Commit graph

1746 commits

Author SHA1 Message Date
Kurt Jaeger
4e90cff927 biology/seqtools: 4.24 -> 4.25
PR:             ports/186299
Submitted by:   pi (myself)
Approved by:    jadawin (mentor)
2014-05-01 16:50:34 +00:00
Steve Wills
4404ec6009 - Stage
- Drop easy_install
- Use auto pkg-plist
- Delete pkg-plist

PR:		ports/188818
Submitted by:	Bartek Rutkowski <ports@robakdesign.com>
Approved by:	portmgr@ (blanket)
2014-04-27 01:59:47 +00:00
Martin Wilke
1cf7eb5d50 - Update to version 1.13.5
PR:		188863
Submitted by:	ports fury
2014-04-26 02:35:37 +00:00
Thomas Zander
50fd87108f - Un-break fetch stage: the name scheme of the source tarballs has changed
- Add LICENSE*
- Remove conflict with hunspell:
  - Rename the 'analyze' binary to 'analyze_t'
  - put a note in pkg-message.in
- Pet portlint

PR:		ports/187569
Submitted by:	Tsurutani Naoki <turutani@scphys.kyoto-u.ac.jp>
Approved by:	thierry (mentor)
MFH:	2014Q2
2014-04-22 19:28:18 +00:00
Rene Ladan
8b3c8800eb Remove expired ports:
2014-04-16 ports-mgmt/pkgsearch: Upstream disappeared
2014-04-17 science/flounder: Unmaintained since 2002
2014-04-17 security/nbaudit: Unmaintained since 2002
2014-04-17 security/saint: Unmaintained since 2002
2014-04-17 graphics/gozer: Unmaintained since 2002
2014-04-17 misc/pdfmap: Unmaintained since 2002
2014-04-17 devel/showgrammar: Unmaintained since 2002
2014-04-17 biology/libgenome: Unmaintained since 2002
2014-04-17 deskutils/narval: Unmaintained since 2002
2014-04-17 devel/fampp: Unmaintained since 2002
2014-04-17 net-p2p/py-fngrab: Unmaintained since 2002
2014-04-17 misc/wmfirew: Unmaintained since 2002
2014-04-17 x11-wm/e16utils: Unmaintained since 2002
2014-04-17 misc/salias: Unmaintained since 2002
2014-04-17 print/latex2slides: Unmaintained since 2002
2014-04-17 lang/sxm: Unmaintained since 2002
2014-04-17 textproc/pybook: Unmaintained since 2002
2014-04-17 mail/mailcrypt: Unmaintained since 2002
2014-04-17 japanese/elvis: Unmaintained since 2002
2014-04-17 devel/prototype: Unmaintained since 2002
2014-04-17 print/wprint: Unmaintained since 2002
2014-04-17 science/euler: Unmaintained since 2002
2014-04-17 multimedia/gopchop: Unmaintained since 2002
2014-04-17 science/gdis: Unmaintained since 2002
2014-04-17 net/googolplex: Unmaintained since 2002
2014-04-17 lang/logo: Unmaintained since 2002
2014-04-17 textproc/roap: Unmaintained since 2002
2014-04-17 x11-wm/afterstep-i18n: Unmaintained since 2002
2014-04-17 games/yamsweeper: Unmaintained since 2002
2014-04-17 net-mgmt/echolot: Unmaintained since 2002
2014-04-17 security/pam_smb: Unmaintained since 2002
2014-04-18 devel/lua-redis-parser: Broken for more than 6 months
2014-04-18 biology/finchtv: Broken for more than 6 months
2014-04-18 net-im/ari-yahoo: Broken for more than 1 year (http://www.icculus.org/ari-yahoo/)
2014-04-18 11:17:45 +00:00
Niclas Zeising
39fc32e828 The FreeBSD x11@ and graphics team proudly presents
a zeising, kwm production, with help from dumbbell, bdrewery:

NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE

This update switches over to use the new xorg stack by default on FreeBSD 9
and 10 stable, on osversions where vt(9) is available.
It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in
/etc/make.conf .
FreeBSD 8-STABLE and released versions of FreeBSD still use
the old version.
A package repository with binary packages for new xorg will
be available soon.

This patch also contains updates of libxcb and related ports, pixman, as well
as some drivers and utilities.

Bump portrevisions for xf86-* ports, as well as virtualbox-ose-additions due
to xserver version change.

