2020-09-15 audio/abraca: Uses deprecated version of python
2020-09-15 audio/ardour5: Uses deprecated version of python
2020-09-15 audio/cplay: Uses deprecated version of python
2020-09-15 audio/cpp-xmms2: Uses deprecated version of python
2020-09-15 audio/p5-xmms2: Uses deprecated version of python
2020-09-15 biology/haplohseq: Uses deprecated version of python
2020-09-15 biology/tophat: Uses deprecated version of python
2020-09-15 chinese/ibus-array: Uses deprecated version of python
2020-09-15 comms/congruity: Uses deprecated version of python
2020-09-15 comms/libbtbb: Uses deprecated version of python
2020-09-15 comms/quisk: Uses deprecated version of python
2020-09-15 databases/mtools-mongodb: Uses deprecated version of python
2020-09-15 databases/mydbf2mysql: Uses deprecated version of python
2020-09-15 databases/ntdb: Uses deprecated version of python
2020-09-15 databases/pgloader: Uses deprecated version of python
2020-09-15 databases/pgtune: Uses deprecated version of python
2020-09-15 databases/postgresql-libpqxx3: Uses deprecated version of python
2020-09-15 databases/postgresql-libpqxx4: Uses deprecated version of python
2020-09-15 databases/py-sqlite3dbm: Uses deprecated version of python
2020-09-15 databases/pydbx: Uses deprecated version of python
2020-09-15 databases/pyspatialite: Uses deprecated version of python
2020-09-15 deskutils/ljcharm: Uses deprecated version of python
2020-09-15 deskutils/mat: Uses deprecated version of python
2020-09-15 devel/aap: Uses deprecated version of python
2020-09-15 devel/apr2: Uses deprecated version of python
2020-09-15 devel/bbfreeze-loader: Uses deprecated version of python
2020-09-15 devel/bicyclerepair: Uses deprecated version of python
2020-09-15 devel/bzrtools: Uses deprecated version of python
2020-09-15 devel/codeville: Uses deprecated version of python
2020-09-15 devel/cvs2svn: Uses deprecated version of python
2020-09-15 devel/cx_Freeze: Uses deprecated version of python
2020-09-15 devel/euca2ools: Uses deprecated version of python
2020-09-15 devel/evolution-gconf-tools: Uses deprecated version of python
2020-09-15 devel/git-bzr-ng: Uses deprecated version of python
2020-09-15 devel/git-cvs: Uses deprecated version of python
2020-09-15 devel/git-remote-hg: Uses deprecated version of python
2020-09-15 devel/grumpy: Uses deprecated version of python
2020-09-15 devel/hg-git: Uses deprecated version of python
2020-09-15 devel/libnxt: Uses deprecated version of python
2020-09-15 devel/libredblack: Uses deprecated version of python
2020-09-15 devel/llvm-cheri: Uses deprecated version of python
2020-09-15 devel/phpsh: Uses deprecated version of python
2020-09-15 devel/py-backports.shutil_which: Uses deprecated version of python
2020-09-15 devel/py-notify: Uses deprecated version of python
2020-09-15 devel/py-pybloomfiltermmap: Uses deprecated version of python
2020-09-15 devel/py-qserve: Uses deprecated version of python
2020-09-15 devel/py-subvertpy: Uses deprecated version of python
2020-09-15 devel/py_static_check: Uses deprecated version of python
2020-09-15 devel/pyst: Uses deprecated version of python
2020-09-15 devel/runsnakerun: Uses deprecated version of python
2020-09-15 devel/tailor: Uses deprecated version of python
2020-09-15 devel/uatraits: Uses deprecated version of python
2020-09-15 dns/nsec3walker: Uses deprecated version of python
2020-09-15 dns/sshfp: Uses deprecated version of python
2020-09-15 editors/medit: Uses deprecated version of python
2020-09-15 emulators/dynagen: Uses deprecated version of python
2020-09-15 emulators/wxmupen64plus: Uses deprecated version of python
2020-09-15 games/diameter: Uses deprecated version of python
2020-09-15 games/kiki: Uses deprecated version of python
