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* Remove outdated PERL_LEVEL checkSunpoet Po-Chuan Hsieh2017-06-011-8/+2
| | | | Notes: svn path=/head/; revision=442335
* Remove outdated PERL_LEVEL checkSunpoet Po-Chuan Hsieh2017-06-011-8/+2
| | | | Notes: svn path=/head/; revision=442334
* Update WWWSunpoet Po-Chuan Hsieh2017-05-301-1/+1
| | | | Notes: svn path=/head/; revision=442081
* biology/diamond: Update to version 0.9.3Joseph Mingrone2017-05-292-4/+4
| | | | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases Approved by: swills (mentor, implicit) Notes: svn path=/head/; revision=441991
* Mark some ports failing on armv6, for errors classified as "clang".Mark Linimon2017-05-271-0/+2
| | | | | | | | | While here, pet portlint. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=441847
* Mark some ports failing on armv6, for errors classified as "???".Mark Linimon2017-05-262-3/+6
| | | | | | | | | While here, pet portlint. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=441814
* biology/molden: Chase recent upstream change of molden distfile.Johannes M Dieterich2017-05-242-4/+4
| | | | | | | | | Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D10864 Notes: svn path=/head/; revision=441560
* - Update to 0.11.2.1Jochen Neumeister2017-05-232-5/+5
| | | | | | | | | | PR: 219396 Submitted by: Yuri Victorovich (Maintainer) <yuri@rawbw.com> Approved by: rene (mentor) Differential Revision: https://reviews.freebsd.org/D10856 Notes: svn path=/head/; revision=441555
* biology/diamond: Update to version 0.9.1Joseph Mingrone2017-05-232-6/+6
| | | | | | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases - License has changed to AGPLv3 Approved by: swills (mentor, implicit) Notes: svn path=/head/; revision=441513
* Revision bump of all ports with USE_GL after consolidation of mesa-libsMatthew Rezny2017-05-233-3/+3
| | | | | | | | Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D10845 Notes: svn path=/head/; revision=441503
* It is possible that r441426 will fix the build problem on armv6. GiveMark Linimon2017-05-211-1/+0
| | | | | | | | | it a try. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=441431
* Mark some ports failing on power64. In cases where the error messageMark Linimon2017-05-211-0/+2
| | | | | | | | | | | | was a stub, provide a real one. While here, pet portlint. Approved by: portmgr (tier-2 blanket) Reported by: swills Notes: svn path=/head/; revision=441429
* Mark BROKEN: checksum and size mismatchAntoine Brodin2017-05-191-0/+2
| | | | | | | Reported by: pkg-fallout Notes: svn path=/head/; revision=441258
* - Update to 5.15.0Wen Heping2017-05-183-3/+14
| | | | Notes: svn path=/head/; revision=441126
* Mark some ports failing on power64. In cases where the error messageMark Linimon2017-05-135-3/+6
| | | | | | | | | | | was a stub, provide a real one. While here, pet portlint. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=440746
* - Update to 0.11.1Martin Wilke2017-05-072-4/+4
| | | | | | | | PR: 219122 Submitted by: maintainer Notes: svn path=/head/; revision=440347
* - Update to 1.5.1Martin Wilke2017-05-072-6/+4
| | | | Notes: svn path=/head/; revision=440343
* bx-python is a python library and associated set of scripts to allow for rapidMartin Wilke2017-05-064-0/+47
| | | | | | | | | | | | | | | | | | | | | | | | | implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are: Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats). Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optomized for use over network filesystems). Data structures for working with intervals on sequences: * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation WWW: https://github.com/bxlab/bx-python PR: 218757 Submitted by: Yuri Victorovich <yuri@rawbw.com> Notes: svn path=/head/; revision=440232
* pysam is a lightweight wrapper of the htslib C-API and provides facilities toMartin Wilke2017-05-065-0/+47
| | | | | | | | | | | | | | | | | | read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages. The module supports compression and random access through indexing. This module provides a low-level wrapper around the htslib C-API as using cython and a high-level API for convenient access to the data within standard genomic file formats. WWW: https://pypi.python.org/pypi/pysam PR: 218745 Submitted by: Yuri Victorovich <yuri@rawbw.com> Notes: svn path=/head/; revision=440231
* - Update to 1.69Wen Heping2017-05-032-4/+4