Apart from these updates, the way shared libraries are handled has been
changed for all xorg ports, as well as libxml2 and freetype, which means
ltverhack is gone and as a consequence shared libraries have been bumped.
The plan is that this change will make library bumps less likely in the
future.
All affected ports have had their portrevisions bumped as a consequence of
this.

Fix some issues where WITH_NEW_XORG weren't detected properly on CURRENT.

Update instructions, hardware support, and more notes can be found on
https://wiki.freebsd.org/Graphics

Thanks to:	all testers, bdrewery and the FreeBSD x11@ team
exp-run by:	bdrewery [1]
PR:		ports/187602 [1]
Approved by:	portmgr (bdrewery), core (jhb)
2014-04-16 18:28:47 +00:00
Rene Ladan
bac6e092c4 Remove expired ports:
2014-04-12 net/pvm++: Unmaintained since 2001
2014-04-12 devel/ixlib: Unmaintained since 2001
2014-04-12 mail/althea: Unmaintained since 2001
2014-04-12 graphics/claraocr: Unmaintained since 2001
2014-04-12 graphics/qvplay: Unmaintained since 2001
2014-04-12 print/guitartex: Unmaintained since 2001
2014-04-12 print/pnm2ppa: Unmaintained since 2001
2014-04-12 graphics/opendis: Unmaintained since 2001
2014-04-12 net/gnome-mud: Unmaintained since 2001
2014-04-12 graphics/maverik: Unmaintained since 2001
2014-04-12 biology/rasmol: Unmaintained since 2001
2014-04-12 mail/mail2procmailrc: Unmaintained since 2001
2014-04-12 science/felt: Unmaintained since 2001
2014-04-12 textproc/pardiff: Unmaintained since 2001
2014-04-12 lang/klone: Unmaintained since 2001
2014-04-12 net/rmsg: Unmaintained since 2001
2014-04-12 net/sharity-light: Unmaintained since 2001
2014-04-12 biology/genpak: Unmaintained since 2001
2014-04-12 net/forg: Unmaintained since 2001
2014-04-12 misc/txt2regex: Unmaintained since 2001
2014-04-12 textproc/ipdf: Unmaintained since 2001
2014-04-12 graphics/plotmtv: Unmaintained since 2001
2014-04-12 devel/happydoc: Unmaintained since 2001
2014-04-12 print/cpp2latex: Unmaintained since 2001
2014-04-12 graphics/svg2swf: Unmaintained since 2001
2014-04-12 devel/flick: Unmaintained since 2001
2014-04-12 mail/smail: Unmaintained since 2001
2014-04-12 net/net-http: Unmaintained since 2001
2014-04-12 security/cfv: Unmaintained since 2001
2014-04-12 graphics/camediaplay: Unmaintained since 2001
2014-04-12 math/umatrix: Unmaintained since 2001
2014-04-13 10:55:38 +00:00
Frederic Culot
5f8ba6d549 - Back to the heap, I don't use this port anymore 2014-04-12 07:42:33 +00:00
Baptiste Daroussin
0542e45bb8 Mark as broken unstaged perl ports
With hat:	portmgr
2014-04-09 09:49:02 +00:00
Baptiste Daroussin
8086bfab37 Support stage 2014-04-07 13:01:26 +00:00
Wen Heping
88e64fdede - Update to 0.5.2
- Add LICENSE
2014-04-06 04:05:43 +00:00
Wen Heping
10b6dcace8 - Update to 2.3.6
- Reset maintainer to ports@
2014-04-06 03:56:03 +00:00
Wen Heping
9eb7654b4f - Update to 4.8
- Reset maintainer to ports@
2014-04-05 10:56:52 +00:00
Antoine Brodin
363d970fb3 Unbreak
Reported by:	pkg-fallout
2014-03-28 00:08:03 +00:00
Sunpoet Po-Chuan Hsieh
b283136f34 - Fix PLIST
- Bump PORTREVISION for package change