2020-09-15 games/lightyears: Uses deprecated version of python
2020-09-15 games/outerspace: Uses deprecated version of python
2020-09-15 games/pachi-game-engine: Uses deprecated version of python
2020-09-15 graphics/caffe: Uses deprecated version of python
2020-09-15 graphics/cloudcompare: Uses deprecated version of python
2020-09-15 graphics/kudu: Uses deprecated version of python
2020-09-15 graphics/pecomato: Uses deprecated version of python
2020-09-15 graphics/py-editobj: Uses deprecated version of python
2020-09-15 graphics/py-mayavi: Uses deprecated version of python
2020-09-15 graphics/pymorph: Uses deprecated version of python
2020-09-15 graphics/tilecache: Uses deprecated version of python
2020-09-15 graphics/uniconvertor: Uses deprecated version of python
2020-09-15 japanese/mailman: Uses deprecated version of python
2020-09-15 java/eclipse-pydev: Uses deprecated version of python
2020-09-15 lang/cdent: Uses deprecated version of python
2020-09-15 lang/julia06: Uses deprecated version of python
2020-09-15 lang/julia07: Uses deprecated version of python
2020-09-15 lang/julia11: Uses deprecated version of python
2020-09-15 lang/tinypy: Uses deprecated version of python
2020-09-15 mail/cleanup-maildir: Uses deprecated version of python
2020-09-15 mail/courier-pythonfilter: Uses deprecated version of python
2020-09-15 mail/getmail: Uses deprecated version of python
2020-09-15 mail/muttils: Uses deprecated version of python
2020-09-15 mail/nohtml: Uses deprecated version of python
2020-09-15 mail/offlineimap: Uses deprecated version of python
2020-09-15 mail/openemm2015: Uses deprecated version of python
2020-09-15 math/blitz++: Uses deprecated version of python
2020-09-15 math/openfst: Uses deprecated version of python
2020-09-15 math/py-fpconst: Uses deprecated version of python
2020-09-15 misc/hb: Uses deprecated version of python
2020-09-15 misc/mtail: Uses deprecated version of python
2020-09-15 misc/wotsap: Uses deprecated version of python
2020-09-15 multimedia/freevo: Uses deprecated version of python
2020-09-15 multimedia/quodlibet: Uses deprecated version of python
2020-09-15 multimedia/tovid: Uses deprecated version of python
2020-09-15 net/ceph13: Uses deprecated version of python
2020-09-15 net/cloud-init-azure: Uses deprecated version of python
2020-09-15 net/exabgp: Uses deprecated version of python
2020-09-15 net/exaddos: Uses deprecated version of python
2020-09-15 net/fb: Uses deprecated version of python
2020-09-15 net/flent: Uses deprecated version of python
2020-09-15 net/flowgrep: Uses deprecated version of python
2020-09-15 net/googlecl: Uses deprecated version of python
2020-09-15 net/mininet: Uses deprecated version of python
2020-09-15 net/nfs-ganesha: Uses deprecated version of python
2020-09-15 net/opensips: Uses deprecated version of python
2020-09-15 net/py-python-ntlm: Uses deprecated version of python
2020-09-15 net/splatd: Uses deprecated version of python
2020-09-15 net-im/centerim-devel: Uses deprecated version of python
2020-09-15 net-im/fugu: Uses deprecated version of python
2020-09-15 net-im/proxy65: Uses deprecated version of python
2020-09-15 net-mgmt/crmsh: Uses deprecated version of python
2020-09-15 net-mgmt/librenms-agent: Uses deprecated version of python
2020-09-15 net-p2p/couchpotato: Uses deprecated version of python
2020-09-15 news/rawdog: Uses deprecated version of python
2020-09-15 ports-mgmt/portell: Uses deprecated version of python
2020-09-15 print/biblio-py: Uses deprecated version of python
2020-09-15 science/brian: Uses deprecated version of python
2020-09-15 science/paraview: Uses deprecated version of python
2020-09-15 security/arm: Uses deprecated version of python
