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* Unbreak the fetch: one of the documentation PDF files was rerolled.danfe2014-01-302-4/+2
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* - Mark BROKEN because it does not fetchdecke2014-01-301-0/+2
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* - fix pkg-plistaz2014-01-302-4/+3
| | | | - add LICENSE
* - Stagify; cleanup Makefile and reorder the knobs a bitdanfe2014-01-291-28/+21
| | | | - Drop the case for long unsupported alpha architecture
* - Fix build on -currentmiwi2014-01-266-26/+60
| | | | | | | | | | - Update MASTER_SITES and WWW: line - Support CXX/CXXFLAGS properly - Support PLIST_FILES - Stage support PR: 184852 Submitted by: Ports Fury
* - Update to 1.9sunpoet2014-01-233-8/+7
| | | | | | - Sort PLIST Changes: http://search.cpan.org/dist/Bio-GFF3/Changes
* Fix properties on pkg-plistbapt2014-01-224-4/+0
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* Support stagebapt2014-01-211-5/+4
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* Support stagebapt2014-01-211-6/+5
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* Support stagebapt2014-01-212-3/+1
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* Support stagebapt2014-01-212-13/+26
| | | | Conver USE_GMAKE
* Stage supportantoine2014-01-181-15/+7
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* - Update to version 1.13.0 and improve FreeBSD support; it also buildsdanfe2014-01-179-140/+378
| | | | | | | | | | 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)
* Reduce over inclusion of bsd.port.mkbapt2014-01-161-2/+1
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* Reduce over inclusion of bsd.port.mkbapt2014-01-161-2/+1
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* Reduce over inclusion of bsd.port.mkbapt2014-01-161-2/+1
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* Reduce over inclusion of bsd.port.mkbapt2014-01-161-7/+3
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* Reduce over inclusion of bsd.port.mkbapt2014-01-161-2/+1
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* Support stagebapt2014-01-161-19/+10
| | | | | Reduce over inclusions of bsd.port.mk Use BROKEN_${ARCH}
* Python cleanup:rene2014-01-143-3/+3
| | | | | | | - USE_PYTHON* = 2.X -> USE_PYTHON* = 2 - USE_PYTHON* = 2.X+ -> USE_PYTHON* = yes Reviewed by: python (mva, rm) Approved by: portmgr-lurkers (mat)
* - Fix build with clangriggs2014-01-132-13/+8
| | | | | | | | - Stage support PR: ports/185655 Submitted by: Tassilo Philipp <tphilipp@potion-studios.com> (maintainer) Approved by: thierry (mentor)
* - add stage supportaz2014-01-062-6/+4
| | | | Approved by: portmgr (blanket infrastructure)
* - add stage supportaz2014-01-063-4/+2
| | | | Approved by: portmgr (blanket infrastructure)
* - support stageaz2014-01-056-135/+143
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* Mark as broken: Invalid checksum, seems like the software was rerolledbapt2014-01-041-0/+2
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* Convert biology to MDOCS and MEXAMPLESadamw2014-01-0314-20/+46
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* - rename AL2 to APACHE20 in Mk/bsd.licenses.db.mkohauer2013-12-311-1/+1
| | | | | | | | | | | | | | - 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@)
* Stage supportantoine2013-12-311-3/+2
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* Stage supportantoine2013-12-311-13/+4
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* - USES=fortran gmake.tijl2013-12-292-16/+15
| | | | | | | - Add dependency on xproto. - Fix build with new CFLAGS. - Staging. - New WWW.
* The hmmer binary was renamed upstream to indicate that it is now anrene2013-12-292-6/+6
| | | | archive file, adjust the port so that fetch and extract work again.
* biology/seqtools: update to 4.24wg2013-12-252-3/+3
| | | | | PR: ports/185162 Submitted by: maintainer
* Several fixes:rene2013-12-242-10/+14
| | | | | | | | | | | | | - 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
* - Fix build with clang/libc++.wen2013-12-202-3/+12
| | | | | | | - Support staging. PR: 184974 Submitted by: tijl@
* - Respect CC/CFLAGSpawel2013-12-202-6/+43
| | | | | PR: ports/184857 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* - biology/tinker: USES=fortran, staging.tijl2013-12-192-22/+20
| | | | | - Add CONFLICTS_INSTALL between hunspell and tinker. Both install bin/analyze.