Reported by:	swills
2014-03-26 14:23:09 +00:00
Sunpoet Po-Chuan Hsieh
0497c7bf52 - Update to 2.0
Changes:	http://search.cpan.org/dist/Bio-GFF3/Changes
2014-03-25 19:34:03 +00:00
Baptiste Daroussin
8b704cb6b6 Does not build with wx 3.0
Remove the contrib component which is not required
Note that is does not build with the unicode version of wx 2.8 as well
2014-03-24 15:18:39 +00:00
Pawel Pekala
c831e86829 Add staging support 2014-03-24 11:06:56 +00:00
Pawel Pekala
030b55b397 - Add staging support
- Unmute install commands
2014-03-24 10:46:35 +00:00
Pawel Pekala
f882a8136a - Add staging support
- Switch to PORTDOCS
2014-03-24 09:01:39 +00:00
Pawel Pekala
9e64a1e656 - Add staging support
- Strip libraries
2014-03-23 21:52:54 +00:00
Pawel Pekala
32dca82a5b Add staging support 2014-03-23 20:50:54 +00:00
Pawel Pekala
805a54b025 - Add staging support
- Strip library
2014-03-23 18:10:41 +00:00
Pawel Pekala
6dc9526345 Add staging support 2014-03-23 18:09:23 +00:00
Pawel Pekala
62fd816b35 Add staging support 2014-03-23 17:43:41 +00:00
Antoine Brodin
a0b36f8e26 Deprecate: Broken for more than 6 months 2014-03-18 18:10:25 +00:00
Emanuel Haupt
3fb1d458f5 Support staging 2014-03-14 12:59:33 +00:00
Emanuel Haupt
a98607e457 Support staging 2014-03-14 12:35:03 +00:00
Martin Wilke
059bf913b9 - Convert USE_GMAKE to USES 2014-03-13 07:41:34 +00:00
Antoine Brodin
cf7b71001e Deprecate a few old unmaintained ports 2014-03-11 21:21:14 +00:00
Gerald Pfeifer
1cd277bdce Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)
2014-03-10 20:55:20 +00:00
Rene Ladan
d6ba8bc3ec biology/ssaha: undeprecate, this port fetches and builds fine.
Submitted by:	Kurt Jaeger via private mail.
2014-03-09 09:39:50 +00:00
Antoine Brodin
c6c742d7cc Deprecate a few unmaintained ports (leaf ports, non staged and unmaintained since more than 12 years) 2014-03-08 22:26:21 +00:00
Antoine Brodin
cda9155ebd Unbreak 2014-03-08 16:39:01 +00:00
Baptiste Daroussin
d574c51a4f Convert b* to USES=zip 2014-03-07 15:52:40 +00:00
Baptiste Daroussin
044f0f8b7c Convert to dos2unix 2014-03-07 11:37:35 +00:00
Alexey Dokuchaev
ae2e4e1956 Update to version 1.13.1. 2014-03-07 07:39:20 +00:00
John Marino
e06d29ed1c biology/fasta3: Checked new distfile and regenerated distinfo to unbreak
Fasta3 distfile was significantly changed.  This should have been released
as a new version (e.g. 36.3.6e), so it's not clear why the distfile was
rerolled.  There are significant changes to makefiles, conf files and even
a few .c and .h files.  They all look like legitimate updates to me
though.

Set DIST_SUBDIR since this port is now known for rerolling, then
regenerate distinfo.  Also add Fasta license and bump revision.
2014-03-02 10:58:50 +00:00
Martin Wilke
4e739fcd1a - Update to 35
PR:		184245
2014-02-27 11:46:11 +00:00
Martin Wilke
a0f669db2a - Update to 5.0.7
PR:		185942
Submitted by:	ports fury
2014-02-27 08:58:36 +00:00
Martin Wilke
5ba557af23 - Stage support
- Update to version 4.4.3

PR:		187041
Submitted by:	ports fury
2014-02-27 08:46:42 +00:00
TAKATSU Tomonari
0cbe65e47c - Repocopy print/py-reportlab to print/py-reportlab1
to preserve version 1.x and to update to 3.0

  print/py-reportlab:
    - Update print/py-reportlab to 3.0 based on print/py-reportlab2
    - Support STAGEDIR
    - Use PYDISTUTILS_AUTOPLIST
      * Remove pkg-plist, accordingly
    - Set CONFLICTS
    - Add PORTSCOUT
    - Replace tab with a single space after WWW: in pkg-descr

  print/py-reportlab1:
    - Support STAGEDIR
    - Add PKGNAMESUFFIX not to duplicate ports with the same name
    - Set CONFLICTS
    - Use PYDISTUTILS_AUTOPLIST
      * Remove pkg-plist, accordingly
    - Make use of PORTDOCS
    - Set OPTIONS_DEFINE explicitly
    - Fix include statement
    - Make docs unconditional to stage
    - Replace tab with a single space after WWW: in pkg-descr

  print/py-reportlab2:
    - Update CONFLICTS
    - Set PORTSCOUT

  dependent ports:
    - Switch dependency from print/py-reportlab to print/py-reportlab1
      * biology/py-biopython
      * deskutils/gourmet
      * deskutils/griffith
      * games/pythonsudoku
      * misc/pdfmap
      * print/py-trml2pdf
      * www/py-satchmo

