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* mark some of the ports that don't build on powerpc64 for meSteve Wills2015-12-134-0/+7
| | | | Notes: svn path=/head/; revision=403676
* - Update maintainer mail addressMartin Wilke2015-12-1112-23/+22
| | | | | | | | | | | | - Update/Remove MASTER_SITE PR: 204755 Submitted by: jwbacon@tds.net (maintainer) Approved by: mat (mentor) Differential Revision: D4493 Notes: svn path=/head/; revision=403506
* - Update to 1.32Wen Heping2015-12-113-6/+8
| | | | | | | | - Add LICENSE - Pet portlint Notes: svn path=/head/; revision=403479
* biology/seqtools: 4.39.2 -> 4.39.3Kurt Jaeger2015-12-052-3/+3
| | | | | | | | | | - Blixem Further improve the display of features in the detail view when they have transparent fill, making sure that they have a visible border. Notes: svn path=/head/; revision=403064
* biology/seqtools: 4.39.1 -> 4.39.2Kurt Jaeger2015-12-012-3/+3
| | | | | | | | | - Blixem: Improve the display of features in the detail view when they have transparent fill. Notes: svn path=/head/; revision=402787
* - Mark BROKEN: checksum mismatch:Dmitry Marakasov2015-11-291-0/+2
| | | | | | | fetch: http://www.platonsoft.nl/spek/xraysoft/unix/platon.tar.gz: size mismatch: expected 12080181, actual 12080357 Notes: svn path=/head/; revision=402567
* Remove expired ports:Rene Ladan2015-11-2815-933/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2015-11-26 audio/pecl-id3: Broken for more than 6 months 2015-11-26 dns/geta: Broken for more than 6 months 2015-11-26 finance/openerp-web: Broken for more than 6 months 2015-11-26 devel/py-async: Further using of this module is not encouraged by upstream 2015-11-26 chinese/kon2: Depends on expiring chinese/cce 2015-11-26 games/linux-skulltag: Depends on expiring audio/linux-fmodapi 2015-11-26 archivers/wzip: Broken for more than 6 months 2015-11-26 databases/sybtcl: Broken for more than 6 months 2015-11-26 biology/povchem: Broken for more than 6 months 2015-11-26 audio/btc: Broken for more than 6 months 2015-11-26 astro/wmglobe: Broken for more than 6 months 2015-11-26 graphics/pyro: Broken for more than 6 months 2015-11-26 graphics/jpeg2ps: Broken for more than 6 months 2015-11-26 chinese/gugod-clean: Broken for more than 6 months 2015-11-26 comms/bforce: Broken for more than 6 months 2015-11-26 cad/geda-docs: Broken for more than 6 months 2015-11-26 chinese/cwtexttf: Broken for more than 6 months 2015-11-26 comms/zmtx-zmrx: Broken for more than 6 months 2015-11-26 astro/sky2000: Broken for more than 6 months 2015-11-26 deskutils/libopensync-plugin-file: Broken for more than 6 months 2015-11-26 databases/sqlite-ext-mobigroup: Broken for more than 6 months 2015-11-26 chinese/bg5ps: Broken for more than 6 months 2015-11-26 deskutils/x-tile: Broken for more than 6 months 2015-11-26 graphics/pure-gl: Broken for more than 6 months 2015-11-26 audio/dvda-author: Broken for more than 6 months 2015-11-26 chinese/oxim: Broken for more than 6 months 2015-11-26 editors/spe: Broken for more than 6 months 2015-11-26 audio/mpdscribble: Broken for more than 6 months 2015-11-26 cad/geda-symcheck: Broken for more than 6 months 2015-11-26 audio/linux-fmodapi: Broken for more than 6 months 2015-11-26 audio/pure-audio: Broken for more than 6 months 2015-11-26 editors/bpatch: Broken for more than 6 months 2015-11-26 benchmarks/geekbench: Broken for more than 6 months 2015-11-26 graphics/icoconvert: Broken for more than 6 months 2015-11-26 cad/geda-utils: Broken for more than 6 months 2015-11-26 deskutils/tomboy-plugin-wordcount: Broken for more than 6 months 2015-11-26 graphics/sketch: Broken for more than 6 months 2015-11-26 ftp/spegla: Broken for more than 6 months 2015-11-26 graphics/clutter-box2d: Broken for more than 6 months 2015-11-26 audio/scmpc: Broken for more than 6 months 2015-11-26 ftp/gnusget: Broken for more than 6 months 2015-11-26 comms/gpsk31: Broken for more than 6 months 2015-11-26 cad/geda-gschem: Broken for more than 6 months 2015-11-26 audio/ampache: Broken for more than 6 months 2015-11-26 cad/slffea: Broken for more than 6 months 2015-11-26 audio/cripple: Broken for more than 6 months 2015-11-26 cad/geda-gattrib: Broken for more than 6 months 2015-11-26 cad/findhier: Broken for more than 6 months 2015-11-26 biology/njplot: Broken for more than 6 months 2015-11-26 audio/wmmp: Broken for more than 6 months 2015-11-26 x11/avant-window-navigator: Broken for more than 6 months 2015-11-26 cad/geda-netlist: Broken for more than 6 months 2015-11-26 deskutils/libopensync-plugin-sunbird: Broken for more than 6 months 2015-11-26 biology/ortep3: Broken for more than 6 months 2015-11-26 astro/aa: Broken for more than 6 months 2015-11-26 french/belote: Broken for more than 6 months 2015-11-26 converters/p5-String-SetUTF8: Broken for more than 6 months 2015-11-26 cad/geda-examples: Broken for more than 6 months 2015-11-26 editors/yasnippet: Broken for more than 6 months 2015-11-26 audio/musica: Broken for more than 6 months 2015-11-26 graphics/rubyphoto: Broken for more than 6 months 2015-11-26 german/bsdpaste: Broken for more than 6 months 2015-11-26 audio/amrcoder: Broken for more than 6 months 2015-11-26 sysutils/bashburn: Broken for more than 6 months 2015-11-26 editors/e93: Broken for more than 6 months 2015-11-26 audio/tepsonic: Broken for more than 6 months 2015-11-26 astro/ephem: Broken for more than 6 months 2015-11-26 chinese/cce: Broken for more than 6 months 2015-11-26 graphics/qcread: Broken for more than 6 months 2015-11-26 databases/py-sqlkit: Broken for more than 6 months 2015-11-26 databases/usogres: Broken for more than 6 months 2015-11-26 cad/libgeda: Broken for more than 6 months 2015-11-26 chinese/p5-Lingua-ZH-BPMFConvert: Broken for more than 6 months 2015-11-26 french/alphabet_sounds_fr: Broken for more than 6 months 2015-11-26 deskutils/mrundlg: Broken for more than 6 months 2015-11-26 databases/erlang-mysql: Broken for more than 6 months 2015-11-26 graphics/linux-XnViewMP: Broken for more than 6 months 2015-11-26 deskutils/akamaru: Broken for more than 6 months 2015-11-26 dns/p5-Net-DNS-ZoneCheck: Broken for more than 6 months 2015-11-26 astro/dgpsip: Broken for more than 6 months 2015-11-26 databases/pecl-handlersocket: Broken for more than 6 months 2015-11-26 audio/cymbaline: Broken for more than 6 months 2015-11-26 french/dico: Broken for more than 6 months 2015-11-26 comms/qpage: Broken for more than 6 months 2015-11-26 audio/sonice: Broken for more than 6 months 2015-11-26 cad/geda-symbols: Broken for more than 6 months 2015-11-26 databases/java-mybatis: Broken for more than 6 months 2015-11-26 databases/openbase-jdbc: Broken for more than 6 months 2015-11-27 www/mediawiki119: Please upgrade to mediawiki-1.25 2015-11-28 www/R-cran-Rpad: Unmaintained upstream Notes: svn path=/head/; revision=402562