* USES=fortran, staging.tijl2013-12-191-9/+5
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* USES=fortran, staging, miscellaneous cleanups.tijl2013-12-192-119/+26
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* Version 2013.12.12, USES=fortran, staging.tijl2013-12-181-30/+17
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* USES=fortran, fix LDFLAGS, staging.tijl2013-12-181-11/+10
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* Fix the build with more standards-compliant compilers such as GCC 4.7. [1]gerald2013-12-134-1/+63
| | | | | | | | 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]
* In preparation for making libtool generate libraries with a sane name, fix allbapt2013-12-1112-19/+19
| | | | LIB_DEPENDS in biology
* Support stagebapt2013-12-111-8/+5
| | | | | USE_GMAKE -> USES=gmake use USES=readline:port
* Support stagebapt2013-12-111-8/+5
| | | | | USE_GMAKE -> USES=gmake Respect CC
* Support stagebapt2013-12-111-3/+3
| | | | | | Convert USE_GMAKE to USES=gmake Add dependency on perl which the port need and was getting by chance bump portrevision, dependencies has changed
* Respect PORT_OPTIONS:MDOCSadamw2013-12-092-8/+8
| | | | | Clean up COMMENT USES=gmake
* - Fix build on headwen2013-12-011-0/+1
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* - Update to 1.28jadawin2013-11-283-62/+60
| | | | Sponsored by: OBS
* - Fix build with clangjadawin2013-11-285-34/+44
| | | | | | | - Support STAGEDIR PR: ports/184242 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* - Fix buildjadawin2013-11-272-10/+42
| | | | | | | - Support STAGEDIR PR: ports/184238 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* biology/lamarc: fix build on currentwg2013-11-262-4/+10
| | | | | PR: ports/184219 Submitted by: KATO Tsuguru <tkato432 yahoo.com>
* Convert to USES=dos2unixbapt2013-11-181-6/+5
| | | | | | While here stagify some of the ports Modernize LIB_DEPENDS Extract zip with bsdtar when possible
* biology/seqtools: update to 4.23wg2013-11-152-4/+4
| | | | | PR: ports/183960 Submitted by: maintainer
* Add stage supportbapt2013-11-131-18/+8
| | | | | Use bsdtar to extract the distfile Rip out USE_GMAKE
* Stage supportbapt2013-11-131-11/+6
| | | | drop USE_GMAKE
* biology/seqtools: Tools for visualising sequence alignmentswg2013-11-108-60/+61
| | | | | | | | | | | | | | | | 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>
* . give maintainership to the submitter;bsam2013-11-071-3/+3
| | | | | | | | | . 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)
* - Update to 1.8sunpoet2013-11-032-3/+3
| | | | Changes: http://search.cpan.org/dist/Bio-GFF3/Changes
* - Install official UGENE documentation (PDF)danfe2013-11-013-3/+21
| | | | - Utilize DIST_SUBDIR as now it's more than one distfile
* - Update to version 1.12.3danfe2013-10-318-79/+325
| | | | | | | | | - 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)
* Update to version 36.3.6dpawel2013-10-305-93/+114
| | | | | PR: ports/181883 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* Update to libmpc version 1.0.1 which brings the following fixes:gerald2013-10-2612-5/+12
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - 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)
* - Remove manual creation and removal of share/applications, as it's now in ↵amdmi32013-10-223-4/+0
| | | | | | the mtree (categories starting with [bce]) Approved by: portmgr (bdrewery)
* Deprecated some ports broken for more than 6 monthbapt2013-10-181-0/+3
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* - Switch to build with lang/ruby19tabthorpe2013-10-111-1/+1
| | | | | | - No PORTREVISION bump, option is off by default With hat: portmgr