PR:		ports/186970
Submitted by:	tota (myself)
Approved by:	Muhammad Moinur Rahman (maintainer)
2014-02-25 12:44:10 +00:00
Emanuel Haupt
094043c26a Remove trailing whitespaces from category biology 2014-02-21 13:35:26 +00:00
Tijl Coosemans
564a799c71 Convert all USE_FORTRAN=yes to "USES=fortran, USE_GCC=yes". In most cases
USE_GCC=yes has been omitted though.

Remove USE_FORTRAN handling from bsd.port.mk and bsd.gcc.mk.

Minor cleanups in some ports like USE_GMAKE, NOPORTDOCS,...

Exp-run:	bdrewery
Approved by:	portmgr (bdrewery)
2014-02-16 17:15:31 +00:00
Emanuel Haupt
5842379229 Support staging 2014-02-16 11:43:07 +00:00
Emanuel Haupt
1f6893241a Support staging 2014-02-16 11:42:09 +00:00
Emanuel Haupt
f035b3ea09 - Support staging
- Use shebangfix
2014-02-16 11:39:42 +00:00
Emanuel Haupt
3c43b72754 Support staging 2014-02-16 11:35:00 +00:00
Emanuel Haupt
92ff3f86fb Support staging 2014-02-16 11:32:43 +00:00
Mathieu Arnold
33ab73cd19 Fix old makeplist bug.
Pointy hat to:	people who blindly use makeplist
Sponsored by:	Absolight
2014-02-12 14:03:25 +00:00
Emanuel Haupt
5005b67362 According to the Porter's Handbook (5.12.2.3.) default options must be added to
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)
2014-02-10 13:54:26 +00:00
Martin Wilke
e6e265ae51 - Stage support 2014-02-10 06:56:52 +00:00
Emanuel Haupt
8305492fd9 Update WWW 2014-02-09 11:13:38 +00:00
Baptiste Daroussin
155aa7f937 Deprecate ports unmaintained for which distillator is not able to find public distfiles
Reported by:	distilator
2014-02-07 18:50:30 +00:00
John Marino
faa78592db biology/libgenome: Fix build on dragonfly 2014-02-05 23:47:48 +00:00
John Marino
5f492e9232 biology/tRNAscan-SE: Fix hardcoded perl path 2014-02-05 23:44:50 +00:00
John Marino
28abc2b0ae biology/wise: Add dragonfly support 2014-02-05 23:42:06 +00:00
Mathieu Arnold
db33716fd3 Drop maintainership on those.
Sponsored by:	Absolight
2014-02-05 17:35:53 +00:00
Rene Ladan
0417f3eeb4 Drop maintainership BOINC ports, old machine running them gave up. 2014-02-04 17:54:29 +00:00
Martin Wilke
6f0f3362e8 - Stage support 2014-01-31 12:47:06 +00:00
Martin Wilke
69310343ab - Stage support 2014-01-31 12:33:11 +00:00
Martin Wilke
271152255b - Stage support 2014-01-31 12:32:55 +00:00
Martin Wilke
5ecf3aa390 - Convert to PYDISTUTILS_AUTOPLIST
- Stage support
- Bump PORTREV
2014-01-31 12:31:24 +00:00
Martin Wilke
73703d71d0 - Convert to PYDISTUTILS_AUTOPLIST
- Stage support
- Bump PORTREV
2014-01-31 12:30:39 +00:00
Alexey Dokuchaev
4e749081cf Unbreak the fetch: one of the documentation PDF files was rerolled. 2014-01-30 13:38:26 +00:00
Bernhard Froehlich
feaa1e68d7 - Mark BROKEN because it does not fetch 2014-01-30 13:11:40 +00:00
Andrej Zverev
a6720a4a32 - fix pkg-plist
- add LICENSE
2014-01-30 07:34:25 +00:00
Alexey Dokuchaev
d526bc887e - Stagify; cleanup Makefile and reorder the knobs a bit
- Drop the case for long unsupported alpha architecture
2014-01-29 12:08:29 +00:00
Martin Wilke
24815166c6 - Fix build on -current
- Update MASTER_SITES and WWW: line
- Support CXX/CXXFLAGS properly
- Support PLIST_FILES
- Stage support

