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Commit Graph

1707 Commits

Author SHA1 Message Date
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
John Marino
b0b3dcecc0 biology/tinker: Regenerate distinfo to unbreak fetch
Apparently the distfile was rerolled.  The sizes of the file are only a few
bytes apart.  Since the master site never changed, it's reasonable just to
regenerate the distinfo and bump the PORTREVISION.

PR:		180664
Approved by:	bapt/culot (mentors, implicit)
2013-08-18 11:38:34 +00:00
Gerald Pfeifer
41e60477bd Replace USE_GCC=4.6+ and USE_GCC=4.4+ by USE_GCC=yes.
Right now this is a noop in the former case and a noop in the latter
case unless lang/gcc44 has been installed explicitly.

This puts a bit more emphasis on standardizing on a canonical version
"current" GCC and makes it easier to update that canonical version
by changing the default in Mk/bsd.gcc.mk and updating the lang/gcc port.

That is, USE_GCC=yes means "use a decent/modern version of GCC" without
having to worry about details.

Approved by:	portmgr (bdrewery)
2013-08-17 16:27:24 +00:00
Alex Kozlov
d4041784dc - Remove MAKE_JOBS_SAFE variable
Approved by:	portmgr (bdrewery)
2013-08-14 22:35:50 +00:00
John Marino
7e734bd16c biology/libgenome: Mark jobs unsafe
Approved by: 	bapt/culot (mentors, implicit)
2013-08-14 09:53:39 +00:00
Dirk Meyer
b83d7bf933 - update libdg to 2.1.0 2013-08-09 14:05:52 +00:00
Sunpoet Po-Chuan Hsieh
1104169569 - Pet portlint: remove blank line among *_DEPENDS 2013-08-06 13:03:54 +00:00
Andrej Zverev
2c25cf429d - Convert to new perl framework
- Trim Makefile header

Approved by:	wen@ (maintainer)
2013-08-06 08:50:49 +00:00
Mathieu Arnold
62a41b423b - Convert to new perl framework
- Remove MAKE_JOBS_SAFE=yes, it's the default.
2013-08-03 13:44:00 +00:00
Andrej Zverev
99ad912735 - Convert to new perl framework
- Trim Makefile header
2013-08-03 08:45:51 +00:00
Mathieu Arnold
4819ca343b - Convert to new perl framework
- Trim Makefile header
- Remove MAKE_JOBS_SAFE=yes, it's the default.
2013-08-02 18:52:07 +00:00
Philippe Audeoud
fc53f40978 - Update to 1.6
- Convert to new perl5 framework
- Changelog: http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-1.6/Changes
2013-08-01 13:15:48 +00:00
Rene Ladan
66fee90926 KDE3 and QT3 expired on 2013-07-01, remove these ports.
Unfortunately, this also affects some ports using QT3 as a GUI toolkit.

Changes to infrastructure files:
- bsd.kde.mk : obsolete, remove
- bsd.qt.mk : note that a CONFLICTS_BUILD line can probably go after a while
- CHANGES : document the removals from bsd.port.mk
- KNOBS : remove KDE and QT (KDE4 and QT4 should be used instead)
- MOVED : add the removed ports

PR:		ports/180745
Submitted by:	rene
Approved by:	portmgr (bapt)
Exp-run by:	bapt
2013-07-26 19:19:20 +00:00
Wen Heping
c65306f29b - Update to 3.0
- Convert to optionsNG
- Drop maintainership
2013-07-20 15:08:45 +00:00
Wen Heping
881d1953d7 - Update to 0.56 2013-07-20 10:04:32 +00:00
Wen Heping
75445be75e - Update to 2.37
Changes: http://cpansearch.perl.org/src/LDS/Bio-Graphics-2.37/Changes
2013-07-20 10:03:10 +00:00
Wen Heping
50ee70d703 - Update to 36.3.6
- Drop maintainership
2013-07-19 14:08:02 +00:00
Martin Wilke
c931ed3f31 - Update to 6.2.06
PR:		180518
Submitted by:	Ports Fury
2013-07-15 14:50:22 +00:00
Martin Wilke
0896ca6624 - Update to 4.4.2
PR:		180515
Submitted by:	Ports Fury
2013-07-15 14:49:02 +00:00
Sunpoet Po-Chuan Hsieh
c2d1a14c7c - Update to 7.31.0
- Bump PORTREVISION for ftp/curl shlib change
- Add TEST_DEPENDS
- Convert to new options framework
- Adjust options:
  - Add COOKIES
  - Add CYASSL, NSS, POLARSSL, THREADED_RESOLVER, TLS_SRP [1]
  - Add GSSAPI and SPNEGO [2]
  - Remove KERBEROS4
  - Rename LIBIDN to IDN
  - Remove TRACKMEMORY [1]
- Sort option handler
- Add SLAVEDIRS: ftp/curl-hiphop
- Cosmetic change
- Cleanup Makefile header
- While I'm here, fix typo (PORTREVSION) in x11-wm/ede/Makefile

