 net/libsocket++: Broken for more than 6 months
2020-05-05 net/ltm: Broken for more than 6 months
2020-05-05 net/lvwimax: Broken for more than 6 months
2020-05-05 net/mono-zeroconf: Broken for more than 6 months
2020-05-05 net/nph: Broken for more than 6 months
2020-05-05 net/p5-Net-RawSock: Broken for more than 6 months
2020-05-05 net/passlogd: Broken for more than 6 months
2020-05-05 net/phamm: Broken for more than 6 months
2020-05-05 net/pim6-tools: Broken for more than 6 months
2020-05-05 net/pim6dd: Broken for more than 6 months
2020-05-05 net/pim6sd: Broken for more than 6 months
2020-05-05 net/proxy-connect: Broken for more than 6 months
2020-05-05 net/rtpbreak: Broken for more than 6 months
2020-05-05 net/s3ql: Broken for more than 6 months
2020-05-05 net/scnc: Broken for more than 6 months
2020-05-05 net/sip_scenario: Broken for more than 6 months
2020-05-05 net/slurm: Broken for more than 6 months
2020-05-05 net/ssmping: Broken for more than 6 months
2020-05-05 net/tcpdstat: Broken for more than 6 months
2020-05-05 net/uplog: Broken for more than 6 months
2020-05-05 net/vblade: Broken for more than 6 months
2020-05-05 net/wizd: Broken for more than 6 months
2020-05-05 net/wmnetload: Broken for more than 6 months
2020-05-05 net/wmnetmon: Broken for more than 6 months
2020-05-05 net/wmpiki: Broken for more than 6 months
2020-05-05 net/xipmsg: Broken for more than 6 months
2020-05-05 net-im/chattahoochie: Broken for more than 6 months
2020-05-05 net-im/jitsi: Broken for more than 6 months
2020-05-05 net-im/mu-conference: Broken for more than 6 months
2020-05-05 net-im/p5-Jabber-Connection: Broken for more than 6 months
2020-05-05 net-im/p5-Net-ICQ2000: Broken for more than 6 months
2020-05-05 net-im/pidgin-guifications: Broken for more than 6 months
2020-05-05 net-im/pidgin-osd: Broken for more than 6 months
2020-05-05 net-im/yoono: Broken for more than 6 months
2020-05-05 net-mgmt/arpalert: Broken for more than 6 months
2020-05-05 net-mgmt/nagios-check_memcached_paranoid: Broken for more than 6 months
2020-05-05 net-mgmt/netwox: Broken for more than 6 months
2020-05-05 net-mgmt/nstreams: Broken for more than 6 months
2020-05-05 net-mgmt/p5-GRNOC-Config: Broken for more than 6 months
2020-05-05 net-mgmt/p5-GRNOC-TL1: Broken for more than 6 months
2020-05-05 net-mgmt/scli: Broken for more than 6 months
2020-05-05 net-mgmt/snmp++: Broken for more than 6 months
2020-05-05 net-mgmt/victorops-nagios: Broken for more than 6 months
2020-05-05 net-p2p/libpdtp: Broken for more than 6 months
2020-05-05 net-p2p/squall: Broken for more than 6 months
2020-05-05 news/crashmail: Broken for more than 6 months
2020-05-05 news/sn: Broken for more than 6 months
2020-05-05 news/xrn: Broken for more than 6 months
2020-05-05 ports-mgmt/managepkg: Broken for more than 6 months
2020-05-05 portuguese/irpf-pt_BR: Broken for more than 6 months
2020-05-05 print/foxitreader: Broken for more than 6 months
2020-05-05 print/pdfcube: Broken for more than 6 months
2020-05-05 print/pmw: Broken for more than 6 months
2020-05-05 print/rprint: Broken for more than 6 months
2020-05-05 russian/p5-cyrillic: Broken for more than 6 months
2020-05-05 russian/tidyup-mail: Broken for more than 6 months
2020-05-05 science/abinit: Broken for more than 6 months
2020-05-05 science/atom: Broken for more than 6 months
2020-05-05 science/cp2k: Broken for more than 6 months
2020-05-05 science/esys-particle: Broken for more than 6 months
2020-05-05 science/openmx: Broken for more than 6 months