PR:		184852
Submitted by:	Ports Fury
2014-01-25 16:48:05 +00:00
Sunpoet Po-Chuan Hsieh
d4310bc023 - Update to 1.9
- Sort PLIST

Changes:	http://search.cpan.org/dist/Bio-GFF3/Changes
2014-01-23 03:28:37 +00:00
Baptiste Daroussin
56fcf8379f Fix properties on pkg-plist 2014-01-21 23:18:05 +00:00
Baptiste Daroussin
2e34754bf6 Support stage 2014-01-20 23:10:10 +00:00
Baptiste Daroussin
090f15acf5 Support stage 2014-01-20 23:06:48 +00:00
Baptiste Daroussin
5221a9dd7a Support stage 2014-01-20 23:00:56 +00:00
Baptiste Daroussin
5da0c9a774 Support stage
Conver USE_GMAKE
2014-01-20 17:02:11 +00:00
Antoine Brodin
6eb2857024 Stage support 2014-01-18 15:55:42 +00:00
Alexey Dokuchaev
9dc680d0e8 - Update to version 1.13.0 and improve FreeBSD support; it also builds
pretty cleanly with GCC v4.2, v4.6, and Clang (modulo a few warnings)
- Sadly, do not use PORTDOCS: since DOCSDIR is set to be inside DATADIR,
  and will get appended to PLIST after @dirrm %%DATADIR%%, which upsets
  sanity checking tools; instead, list the docs explicitly in DISTFILES
  and add them to pkg-plist (guarded by %%PORTDOCS%%)

Tested on:	i386 (only)
2014-01-16 17:17:15 +00:00
Baptiste Daroussin
0adb5c3f94 Reduce over inclusion of bsd.port.mk 2014-01-15 22:52:28 +00:00
Baptiste Daroussin
b6b54b0a88 Reduce over inclusion of bsd.port.mk 2014-01-15 22:51:26 +00:00
Baptiste Daroussin
3b82ca9795 Reduce over inclusion of bsd.port.mk 2014-01-15 22:50:50 +00:00
Baptiste Daroussin
281fdcd544 Reduce over inclusion of bsd.port.mk 2014-01-15 22:50:18 +00:00
Baptiste Daroussin
06600f966f Reduce over inclusion of bsd.port.mk 2014-01-15 22:48:32 +00:00
Baptiste Daroussin
9d0066d3ff Support stage
Reduce over inclusions of bsd.port.mk
Use BROKEN_${ARCH}
2014-01-15 22:44:13 +00:00
Rene Ladan
50f8eaece1 Python cleanup:
- USE_PYTHON* = 2.X -> USE_PYTHON* = 2
- USE_PYTHON* = 2.X+ -> USE_PYTHON* = yes
Reviewed by:	python (mva, rm)
Approved by:	portmgr-lurkers (mat)
2014-01-13 21:00:02 +00:00
Thomas Zander
368c138aae - Fix build with clang
- Stage support

PR:		ports/185655
Submitted by:	Tassilo Philipp <tphilipp@potion-studios.com> (maintainer)
Approved by:	thierry (mentor)
2014-01-12 19:07:28 +00:00
Andrej Zverev
f09fca2358 - add stage support
Approved by:	portmgr (blanket infrastructure)
2014-01-06 09:57:19 +00:00
Andrej Zverev
2c6b14778c - add stage support
Approved by:	portmgr (blanket infrastructure)
2014-01-06 09:44:19 +00:00
Andrej Zverev
f41a84cc7d - support stage 2014-01-05 12:07:20 +00:00
Baptiste Daroussin
4be4ab0c7e Mark as broken: Invalid checksum, seems like the software was rerolled 2014-01-03 19:46:05 +00:00
Adam Weinberger
955d37365b Convert biology to MDOCS and MEXAMPLES 2014-01-03 15:46:52 +00:00
Olli Hauer
4fb1cfb1cd - rename AL2 to APACHE20 in Mk/bsd.licenses.db.mk
- svn move Templates/Licenses/AL2 Templates/Licenses/APACHE20
- add APACHE10 and APACHE11 to Mk/bsd.licenses.db.mk
- add entry in UPDATING
- bulk change all ports AL2 => APACHE20