Changes:	http://curl.haxx.se/changes.html
PR:		ports/172325 (-exp run), ports/177369 (based on) [1]
Submitted by:	Hirohisa Yamaguchi <umq@ueo.co.jp> [1], hrs (via email) [2]
Exp run by:	miwi
2013-07-11 16:26:26 +00:00
Baptiste Daroussin
0e92144c9f Convert from USE_MOTIF to USES=motif 2013-07-10 07:33:24 +00:00
Baptiste Daroussin
bad37a6cd4 Convert from USE_MOTIF to USES=motif
While here:
- trim headers
- Remove indefinite article from comment
- convert USE_GMAKE to USES=gmake
2013-07-09 21:49:35 +00:00
Antoine Brodin
4cf302d6b0 Fix some PORT_OPTIONS conversions 2013-06-30 20:53:06 +00:00
Baptiste Daroussin
5b4f8f3bbd Convert to USES=imake
Trim headers
2013-06-28 18:32:25 +00:00
Raphael Kubo da Costa
9db47c1f7c Fix some screw ups introduced in r319847.
I'm not sure if the submitter of ports/179224 didn't even test his patch or
if the distfile was re-rolled in a bizarre way.

Anyway, fix distfile and also cd into the correct directories to actually
build the port.

PR:		ports/179790
2013-06-24 18:09:52 +00:00
Boris Samorodov
747a2e993f Remove stale (since r321246) pkg-plist file. 2013-06-19 21:04:36 +00:00
Boris Samorodov
e92c6f2a98 . introdice optionsNG to the port;
. remove shlib ABI version from LIB_DEPENDS;
. introduce EXAMPLE option (do not install examples to DOCSDIR);
. bump PORTREVISION;
. get use of PLIST_FILES, PORTDOCS and PORTEXAMPLES at Makefile;
. get rid of pkg-plist;
. trim Makefile heades;
. remove acticle from COMMENT;
. simplify install commands.
2013-06-19 20:06:59 +00:00
Boris Samorodov
6c45647e07 . NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. introduce EXAMPLES option (do not install examples to DOCSDIR);
. bump PORTREVISION;
. make use of PLIST_FILES, PORTDOCS and PORTEXAMPLES at Makefile;
. get rid of pkg-plist;
. simpify install commands.
2013-06-19 20:01:30 +00:00
Boris Samorodov
75e93c8196 . NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. mute mdir commands and unmute install commands;
. do not use mkdir for parent directories (mkdir implies "-p");
. introduce EXAMPLE option (do not install examples to DOCSDIR);
. bump PORTREVISION;
. make use of PLIST_FILES, PORTDOCS and PORTEXAMPLES at Makefile;
. get rid of pkg-plist;
. use standard DOCSDIR and EXAMPLESDIR (instead of a PREFIX/foo/bar path);
. trim Makefile headers.
2013-06-19 19:54:13 +00:00
Boris Samorodov
0c61d2954c . NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. pet portlint: use {} instaed of () at variable;
. use PLIST_FILES, PORTDATA and PORTDOCS at Makefile;
. get rid of pkg-plist;
. remove article from COMMENT;
. trim Makefile headers.
2013-06-19 19:20:25 +00:00
Boris Samorodov
8def27fa74 . NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. mute mkdir;
. use PLIST_FILES and PORTDOCS at Makefile;
. remove pkg-plist;
. trim Makefile headers;
. remove article from COMMENT;
. pet portlint -- use opne space after WWW: at pkg-descr.
2013-06-19 19:15:14 +00:00
Boris Samorodov
de034ce0d6 Use optionsNG for DOCS. 2013-06-19 19:07:35 +00:00
Boris Samorodov
6c227ca468 . NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. use PORTDOCS at Makefile (thus simplify pkg-plist);