* Update BioCocoa to the latest release.theraven2013-10-093-75/+68
| | | | Approved by: bapt (mentor)
* - Update to 0.5.1wen2013-10-043-4/+4
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* - Update to 1.7sunpoet2013-10-043-12/+12
| | | | | | - Support STAGEDIR Changes: http://search.cpan.org/dist/Bio-GFF3/Changes
* biology/avida: add <unistd.h>, <typoinfo> for modern compilersmarino2013-10-022-0/+20
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* - Remove NO_STAGE as these have been tested to be safebdrewery2013-09-252-2/+0
| | | | With hat: portmgr
* Use value of BOINC_CLIENT_HOME in pkg-messagerene2013-09-242-2/+3
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* - Add stagedir supportrene2013-09-241-12/+17
| | | | - Rewrap lines
* Respect 'make check-sanity' for this port too.rene2013-09-241-2/+1
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* Fix NO_STAGE attributionbapt2013-09-231-1/+1
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* Add NO_STAGE all over the place in preparation for the staging support (cat: ↵bapt2013-09-2094-114/+117
| | | | biology)
* Mark BROKEN, fails checksumbdrewery2013-09-181-0/+2
| | | | With hat: portmgr
* Add an explicit dependency on pkgconfantoine2013-09-081-1/+1
| | | | Approved by: portmgr (bapt)
* - Use single space after WWW:sunpoet2013-09-081-1/+1
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* - convert to the new perl5 frameworkaz2013-09-074-4/+7
| | | | Approved by: portmgr (bapt@, blanket)
* - Make ports use the libc provided iconv implementation on 10-CURRENTmadpilot2013-09-053-3/+5
| | | | | | | | | | 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)
* - Add WWWsunpoet2013-08-301-2/+1
| | | | | - Use single space after WWW: - Remove Author line
* - Disconnect ports removed in r325546bdrewery2013-08-291-1/+0
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* Update to latest GNUstep core libraries.theraven2013-08-298-412/+85
| | | | | | | | | | | 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
* Make sure to respect CC and CXX, this fixes the build on head without gccbapt2013-08-281-2/+2
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* Update math/gsl to 1.16 and adjust some dependent portsbf2013-08-271-2/+2
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* - Update to 2.3.5wen2013-08-204-442/+9
| | | | | | - Add LICENSE - Remove pkg-message since license changed upstream - Do not install test files as example
* biology/tinker: Regenerate distinfo to unbreak fetchmarino2013-08-182-2/+3
| | | | | | | | | 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)
* Replace USE_GCC=4.6+ and USE_GCC=4.4+ by USE_GCC=yes.gerald2013-08-181-1/+1
| | | | | | | | | | | | | | 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)
* - Remove MAKE_JOBS_SAFE variableak2013-08-1510-10/+0
| | | | Approved by: portmgr (bdrewery)
* biology/libgenome: Mark jobs unsafemarino2013-08-141-0/+2
| | | | Approved by: bapt/culot (mentors, implicit)
* - update libdg to 2.1.0dinoex2013-08-092-5/+5
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* - Pet portlint: remove blank line among *_DEPENDSsunpoet2013-08-061-1/+0
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* - Convert to new perl frameworkaz2013-08-062-2/+4
| | | | | | - Trim Makefile header Approved by: wen@ (maintainer)
* - Convert to new perl frameworkmat2013-08-032-2/+2
| | | | - Remove MAKE_JOBS_SAFE=yes, it's the default.
* - Convert to new perl frameworkaz2013-08-032-2/+2
| | | | - Trim Makefile header
* - Convert to new perl frameworkmat2013-08-038-24/+19
| | | | | - Trim Makefile header - Remove MAKE_JOBS_SAFE=yes, it's the default.