* biology/platon: fix fetchingRuslan Makhmatkhanov2015-11-193-6/+4
| | | | | | | | | | | | | Add working mirror. Also update file size in distinfo - checksum is not changed and I dunno why. But with old file size it warns that expected size was different. PR: 204491 Submitted by: Walter Schwarzenfeld <w.litter@aon.at> Notes: svn path=/head/; revision=401960
* - Switch to options helpersDmitry Marakasov2015-11-191-1/+1
| | | | Notes: svn path=/head/; revision=401907
* biology/seqtools: Fix distinfo, WWWKurt Jaeger2015-11-182-3/+3
| | | | | | | | | - Side effect of the seqtools automated build system Submitted by: pkg-fallout Notes: svn path=/head/; revision=401862
* biology/seqtools: 4.39.0 -> 4.39.1Kurt Jaeger2015-11-132-3/+3
| | | | | | | | - Fix a bug in Belvu where the display was being initialised in command-line-only modes. Notes: svn path=/head/; revision=401527
* - Update to 1.14.6Danilo Egea Gondolfo2015-11-093-4/+4
| | | | Notes: svn path=/head/; revision=401113
* Mark a few ports BROKEN: unfetchableAntoine Brodin2015-11-091-0/+2
| | | | Notes: svn path=/head/; revision=401096
* biology/seqtools: 4.36 -> 4.39.0Kurt Jaeger2015-11-082-3/+3
| | | | | | | | | | | | | | | | | - Blixem o There is now an optional setting to highlight "maybe-canonical" splice sites in Blixem. This can be used to help identify problems where the strand is incorrect in the input data - it highlights splice sites in a different colour if they would be canonical were they on the other strand. o Fixed a bug with colinearity lines when an alignment's cigar string contains introns. o There are now separate feedback boxes for the selected sequence name coordinates. Hover over each box to see a tooltip describing its contents. Notes: svn path=/head/; revision=401065
* - Update to 1.14.5Danilo Egea Gondolfo2015-11-063-4/+4
| | | | Notes: svn path=/head/; revision=400926
* Fix ports that confused the meaning of WRKDIR and WRKSRC.Mathieu Arnold2015-11-051-5/+5
| | | | | | | | | | | PR: 204056 Submitted by: mat Reviewed by: bapt Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D2735 Notes: svn path=/head/; revision=400848
* biology/seaview: Broken, Does not fetch (checksum mismatch)John Marino2015-11-021-0/+2
| | | | Notes: svn path=/head/; revision=400638
* - Update to 2015.09.21Guido Falsi2015-10-275-25/+60
| | | | | | | | | | | | | | | - Add License - Add SIMD option disabled by default to avoid creating official packags with CPU specific optimizations - Add pkg-message explaining how to get an optimized binary - Assign maintainership to submitter PR: 203334 Submitted by: jwbacon at tds.net Approved by: Maintainer timeout Notes: svn path=/head/; revision=400336
* Deprecate ports broken for more than 6 monthsAntoine Brodin2015-10-254-0/+8
| | | | Notes: svn path=/head/; revision=400160
* biology/seaview: Update version 4.5.4.7=>4.5.4.8Muhammad Moinur Rahman2015-10-202-3/+3
| | | | Notes: svn path=/head/; revision=399820
* - Update to 36.3.8Danilo Egea Gondolfo2015-10-162-4/+4
| | | | | | | | | | - Pass maintainership to submitter PR: 203817 Submitted by: Wendell Borges <wendell@bsd.com.br> Notes: svn path=/head/; revision=399468
* - Add LICENSE_FILEDmitry Marakasov2015-10-141-1/+2
| | | | | | | - Switch to options helpers Notes: svn path=/head/; revision=399316
* - Pet portlintDmitry Marakasov2015-10-141-4/+5
| | | | | | | | - Add LICENSE - Drop unneeded WX_UNICODE Notes: svn path=/head/; revision=399306