. use plain install instead of a .for loop;
. trim Makefile headers.
2013-06-19 19:05:47 +00:00
Boris Samorodov
0ed60a672e . NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. use PLIST_FILES, PORTDATA and PORTDOCS;
. use standard DATADIR and DOCSDIR (rather PREFIX/foo/bar);
. remove pkg-plist.
2013-06-19 19:01:47 +00:00
Boris Samorodov
c23d4e5464 . NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. trim Makefile headers.
2013-06-19 18:56:37 +00:00
Boris Samorodov
a4c819f709 . add license (GPLv2);
. bump PORTREVISION;
. NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. trim Makefile headers.
2013-06-19 18:53:54 +00:00
Boris Samorodov
e4da7811ba . NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. use f instead of file for a variable (portlint warns against file);
. do not mute install commands;
. remove article from COMMENT;
. trim Makefile headers;
. pet portlint: use one space after WWW: at pkg-descr.
2013-06-19 18:51:16 +00:00
Boris Samorodov
f257e1ad16 . remove pkg-plist (along with the previous commit). 2013-06-19 18:44:32 +00:00
Boris Samorodov
cb68e7ac4a . NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. use PORTDOCS and PORTDATA at makefile;
. mute mkdirs;
. add padding to PKGMESSAGE;
. remove article from COMMENT.
2013-06-19 18:43:13 +00:00
Boris Samorodov
52d1606f7c . NOPORTEXAMPLES -> PORT_OPTIONS:MEXAMPLES;
. use PORTEXAMPLES at Makefile;
. trim Makefile headers.
2013-06-19 18:38:46 +00:00
Boris Samorodov
7ce5fafe53 . add license (GPLv2);
. bump PORTREVISION;
. trim article from COMMENT;
. trim Makefile headers.
2013-06-19 16:36:53 +00:00
Boris Samorodov
2f705dfa96 . pet portlint: add USE_LDCONFIG;
. bump PORTREVISION.
2013-06-19 15:43:56 +00:00
Boris Samorodov
0fe9c450a3 . trim Makefile headers;
. remove the indefinite article from COMMENT.
2013-06-19 15:39:18 +00:00
Boris Samorodov
3d4edf2fac . NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. use PLIST_FILES and PORTDOCS;
. remove pkg-plist (4 lines).
2013-06-19 14:10:02 +00:00
Boris Samorodov
1eb6ad8592 . NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. remove LICENSE_FILE for a standard license (GPLv2);
. trim Makefile headers.
2013-06-19 13:35:55 +00:00
Boris Samorodov
f0b8908924 Index: Makefile
===================================================================
--- Makefile	(revision 321238)
+++ Makefile	(working copy)
@@ -1,9 +1,5 @@
-# New ports collection makefile for:	seqio
-# Date created:				17 August 2001
-# Whom:					Tony Maher
-#
+# Created by: Tony Maher
 # $FreeBSD$
-#

 PORTNAME=	seqio
 PORTVERSION=	1.2.2
@@ -13,38 +9,32 @@
 DISTNAME=	${PORTNAME}

 MAINTAINER=	ports@FreeBSD.org
-COMMENT=	A set of C functions which can read/write biological sequence files
+COMMENT=	Set of C functions which can read/write biological sequence files

 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}

 EXAMPLES=	example1.c example2.c example3.c example4.c seqio.c \
 		seqio.h Makefile
 PROGRAMS=	fmtseq grepseq idxseq typeseq wcseq
+PLIST_FILES+=	${PROGRAMS:S,^,bin/,}
+PORTEXAMPLES=	*
+PORTDOCS=	*