2020-09-15 security/ismtp: Uses deprecated version of python
2020-09-15 security/py-halberd: Uses deprecated version of python
2020-09-15 security/switzerland: Uses deprecated version of python
2020-09-15 security/tsshbatch: Uses deprecated version of python
2020-09-15 shells/lshell: Uses deprecated version of python
2020-09-15 sysutils/abck: Uses deprecated version of python
2020-09-15 sysutils/condor: Uses deprecated version of python
2020-09-15 sysutils/farbot: Uses deprecated version of python
2020-09-15 sysutils/fusefs-wikipediafs: Uses deprecated version of python
2020-09-15 sysutils/heartbeat: Uses deprecated version of python
2020-09-15 sysutils/isomd5sum: Uses deprecated version of python
2020-09-15 sysutils/py-stdiff: Uses deprecated version of python
2020-09-15 sysutils/tren: Uses deprecated version of python
2020-09-15 textproc/doclifter: Uses deprecated version of python
2020-09-15 textproc/ibus-el: Uses deprecated version of python
2020-09-15 textproc/p5-WWW-Google-SiteMap: Deprecated upstream, see textproc/p5-Search-Sitemap
2020-09-15 textproc/plover: Uses deprecated version of python
2020-09-15 textproc/py-esmre: Uses deprecated version of python
2020-09-15 textproc/py-libxslt: Uses deprecated version of python
2020-09-15 textproc/py-pdfminer: Uses deprecated version of python
2020-09-15 textproc/translate-toolkit: Uses deprecated version of python
2020-09-15 www/bluefish: Uses deprecated version of python
2020-09-15 www/calendarserver: Uses deprecated version of python
2020-09-15 www/geeknote: Uses deprecated version of python
2020-09-15 www/go-appengine-sdk: Uses deprecated version of python
2020-09-15 www/google-appengine: Uses deprecated version of python
2020-09-15 www/libhpack: Uses deprecated version of python
2020-09-15 www/mkapachepw: Uses deprecated version of python
2020-09-15 www/mod_pagespeed: Uses deprecated version of python
2020-09-15 www/mod_python35: Uses deprecated version of python
2020-09-15 www/py-qp: Uses deprecated version of python
2020-09-15 www/py-url: Uses deprecated version of python
2020-09-15 www/pyblosxom: Uses deprecated version of python
2020-09-15 www/pyjamas: Uses deprecated version of python
2020-09-15 www/roundup: Uses deprecated version of python
2020-09-15 www/varnish-libvmod-awsrest: Uses deprecated version of python
2020-09-15 www/waccess: Uses deprecated version of python
2020-09-15 www/wadcomblog: Uses deprecated version of python
2020-09-15 www/webcheck: Uses deprecated version of python
2020-09-15 www/woof: Uses deprecated version of python
2020-09-15 x11-drivers/xf86-video-qxl: uses deprecated version of python
2020-09-15 x11-fm/twander: Uses deprecated version of python
2020-09-15 x11-wm/compizconfig-python: Uses deprecated version of python
2020-09-15 x11-wm/fvwm-crystal: Uses deprecated version of python
For some reason the -deps archive had a wrong size, perhaps because it was regenerated and not uploaded.
-deps was generated by me.
Updating distinfo.
Reported by: fallout
Extend the expiration of unmaintained leaf ports that are broken with
-fno-common and previously had a short expiration date. The new date is set
to 2021-04-01, meaning the ports will be in the 2021Q2 branch, giving people
until 2021-06-30 (10 months from now) to fix issues.
Improve the wording of the deprecation message, mentioning both llvm 11 and
-fno-common.
Bump portrevision to force reinstall. This way the warning message about
deprecation will be displayed to users installing or reinstalling the
software.
MFH: 2020Q3 (maybe)
After switch to meson libp11-kit.so no longer has symbols
in the LIBP11_KIT_1.0 namespace. As a workaround, bump
PORTREVISION of consumers to get those rebuilt.
See more details in the comments of the linked PR.
