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* Upgrade from 3.6.6 to 3.6.7. Be sure to not extract the zlibMikhail Teterin2015-03-242-3/+4
| | | | | | | subdirectory. Notes: svn path=/head/; revision=382123
* 6 ports categories: Remove $PTHREAD_LIBSJohn Marino2015-03-243-10/+8
| | | | | | | | | Categories: cad, devel, java, x11-fm, biology, deskutils approved by: PTHREAD blanket Notes: svn path=/head/; revision=382111
* biology/seaview: Update version 4.5.3.4=>4.5.4Muhammad Moinur Rahman2015-03-243-41/+5
| | | | | | | - Remove dependency for libpdf as removed by upstream Notes: svn path=/head/; revision=382078
* - Update to version 1.16.1Alexey Dokuchaev2015-03-233-8/+8
| | | | | | | | | | - Explicitly list all required Qt components in USE_QT4 instead of relying on them being silently picked up through `www/webkit-qt4' dependency - Group *_build components together while here - Remove one REINPLACE_CMD call that is no longer needed Notes: svn path=/head/; revision=381974
* biology/segan: Limit GCC to 4.8 while waiting for updateJohn Marino2015-03-211-1/+1
| | | | | | | | | | | | Due to questionable c++, GCC 4.9 and newer cannot build seqan. An update has been in the works that will enable clang compilers and all versions of GCC to build seqan, but it is not quite ready yet. While waiting for it, limit the version of GCC used to 4.8. PR: 196851 Notes: svn path=/head/; revision=381791
* For the new USE_GITHUB with only GH_TAGNAME set default DISTNAME toBryan Drewery2015-03-201-2/+2
| | | | | | | | | | | | | include GH_PROJECT/GH_ACCOUNT/GH_TAGNAME. This prevents the distfile having the same name despite changing one of these values and causing a bad checksum. Differential Revision: https://reviews.freebsd.org/D2103 Reviewed by: mat With hat: bdrewery Notes: svn path=/head/; revision=381777
* Convert to new USE_GITHUB.Mathieu Arnold2015-03-202-11/+4
| | | | | | | | | While there, cleanup. Sponsored by: Absolight Notes: svn path=/head/; revision=381726
* Fix packaging as a user (pkg already takes care of credentials)Baptiste Daroussin2015-03-181-2/+2
| | | | | | | Strip binaries Notes: svn path=/head/; revision=381580
* - Simplify MASTER_SITESDmitry Marakasov2015-03-171-3/+9
| | | | | | | - Strip libraries Notes: svn path=/head/; revision=381464
* biology/seaview: UNBREAKMuhammad Moinur Rahman2015-03-163-15/+38
| | | | | | | | | | | | | - Update version 4.5.2=>4.5.3.4 - Add LICENSE (GPLv3) - Remove PDFLIBS as OPTIONS as it is no loner an optional requirement PR: 198602 Submitted by: pi Approved by: bapt marino (implicit) Notes: svn path=/head/; revision=381381
* Some OCD cleanups on some of the perl@ ports.Adam Weinberger2015-03-125-984/+976
| | | | | | | | | | | | | | | | - Remove dependencies in core - Put testing depends in TEST_DEPENDS - Remove unnecessary bsd.port.options.mk inclusions - Remove checks for Perl versions that no longer exist in the ports tree - Sort plists, some of which were so jumbled that I have to assume the plist was randomized before committing A lot of the plist changes in this commit are moving PERL5_MAN3 after SITE_PERL. It's repo churn now, but it makes updating the ports later far easier. Notes: svn path=/head/; revision=381151
* - Add empty directory to plistDmitry Marakasov2015-03-111-0/+1
| | | | Notes: svn path=/head/; revision=380989
* Update from 7.1.1 to 7.1.2.Mikhail Teterin2015-03-112-3/+3
| | | | Notes: svn path=/head/; revision=380981
* Unbreak by upgrading to March 5, 2015 "release" from upstream.Mikhail Teterin2015-03-085-106/+103
| | | | | | | | | | | | | | | Reduce restrictions from RESTRICTED to NO_CDROM -- the licensing allows use by academic community as long as it is not redistributed. Upstream still do not version their "releases", so next time they reroll the tarball, the download will start breaking again. But this time, it will be possible to fetch it from FreeBSD mirrors. Hide most of the optional data files under the DOCS-option and streamline various build-related scriptlets. Notes: svn path=/head/; revision=380806