+OPTIONS_DEFINE=	DOCS EXAMPLES
+
+.include <bsd.port.options.mk>
+
 do-install:
-	cd ${WRKSRC}; \
-	for file in ${PROGRAMS}; do \
-		${INSTALL_PROGRAM} $$file ${PREFIX}/bin; \
-	done
-.if !defined(NOPORTEXAMPLES)
-	${MKDIR} ${EXAMPLESDIR}
-	cd ${WRKSRC}; \
-	for file in ${EXAMPLES}; do \
-		${INSTALL_DATA} $$file ${EXAMPLESDIR}; \
-	done
+	${INSTALL_PROGRAM} ${PROGRAMS:S,^,${WRKSRC}/,} ${PREFIX}/bin
+.if ${PORT_OPTIONS:MEXAMPLES}
+	@${MKDIR} ${EXAMPLESDIR}
+	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/,} ${EXAMPLESDIR}
 .endif
-.if !defined(NOPORTDOCS)
-	${MKDIR} ${DOCSDIR}
-	${MKDIR} ${DOCSDIR}/html
+.if ${PORT_OPTIONS:MDOCS}
+	@${MKDIR} ${DOCSDIR}/html
 	${INSTALL_DATA} ${WRKSRC}/bioseq.txt ${DOCSDIR}
-	cd ${WRKSRC}/doc; \
-	for file in *.doc; do \
-		${INSTALL_DATA} $$file ${DOCSDIR}; \
-	done
-	cd ${WRKSRC}/html; \
-	for file in *.html; do \
-		${INSTALL_DATA} $$file ${DOCSDIR}/html; \
-	done
+	${INSTALL_DATA} ${WRKSRC}/doc/*.doc ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/html/*.html ${DOCSDIR}/html
 .endif

 .include <bsd.port.mk>
2013-06-19 13:09:19 +00:00
Boris Samorodov
4392a3472d . NOPORTDOCS -> PORT_OPTIONS:MDOCS;
. use PLIST_FILES and PORTDOCS;
. get rid of  pkg-plist;
. pet portlint: use one space after WWW: at pkg-descr;
. trim Makefile headers;
. remove the indefinite article from COMMENT.
2013-06-19 12:43:28 +00:00
Andrej Zverev
b62e166e01 - Avoid of using SITE_PERL
- Remove depend on DB_File.pm since it part of perl distribution

PR:		ports/178877
Submitted by:	az
Approved by:	matainer (timeout)
2013-06-07 06:51:42 +00:00
Martin Wilke
db74061cad - Update to 3.6.9.5
PR:		179224
Submitted by:	Ports Fury
2013-06-04 10:02:30 +00:00
Martin Wilke
0ed7cc3196 - Fix build with clang
PR:		179215
Submitted by:	Ports Fury
2013-06-04 08:26:03 +00:00
Wen Heping
b3107f6cbf - Trim Makefile headers 2013-06-01 14:22:35 +00:00
Martin Wilke
727fa1d184 - Update to 6.2.05
PR:		179061
Submitted by:	Ports Fury
2013-05-29 05:25:49 +00:00
Wen Heping
e5c64e2888 - Update to 3.5.1
- Trim Makefile headers
- Convert to optionsNG
- Update WWW, MASTER_SITES and COMMENT
2013-05-26 07:49:47 +00:00
Martin Wilke
3781b13d04 - Update to 6.2.04
PR:		178590
Submitted by:	Ports Fury
2013-05-21 08:19:03 +00:00
Baptiste Daroussin
9f1de9b900 Convert USE_NCURSES by USES=ncurses
Convert USE_READLINE by USES=readline
2013-05-06 15:34:17 +00:00
Baptiste Daroussin
dc9dfec602 Fix build by adding an explicit dep on pkgconf 2013-05-03 20:48:34 +00:00
Frederic Culot
ec91efa233 - Update to 1.13.0
- Improve COMMENT (remove leading article, add missing space)
- Remove unneeded BSD license file
- Trim Makefile's header
- Pet portlint (move LICENSE section earlier, change tab to space in WWW link)

Changes:	http://sourceforge.net/p/staden/news/2013/03/iolib-1130-released/
2013-04-30 15:41:49 +00:00
Xin LI
59816216bc Workaround the way mopac installs executables.
PR:		ports/171932
Reported by:	Jinsong Zhao <jszhao yeah net>
2013-04-29 17:30:09 +00:00
Martin Wilke
3cf5f6199d - Update to 6.2.02
PR:		178031
Submitted by:	Ports Fury
2013-04-29 14:23:03 +00:00
Rene Ladan
59140a81a3 Use bsd.port.options.mk instead of bsd.port.{pre|post}.mk 2013-04-29 12:20:35 +00:00
Marcus von Appen
821843ca06 - Convert USE_ICONV=yes to USES=iconv
- Change USE_GNOME=pkgconfig|gnomehack to USES=pathfix|pkgconfig while here