PR: 248819
Reported by: John Hein
2020-08-26 audio/timidity++-tcltk: Broken for more than 6 months
2020-08-26 biology/pbcopper: Broken for more than 6 months
2020-08-26 devel/ace: Broken for more than 6 months
2020-08-26 devel/bin86: Broken for more than 6 months
2020-08-26 devel/erlang-oserl: Broken for more than 6 months
2020-08-20 emulators/qemu40: Please consider using qemu or qemu41
2020-08-26 games/linux-darwinia-demo: Broken for more than 6 months
2020-08-26 games/linux-defcon: Broken for more than 6 months
2020-08-26 games/linux-uplink-demo: Broken for more than 6 months
2020-08-26 games/xevil: Broken for more than 6 months
2020-08-26 games/xminesweep: Broken for more than 6 months
2020-08-26 graphics/backfract: Broken for more than 6 months
2020-08-26 japanese/kanjipad: Broken for more than 6 months
2020-08-26 japanese/xdtp: Broken for more than 6 months
2020-08-26 korean/hpscat: Broken for more than 6 months
2020-08-26 math/barvinok: Broken for more than 6 months
2020-08-26 math/openmesh: Broken for more than 6 months
2020-08-26 math/rehearse: Broken for more than 6 months
2020-08-26 net/hinfo: Broken for more than 6 months
2020-08-26 science/fleur: Broken for more than 6 months
2020-08-26 science/lm: Broken for more than 6 months
2020-08-26 security/ddos_scan: Broken for more than 6 months
2020-08-26 security/gag: Broken for more than 6 months
2020-08-26 security/py-keystone: Broken for more than 6 months
2020-08-26 sysutils/mono-kmod: mastersite disappeared, unfetchable
2020-08-26 x11-themes/gtk-cleanice-engine: Broken for more than 6 months
2020-08-26 x11-wm/aewm: Broken for more than 6 months
LLVM 11 switched from -fcommon to -fno-common by default. This revealed a
slight misposition of names in paml.h, which caused one symbol per enum
that's not used anywhere.
The fix just moves the names back so that the enums are named that, rather
than creating new unused symbols.
Reviewed by: zeising
Approved by: jrm (maintainer)
MFH: 2020Q3
2020-08-15 archivers/py-backports.lzma: Uses deprecated version of python
2020-08-15 archivers/py-bup: Uses deprecated version of python
2020-08-15 archivers/py-librtfcomp: Uses deprecated version of python
2020-08-15 audio/blop-lv2: Uses deprecated version of python
2020-08-15 audio/bs2b-lv2: Uses deprecated version of python
2020-08-15 audio/py-gmusicproxy: Uses deprecated version of python
2020-08-15 audio/py-karaoke: Uses deprecated version of python
2020-08-15 audio/py-openal: Uses deprecated version of python
2020-08-15 audio/py-py-jack: Uses deprecated version of python
2020-08-15 audio/py-xmms2: Uses deprecated version of python
2020-08-15 audio/triceratops-lv2: Uses deprecated version of python
2020-08-15 biology/py-biom-format: Uses deprecated version of python
2020-08-15 comms/py-bulksms: Uses deprecated version of python
2020-08-15 comms/py-gammu: Uses deprecated version of python
2020-08-15 databases/py-geoalchemy: Uses deprecated version of python
2020-08-15 databases/py-htsql-mysql: Uses deprecated version of python
2020-08-15 databases/py-htsql-pgsql: Uses deprecated version of python
2020-08-15 databases/py-mysql2pgsql: Uses deprecated version of python
2020-08-15 databases/py-oursql: Uses deprecated version of python
2020-08-15 databases/py-pyPgSQL: Uses deprecated version of python
2020-08-15 databases/py-pyhs: Uses deprecated version of python
2020-08-15 databases/py-pytc: Uses deprecated version of python
2020-08-15 databases/py-riak: Uses deprecated version of python
2020-08-15 databases/py-umemcache: Uses deprecated version of python
2020-08-15 devel/py-Breve: Uses deprecated version of python
2020-08-15 devel/py-PyODE: Uses deprecated version of python
2020-08-15 devel/py-akismet: Uses deprecated version of python
2020-08-15 devel/py-aspects: Uses deprecated version of python
2020-08-15 devel/py-backports.tempfile: Uses deprecated version of python
2020-08-15 devel/py-backports.weakref: Uses deprecated version of python