| | | | | | | | | PR: 218903 Submitted by: wen@ Approved by: maintainer Notes: svn path=/head/; revision=440010
* devel/boost-*: update to 1.64.0Jan Beich2017-05-021-1/+1
| | | | | | | | | | | Changes: http://www.boost.org/users/history/version_1_64_0.html PR: 218835 Approved by: office (bapt) Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D10472 Notes: svn path=/head/; revision=439934
* Update math/gsl to 2.3Tobias C. Berner2017-05-021-0/+1
| | | | | | | | | | | | | | | | | | This release introduces some new features and fixes several bugs: http://savannah.gnu.org/forum/forum.php?forum_id=8751 * update to 2.3 and take maintainership * update math/py-gsl to 2.2.0 for gsl2 support * update math/rubygem-rb-gsl to 2.1.0.2 for gsl2 support PR: 218952 Exp-run by: antoine Reviewed by: mat, rakuco Approved by: rakuco (mentor) Differential Revision: https://reviews.freebsd.org/D10522 Notes: svn path=/head/; revision=439928
* Provide error messages for some ports failing on aarch64, and, in aMark Linimon2017-05-012-0/+5
| | | | | | | | | | | few cases, other tier-2 archs. While here, pet portlint. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=439905
* 2017-04-30 devel/stormlib-ghost++: Unfetchable for more than six months ↵Larry Rosenman2017-04-305-79/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | (google code has gone away) 2017-04-30 devel/py-coil: Unfetchable for more than six months (google code has gone away) 2017-04-30 devel/py-cmdln: Unfetchable for more than six months (google code has gone away) 2017-04-30 devel/privman: Unfetchable for more than six months (google code has gone away) 2017-04-30 devel/c-unit: Unfetchable for more than six months (google code has gone away) 2017-04-30 devel/py-px: Unfetchable for more than six months (google code has gone away) 2017-04-30 devel/nglogc: Unfetchable for more than six months (google code has gone away) 2017-04-30 devel/bncsutil-ghost++: Unfetchable for more than six months (google code has gone away) 2017-04-30 devel/liblouisxml: Unfetchable for more than six months (google code has gone away) 2017-04-30 devel/nxt-python: Unfetchable for more than six months (google code has gone away) 2017-04-30 devel/spdict: Unfetchable for more than six months (google code has gone away) 2017-04-30 devel/guiloader-c++: Unfetchable for more than six months (google code has gone away) 2017-04-30 devel/streamhtmlparser: Unfetchable for more than six months (google code has gone away) 2017-04-30 devel/winpdb: Unfetchable for more than six months (google code has gone away) 2017-04-30 net/opendpi: Unfetchable for more than six months (google code has gone away) 2017-04-30 net/py-pybeanstalk: Unfetchable for more than six months (google code has gone away) 2017-04-30 net-im/qwit: Unfetchable for more than six months (google code has gone away) 2017-04-30 net-im/linux-instantbird: Unfetchable for more than six months (google code has gone away) 2017-04-30 net-im/jabber-pyicq: Unfetchable for more than six months (google code has gone away) 2017-04-30 net-im/qwit-devel: Unfetchable for more than six months (google code has gone away) 2017-04-30 net-im/naim: Unfetchable for more than six months (google code has gone away) 2017-04-30 net-im/pwytter: Unfetchable for more than six months (google code has gone away) 2017-04-30 sysutils/sievelog: Unfetchable for more than six months (google code has gone away) 2017-04-30 sysutils/ldapenter: Unfetchable for more than six months (google code has gone away) 2017-04-30 sysutils/py-danzfs: Unfetchable for more than six months (google code has gone away) 2017-04-30 sysutils/plasma-applet-apcups: Unfetchable for more than six months (google code has gone away) 2017-04-30 sysutils/scanmem: Unfetchable for more than six months (google code has gone away) 2017-04-30 sysutils/pdsh: Unfetchable for more than six months (google code has gone away) 2017-04-30 deskutils/superswitcher: Unfetchable for more than six months (google code has gone away) 2017-04-30 deskutils/plasma-applet-playwolf: Unfetchable for more than six months (google code has gone away) 2017-04-30 deskutils/nagaina: Unfetchable for more than six months (google code has gone away) 2017-04-30 deskutils/vboxgtk: Unfetchable for more than six months (google code has gone away) 2017-04-30 deskutils/libgcal: Unfetchable for more than six months (google code has gone away) 2017-04-30 math/carve: Unfetchable for more than six months (google code has gone away) 2017-04-30 math/foma: Unfetchable for more