Reviewed by:	bapt, kwm
2013-04-27 08:50:46 +00:00
Bryan Drewery
6539776faf Remove unneeded escaping 2013-04-26 16:23:13 +00:00
Martin Wilke
ff0810582d - Update to 5.0.6
PR:		178032
Submitted by:	Ports Fury
2013-04-26 06:57:37 +00:00
Glen Barber
8b8bc02a97 Update MASTERSITES for my server to use https
Approved by:	wen (maintainer, implicit)
2013-04-26 04:03:54 +00:00
Alex Kozlov
e159824929 - Convert USE_GETTEXT to USES (part 3)
Approved by:	portmgr (bapt)
2013-04-24 18:10:30 +00:00
Baptiste Daroussin
992586fa08 Finish converting the whole ports tree to USES=pkgconfig 2013-04-23 14:20:25 +00:00
Eitan Adler
5190f14f8d For perl@ owned ports:
- Fix COMMENT
- Trim header
2013-03-29 00:44:53 +00:00
Martin Wilke
f811ff18d3 - Update to 4.4.1
PR:		177257
Submitted by:	Ports Fury
2013-03-26 01:08:40 +00:00
Martin Wilke
78d7633e69 - Mark broken checksum mismatch
Reported by:	pointyhat http://pointyhat.freebsd.org/errorlogs/i386-errorlogs/a.8.20130324140101.pointyhat/dotter-20021204.log
2013-03-25 01:41:31 +00:00
Martin Wilke
fbdc28e4dd - Update to 6.2.01
PR:		177261
Submitted by:	ports fury
2013-03-24 16:13:57 +00:00
Max Brazhnikov
ffd97a0193 - convert USE_CMAKE to USES
- while here clean up some ports from CMAKE_VERBOSE, which is intended
  for users

Approved by:	portmgr (miwi)
2013-03-22 20:06:14 +00:00
Vanilla I. Shu
42ef81ca40 Fix build with protobuf-2.5.0
Obtained from:	miwi@
2013-03-21 14:09:22 +00:00
Jason Helfman
82c28cbbf5 - adopt optionsNG
- trim historical header
- tighten COMMENT

Approved by:	portmgr (miwi)
2013-03-18 23:35:01 +00:00
Vanilla I. Shu
5e191b87d1 1: Upgrade protobuf to 2.5.0.
2: bump revision.
3: document UPDATING.
2013-03-18 15:14:27 +00:00
Jason Helfman
3005e8f2fc - adoption of optionsNG
- trim historical header

Approved by:	portmgr (miwi)
2013-03-18 06:55:42 +00:00
Jason Helfman
4153f3e96b - adoption of optionsNG
- trim historical header
- fix mixture of DOCS/EXAMPLES -> EXAMPLES
- add shared description for GLUT to bodm

Approved by:	portmgr (miwi)
2013-03-18 06:54:39 +00:00
Jason Helfman
21ff3eb3b7 - adoption of optionsNG
- trim historical header
- tighten COMMENT

Approved by:	portmgr (miwi)
2013-03-18 06:50:12 +00:00
Jason Helfman
aa6aea716d - adoption of optionsNG
- trim historical header
- use tabs in favor of spaces

Approved by:	portmgr (miwi)
2013-03-18 06:48:55 +00:00
Martin Wilke
1b607e2b11 - Update to 2012.06.20
PR:		176544
Submitted by:	Ports Fury
2013-03-14 05:27:58 +00:00
Baptiste Daroussin
9250d94365 Convert USE_BISON to USES= bison
It brings bison as a build dependency in case it is set the following way:
USES= bison or USES= bison:build

it brings bison as a run dependency in case it is set the following way:
USES= bison:run

it brings bison both as a run and build dependency in case it the set the following way:
USES= bison:both

While here trim some headers
Convert some USE_GNOME= gnomehack to USES= pathfix
2013-03-08 11:32:11 +00:00
Rene Ladan
a155d81752 Remove compatibility with FreeBSD 7.X
While here pet Makefile headers.
2013-03-06 23:31:58 +00:00
Eitan Adler
0a035043de Add missing item to pkg-plist reported by QAT but not reported by poudriere. 2013-03-03 15:22:43 +00:00
Eitan Adler
0bf06bbddc Update to 2.33 2013-03-03 01:45:00 +00:00
Martin Wilke
ac8c5f4481 - Update to 2.4.1
PR:		176552
Submitted by:	Ports Fury
2013-03-02 14:50:25 +00:00
Alexey Dokuchaev
bb8c521c72 Unbreak on 7.X and i386 systems.
Reported by:	QAT
2013-02-25 13:00:15 +00:00
Alexey Dokuchaev
53bda2f119 Add Unipro UGENE, a free open-source crowss-platform bioinformatics software.
PR:		ports/173387
Submitted by:	Hannes Hauswedell
2013-02-23 04:50:48 +00:00
Frederic Culot
417a7b673b - Update to 0.52 [1]
- Capitalize names (Perl) in COMMENT