2020-08-15 devel/py-cfgparse: Uses deprecated version of python
2020-08-15 devel/py-ciphon: Uses deprecated version of python
2020-08-15 devel/py-cjson: Uses deprecated version of python
2020-08-15 devel/py-clonedigger: Uses deprecated version of python
2020-08-15 devel/py-cuisine: Uses deprecated version of python
2020-08-15 devel/py-deliciousapi: Uses deprecated version of python
2020-08-15 devel/py-dialog: Uses deprecated version of python
2020-08-15 devel/py-efl: Uses deprecated version of python
2020-08-15 devel/py-ezpyinline: Uses deprecated version of python
2020-08-15 devel/py-fsm: Uses deprecated version of python
2020-08-15 devel/py-gdbgui: Uses deprecated version of python
2020-08-15 devel/py-gearman: Uses deprecated version of python
2020-08-15 devel/py-generate: Uses deprecated version of python
2020-08-15 devel/py-geotypes: Uses deprecated version of python
2020-08-15 devel/py-gitosis: Uses deprecated version of python
2020-08-15 devel/py-google-apputils: Uses deprecated version of python
2020-08-15 devel/py-hghooks: Uses deprecated version of python
2020-08-15 devel/py-instant: Uses deprecated version of python
2020-08-15 devel/py-jcc: Uses deprecated version of python
2020-08-15 devel/py-json-py: Uses deprecated version of python
2020-08-15 devel/py-json-sempai: Uses deprecated version of python
2020-08-15 devel/py-jsonlib: Uses deprecated version of python
2020-08-15 devel/py-jsonlib2: Uses deprecated version of python
2020-08-15 devel/py-jsonrpclib: Uses deprecated version of python
2020-08-15 devel/py-kayako: Uses deprecated version of python
2020-08-15 devel/py-kid: Uses deprecated version of python
2020-08-15 devel/py-kjbuckets: Uses deprecated version of python
2020-08-15 devel/py-kqueue: Uses deprecated version of python
2020-08-15 devel/py-log4py: Uses deprecated version of python
2020-08-15 devel/py-mwlib.ext: Uses deprecated version of python
2020-08-15 devel/py-mx-experimental: Uses deprecated version of python
2020-08-15 devel/py-option_merge: Uses deprecated version of python
2020-08-15 devel/py-prioritized_methods: Uses deprecated version of python
2020-08-15 devel/py-protocols: Uses deprecated version of python
2020-08-15 devel/py-ptrace: Uses deprecated version of python
2020-08-15 devel/py-pydoop: Uses deprecated version of python
2020-08-15 devel/py-pyke: Uses deprecated version of python
2020-08-15 devel/py-pymtbl: Uses deprecated version of python
2020-08-15 devel/py-pyshapelib: Uses deprecated version of python
2020-08-15 devel/py-pytemplate: Uses deprecated version of python
2020-08-15 devel/py-python2-pythondialog: Uses deprecated version of python
2020-08-15 devel/py-pyutil: Uses deprecated version of python
2020-08-15 devel/py-pyvalid: Uses deprecated version of python
2020-08-15 devel/py-pyxml2obj: Uses deprecated version of python
2020-08-15 devel/py-qpid: Uses deprecated version of python
2020-08-15 devel/py-repoze.what-pylons: Uses deprecated version of python
2020-08-15 devel/py-repoze.who-friendlyform: Uses deprecated version of python
2020-08-15 devel/py-robotframework-ride: Uses deprecated version of python
2020-08-15 devel/py-ruamel.ordereddict: Uses deprecated version of python
2020-08-15 devel/py-sanetime: Uses deprecated version of python
2020-08-15 devel/py-selectors34: Uses deprecated version of python
2020-08-15 devel/py-sqlcc: Uses deprecated version of python
2020-08-15 devel/py-statgrab: Uses deprecated version of python
2020-08-15 devel/py-tconfpy: Uses deprecated version of python
2020-08-15 devel/py-terminable_thread: Uses deprecated version of python
2020-08-15 devel/py-trace2html: Uses deprecated version of python
2020-08-15 devel/py-tvrage: Uses deprecated version of python
2020-08-15 devel/py-tw.forms: Uses deprecated version of python
2020-08-15 devel/py-uncompyle2: Uses deprecated version of python
2020-08-15 devel/py-yum-metadata-parser: Uses deprecated version of python
2020-08-15 devel/rubygem-warden127: No longer needed