- math/openfst/pkg-plist: remove share/licenses/openfst-1.3.4

PR:		ports/184785
Submitted by:	ohauer
Reviewed by:	tabthorpe
Approved by:	portmgr (tabthorpe@)
2013-12-30 20:55:18 +00:00
Antoine Brodin
b5fdf54ec6 Stage support 2013-12-30 18:27:32 +00:00
Antoine Brodin
9d9aec7824 Stage support 2013-12-30 18:08:14 +00:00
Tijl Coosemans
ec8db877f4 - USES=fortran gmake.
- Add dependency on xproto.
- Fix build with new CFLAGS.
- Staging.
- New WWW.
2013-12-29 14:30:20 +00:00
Rene Ladan
94066acc1a The hmmer binary was renamed upstream to indicate that it is now an
archive file, adjust the port so that fetch and extract work again.
2013-12-29 10:41:50 +00:00
William Grzybowski
1f6544c522 biology/seqtools: update to 4.24
PR:		ports/185162
Submitted by:	maintainer
2013-12-24 17:23:23 +00:00
Rene Ladan
652c8e10fe Several fixes:
- install files as the BOINC user/group, this ensures that work units can
  be downloaded and sent
- try to remove ~boinc/projects if empty
- do not specify -o and -g parameters to ${INSTALL}, this ensures the
  package can be built as user
- only extract the hmmer binary from the hmmer distribution file, this
  ensures correct permissions when modifying app_info.xml as user
- Bump PORTREVISION

Reviewed by:	bapt
2013-12-23 18:03:15 +00:00
Wen Heping
1fc27b753e - Fix build with clang/libc++.
- Support staging.

PR:		184974
Submitted by:	tijl@
2013-12-20 15:29:07 +00:00
Pawel Pekala
91571f28bb - Respect CC/CFLAGS
PR:		ports/184857
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
2013-12-20 13:27:13 +00:00
Tijl Coosemans
1555ae4f31 - biology/tinker: USES=fortran, staging.
- Add CONFLICTS_INSTALL between hunspell and tinker.
  Both install bin/analyze.
2013-12-18 18:27:04 +00:00
Tijl Coosemans
f0d679be01 USES=fortran, staging. 2013-12-18 17:24:51 +00:00
Tijl Coosemans
bd36806845 USES=fortran, staging, miscellaneous cleanups. 2013-12-18 16:23:08 +00:00
Tijl Coosemans
9eba83c71f Version 2013.12.12, USES=fortran, staging. 2013-12-17 21:55:24 +00:00
Tijl Coosemans
23f82b30c6 USES=fortran, fix LDFLAGS, staging. 2013-12-17 21:24:17 +00:00
Gerald Pfeifer
2291db64ec Fix the build with more standards-compliant compilers such as GCC 4.7. [1]
On the way replace USE_GMAKE by USES=gmake.

PR:		184566 [1], 182136
Submitted by:	Christoph Moench-Tegeder <cmt@burggraben.net> [1]
Approved by:	maintainer (Jason Bacon <jwbacon@tds.net>) [1]
2013-12-13 09:34:40 +00:00
Baptiste Daroussin
a2275161bd In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology
2013-12-11 14:43:51 +00:00
Baptiste Daroussin
732ab835ac Support stage
USE_GMAKE -> USES=gmake
use USES=readline:port
2013-12-10 17:54:12 +00:00
Baptiste Daroussin
67c403a63a Support stage
USE_GMAKE -> USES=gmake
Respect CC
2013-12-10 17:25:38 +00:00
Baptiste Daroussin
46c85cde39 Support stage
Convert USE_GMAKE to USES=gmake
Add dependency on perl which the port need and was getting by chance
bump portrevision, dependencies has changed
2013-12-10 17:21:46 +00:00
Adam Weinberger
6507f2bc7a Respect PORT_OPTIONS:MDOCS
Clean up COMMENT
USES=gmake
2013-12-09 01:28:41 +00:00
Wen Heping
7c42586279 - Fix build on head 2013-12-01 01:58:31 +00:00
Philippe Audeoud
ad6d50d019 - Update to 1.28
Sponsored by:	OBS
2013-11-28 15:05:08 +00:00
Philippe Audeoud
ee7ae13fca - Fix build with clang
- Support STAGEDIR