2020-05-05 science/p5-Geo-ReadGRIB: Broken for more than 6 months
2020-05-05 science/py-tensorflow-estimator: Broken for more than 6 months
2020-05-05 security/firewalk: Broken for more than 6 months
2020-05-05 security/hmap: Broken for more than 6 months
2020-05-05 security/ipfcount: Broken for more than 6 months
2020-05-05 security/libbf: Broken for more than 6 months
2020-05-05 security/log2timeline: Broken for more than 6 months
2020-05-05 security/opencdk: Broken for more than 6 months
2020-05-05 security/pad: Broken for more than 6 months
2020-05-05 security/pam_fprint: Broken for more than 6 months
2020-05-05 security/pam_per_user: Broken for more than 6 months
2020-05-05 security/razorback-dispatcher: Broken for more than 6 months
2020-05-05 security/ruby-camellia: Broken for more than 6 months
2020-05-05 security/scanhill: Broken for more than 6 months
2020-05-05 security/sinfp: Broken for more than 6 months
2020-05-05 security/ssh_askpass_gtk2: Broken for more than 6 months
2020-05-05 security/subweb: Broken for more than 6 months
2020-05-05 security/unssh: Broken for more than 6 months
2020-05-05 security/xspy: Broken for more than 6 months
2020-05-05 shells/osh: Broken for more than 6 months
2020-05-05 shells/shell-include: Broken for more than 6 months
2020-05-05 sysutils/abgx360gui: Broken for more than 6 months
2020-05-05 sysutils/autojump: Broken for more than 6 months
2020-05-05 sysutils/backupchecker: Broken for more than 6 months
2020-05-05 sysutils/cdf: Broken for more than 6 months
2020-05-05 sysutils/cdls: Broken for more than 6 months
2020-05-05 sysutils/circonus-agent: Broken for more than 6 months
2020-05-05 sysutils/cloop-utils: Broken for more than 6 months
2020-05-05 sysutils/confman: Broken for more than 6 months
2020-05-05 sysutils/detach: Broken for more than 6 months
2020-05-05 sysutils/disktool: 64-bit unsupported
2020-05-05 sysutils/downtime: Broken for more than 6 months
2020-05-05 sysutils/fusefs-fusexmp_fh: Broken for more than 6 months
2020-05-05 sysutils/fusefs-gunzip: Broken for more than 6 months
2020-05-05 sysutils/goss: Broken for more than 6 months
2020-05-05 sysutils/gpte: Broken for more than 6 months
2020-05-05 sysutils/hidesvn: Broken for more than 6 months
2020-05-05 sysutils/hoz: Broken for more than 6 months
2020-05-05 sysutils/intel-qcu: Broken for more than 6 months
2020-05-05 sysutils/iogen: Broken for more than 6 months
2020-05-05 sysutils/jailctl: Broken for more than 6 months
2020-05-05 sysutils/jx: Broken for more than 6 months
2020-05-05 sysutils/linux-crashplan: Broken for more than 6 months
2020-05-05 sysutils/mkfile: Broken for more than 6 months
2020-05-05 sysutils/mpiexec: Broken for more than 6 months
2020-05-05 sysutils/nfsping: Broken for more than 6 months
2020-05-05 sysutils/phantom: Broken for more than 6 months
2020-05-05 sysutils/ptools: Broken for more than 6 months
2020-05-05 sysutils/realsync: Broken for more than 6 months
2020-05-05 sysutils/rmonitor: Broken for more than 6 months
2020-05-05 sysutils/roottail: Broken for more than 6 months
2020-05-05 sysutils/sb16config: Broken for more than 6 months
2020-05-05 sysutils/sbase: Broken for more than 6 months
2020-05-05 sysutils/setquota: Broken for more than 6 months
2020-05-05 sysutils/sortu: Broken for more than 6 months
2020-05-05 sysutils/stmpclean: Broken for more than 6 months
2020-05-05 sysutils/tmate-slave: Broken for more than 6 months
2020-05-05 sysutils/tss: Broken for more than 6 months
2020-05-05 sysutils/vstrip: Broken for more than 6 months