2020-08-15 dns/py-dnschain: Uses deprecated version of python
2020-08-15 dns/py-idnkit2: Uses deprecated version of python
2020-08-15 games/colobot: Uses deprecated version of python
2020-08-15 games/endgame-singularity: Uses deprecated version of python
2020-08-15 games/katawa-shoujo: Uses deprecated version of RenPy
2020-08-15 games/pyfa: Uses deprecated version of python
2020-08-15 games/renpy6: Uses deprecated version of python
2020-08-15 games/solarwolf: Uses deprecated version of python
2020-08-15 games/thudboard: Uses deprecated version of python
2020-08-15 graphics/djvusmooth: Uses deprecated version of python
2020-08-15 graphics/py-glewpy: Uses deprecated version of python
2020-08-15 graphics/py-openexr: Uses deprecated version of python
2020-08-15 graphics/py-poppler: Uses deprecated version of python
2020-08-15 graphics/py-pygooglechart: Uses deprecated version of python
2020-08-15 graphics/py-sane: Uses deprecated version of python
2020-08-15 graphics/py-stltools: Uses deprecated version of python
2020-08-15 graphics/sk1: Uses deprecated version of python
2020-08-15 japanese/py-mecab: Uses deprecated version of python
2020-08-15 japanese/py-tegaki-gtk: Uses deprecated version of python
2020-08-15 lang/py-mx-base: Uses deprecated version of python
2020-08-15 mail/mailpile: Uses deprecated version of python
2020-08-15 math/py-ffc: Uses deprecated version of python
2020-08-15 math/py-fiat: Uses deprecated version of python
2020-08-15 math/py-nzmath: Uses deprecated version of python
2020-08-15 math/py-pymc: Uses deprecated version of python
2020-08-15 math/py-ufl: Uses deprecated version of python
2020-08-15 misc/py-socli: Uses deprecated version of python
2020-08-15 misc/py-yolk: Uses deprecated version of python
2020-08-15 multimedia/py-flvlib: Uses deprecated version of python
2020-08-15 net/py-gspreadsheet: Uses deprecated version of python
2020-08-15 net/py-libnet: Uses deprecated version of python
2020-08-15 net/py-netlib: Uses deprecated version of python
2020-08-15 net/py-pynmsg: Uses deprecated version of python
2020-08-15 net/py-rainbowstream: Uses deprecated version of python
2020-08-15 net/py-wolframalpha: Uses deprecated version of python
2020-08-15 net-im/empathy: Uses deprecated version of python
2020-08-15 net-im/farsight2: Uses deprecated version of python
2020-08-15 net-im/py-xmpppy: Uses deprecated version of python
2020-08-15 net-im/telepathy-farsight: Uses deprecated version of python
2020-08-15 net-im/telepathy-python: Uses deprecated version of python
2020-08-15 net-im/telepathy-rakia: Uses deprecated version of python
2020-08-15 net-mgmt/py-pynsca: Uses deprecated version of python
2020-08-15 net-mgmt/py-yapsnmp: Uses deprecated version of python
2020-08-15 net-p2p/py-py2play: Uses deprecated version of python
2020-08-15 news/py-yenc: Uses deprecated version of python
2020-08-15 print/py-pyscript: Uses deprecated version of python
2020-08-15 print/py-stapler: Uses deprecated version of python
2020-08-15 print/py-trml2pdf: Uses deprecated version of python
2020-08-15 science/py-PyQuante: Uses deprecated version of python
2020-08-15 science/py-mlpy: Uses deprecated version of python
2020-08-15 science/py-ws2300: Uses deprecated version of python
2020-08-15 security/py-PF: Uses deprecated version of python
2020-08-15 security/py-cracklib: Uses deprecated version of python
2020-08-15 security/py-fteproxy: Uses deprecated version of python
2020-08-15 security/py-onetime: Uses deprecated version of python
2020-08-15 security/py-pydeep: Uses deprecated version of python
2020-08-15 security/py-slowaes: Uses deprecated version of python
2020-08-15 security/py-sslstrip: Uses deprecated version of python
2020-08-15 security/py-volatility: Uses deprecated version of python
2020-08-15 sysutils/py-analyzemft: Uses deprecated version of python
2020-08-15 sysutils/py-cdmi: Uses deprecated version of python
2020-08-15 sysutils/py-ezjailremote: Uses deprecated version of python