PR:		ports/176003 [1]
Submitted by:	Gea-Suan Lin <gslin@gslin.org>
2013-02-16 14:58:51 +00:00
Ruslan Makhmatkhanov
a699fc1724 - remove empty files 2013-02-15 08:57:19 +00:00
Martin Wilke
c23a507726 - Fix build with clang
PR:		175034
Submitted by:	Ports Fury
2013-02-10 07:55:45 +00:00
Philippe Audeoud
9b5140c936 - Update to 1.27
- Changelog: http://cpansearch.perl.org/src/TFRAYNER/Bio-MAGETAB-1.27/Changes
2013-02-05 14:45:14 +00:00
Marcelo Araujo
6faa1b7774 - Update to 20121109.
PR:		ports/175014
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
2013-02-04 10:07:30 +00:00
Thomas Abthorpe
49626f567a - Strip header at request of original creator
Submitted by:	trevor
With hat:	portmgr
2013-01-27 05:55:20 +00:00
Philippe Audeoud
fad40cef87 - Update to 2.32
- Changelog: http://cpansearch.perl.org/src/LDS/Bio-Graphics-2.32/Changes
2013-01-24 14:36:55 +00:00
Max Brazhnikov
81c27c891a Bump PORTREVISION after DESKTOP_ENTRIES update 2013-01-23 15:00:18 +00:00
Marcelo Araujo
05e78fe84a - Update to 9.03.
PR:		ports/172499
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
2013-01-14 08:04:38 +00:00
Max Brazhnikov
5dd37213f5 - Update DESKTOP_ENTRIES:
* rephrase Comment field or use port ${COMMENT} if appropriate
  * adjust Icon field according to the Desktop Entry Specification
  * update Categories field: remove deprecated category Application;
    set main category, if missing
- Remove indefinite article and/or rephrase COMMENT
- Trim Makefile header
- Other minor changes
2013-01-07 02:07:26 +00:00
Rene Ladan
b29162eed1 Take over maintainership.
Approved by:	pav (previous maintainer)
2012-12-28 21:59:42 +00:00
Rene Ladan
b06829187f Use the new project URL to let the application attach coorectly to the
project, and some cleanups:
- use optionsNG
- update commands in pkg-install.in
- improve %%AMD64%% comment handling
- convert Makefile header
- remove unused variable SIMAP_URL

Bump PORTREVISION

PR:		ports/174748
Submitted by:	myself
Approved by:	maintainer (pav@)
2012-12-27 20:12:06 +00:00
Andrej Zverev
14d750125f Cleanup supporting perl version 5.8 and 5.10,
lang/perl5.8 and lang/5.10 will be removed from ports tree soon.
2012-12-17 15:39:36 +00:00
Wen Heping
b7e651129e - Update to 1.5
Changes: http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-1.5/Changes
2012-12-16 04:22:15 +00:00
Eitan Adler
1c155b4991 Update to 5.0.4 2012-12-14 17:47:16 +00:00
Max Brazhnikov
4beaa15d30 - Mark conflict with science/openbabel
- Trim Makefile header
2012-12-11 14:24:51 +00:00
Max Brazhnikov
5bf9bfc399 science/openbabel:
- Update openbabel to 2.3.2
- Switch to CMake build system
- Add PYTHON and CAIRO options
- Don't rename babel binary, mark conflict with ancient biology/babel

science/py-openbabel:
- Merge py-openbabel to openbabel

other:
- chase openbabel update
2012-12-11 14:19:54 +00:00
Baptiste Daroussin
db767ee750 Remove hardcoded extract dependency on diablo-jdk16, directly use USE_ZIP
instead given that jar files are just zip files, remove hardcoded do extract
target.