2020-05-05 sysutils/watchdog: Broken for more than 6 months
2020-05-05 sysutils/wmbsdbatt: Broken for more than 6 months
2020-05-05 sysutils/wmcpuload: Broken for more than 6 months
2020-05-05 sysutils/wmcube: Broken for more than 6 months
2020-05-05 sysutils/wtail: Broken for more than 6 months
2020-05-05 textproc/csv2latex: Broken for more than 6 months
2020-05-05 textproc/da-hyphen: Broken for more than 6 months
2020-05-05 textproc/glark: Broken for more than 6 months
2020-05-05 textproc/html2tex: Broken for more than 6 months
2020-05-05 textproc/htmlsection: Broken for more than 6 months
2020-05-05 textproc/kenlm: Broken for more than 6 months
2020-05-05 textproc/libguess: Broken for more than 6 months
2020-05-05 textproc/libxml++26-reference: Broken for more than 6 months
2020-05-05 textproc/no-hunspell: Broken for more than 6 months
2020-05-05 textproc/p5-MARC: Broken for more than 6 months
2020-05-05 textproc/p5-texcount: Broken for more than 6 months
2020-05-05 textproc/pcrs: Broken for more than 6 months
2020-05-05 textproc/pear-Structures_DataGrid_DataSource_RSS: Broken for more than 6 months
2020-05-05 textproc/pear-Structures_DataGrid_DataSource_XML: Broken for more than 6 months
2020-05-05 textproc/permute: Broken for more than 6 months
2020-05-05 textproc/pocketreader: Broken for more than 6 months
2020-05-05 textproc/py-sgrep: Broken for more than 6 months
2020-05-05 textproc/rss2html: Broken for more than 6 months
2020-05-05 textproc/ruby-xmlparser: Broken for more than 6 months
2020-05-05 textproc/sv-hyphen: Broken for more than 6 months
2020-05-05 textproc/tclExpat: Broken for more than 6 months
2020-05-05 textproc/tex2im: Broken for more than 6 months
2020-05-05 textproc/topic: Broken for more than 6 months
2020-05-05 textproc/uz-hunspell: Broken for more than 6 months
2020-05-05 textproc/xmlprpr: Broken for more than 6 months
2020-05-05 www/ach: Broken for more than 6 months
2020-05-05 www/apache-forrest: Broken for more than 6 months
2020-05-05 www/apercu: Broken for more than 6 months
2020-05-05 www/cblog: Broken for more than 6 months
2020-05-05 www/drood: Broken for more than 6 months
2020-05-05 www/drraw: Broken for more than 6 months
2020-05-05 www/flood: Broken for more than 6 months
2020-05-05 www/grafana2: Broken for more than 6 months
2020-05-05 www/imgsizer: Broken for more than 6 months
2020-05-05 www/jdresolve: Broken for more than 6 months
2020-05-05 www/linkcheck: Broken for more than 6 months
2020-05-05 www/madsonic-standalone: Broken for more than 6 months
2020-05-05 www/mod_auth_external2: Broken for more than 6 months
2020-05-05 www/mod_chroot: Broken for more than 6 months
2020-05-05 www/mod_cvs2: Broken for more than 6 months
2020-05-05 www/mod_domaintree: Broken for more than 6 months
2020-05-05 www/mod_encoding: Broken for more than 6 months
2020-05-05 www/mod_flickr: Broken for more than 6 months
2020-05-05 www/mod_gzip2: Broken for more than 6 months
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- Remove option for net/openmpi2 from science/pnetcdf (net/openmpi2 is deprecated and will be removed)
- Fix science/gromacs plist when MPI option is enabled
- Bump PORTREVISION for all the consumers of net/openmpi
GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate
the proportion of phenotypic variance explained by genome- or chromosome-wide
SNPs for complex traits (the GREML method), and has subsequently extended for
many other analyses to better understand the genetic architecture of complex
traits.