PR:		ports/184242
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
2013-11-27 16:07:51 +00:00
Philippe Audeoud
9a5536a62b - Fix build
- Support STAGEDIR

PR:		ports/184238
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
2013-11-27 13:16:47 +00:00
William Grzybowski
38592c3bf2 biology/lamarc: fix build on current
PR:		ports/184219
Submitted by:	KATO Tsuguru <tkato432 yahoo.com>
2013-11-26 15:37:05 +00:00
Baptiste Daroussin
51c60ddf7f Convert to USES=dos2unix
While here stagify some of the ports
Modernize LIB_DEPENDS
Extract zip with bsdtar when possible
2013-11-18 13:45:44 +00:00
William Grzybowski
75a509365b biology/seqtools: update to 4.23
PR:		ports/183960
Submitted by:	maintainer
2013-11-14 20:09:00 +00:00
Baptiste Daroussin
0169c8b869 Add stage support
Use bsdtar to extract the distfile
Rip out USE_GMAKE
2013-11-12 22:02:02 +00:00
Baptiste Daroussin
b2ac854afe Stage support
drop USE_GMAKE
2013-11-12 21:54:36 +00:00
William Grzybowski
20139c3cfa biology/seqtools: Tools for visualising sequence alignments
Blixem is an interactive browser of pairwise alignments that have
been stacked up in a "master-slave" multiple alignment; it is not
a 'true' multiple alignment but a 'one-to-many' alignment.

Belvu is a multiple sequence alignment viewer and phylogenetic tool.

Dotter is a graphical dot-matrix program for detailed comparison
of two sequences.

WWW: http://www.sanger.ac.uk/resources/software/seqtools/

PR:		ports/183801
Submitted by:	Kurt Jaeger <fbsd-ports opsec.eu>
2013-11-10 11:01:02 +00:00
Boris Samorodov
6807405893 . give maintainership to the submitter;
. add one month to DEPRACATION_DATE;

while here: strip the indefinite article from COMMENT.

PR:		ports/183742
Submitted by:	Kurt Jaeger <fbsd-ports@opsec.eu> (assigned maintainer)
2013-11-07 13:18:51 +00:00
Sunpoet Po-Chuan Hsieh
a0d361d097 - Update to 1.8
Changes:	http://search.cpan.org/dist/Bio-GFF3/Changes
2013-11-02 19:55:32 +00:00
Alexey Dokuchaev
0b0738811e - Install official UGENE documentation (PDF)
- Utilize DIST_SUBDIR as now it's more than one distfile
2013-11-01 15:20:28 +00:00
Alexey Dokuchaev
c5854fe3e1 - Update to version 1.12.3
- Conditionalize dependency on `devel/libexecinfo'
- Try to detect SSE2 support
- Convert to USES=qmake and stafigy
- Improve grammar in port description while here

Approved by:	maintainer (implicit)
2013-10-31 15:30:04 +00:00
Pawel Pekala
dfc46ed8d1 Update to version 36.3.6d
PR:		ports/181883
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
2013-10-29 19:32:15 +00:00
Gerald Pfeifer
3be3e90f93 Update to libmpc version 1.0.1 which brings the following fixes:
- Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui
 - 0^0, which returned (NaN,NaN) previously, now returns (1,+0).
 - Removed compatibility with K&R compilers, which was untestable due
   to lack of such compilers.
 - New functions
   . mpc_log10
   . mpc_mul_2si, mpc_div_2si
 - Speed-ups
   . mpc_fma
 - Bug fixes
   . mpc_div and mpc_norm now return a value indicating the effective
     rounding direction, as the other functions.
   . mpc_mul, mpc_sqr and mpc_norm now return correct results even if
     there are over- or underflows during the computation.
   . mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has
     infinite part and equals output variable is corrected.
   . mpc_fr_sub: Wrong return value for imaginary part is corrected.

Convert to the new LIB_DEPENDS standard and remove hard-coded
.so versions from a couple of dependent ports.

Bump PORTREVISIONS of all dependent ports.