* - Update to 1.6jadawin2013-08-012-4/+5
| | | | | - Convert to new perl5 framework - Changelog: http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-1.6/Changes
* KDE3 and QT3 expired on 2013-07-01, remove these ports.rene2013-07-276-187/+0
| | | | | | | | | | | | | | | | 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
* - Update to 3.0wen2013-07-203-32/+46
| | | | | - Convert to optionsNG - Drop maintainership
* - Update to 0.56wen2013-07-203-3/+13
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* - Update to 2.37wen2013-07-203-3/+7
| | | | Changes: http://cpansearch.perl.org/src/LDS/Bio-Graphics-2.37/Changes
* - Update to 36.3.6wen2013-07-195-23/+30
| | | | - Drop maintainership
* - Update to 6.2.06miwi2013-07-154-13/+23
| | | | | PR: 180518 Submitted by: Ports Fury
* - Update to 4.4.2miwi2013-07-152-3/+3
| | | | | PR: 180515 Submitted by: Ports Fury
* - Update to 7.31.0sunpoet2013-07-121-0/+1
| | | | | | | | | | | | | | | | | | | | | | | - 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
* Convert from USE_MOTIF to USES=motifbapt2013-07-101-6/+2
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* Convert from USE_MOTIF to USES=motifbapt2013-07-103-7/+4
| | | | | | | While here: - trim headers - Remove indefinite article from comment - convert USE_GMAKE to USES=gmake
* Fix some PORT_OPTIONS conversionsantoine2013-07-011-1/+1
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* Convert to USES=imakebapt2013-06-291-10/+4
| | | | Trim headers
* Fix some screw ups introduced in r319847.rakuco2013-06-252-4/+4
| | | | | | | | | | 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
* Remove stale (since r321246) pkg-plist file.bsam2013-06-201-39/+0
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* . introdice optionsNG to the port;bsam2013-06-202-98/+26
| | | | | | | | | | | . 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.
* . NOPORTDOCS -> PORT_OPTIONS:MDOCS;bsam2013-06-202-18/+14
| | | | | | | | . 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.
* . NOPORTDOCS -> PORT_OPTIONS:MDOCS;bsam2013-06-202-42/+17
| | | | | | | | | | | . 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.
* . NOPORTDOCS -> PORT_OPTIONS:MDOCS;bsam2013-06-202-34/+11
| | | | | | | | . 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.
* . NOPORTDOCS -> PORT_OPTIONS:MDOCS;bsam2013-06-203-13/+12
| | | | | | | | | . 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.
* Use optionsNG for DOCS.bsam2013-06-201-2/+2
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* . NOPORTDOCS -> PORT_OPTIONS:MDOCS;bsam2013-06-202-12/+9
| | | | | | . use PORTDOCS at Makefile (thus simplify pkg-plist); . use plain install instead of a .for loop; . trim Makefile headers.
* . NOPORTDOCS -> PORT_OPTIONS:MDOCS;bsam2013-06-202-13/+11
| | | | | | . use PLIST_FILES, PORTDATA and PORTDOCS; . use standard DATADIR and DOCSDIR (rather PREFIX/foo/bar); . remove pkg-plist.
* . NOPORTDOCS -> PORT_OPTIONS:MDOCS;bsam2013-06-201-10/+11
| | | | . trim Makefile headers.
* . add license (GPLv2);bsam2013-06-201-8/+9
| | | | | | . bump PORTREVISION; . NOPORTDOCS -> PORT_OPTIONS:MDOCS; . trim Makefile headers.
* . NOPORTDOCS -> PORT_OPTIONS:MDOCS;bsam2013-06-202-12/+12
| | | | | | | | . 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.
* . remove pkg-plist (along with the previous commit).bsam2013-06-201-17/+0
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* . NOPORTDOCS -> PORT_OPTIONS:MDOCS;bsam2013-06-201-4/+14
| | | | | | | . use PORTDOCS and PORTDATA at makefile; . mute mkdirs; . add padding to PKGMESSAGE; . remove article from COMMENT.
* . NOPORTEXAMPLES -> PORT_OPTIONS:MEXAMPLES;bsam2013-06-202-20/+8
| | | | | . use PORTEXAMPLES at Makefile; . trim Makefile headers.
* . add license (GPLv2);bsam2013-06-201-6/+5
| | | | | | . bump PORTREVISION; . trim article from COMMENT; . trim Makefile headers.
* . pet portlint: add USE_LDCONFIG;bsam2013-06-191-0/+2
| | | | . bump PORTREVISION.
* . trim Makefile headers;bsam2013-06-191-6/+2
| | | | . remove the indefinite article from COMMENT.
* . NOPORTDOCS -> PORT_OPTIONS:MDOCS;bsam2013-06-192-5/+8
| | | | | . use PLIST_FILES and PORTDOCS; . remove pkg-plist (4 lines).