- Fix some whitespace issues
- Suggest the user to configure their user name and team ID. [1]
- Link to a website where statistics are updated more often.
Suggested by: netchild [1]
Special thanks to netchild for inspiring bringing back this piece software
to ports!
Reviewed by: netchild, pi, salvadore
Differential Revision: https://reviews.freebsd.org/D24127
Chase r527795 and put a deprecation notice on all openjfx8-devel
dependent ports too.
Also deprecate devel/gradle4 which is only needed to build igv and
openjfx8-devel.
Kallisto no longer builds in hdf5 by default, but it is still required
for some downstream tools like Sleuth. Forcing it ON for now, but will
disable it in a future upgrade.
Reported by: portscout
* Fix build on i386 [1]
* Fix science/code_saturne build with new openblas [2]
* Avoid installing private headers [3]
* Prevent build from optimizing for host by correcting build confg [4]
* Bump portrevision of dependent ports [5]
This is correcting issues from r523749 [1][2][4] and r515970 [3]
PR: 231371
Reported by: build cluster [1]
Reported by: Dima Pasechnik <dimpase+freebsd@gmail.com> [2]
Reported by: many [5]
Reviewed by: mat, bapt
Approved by: implicit, since this is a build fix
* Bug fix for long sequences.
* Unbreak '/dev/tty' problem during a build
* Update maintainer's mail address
PR: 243206
Submitted by: mzaki@e-mail.ne.jp (maintainer)
- Bump PORTREVISION for dependency change
The circular dependency among p5-Bio-Cluster, p5-Bio-DB-NCBIHelper, p5-Bio-Variation and this port has been resolved in p5-Bio-Variation 1.7.5 update.
Bio::DB::NCBIHelper provides a single place to setup some common methods for
querying NCBI web databases. This module just centralizes the methods for
constructing a URL for querying NCBI GenBank and NCBI GenPept and the common
HTML stripping done in postprocess_data().
WWW: https://metacpan.org/release/Bio-DB-NCBIHelper
Bio::DB::EMBL allows the dynamic retrieval of sequence objects Bio::Seq from the
EMBL database using the dbfetch script at EBI.
In order to make changes transparent we have host type (currently only ebi) and
location (defaults to ebi) separated out. This allows later additions of more
servers in different geographical locations.
The functionality of this module is inherited from Bio::DB::DBFetch which
implements Bio::DB::WebDBSeqI.
WWW: https://metacpan.org/release/Bio-DB-EMBL
Unsure why this was marked unfetchable. Fetch works fine and the port is
still useful, though it cannot be upgraded to newer releases, which are
closed-source.
java/openjdk6 support was removed from Mk/bsd.java.mk (r512662) and
java/openjdk6 and java/openjdk6-jre were removed from the ports tree
(r512663). Now this patch completely removes remaining stuff from the
ports tree.
PR: 241953 (exp-run)
Reviewed by: glewis
Approved by: portmgr (antoine)
Differential Revision: https://reviews.freebsd.org/D22342
- Remove BROKEN=. Version 4.9i became unfetchable when the author pulled
the tarball to prevent users from downloading a version with new, serious
bugs.
Upstream changes described by the author:
- mcmctree: Initial values have ages that are too old, exceeding max
bounds. In theory bounds in mcmctree are always soft so that the node
ages will move to the area of posterior mode when burnin is long enough.
In practice the poor starting values are problematic and requires long
burn-in. I have rewritten the code for generating initial values to
respect the min and max bounds specified in the fossil calibrations.
- codeml: A bug introduced in 4.9i caused the clade labels ($) to be
ignored. This affects the branch, branch-site and clade models. If
your tree has branch labels (#) only and no clade models, everything
will be fine. If you have used the clade label ($) in the tree with or
without the branch label (#), either the program will abort or the
results will be incorrect. The clade label ($) is supposed to label
all branches in the clade as well as the branch itself, but all clade
labels in the tree are ignored in 4.9i. Earlier versions are correct.