PR:		183141
Approved by:	portmgr (bdrewery)
2013-10-26 00:52:33 +00:00
Dmitry Marakasov
a2105d9f79 - Remove manual creation and removal of share/applications, as it's now in the mtree (categories starting with [bce])
Approved by:	portmgr (bdrewery)
2013-10-22 13:57:35 +00:00
Baptiste Daroussin
79238694b3 Deprecated some ports broken for more than 6 month 2013-10-18 07:19:25 +00:00
Thomas Abthorpe
84e9967fe5 - Switch to build with lang/ruby19
- No PORTREVISION bump, option is off by default

With hat:	portmgr
2013-10-10 18:08:34 +00:00
David Chisnall
9443e7435f Update BioCocoa to the latest release.
Approved by:	bapt (mentor)
2013-10-08 18:34:45 +00:00
Wen Heping
3e2d8d2bfb - Update to 0.5.1 2013-10-04 08:09:02 +00:00
Sunpoet Po-Chuan Hsieh
10c66b58b4 - Update to 1.7
- Support STAGEDIR

Changes:	http://search.cpan.org/dist/Bio-GFF3/Changes
2013-10-03 16:19:59 +00:00
John Marino
a7256f135f biology/avida: add <unistd.h>, <typoinfo> for modern compilers 2013-10-01 22:00:47 +00:00
Bryan Drewery
2d8b17ea39 - Remove NO_STAGE as these have been tested to be safe
With hat:	portmgr
2013-09-25 00:54:08 +00:00
Rene Ladan
70f577a3ad Use value of BOINC_CLIENT_HOME in pkg-message 2013-09-24 12:00:40 +00:00
Rene Ladan
daefaaa864 - Add stagedir support
- Rewrap lines
2013-09-23 22:01:22 +00:00
Rene Ladan
e6b40643d7 Respect 'make check-sanity' for this port too. 2013-09-23 19:54:50 +00:00
Baptiste Daroussin
f45d0a8198 Fix NO_STAGE attribution 2013-09-22 18:05:04 +00:00
Baptiste Daroussin
7055ff02f1 Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
Bryan Drewery
444ad25cd4 Mark BROKEN, fails checksum
With hat:	portmgr
2013-09-18 14:44:58 +00:00
Antoine Brodin
1a72d776a0 Add an explicit dependency on pkgconf
Approved by:	portmgr (bapt)
2013-09-08 08:29:00 +00:00
Sunpoet Po-Chuan Hsieh
7684922546 - Use single space after WWW: 2013-09-07 17:20:21 +00:00
Andrej Zverev
6f12870030 - convert to the new perl5 framework
Approved by:	portmgr (bapt@, blanket)
2013-09-07 07:44:26 +00:00
Guido Falsi
642be1b81d - Make ports use the libc provided iconv implementation on 10-CURRENT
after r254273
- Fix a bunch of ports to properly work after this
- Mark converters/libiconv as IGNORE for systems with iconv in libc

Reviewed by:	bapt
Approved by:	portmgr (bapt)
Discussed with:	bapt, bsam (who both contributed ideas and code)
2013-09-04 18:06:07 +00:00
Sunpoet Po-Chuan Hsieh
1b0d3f744b - Add WWW
- Use single space after WWW:
- Remove Author line
2013-08-29 17:16:52 +00:00
Bryan Drewery
52c6ac3e26 - Disconnect ports removed in r325546 2013-08-29 02:28:57 +00:00
David Chisnall
3bec8741ff Update to latest GNUstep core libraries.
Update dependent packages with more recent releases.
Remove old and bit-rotted ones.
Switch to using clang 3.3 and libobjc2 1.7 by default, so modern Objective-C features work out of the box and remove a lot of configurable options for sub-optimal (and, often, unsupported / deprecated upstream) configurations.
Take maintainership of GNUstep-related ports.

Several of the ports left in have scary warnings which mean that they are likely broken in lots of cases.  Future commits will fix them.

Approved by:	bapt
2013-08-28 18:26:01 +00:00
Baptiste Daroussin
dcf5d98f78 Make sure to respect CC and CXX, this fixes the build on head without gcc 2013-08-28 06:04:51 +00:00
Brendan Fabeny
6c4fa199d0 Update math/gsl to 1.16 and adjust some dependent ports 2013-08-26 16:06:37 +00:00
Wen Heping
b057defb54 - Update to 2.3.5
- Add LICENSE
- Remove pkg-message since license changed upstream
- Do not install test files as example
2013-08-20 14:11:56 +00:00