* . NOPORTDOCS -> PORT_OPTIONS:MDOCS;bsam2013-06-192-11/+8
| | | | | . remove LICENSE_FILE for a standard license (GPLv2); . trim Makefile headers.
* Index: Makefilebsam2013-06-191-27/+17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | =================================================================== --- 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>
* . NOPORTDOCS -> PORT_OPTIONS:MDOCS;bsam2013-06-193-12/+11
| | | | | | | | . 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.
* - Avoid of using SITE_PERLaz2013-06-071-2/+1
| | | | | | | | - Remove depend on DB_File.pm since it part of perl distribution PR: ports/178877 Submitted by: az Approved by: matainer (timeout)
* - Update to 3.6.9.5miwi2013-06-043-19/+33
| | | | | PR: 179224 Submitted by: Ports Fury
* - Fix build with clangmiwi2013-06-041-0/+10
| | | | | PR: 179215 Submitted by: Ports Fury
* - Trim Makefile headerswen2013-06-013-15/+3
|
* - Update to 6.2.05miwi2013-05-292-5/+4
| | | | | PR: 179061 Submitted by: Ports Fury
* - Update to 3.5.1wen2013-05-265-105/+22
| | | | | | - Trim Makefile headers - Convert to optionsNG - Update WWW, MASTER_SITES and COMMENT
* - Update to 6.2.04miwi2013-05-212-3/+3
| | | | | PR: 178590 Submitted by: Ports Fury
* Convert USE_NCURSES by USES=ncursesbapt2013-05-061-2/+1
| | | | Convert USE_READLINE by USES=readline
* Fix build by adding an explicit dep on pkgconfbapt2013-05-041-0/+1
|
* - Update to 1.13.0culot2013-04-306-15/+45
| | | | | | | | | - 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/
* Workaround the way mopac installs executables.delphij2013-04-302-1/+4
| | | | | PR: ports/171932 Reported by: Jinsong Zhao <jszhao yeah net>
* - Update to 6.2.02miwi2013-04-293-3/+4
| | | | | PR: 178031 Submitted by: Ports Fury
* Use bsd.port.options.mk instead of bsd.port.{pre|post}.mkrene2013-04-291-2/+2
|
* - Convert USE_ICONV=yes to USES=iconvmva2013-04-271-1/+1
| | | | | | - Change USE_GNOME=pkgconfig|gnomehack to USES=pathfix|pkgconfig while here Reviewed by: bapt, kwm
* Remove unneeded escapingbdrewery2013-04-271-6/+2
|
* - Update to 5.0.6miwi2013-04-262-3/+3
| | | | | PR: 178032 Submitted by: Ports Fury
* Update MASTERSITES for my server to use httpsgjb2013-04-261-1/+1
| | | | Approved by: wen (maintainer, implicit)
* - Convert USE_GETTEXT to USES (part 3)ak2013-04-251-1/+1
| | | | Approved by: portmgr (bapt)
* Finish converting the whole ports tree to USES=pkgconfigbapt2013-04-231-1/+1
|
* For perl@ owned ports:eadler2013-03-293-8/+4
| | | | | - Fix COMMENT - Trim header
* - Update to 4.4.1miwi2013-03-262-25/+17
| | | | | PR: 177257 Submitted by: Ports Fury
* - Mark broken checksum mismatchmiwi2013-03-251-0/+2
| | | | Reported by: pointyhat http://pointyhat.freebsd.org/errorlogs/i386-errorlogs/a.8.20130324140101.pointyhat/dotter-20021204.log
* - Update to 6.2.01miwi2013-03-255-168/+164
| | | | | PR: 177261 Submitted by: ports fury
* - convert USE_CMAKE to USESmakc2013-03-232-4/+2
| | | | | | | - while here clean up some ports from CMAKE_VERBOSE, which is intended for users Approved by: portmgr (miwi)
* Fix build with protobuf-2.5.0vanilla2013-03-212-0/+34
| | | | Obtained from: miwi@
* - adopt optionsNGjgh2013-03-191-19/+28
| | | | | | | - trim historical header - tighten COMMENT Approved by: portmgr (miwi)
* 1: Upgrade protobuf to 2.5.0.vanilla2013-03-181-0/+1
| | | | | 2: bump revision. 3: document UPDATING.