- 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
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
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.
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.
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.
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
- 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
This port can't use Altivec. Instead, it's possible to use GCC's translation layer from SSE. Adjust build flags to do it.
PR: 239645
Approved by: yuri (maintainer), tcberner (mentor)
Differential Revision: https://reviews.freebsd.org/D21160
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.
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, everything INDEX-11 shows with a dependency on lang/gcc9 now.
PR: 238330
Now it builds with gradle-5.
Improvements im Makefile to simplify the port update process, in line with some other gradle-based ports.
Reported by: repology
GCC 8 and 9 are incompatible in handling const variables with OpenMP
default(none). All const variables default to shared even with default(none)
present. 8 errors out if a const variable is explicitly defined as shared and
9 requires an explicit definition.
Using an upstream trunk patch for now, which checks the compiler version.
Also discussing more portable approaches to avoid future issues.
Reported by: jrm
GCC 9 requires OpenMP variables to be explicitly defined as shared or private
where earlier versions fell back on default. New patch sent upstream.
PR: 238471
Reported by: gerald
*** File 'Makefile.config.FreeBSD.powerpc' is missing. Please run ./configure
The configuration script may have other problems as well. This needs
to be addressed by upstream (if there is interest).
Approved by: portmgr (tier-2 blanket)
configure and Makefile.in provided in tarballs have -lstdc++ hard-coded in them.
The previous version of the port patches these to be -lc++, which still might fail on gcc systems, depending on which C++ library is used.
This change adds USES=autoreconf which makes it to regenerate configure and Makefile.in and hopefully have the proper C++ library in these files.
GNU libtool links with the C compiler, not with the C++ compiler, in this project. This is what I think triggers link failures due to a wrong C++
library getting into the link lines. GNU libtool likely chooses C compiler because this project has its 'main' functions in .c files,
but also includes C++ object modules. This likely causes GNU tools confusion and it uses the C compiler to link and fails due to wrong C++ libraries added there.
Use new GCC from ports on GCC architectures.
Merge 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5, fixes build on GCC architectures.
Also include sys/endian.h and use bswap32 and bswap64 for byte-swapping (PR at https://github.com/bcgsc/abyss/pull/287 ).
PR: 238737
Approved by: yuri (maintainer), mat (mentor)
Differential Revision: https://reviews.freebsd.org/D20717
Autoconf reports that HAVE_ASM_BSR is true (1). However, it's a false
positive.
I do not have enough knowledge of autoconf to fix this problem correctly,
so fix src/config.h in post-configure. Patches welcome.
A proper fix will most likely also fix the build on other tier-2 archs,
but I have not taken the time to test that yet.
Approved by: portmgr (tier-2 blanket)
The BOLT-LMM software package currently consists of two main algorithms, the
BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML
algorithm for variance components analysis (i.e., partitioning of
SNP-heritability and estimation of genetic correlations).
GEMMA is a software toolkit for fast application of linear mixed models (LMMs)
and related models to genome-wide association studies (GWAS) and other
large-scale data sets.
VSEARCH supports de novo and reference based chimera detection, clustering,
full-length and prefix dereplication, rereplication, reverse complementation,
masking, all-vs-all pairwise global alignment, exact and global alignment
searching, shuffling, subsampling and sorting. It also supports FASTQ file
analysis, filtering, conversion and merging of paired-end reads.
The aim of this project is to create an alternative to the USEARCH tool
developed by Robert C. Edgar (2010).
- Expire after the last version without /usr/lib/libomp.so
- Drop SOVERSION for seamless transition (i.e., avoid conditionals)
PR: 236907
Approved by: bapt (maintainer)
Differential Revision: https://reviews.freebsd.org/D19767
fastp is a tool designed to provide fast all-in-one preprocessing for FastQ
files. This tool is developed in C++ with multithreading supported to afford
high performance.
- 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
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2019-03-12 devel/physfs-devel: is the same as devel/physfs, serving no purpose
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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