* Unbreak by updating from 7.0.1 to 7.1.1. Hopefully, the authors willMikhail Teterin2015-03-082-6/+4
| | | | | | | | | | stop rerolling releases (and breaking downstream checksums) now. While here, allow parallel builds (seems to work again now) and stop extraction of unused subdirectories. Notes: svn path=/head/; revision=380785
* biology/samtools: update 1.1 -> 1.2Bartek Rutkowski2015-03-062-4/+5
| | | | | | | | PR: 198292 Submitted by: Reed Cartwright <cartwright@asu.edu> Notes: svn path=/head/; revision=380597
* biology/htslib: update 1.1 -> 1.2.1Bartek Rutkowski2015-03-066-23/+45
| | | | | | | | PR: 198291 Submitted by: Reed Cartwright <cartwright@asu.edu> Notes: svn path=/head/; revision=380596
* Add a run dependency used by update_blastdb.plTilman Keskinoz2015-03-061-1/+2
| | | | | | | | PR: 198331 Submitted by: maintainer Notes: svn path=/head/; revision=380582
* - Update to 1.13.10Danilo Egea Gondolfo2015-03-043-4/+4
| | | | Notes: svn path=/head/; revision=380435
* Remove Authors from pkg-descrBaptiste Daroussin2015-03-021-1/+0
| | | | Notes: svn path=/head/; revision=380301
* Remove TEST dependency on p5-Test-Simple when the version in core isAdam Weinberger2015-02-261-1/+0
| | | | | | | | | sufficient. Thanks to az for showing me the light here. Notes: svn path=/head/; revision=380025
* Update Unipro UGENE to version 1.16.0 (documentation was also rerolled).Alexey Dokuchaev2015-02-243-9/+18
| | | | Notes: svn path=/head/; revision=379787
* Mark BROKEN: Fails to link, tries to use internal fltk symbolsAntoine Brodin2015-02-211-0/+2
| | | | | | | | | | | | | | c++ -o seaview seaview.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o resource.o nexus.o viewasprots.o racnuc_fetch.o concatenate.o statistics.o trees.o treedraw.o addbootstrap.o least_squares_brl.o pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o Fl_Native_File_Chooser_FLTK.o raa_acnuc.o parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o bionj.o phyml_util.o \ -L/usr/local/lib -lfltk_images -lfltk \ -lXft -lXext -lfontconfig -ljpeg -lpng -lXinerama -L/usr/local/lib -lpdf \ -lX11 -lm -lz -pthread seaview.o: In function `clipboard_contains_alignment(char const*)': seaview.cxx:(.text+0x1c14): undefined reference to `fl_selection_buffer' Reported by: pkg-fallout Notes: svn path=/head/; revision=379482
* biology/seqtools: 4.31 -> 4.32Kurt Jaeger2015-02-122-3/+3
| | | | | | | | | | | | | | | | | | - Blixem o Previously-unsupported GFF feature types can now be displayed as a new 'basic feature' type. o Styles are now applied to the detail view as well as the big picture, so feature display is more consistent across the two views. o Fix a bug where styles were not being applied to dynamically-loaded features. - Dotter o Added a 'maximise' button for the greyramp tool. o Small fixes to inconsistencies in context-sensitive menus and keyboard shortcuts. Notes: svn path=/head/; revision=378870
* Mark BROKEN: Checksum and size mismatchAntoine Brodin2015-01-311-0/+1
| | | | | | | Reported by: pkg-fallout Notes: svn path=/head/; revision=378195
* - Update to 3.6.6Wen Heping2015-01-313-5/+5
| | | | | | | | PR: 197039 Submitted by: antont@inbox.lv Notes: svn path=/head/; revision=378190
* - Update to 1.13.9Danilo Egea Gondolfo2015-01-303-4/+4
| | | | Notes: svn path=/head/; revision=378185
* misc/otter & biology/ariadne: Not jobs safeJohn Marino2015-01-211-0/+2
| | | | | | | | | The otter port tries to build libotter.a before an object is completely built (share.o in my case) and ariadne tries to start building in a directory before it is created (under multiple jobs). Notes: svn path=/head/; revision=377623
* biology/py-biopython:Max Brazhnikov2015-01-191-3/+5
| | | | | | | | | - Convert to options framework Approved by: portmgr blanket Notes: svn path=/head/; revision=377466
* Designatate 4 ports as unsafe for parallel buildingJohn Marino2015-01-191-0/+1