* - adoption of optionsNGjgh2013-03-181-15/+12
| | | | | | - trim historical header Approved by: portmgr (miwi)
* - adoption of optionsNGjgh2013-03-182-130/+129
| | | | | | | | - trim historical header - fix mixture of DOCS/EXAMPLES -> EXAMPLES - add shared description for GLUT to bodm Approved by: portmgr (miwi)
* - adoption of optionsNGjgh2013-03-181-11/+8
| | | | | | | - trim historical header - tighten COMMENT Approved by: portmgr (miwi)
* - adoption of optionsNGjgh2013-03-181-26/+26
| | | | | | | - trim historical header - use tabs in favor of spaces Approved by: portmgr (miwi)
* - Update to 2012.06.20miwi2013-03-146-191/+173
| | | | | PR: 176544 Submitted by: Ports Fury
* Convert USE_BISON to USES= bisonbapt2013-03-081-6/+2
| | | | | | | | | | | | | | 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
* Remove compatibility with FreeBSD 7.Xrene2013-03-072-14/+2
| | | | While here pet Makefile headers.
* Add missing item to pkg-plist reported by QAT but not reported by poudriere.eadler2013-03-031-0/+1
|
* Update to 2.33eadler2013-03-032-3/+3
|
* - Update to 2.4.1miwi2013-03-023-124/+45
| | | | | PR: 176552 Submitted by: Ports Fury
* Unbreak on 7.X and i386 systems.danfe2013-02-254-1/+37
| | | | Reported by: QAT
* Add Unipro UGENE, a free open-source crowss-platform bioinformatics software.danfe2013-02-236-0/+1218
| | | | | PR: ports/173387 Submitted by: Hannes Hauswedell
* - Update to 0.52 [1]culot2013-02-163-13/+26
| | | | | | | - Capitalize names (Perl) in COMMENT PR: ports/176003 [1] Submitted by: Gea-Suan Lin <gslin@gslin.org>
* - remove empty filesrm2013-02-151-0/+0
|
* - Fix build with clangmiwi2013-02-103-24/+26
| | | | | PR: 175034 Submitted by: Ports Fury
* - Update to 1.27jadawin2013-02-052-3/+3
| | | | - Changelog: http://cpansearch.perl.org/src/TFRAYNER/Bio-MAGETAB-1.27/Changes
* - Update to 20121109.araujo2013-02-044-43/+25
| | | | | PR: ports/175014 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* - Strip header at request of original creatortabthorpe2013-01-271-5/+1
| | | | | Submitted by: trevor With hat: portmgr
* - Update to 2.32jadawin2013-01-242-7/+4
| | | | - Changelog: http://cpansearch.perl.org/src/LDS/Bio-Graphics-2.32/Changes
* Bump PORTREVISION after DESKTOP_ENTRIES updatemakc2013-01-231-0/+1
|
* - Update to 9.03.araujo2013-01-145-219/+35
| | | | | PR: ports/172499 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* - Update DESKTOP_ENTRIES:makc2013-01-071-2/+2
| | | | | | | | | | * 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
* Take over maintainership.rene2012-12-291-1/+1
| | | | Approved by: pav (previous maintainer)
* Use the new project URL to let the application attach coorectly to therene2012-12-282-18/+15
| | | | | | | | | | | | | | | 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@)
* Cleanup supporting perl version 5.8 and 5.10,az2012-12-171-7/+1
| | | | lang/perl5.8 and lang/5.10 will be removed from ports tree soon.