2020-08-15 sysutils/py-gmailfs-fuse: Uses deprecated version of python
2020-08-15 sysutils/py-ploy_ec2: Uses deprecated version of python
2020-08-15 sysutils/py-ploy_fabric: Uses deprecated version of python
2020-08-15 sysutils/py-scriptine: Uses deprecated version of python
2020-08-15 sysutils/py-superlance: Uses deprecated version of python
2020-08-15 textproc/py-bugzillatools: Uses deprecated version of python
2020-08-15 textproc/py-elib.intl: Uses deprecated version of python
2020-08-15 textproc/py-errorhandler: Uses deprecated version of python
2020-08-15 textproc/py-hyperestraier-python: Uses deprecated version of python
2020-08-15 textproc/py-pyes: Uses deprecated version of python
2020-08-15 textproc/py-pyhwp: Uses deprecated version of python
2020-08-15 textproc/py-sphinx_numfig: Uses deprecated version of python
2020-08-15 www/py-HTMLgen: Uses deprecated version of python
2020-08-15 www/py-albatross: Uses deprecated version of python
2020-08-15 www/py-amf: Uses deprecated version of python
2020-08-15 www/py-apachelog: Uses deprecated version of python
2020-08-15 www/py-aws-requests-auth: Uses deprecated version of python
2020-08-15 www/py-clientform: Uses deprecated version of python
2020-08-15 www/py-django-appmedia: Uses deprecated version of python
2020-08-15 www/py-django-evolution: Uses deprecated version of python
2020-08-15 www/py-fedex: Uses deprecated version of python
2020-08-15 www/py-formalchemy: Uses deprecated version of python
2020-08-15 www/py-frappe-bench: Uses deprecated version of python
2020-08-15 www/py-funkload: Uses deprecated version of python
2020-08-15 www/py-goobook: Uses deprecated version of python
2020-08-15 www/py-poster: Uses deprecated version of python
2020-08-15 www/py-pyquery: Uses deprecated version of python
2020-08-15 www/py-pysearch: Uses deprecated version of python
2020-08-15 www/py-pywebdav: Uses deprecated version of python
2020-08-15 www/py-slimmer: Uses deprecated version of python
2020-08-15 www/py-surl: Uses deprecated version of python
2020-08-15 www/py-tmdb3: Uses deprecated version of python
2020-08-15 www/py-trello: Uses deprecated version of python
2020-08-15 www/py-uliweb: Uses deprecated version of python
2020-08-15 www/py-wsgiauth: Uses deprecated version of python
2020-08-15 x11-toolkits/py-wax: Uses deprecated version of python
2020-08-15 x11-toolkits/py-wxPython-common: Uses deprecated version of python
2020-08-15 x11-toolkits/py-wxPython28-common: Uses deprecated version of python
Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/htslib/tags
Bump PORTREVISION on dependents that don't require additional patching
PR: 248089
0.46.2 has long-standing regressions that are not being addressed, including
a seg fault when using --genomebam.
Also revert to bundled htslib in preparation for biology/htslib upgrade
to 1.10. Kallisto source contains modified bits of htslib 1.4.1 that are
incompatible with htslib > 1.9.
bio-shell, providing BioRuby Shell, is a command-line interface for BioRuby, an
open source bioinformatics library for Ruby.
This code has historically been part of the BioRuby gem, but has been split into
its own gem as part of an effort to modularize BioRuby. bio-shell and many more
plugins are available at biogems.info.
WWW: https://github.com/bioruby/bioruby-shell
bio-old-biofetch-emulator emulates Bio::Fetch object in BioRuby as if
discontinued BioRuby BioFetch server were still alive. It overrides methods and
objects in Bio::Fetch, and if the old BioRuby BioFetch server's URL is given, it
intercepts all requests and converts them into existing web services such as
TogoWS, KEGG REST API, NCBI E-Utilities, and GenomeNet(genome.jp).
WWW: https://github.com/ngoto/bioruby-old-biofetch-emulator
bio-executables is a collection of miscellaneous utilities for bioinformatics
that were formerly part of the BioRuby core ("bio" gem). Because of reducing
complexity, they were moved to this gem.