| | | | | | | | | All had similar errors that it couldn't find something during the build, yet built on a subsequent pass with no adjustments. Most I've seen before on previous bulk runs. Notes: svn path=/head/; revision=377443
* - Pass maintainership to submitterWen Heping2015-01-191-1/+1
| | | | | | | | PR: 196859 Submitted by: Joseph Mingrone<jrm@ftfl.ca> Notes: svn path=/head/; revision=377397
* - Simplify MakefileSunpoet Po-Chuan Hsieh2015-01-182-135/+130
| | | | | | | | | - Use tab instead of space - Sort PLIST - Pass maintainership to perl@ Notes: svn path=/head/; revision=377369
* - Update to 1.13.8Danilo Egea Gondolfo2015-01-143-4/+4
| | | | Notes: svn path=/head/; revision=377013
* Mark BROKEN: UnfetchableAntoine Brodin2015-01-101-0/+1
| | | | | | | Reported by: pkg-fallout Notes: svn path=/head/; revision=376682
* Update to version 1.15.1.Alexey Dokuchaev2015-01-063-10/+10
| | | | Notes: svn path=/head/; revision=376383
* biology/tinker: 6.2.6 -> 7.0.1Kurt Jaeger2015-01-046-65/+94
| | | | | | | | PR: 196376 Submitted by: Nikola Kolev <koue@chaosophia.net> Notes: svn path=/head/; revision=376238
* - Convert USE_PYTHON -> USES leftovers missed in the previous commitsMarcus von Appen2015-01-041-1/+1
| | | | | | | | Spotted by: antoine With hat: python Notes: svn path=/head/; revision=376179
* Update to upstream version 36Thomas Zander2015-01-012-7/+6
| | | | | | | | PR: 196339 Submitted by: koue@chaosophia.net Notes: svn path=/head/; revision=376018
* Remove expired ports:Rene Ladan2015-01-017-166/+0
| | | | | | | | | | 2015-01-01 biology/boinc-simap: Project shutting down, see http://boincsimap.org/boincsimap/forum_thread.php?id=88 2015-01-01 security/openssh-portable-base: Overwrite-base option/port/pkg will be removed. There is no real need for foot-shooting. 2015-01-01 devel/cedet: Fails to build, use Emacs' builtin cedet package instead 2015-01-01 devel/ecb: does not work with newer Emacs versions, use the elpa package instead Notes: svn path=/head/; revision=375913
* Fix PKGNAMEPREFIX of biology/ncbi-blast+, so that the resulting package isMichael Gmelin2014-12-311-1/+2
| | | | | | | | | named like the port. Approved by: mentors (implicit) Notes: svn path=/head/; revision=375866
* Rename biology/ncbi-blast to biology/ncbi-blast+Michael Gmelin2014-12-305-2/+2
| | | | | | | Approved by: mentors (implicit) Notes: svn path=/head/; revision=375848
* - Update to 5.11.0Wen Heping2014-12-303-5/+28
| | | | | | | | PR: 196377 Submitted by: koue@chaosophia.net Notes: svn path=/head/; revision=375831
* Convert to USES=autoreconfBaptiste Daroussin2014-12-281-2/+2
| | | | Notes: svn path=/head/; revision=375747
* Bump portrevision after png updateBaptiste Daroussin2014-12-253-1/+3
| | | | Notes: svn path=/head/; revision=375598
* Change libpng15.so to libpng.so in LIB_DEPENDS to prepare the upgradeAntoine Brodin2014-12-253-4/+4
| | | | Notes: svn path=/head/; revision=375594
* Change my non-FreeBSD MAINTAINER mail to bofh@Muhammad Moinur Rahman2014-12-241-1/+1
| | | | | | | Approved by: bapt Notes: svn path=/head/; revision=375378
* Cleanup plistBaptiste Daroussin2014-12-207-8/+0
| | | | Notes: svn path=/head/; revision=375014
* - Upadate biology/mopac to version 1.15Pawel Pekala2014-12-166-41/+17
| | | | | | | | | | | | - Bump affected ports - Switch ports to new mastersite, add LICENSE - Reformat ports pkg descriptions PR: 194493 Submitted by: tkato432@yahoo.com Notes: svn path=/head/; revision=374828
* Samtools implements various utilities for post-processing alignments in thePawel Pekala2014-12-158-0/+169
| | | | | | | | | | | | | SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu> Notes: svn path=/head/; revision=374767
* HTSlib is an implementation of a unified C library for accessing common filePawel Pekala2014-12-146-0/+131
| | | | | | | | | | | | | formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing data. It is the core library used by samtools and bcftools. WWW: http://www.htslib.org/ PR: 195591 Submitted by: Reed A. Cartwright <cartwright@asu.edu> Notes: svn path=/head/; revision=374729
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