* - Update to 1.5wen2012-12-162-3/+3
| | | | Changes: http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-1.5/Changes
* Update to 5.0.4eadler2012-12-152-3/+3
|
* - Mark conflict with science/openbabelmakc2012-12-111-6/+4
| | | | - Trim Makefile header
* science/openbabel:makc2012-12-112-2/+13
| | | | | | | | | | | | | - 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
* Remove hardcoded extract dependency on diablo-jdk16, directly use USE_ZIPbapt2012-12-111-8/+1
| | | | | | | instead given that jar files are just zip files, remove hardcoded do extract target. Reported by: linimon, matthew
* Decommissioning java 1.5 (EOLed since October 2009):bapt2012-12-101-6/+2
| | | | suppress any reference to JAVA_VERSION= 1.5+ (part2)
* Decommissioning java 1.5 (EOLed since October 2009):bapt2012-12-102-2/+2
| | | | suppress any reference to USE_JAVA= 1.5+ (part1)
* - Support CC properlypawel2012-12-083-35/+26
| | | | | | | | | - Switch to PLIST_FILES - Add option for GTK2 support PR: ports/174174 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Feature safe: yes
* Update to 2.31.tobez2012-12-073-9/+11
| | | | | | Changes: http://search.cpan.org/dist/Bio-Graphics/Changes Feature safe: yes
* - Reset MAINTAINER due to unrecoverable email bouncezi2012-12-051-1/+1
| | | | | Reported by: portscout Feature safe: yes
* - Fix build with clanggahr2012-12-031-0/+56
| | | | Feature safe: yes
* - Update to version 6.1.01sperber2012-12-0115-753/+788
| | | | | | | | | | | - 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
* - Update to version 5.0.2sperber2012-12-017-275/+79
| | | | | | | | | | - 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
* 2012-11-26 benchmarks/gsbench: No more public distfilesbapt2012-11-284-51/+0
| | | | | | | | | | | 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
* - Update to version 2.0wen2012-11-156-80/+60
| | | | | | | | | - Update pkg-descr PR: 172497 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Feature safe: yes
* - Update to version 4.4.0pawel2012-10-315-76/+56
| | | | | | | | | | | | | | - 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
* Update to version 2.12.4pawel2012-10-312-10/+4
| | | | | | PR: ports/172218 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Feature safe: yes
* - Reset maintainer to perl@wen2012-10-301-1/+1
| | | | Feature safe: yes
* - Update to 1.4wen2012-10-302-8/+4
| | | | | | | Changes: http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-1.4/Changes - Trim Makefile headers Feature safe: yes
* - Trim Makefile headerswen2012-10-301-6/+2
| | | | | | - Reset maintainer to perl@ Feature safe: yes
* Deprecate a bunch of ports that are either abandonware and/or for which no morebapt2012-10-261-0/+3
| | | | | | | public distfiles are available, or for which are -devel version with a more recent stable version for long Feature safe: yes
* 2012-10-20 chinese/wangttf: No more public distfilesbapt2012-10-266-100/+0
| | | | | | | | | | 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
* - Update to 1.26wen2012-10-252-8/+4
| | | | | | Changes: http://cpansearch.perl.org/src/TFRAYNER/Bio-MAGETAB-1.26/Changes Feature safe: yes
* - cleanup commentsdinoex2012-10-131-5/+0
| | | | Feature safe: yes
* - Update to 1.5.3wen2012-10-083-11/+37
| | | | - Trim Makefile headers
* - Take maintainershipwen2012-10-017-7/+7
|
* - Reassign to the heap at maintainer's requesttabthorpe2012-10-0120-131/+40
|
* Add new ports biology/plink [1] and biology/plinkseq [2]:makc2012-09-279-0/+138
| | | | | | | | | | 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>
* - update to 1.60rm2012-09-254-133/+140
| | | | | | | | | | | | | 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)
* Mea culpa, s/Whom/Created by/danfe2012-09-231-1/+1
|
* - Adjust "Created by" tag to include more complete submitter's informationdanfe2012-09-231-5/+4
| | | | | - Mute MKDIRs, remove trailing dot from RESTRICTED, drop leading indefinite article from COMMENT where appropriate