This code has historically been part of the BioRuby gem, but has been split into
its own gem as part of an effort to modularize BioRuby. bio-executables and many
more plugins are available at biogems.info.
WWW: https://github.com/bioruby/bioruby-executables
From ChangeLog: https://github.com/stephaneguindon/phyml/releases/tag/v3.3.20200621
This release fixes a few minor bugs (see recent commits). The manual also gives
extra XML configuration information in order to apply fancy substitution models
(e.g., CAT-like) on single- or multiple-gene data sets
Reported by: portscout
Chase the devel/libffi update
Bump portrevision of all dependent ports to chace shard library version bump
in libffi.
Update LIB_DEPENDS lines where needed to not require a specific version of
libffi.so.
PR: 247028 (for tracking)
In file included from ebwt.h:43,
from ebwt_build.cpp:11:
processor_support.h:52:22: error: extended character “ is not valid in an identifier
52 | std::cerr << “ERROR: please define __cpuid() for this build.\n”;
| ^
processor_support.h:52:72: error: extended character ” is not valid in an identifier
52 | std::cerr << “ERROR: please define __cpuid() for this build.\n”;
| ^
http://package18.nyi.freebsd.org/data/121amd64-default-PR244494/2020-06-10_18h04m44s/logs/errors/bowtie-1.1.2_9.log
PR: 246700
Picard is a set of command line tools for manipulating high-throughput
sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file
formats are defined in the Hts-specs repository.
Bioawk is an extension to Brian Kernighan's awk, adding the support of several
common biological data formats, including optionally gzip'ed BED, GFF, SAM,
VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few
built-in functions and an command line option to use TAB as the input/output
delimiter. When the new functionality is not used, bioawk is intended to behave
exactly the same as the original BWK awk.
The Subread package comprises a suite of software programs for processing
next-gen sequencing read data including:
Subread: a general-purpose read aligner
Subjunc: a read aligner developed for aligning RNA-seq reads
featureCounts: a software program developed for counting reads to genomic
features such as genes, exons, promoters and genomic bins.
Sublong: a long-read aligner that is designed based on seed-and-vote.
exactSNP: discovers SNPs by testing signals against local background noise.
utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:81:5: error: 'get_deleter' declared as a 'virtual' field
This may have something to do with compiler:openmp in USES. However,
it has broken for more than 6 months at this point.
Approved by: portmgr (tier-2 blanket)
- Repocopy textproc/py-sphinx to textproc/py-sphinx18
Update it to 1.8.5 (latest version from 1.8.X).
This version supports Python 2 and 3.
Add test target.
- textproc/py-sphinx: Update to 3.0.2
Python 3 only (3.5+).
Add test target.
- Mk/Uses/python.mk: Add PY_SPHINX
Shared macro to use with flavors and not break
ports with USES=python (all versions).
Python >=3.5 --> textproc/py-sphinx (v3.0.2)
Python < 3.5 --> textproc/py-sphinx18 (v1.8.5)
All ports that uses sphinx were changed to use the new variable
${PY_SPHINX} in the dependency line, exceptions:
* Ports that fails to build with sphinx 3.0.2 because of code.
They are pointing to textproc/py-sphinx18 directly.
There aren't many ports.
* Ports that doesn't know Python flavors.
- Add several patches to fix Sphinx consumers
The most common issues are related with pkg-plist, the output
files from Sphinx changes between versions, keep this dynamically
is the better approach.
This will save time in future sphinx updates.
PR: 245629
Exp-run by: antoine
Use GCC instead of Clang:
/usr/lib/clang/10.0.0/include/mmintrin.h:216:19: error: use of undeclared identifier '__builtin_ia32_punpckhbw'
return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
Some changes have been made in this release that break backwards
compatibility. Let USES=gmake force users to upgrade to this version so
port maintainers don't have to support older versions.
PR: 245725
Exp-run by: antoine
Approved by: portmgr (antoine)
Adjusted for ports rescued since r534032
2020-05-05 audio/festvox-czech: Broken for more than 6 months
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2020-05-05 x11-wm/ratmenu: Broken for more than 6 months
- 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
