Commit Graph

2830 Commits

Author SHA1 Message Date
Sunpoet Po-Chuan Hsieh
4453cd341c Convert REINPLACE_CMD to patch file 2020-09-29 18:23:04 +00:00
Sunpoet Po-Chuan Hsieh
7d33b22118 Update PYTHON option to use Python 3 2020-09-27 19:30:20 +00:00
Mark Linimon
56ba7b05c4 Allow building on powerpc64le.
Approved by:	portmgr (tier-2 blanket)
2020-09-27 07:44:15 +00:00
Mark Linimon
694ca2a5d8 Canonicalize powerpc64le CXXFLAGS to be the same as powerpc64.
Approved by:	portmgr (tier-2 blanket)
2020-09-27 07:41:33 +00:00
Yuri Victorovich
8e7137a413 biology/abyss: Update 2.2.4 -> 2.2.5
Reported by:	portscout
2020-09-27 06:59:05 +00:00
Yuri Victorovich
655b66b2e4 biology/ncbi-cxx-toolkit: Fix build on 13
Reported by:	fallout
2020-09-27 04:57:44 +00:00
Joseph Mingrone
7f9181e95c biology/py-biom-format: Fix fetch and relax scipy requirement
- The broken fetch was due to a commit error.

- The relaxing of the scipy constraint is temporary until scipy can be
  updated.
2020-09-26 09:10:37 +00:00
Yuri Victorovich
9ea8f6721b biology/ncbi-cxx-toolkit: Update 21.0.0 -> 22.0.0 2020-09-25 06:57:43 +00:00
Joseph Mingrone
fd1ca09f9f biology/py-biom-format: Update to version 2.1.8
Upstream changes:
https://github.com/biocore/biom-format/releases/tag/2.1.8
2020-09-25 01:03:03 +00:00
Yuri Victorovich
9c49891589 biology/py-scikit-bio: Fix build on the i386 architecture
Reported by:	fallout
MFH:		2020Q3
2020-09-24 23:16:26 +00:00
Mark Linimon
7b6fb490d7 Also enable on powerpc64le.
Approved by:	portmgr (tier-2 blanket)
2020-09-24 20:38:59 +00:00
Mark Linimon
fbf95f4a64 Also enable on powerpc64le.
Approved by:	portmgr (tier-2 blanket)
2020-09-24 20:29:35 +00:00
Joseph Mingrone
f244f722da biology/py-biom-format: Restore in preparation for an update to v2.1.8
Version 2.1.8 supports python 3
2020-09-24 19:31:43 +00:00
Jason W. Bacon
12d8a81d51 biology/gmap: Upgrade to 2020.09.12
First upgrade in 5 years, so numerous improvements
Unsure if powerpc is still supported upstream
Code mentions power8, but does not build on my Mac G5
2020-09-22 00:55:39 +00:00
Stefan Eßer
136b2d0c4c Fix build with -fno-common 2020-09-21 18:14:57 +00:00
Antoine Brodin
9e6683e879 Unbreak bulk -a 2020-09-19 14:15:42 +00:00
Rene Ladan
b2e5755eb8 Remove expired ports:
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
2020-09-19 13:01:00 +00:00
Jason W. Bacon
57b67ec18e biology/subread: Add -fcommon for clang 11
Reported by:    pkg-fallout
2020-09-18 00:57:35 +00:00
Jason W. Bacon
719076a220 biology/canu: Upgrade to 2.1
Numerous functional improvements for ease of use and output quality
A few bug fixes

Reported by:    portscout
2020-09-14 22:27:37 +00:00
Yuri Victorovich
b0453c9897 biology/py-pyfaidx: Update 0.5.5.2 -> 0.5.9.1 2020-09-13 19:05:30 +00:00
Yuri Victorovich
f99bcb9c0e biology/gatk: Fix build
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
2020-09-08 19:25:36 +00:00
Yuri Victorovich
b82fb7ff7d biology/viennarna: Update 2.4.14 -> 2.4.15 2020-09-07 21:49:07 +00:00
Yuri Victorovich
2353dc4187 biology/gatk: Update 4.1.8.0 -> 4.1.8.1 2020-09-06 02:16:44 +00:00
Fernando Apesteguía
0add9fcff9 biology/mapm3: Reformat patches.
Make them compliant with the expected format.
2020-09-04 12:24:23 +00:00
Fernando Apesteguía
64680c4bd0 biology/mapm3: Fix build with llvm11, gcc10
Another instance of -fno-common issue.