* - Fix typoSunpoet Po-Chuan Hsieh2015-10-101-1/+1
| | | | | | | Approved by: portmgr (blanket) Notes: svn path=/head/; revision=399072
* - Update to 1.14.4Danilo Egea Gondolfo2015-10-073-4/+4
| | | | Notes: svn path=/head/; revision=398730
* - Update to 1.14.3Danilo Egea Gondolfo2015-10-013-4/+4
| | | | Notes: svn path=/head/; revision=398397
* biology/seaview: Update version 4.5.4.6=>4.5.4.7Muhammad Moinur Rahman2015-10-012-4/+3
| | | | Notes: svn path=/head/; revision=398266
* biology/grappa: define license (GPLv2)Ruslan Makhmatkhanov2015-09-251-0/+2
| | | | | | | | | | | As per the web site, the license for GRAPPA is GPLv2 https://www.cs.unm.edu/~moret/GRAPPA/ PR: 202426 Submitted by: George <george@nycbug.org> Notes: svn path=/head/; revision=397864
* BWA is a program for aligning sequencing reads against a large referenceRuslan Makhmatkhanov2015-09-258-0/+84
| | | | | | | | | | | | | genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads. WWW: http://sourceforge.net/projects/bio-bwa/ PR: 203158 Submitted by: Jason Bacon <jwbacon@tds.net> Notes: svn path=/head/; revision=397851
* Fast indexing and retrieval of FASTA records from flat file data bases.Ruslan Makhmatkhanov2015-09-255-0/+85
| | | | | | | | | | WWW: http://sourceforge.net/projects/cdbfasta/ PR: 203233 Submitted by: Jason Bacon <jwbacon@tds.net> Notes: svn path=/head/; revision=397850
* Simple and quick FastQ and FastA tool for file reading and conversion.Ruslan Makhmatkhanov2015-09-254-0/+39
| | | | | | | | | | WWW: https://github.com/fstrozzi/Fastool PR: 203293 Submitted by: Jason Bacon <jwbacon@tds.net> Notes: svn path=/head/; revision=397849
* FastTree infers approximately-maximum-likelihood phylogenetic trees fromRuslan Makhmatkhanov2015-09-254-0/+41
| | | | | | | | | | | | | alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. WWW: http://www.microbesonline.org/fasttree/ PR: 203295 Submitted by: Jason Bacon <jwbacon@tds.net> Notes: svn path=/head/; revision=397848
* The FASTX-Toolkit is a collection of command line tools for Short-ReadsRuslan Makhmatkhanov2015-09-255-0/+57
| | | | | | | | | | | | FASTA/FASTQ files preprocessing. WWW: http://hannonlab.cshl.edu/fastx_toolkit/ PR: 203318 Submitted by: Jason Bacon <jwbacon@tds.net> Notes: svn path=/head/; revision=397847
* Gordon's text utilities.Ruslan Makhmatkhanov2015-09-255-0/+50
| | | | | | | | | | WWW: https://github.com/agordon/libgtextutils PR: 203309 Submitted by: Jason Bacon <jwbacon@tds.net> Notes: svn path=/head/; revision=397846
* Typos, whitespace and capitalization fixes (A-F).Jimmy Olgeni2015-09-201-1/+1
| | | | Notes: svn path=/head/; revision=397395
* - Use compiler:openmp instead of gccWen Heping2015-09-191-4/+1
| | | | | | | | | - Minor cleanup Reported by: danfe@ Notes: svn path=/head/; revision=397322
* CD-HIT is a very widely used program for clustering and comparing protein orWen Heping2015-09-195-0/+81
| | | | | | | | | | | | nucleotide sequences. WWW: http://weizhong-lab.ucsd.edu/cd-hit/ PR: 203183 Submitted by: jwbacon@tds.net Notes: svn path=/head/; revision=397318
* Make all GNUstep ports install into the System domain so that the Local ↵David Chisnall2015-09-192-66/+66