Reported by:	linimon, matthew
2012-12-11 07:26:38 +00:00
Baptiste Daroussin
7c354b1913 Decommissioning java 1.5 (EOLed since October 2009):
suppress any reference to JAVA_VERSION=	1.5+ (part2)
2012-12-10 13:18:28 +00:00
Baptiste Daroussin
580b0c7423 Decommissioning java 1.5 (EOLed since October 2009):
suppress any reference to USE_JAVA=	1.5+ (part1)
2012-12-10 11:25:27 +00:00
Pawel Pekala
e8c48e4d84 - Support CC properly
- Switch to PLIST_FILES
- Add option for GTK2 support

PR:		ports/174174
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
Feature safe:	yes
2012-12-07 22:22:06 +00:00
Anton Berezin
c25a46dd74 Update to 2.31.
Changes: http://search.cpan.org/dist/Bio-Graphics/Changes

Feature safe:	yes
2012-12-07 13:49:15 +00:00
Ryan Steinmetz
33a2019014 - Reset MAINTAINER due to unrecoverable email bounce
Reported by:	portscout
Feature safe:	yes
2012-12-04 20:28:16 +00:00
Pietro Cerutti
a6f872f2b0 - Fix build with clang
Feature safe:	yes
2012-12-03 11:27:47 +00:00
Armin Pirkovitsch
2b222ce70c - Update to version 6.1.01
- Add MAKE_JOBS_SAFE
- Convert to optionsng
- Trim Makefile header

PR:           ports/171971
Submitted by: KATO Tsuguru <tkato432 _at_ yahoo.com>
Approved by:  beat (mentor)
Feature safe: yes
2012-12-01 00:00:43 +00:00
Armin Pirkovitsch
f50819ce60 - Update to version 5.0.2
- Add MAKE_JOBS_UNSAFE
- Convert to optionsng

PR:           ports/171970
Submitted by: KATO Tsuguru <tkato432 _at_ yahoo.com>
Approved by:  beat (mentor)
Feature safe: yes
2012-11-30 23:51:49 +00:00
Baptiste Daroussin
18210032c9 2012-11-26 benchmarks/gsbench: No more public distfiles
2012-11-26 benchmarks/xengine: No more public distfiles
2012-11-26 biology/belvu: No more public distfiles
2012-11-26 multimedia/kaffeine-mozilla: No more public distfiles
2012-11-26 www/gnustep-ticker: Abandonware
2012-11-26 net/tryst-examples: Abandonware
2012-11-26 net/tryst: Abandonware

Feature safe:	yes
2012-11-28 09:05:54 +00:00
Wen Heping
2a3cdaf773 - Update to version 2.0
- Update pkg-descr

PR:		172497
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>

Feature safe:	yes
2012-11-15 07:04:29 +00:00
Pawel Pekala
ff942cf270 - Update to version 4.4.0
- Mark MAKE_JOBS_SAFE
- Make dependency on print/pdflib optional
- Switch to PLIST_FILES

While here:
- Add missing deps
- Add desktop entry

PR:		ports/172498
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
Feature safe:	yes
2012-10-30 20:31:14 +00:00
Pawel Pekala
987bb3de6b Update to version 2.12.4
PR:		ports/172218
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
Feature safe:	yes
2012-10-30 17:53:39 +00:00
Wen Heping
cb1e050008 - Reset maintainer to perl@
Feature safe:	yes
2012-10-30 02:03:29 +00:00
Wen Heping
68d3450c97 - Update to 1.4
Changes: http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-1.4/Changes
- Trim Makefile headers

Feature safe:	yes
2012-10-30 01:59:37 +00:00
Wen Heping
a2845e428a - Trim Makefile headers
- Reset maintainer to perl@

Feature safe:	yes
2012-10-30 01:47:15 +00:00
Baptiste Daroussin
da6c3af5fc Deprecate a bunch of ports that are either abandonware and/or for which no more
public distfiles are available, or for which are -devel version with a more
recent stable version for long

Feature safe:	yes
2012-10-26 14:57:50 +00:00
Baptiste Daroussin
3db2e90933 2012-10-20 chinese/wangttf: No more public distfiles
2012-10-20 chinese/stardict-dict-zh_TW: No more public distfiles
2012-10-20 chinese/stardict-dict-zh_CN: No more public distfiles
2012-10-20 chinese/mingunittf: No more public distfiles
2012-10-20 chinese/dfsongsd: No more public distfiles
2012-10-20 biology/dna-qc: No more public distfiles

Feature safe:	yes
2012-10-25 23:05:56 +00:00
Wen Heping
5c73d4b55d - Update to 1.26
Changes: http://cpansearch.perl.org/src/TFRAYNER/Bio-MAGETAB-1.26/Changes