While here:

 * strip executables
 * add license

PR:	249077
Submitted by:	tphilipp@potion-studios.com (maintainer)
MFH:	2020Q3 (build fix, -fno-common)
2020-09-04 11:28:24 +00:00
Joseph Mingrone
3a2ec6d491 biology/hyphy: Update to version 2.5.18 and add AVX option
The AVX option is off by default, because hyphy will crash on systems
without advanced vector extensions support.
2020-09-02 17:47:10 +00:00
Yuri Victorovich
d50977910e biology/py-ete3: Update 3.1.1 -> 3.1.2
Reported by:	portscout
2020-09-02 03:54:04 +00:00
Joseph Mingrone
bc66849a97 biology/diamond: Update to version 2.0.4
Upstream changes:
https://github.com/bbuchfink/diamond/releases/tag/v2.0.3
https://github.com/bbuchfink/diamond/releases/tag/v2.0.4

Port changes:
Remove a patch that was upstreamed:
https://github.com/bbuchfink/diamond/pull/378
2020-08-30 16:14:22 +00:00
Jason W. Bacon
6ded3faed8 biology/picard-tools: Remove extraneous file
Reported by:    Roman Bogorodskiy
2020-08-30 14:06:54 +00:00
Niclas Zeising
a1b290c54d Extend expiration of ports broken with -fno-common
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)
2020-08-30 09:47:49 +00:00
Roman Bogorodskiy
8ccd925b80 Chase security/p11-kit update
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
2020-08-30 03:10:23 +00:00
Tobias C. Berner
84824b9b09 biology/: Fix build with clang11 and deprecate ports@ ports 2020-08-29 08:34:51 +00:00
Tobias C. Berner
159fcd4b30 biology/phyml: fix build on recent current
mostly backport of:
	3574fb82d5

Obtained from:	3574fb82d5
2020-08-29 08:34:27 +00:00
Tobias C. Berner
7f618356c8 biology/cufflinks: fix build on recent current 2020-08-28 18:24:04 +00:00
Tobias C. Berner
6b8c279e7b biology/bwa: fix build on recent current
Obtained from:	2a1ae7b6f3
2020-08-28 11:17:13 +00:00
Rene Ladan
09df8f4601 Remove expired ports:
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
2020-08-27 11:25:47 +00:00
Yuri Victorovich
49bf1df227 biology/hhsuite: Update 3.2.0 -> 3.3.0
Reported by:	portscout
2020-08-27 04:28:24 +00:00
Kyle Evans
349be39472 biology/paml: fix the build with LLVM 11
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
2020-08-20 17:07:03 +00:00
Joseph Mingrone
9c4faf08b0 biology/hyphy: Update to version 2.5.17
Upstream changes:
https://github.com/veg/hyphy/releases/tag/2.5.16
https://github.com/veg/hyphy/releases/tag/2.5.17
2020-08-20 16:15:22 +00:00
Danilo G. Baio
91987153e5 devel/ipython: Update to 7.17.0
IPython 7.17+ supports Python 3.7 and above, following NEP 29.
Update consumers to use Python >= 3.7 (avoid break bulk -a).

Changelog:	https://ipython.readthedocs.io/en/latest/whatsnew/version7.html?highlight=7.17#ipython-7-17

Approved by:	dbaio (python, maintainer)
2020-08-15 12:50:57 +00:00
Rene Ladan
b6cb229310 Remove deprecated ports:
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
2020-08-15 10:50:58 +00:00
Yuri Victorovich
c6113702a3 biology/graphlan: Remove the 2.7 limitation on python because it's no longer needed 2020-08-14 04:59:29 +00:00
Yuri Victorovich
152f1a83b5 biology/groopm: Remove python's 2.7 restriction placed here by mistake 2020-08-13 19:19:23 +00:00
Joseph Mingrone
c565364c26 biology/diamond: Update to version 2.0.2
Upstream changes:
https://github.com/bbuchfink/diamond/releases/tag/v2.0.1
https://github.com/bbuchfink/diamond/releases/tag/v2.0.2
2020-08-07 11:20:11 +00:00
Yuri Victorovich
1856336100 biology/py-gtfparse: Update 1.2.0 -> 1.2.1
Reported by:	portscout
2020-08-07 04:13:00 +00:00
Jason W. Bacon
7197facae5 biology/samtools: Upgrade to 1.10
Numerous bug fixes and enhancements:
https://github.com/samtools/samtools/releases/tag/1.10

Take maintainership per ports/248089

PR:             ports/248089
2020-08-03 18:22:06 +00:00
Jason W. Bacon
3d154d8bbc biology/bcftools: Upgrade to 1.10.2
Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/bcftools/tags

Take maintainership per ports/248089.

PR:             ports/248089
2020-08-03 18:16:54 +00:00
Jason W. Bacon
551f57c4e0 biology/vt: Patch to work with htslib 1.10.2
Minor API changes requiring type casts
2020-08-03 17:42:32 +00:00
Jason W. Bacon
fb3f006dcf biology/htslib: Upgrade to 1.10.2
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
2020-08-03 17:40:04 +00:00
Jason W. Bacon
c3b030a079 biology/kallisto: Revert to 0.46.1
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.
2020-08-03 15:45:21 +00:00