* - Reassign to the heap at maintainer's requesttabthorpe2012-09-221-6/+2
|
* Deprecated a bunch a ports with nor more public distfiles (thanks ehaupt'sbapt2012-09-211-0/+3
| | | | distilator
* Mark as broken on sparc64: depends on thread-local storage, which is notlinimon2012-09-081-0/+4
| | | | | | available on sparc64. Hat: portmgr
* Fix build with clangbapt2012-08-241-0/+13
|
* - Submitter is now maintainerscheidell2012-08-071-1/+1
| | | | | PR: ports/169920 Approved by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Update to version 6.903scheidell2012-08-074-44/+119
| | | | | | PR: ports/169920 Submitted by: "Reed A. Cartwright" <cartwright@asu.edu> Approved by: maintainer (timeout, 21 days)
* Switch from libglut to freeglut and retire libglut. Libglut hasn't beenkwm2012-08-053-3/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* Fix typos in COMMENTcs2012-07-291-1/+1
| | | | Approved by: portmgr@ (implicit)
* Fix typos in COMMENTcs2012-07-252-2/+2
|
* Fix typos in COMMENTcs2012-07-241-1/+1
|
* Replace USE_GCC=4.4+ by USE_GCC=4.6+ since GCC 4.4 is on its way out.gerald2012-07-221-1/+1
| | | | Approved by: maintainer
* - Update to 1.23sunpoet2012-07-202-5/+5
| | | | | | | - Add LICENSE - Remove WRKSRC Changes: http://search.cpan.org/dist/Bio-MAGETAB/Changes
* - Remove SITE_PERL from *_DEPENDSaz2012-06-301-2/+2
| | | | Approved by: portmgr@ (bapt@)
* - Remove SITE_PERL from *_DEPENDSaz2012-06-301-39/+39
| | | | Approved by: portmgr@ (bapt@)
* - reset MAINTAINERdinoex2012-06-262-2/+2
|
* s/X11BASE/LOCALBASE/, or equivalent.dougb2012-06-251-1/+1
| | | | The X11BASE variable is long gone, however these ports were not updated.
* - Update to 2.29sunpoet2012-06-182-4/+3
| | | | Changes: http://search.cpan.org/dist/Bio-Graphics/Changes
* - Update to version 2.1.8sylvio2012-06-186-171/+21
| | | | | | | | | | | Remove file: files/patch-Makefile.in files/patch-configure files/patch-src__control__defaults.h pkg-plist PR: ports/168994 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* - Update to version 2.12.3sylvio2012-06-183-30/+54
| | | | | PR: ports/168993 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
* - Update to 0.50sunpoet2012-06-133-22/+37
| | | | | - Add TEST_DEPENDS - Sort PLIST
* - Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} orswills2012-06-114-4/+4
| | | | | | | | RUN_DEPENDS=${BUILD_DEPENDS} to use := which portlint has warned about for a while. PR: ports/168208 Approved by: portmgr (miwi)
* - Fix maintainer emailamdmi32012-06-071-1/+1
| | | | Submitted by: maintainer via private email
* SeqAn is an open source C++ library of efficient algorithmsamdmi32012-06-078-0/+2230
| | | | | | | | | | | and data structures for the analysis of sequences with the focus on biological data. The library is licensed under the 3-clause BSD license except the applications which are GPL. WWW: http://www.seqan.de/ PR: 167571 Submitted by: Hannes <h2+fbsdports@fsfe.org>
* - Remove SITE_PERL from *_DEPENDSaz2012-06-041-1/+1
|
* - Update to 0.49sunpoet2012-06-032-4/+3
|
* Set maintainership back to ports@cs2012-06-032-2/+2
|
* - update png to 1.5.10dinoex2012-06-0115-16/+19
|
* Remove non-serving mirrorcs2012-05-201-2/+1
|
* - Adjust BOINC_* variables to be consistent with new system in boinc-clientpav2012-05-162-9/+9
|
* - Update to 0.48sunpoet2012-05-032-5/+5
| | | | - Add BUILD_DEPENDS
* - Update to 1.3culot2012-04-262-3/+3
| | | | Changes: http://search.cpan.org/dist/Bio-GFF3/Changes
* - Update to 2.28wen2012-04-173-3/+4
| | | | ChangeLog: http://cpansearch.perl.org/src/LDS/Bio-Graphics-2.28/Changes
* - Update to 1.2culot2012-04-163-16/+18
| | | | | | | - Add LICENSE (Artistic 1 & GPL 1) - Add TEST_DEPENDS Changes: http://search.cpan.org/dist/Bio-GFF3/Changes
* - Update to 0.47wen2012-04-112-3/+3
|
* - Update to 1.0wen2012-03-223-4/+7
| | | | | | - Reset maintainer to perl@ Feature safe: yes
generated by cgit (git 2.34.1) at 2024-12-15 08:27:47 +0800