| | | | | | | | | | | | | | domain is available for stuff built from source. Some ports were already installing in the System domain, for these just remove the Makefile lines explicitly specifying the install domain. The rest are installed in the Local domain, remove any overrides, update their pkg-plists and any explicit paths in the Makefiles and then bump port revision. Approved by: bapt (mentor) Differential Revision: https://reviews.freebsd.org/D2977 Notes: svn path=/head/; revision=397315
* - Update to 1.14.2Danilo Egea Gondolfo2015-09-173-4/+5
| | | | Notes: svn path=/head/; revision=397111
* Remove ansi version fo wxGTK 2.8 and only keep the unicode versionBaptiste Daroussin2015-09-162-1/+2
| | | | | | | | | | | All applications in the ports tree works correctly with unicode version of wxGTK Newer version of wxGTK are unicode only (3.0+) Note that now WX_UNICODE macro is noop Notes: svn path=/head/; revision=397077
* biology/seaview: Update version 4.5.4.4=>4.5.4.6Muhammad Moinur Rahman2015-09-152-5/+5
| | | | Notes: svn path=/head/; revision=396964
* Make it so that the default Perl is always called perl5.Mathieu Arnold2015-09-145-72/+72
| | | | | | | | | | | | | | | | | | | - Move Perl's man1 files along with its man3 files. - Move where Perl installs its modules man1 pages. - Convert the ports installing man1 pages. - Make different Perl versions installable at the same time. Though you should note that only the default version can be used to install Perl modules, and the non default Perl versions cannot use the modules installed via ports if they contain .so as they are installed in a version specific directory. Reviewed by: bapt (the Mk bits) Exp-run by: antoine Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D3542 Notes: svn path=/head/; revision=396892
* Enfoce unicode version of wxGTKBaptiste Daroussin2015-09-131-0/+1
| | | | Notes: svn path=/head/; revision=396851
* - Update to 1.14.1Danilo Egea Gondolfo2015-09-133-5/+5
| | | | Notes: svn path=/head/; revision=396842
* - Add LICENSESunpoet Po-Chuan Hsieh2015-09-032-8/+8
| | | | | | | | | | | | - Add NO_ARCH - Use BROKEN_RUBY22 - While I'm here, use single space after WWW: Approved by: portmgr (blanket) With hat: ruby Notes: svn path=/head/; revision=395991
* - Unbreak on PowerPC by using atomicops implementation for Linux and GCCAlexey Dokuchaev2015-09-022-12/+40
| | | | | | | | | | __sync_* functions family - Remove BROKEN_ia64: it never had been first-class architecture, killed officially in -CURRENT for a while now - Sanitize installation commands and sort the knobs while I am here Notes: svn path=/head/; revision=395830
* - Do not falsely advertise that PowerPC build runs out of space and failsAlexey Dokuchaev2015-09-021-11/+5
| | | | | | | - Remove redundant PKGMESSAGE assignment and sanitize symlinks while here Notes: svn path=/head/; revision=395829
* Unbreak the build on PowerPC (at least) by always using va_copy() macro forAlexey Dokuchaev2015-09-022-20/+7
| | | | | | | copying variable argument lists, not just on AMD64. Notes: svn path=/head/; revision=395828
* Unbreak the build on PowerPC, it had nothing to do with "error in pthreads":Alexey Dokuchaev2015-09-022-2/+20
| | | | | | | | | | | configure script was passing `-faltivec' to the compiler, while this flag is non-standard and only supported on Mac OS X/Darwin systems. Also replace Apple-specific Altivec detection with querying the "hw.altivec" sysctl instead. Notes: svn path=/head/; revision=395826
* - Switch to options helpersDmitry Marakasov2015-09-021-6/+2
| | | | Notes: svn path=/head/; revision=395817
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