Feature safe:	yes
2012-10-25 00:18:32 +00:00
Dirk Meyer
851945b1eb - cleanup comments
Feature safe: yes
2012-10-13 13:39:56 +00:00
Wen Heping
27c347dbdd - Update to 1.5.3
- Trim Makefile headers
2012-10-08 03:17:02 +00:00
Wen Heping
baa9b66158 - Take maintainership 2012-10-01 14:55:55 +00:00
Thomas Abthorpe
d46aafc64e - Reassign to the heap at maintainer's request 2012-10-01 14:45:16 +00:00
Max Brazhnikov
ecd280d820 Add new ports biology/plink [1] and biology/plinkseq [2]:
PLINK is a free, open-source whole genome association analysis toolset.
PLINK/SEQ is an open-source C/C++ library for working with human
genetic variation data.

PR:		ports/171918 [1]
PR:		ports/171922 [2]
Submitted by:	Jason Bacon <jwbacon at tds.net>
2012-09-27 09:59:25 +00:00
Ruslan Makhmatkhanov
9f67b5e7f1 - update to 1.60
while here:
- convert Makefile header into two-line format
- update COMMENT (indefinite article removed)
- change USE_PYTHON to just -2.7
- remove py-reportlab from BUILD_DEPENDS and kick PYTHON_SITELIBDIR from there
- tab -> space change in pkg-descr:WWW

PR:		171115
Submitted by:	wen
Approved by:	Mauricio Herrera Cuadra <mauricio at arareko dot net> (maintainer)
2012-09-25 08:06:42 +00:00
Alexey Dokuchaev
bd4927ffa4 Mea culpa, s/Whom/Created by/ 2012-09-23 15:40:58 +00:00
Alexey Dokuchaev
e6bc1ecae5 - Adjust "Created by" tag to include more complete submitter's information
- Mute MKDIRs, remove trailing dot from RESTRICTED, drop leading indefinite
  article from COMMENT where appropriate
2012-09-23 15:38:58 +00:00
Thomas Abthorpe
f48ef480ea - Reassign to the heap at maintainer's request 2012-09-22 15:34:16 +00:00
Baptiste Daroussin
6b968aca1e Deprecated a bunch a ports with nor more public distfiles (thanks ehaupt's
distilator
2012-09-20 22:26:26 +00:00
Mark Linimon
3fd15ea0ae Mark as broken on sparc64: depends on thread-local storage, which is not
available on sparc64.

Hat:		portmgr
2012-09-08 08:30:39 +00:00
Baptiste Daroussin
0ff48b2c81 Fix build with clang 2012-08-24 10:18:51 +00:00
Michael Scheidell
1217f4c6f2 - Submitter is now maintainer
PR:		ports/169920
Approved by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
2012-08-07 13:54:02 +00:00
Michael Scheidell
2c946497ba - Update to version 6.903
PR:		ports/169920
Submitted by:	"Reed A. Cartwright" <cartwright@asu.edu>
Approved by:	maintainer (timeout, 21 days)
2012-08-07 12:26:39 +00:00
Koop Mast
5aa7246575 Switch from libglut to freeglut and retire libglut. Libglut hasn't been
developed in years and has been dropped from the MESA 8.0 distribution.
Freeglut is a rewrite of glut and is actively developed and is used by
many linux distributions instead of libglut.

Bump all ports that directly depend on libglut because of the shlib version
change.

There are some extra items in this patch.

*) Because freeglut doesn't have the same dependancies as libglut, some ports
	need extra dependencies added to USE_XORG to make them build.
*) Mark graphics/f90gl broken, f90gl depends on a header that is only shipped
	with libglut.
*) Remove option for libglut/freeglut selection in games/cake, only freeglut
	remains now.
*) While here fix a png related build issue games/vegastrike.

Thanks to miwi for running the exp-run.

Approved by:	portmgr (miwi)

Collaboration with:	zeising@
Obtained from:	xorg-dev staging area.
2012-08-04 22:52:02 +00:00
Carlo Strub
db5e2bc177 Fix typos in COMMENT
Approved by:	portmgr@ (implicit)
2012-07-29 11:17:02 +00:00
Carlo Strub
d5fda8cb2c Fix typos in COMMENT 2012-07-25 06:32:06 +00:00
Carlo Strub
1863cc77b0 Fix typos in COMMENT 2012-07-24 07:19:21 +00:00