than six months (google code has gone away) 2017-04-30 math/libjbigi: Unfetchable for more than six months (google code has gone away) 2017-04-30 multimedia/gcap: Unfetchable for more than six months (google code has gone away) 2017-04-30 multimedia/freetuxtv: Unfetchable for more than six months (google code has gone away) 2017-04-30 multimedia/bangarang: Unfetchable for more than six months (google code has gone away) 2017-04-30 multimedia/opencinematools: Unfetchable for more than six months (google code has gone away) 2017-04-30 multimedia/vstream-client: Unfetchable for more than six months (google code has gone away) 2017-04-30 biology/treeviewx: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/pylot: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/xpi-pencil: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/mod_myvhost: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/feedonfeeds: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/mod_jail: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/jspacker: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/cocoon: Overly complex port with no maintainer since 2008, requires openjdk 1.6 2017-04-30 www/mod_authz_unixgroup24: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/trac-down: Upstream is gone www/tengine 2017-04-30 www/arora: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/py-postmarkup: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/py-dotcloud.cli: deprecated in upstream 2017-04-30 www/closure-linter: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/httpsqs: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/sventon: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/mod_authnz_external22: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/mod_authn_otp: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/php-plurk-api: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/py-django-app-plugins: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/mod_authz_unixgroup22: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/squidstats: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/mod_log_firstbyte: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/gaeo: Unfetchable for more than six months (google code has gone away) 2017-04-30 www/xpi-pentadactyl: Unfetchable for more than six months (google code has gone away) 2017-04-30 net-mgmt/py-flowtools: Unfetchable for more than six months (google code has gone away) 2017-04-30 chinese/ydict: Unfetchable for more than six months (google code has gone away) 2017-04-30 chinese/py-cconv: Unfetchable for more than six months (google code has gone away) 2017-04-30 chinese/fqterm: Unfetchable for more than six months (google code has gone away) 2017-04-30 chinese/libgooglepinyin: Unfetchable for more than six months (google code has gone away) 2017-04-30 chinese/p5-cconv: Unfetchable for more than six months (google code has gone away) 2017-04-30 chinese/fcitx-googlepinyin: Unfetchable for more than six months (google code has gone away) 2017-04-30 chinese/php-cconv: Unfetchable for more than six months (google code has gone away) 2017-04-30 chinese/ibus-table-chinese: Unfetchable for more than six months (google code has gone away) 2017-04-30 databases/jdbm2: Unfetchable for more than six months (google code has gone away) 2017-04-30 databases/akonadi-googledata: Unfetchable for more than six months (google code has gone away) 2017-04-30 lang/ofc: Unfetchable for more than six months (google code has gone away) 2017-04-30 comms/esmska: Unfetchable for more than six months (google code has gone away) 2017-04-30 x11/keynav: Unfetchable for more than six months (google code has gone away) 2017-04-30 x11/hotwire-shell: Unfetchable for more than six months (google code has gone away) 2017-04-30 security/fuzzdb: Unfetchable for more than six months (google code has gone away) 2017-04-30 security/truecrack: Unfetchable for more than six months (google code has gone away) 2017-04-30 security/skipfish: Unfetchable for more than six months (google code has gone away) 2017-04-30 security/py-yara-editor: Unfetchable for more than six months (google code has gone away) 2017-04-30 security/nmapsi4: Unfetchable for more than six months (google code has gone away) 2017-04-30 security/cmd5checkpw: Unfetchable for more than six months (google code has gone away) 2017-04-30 net-p2p/unworkable: Unfetchable for more than six months (google code has gone away) 2017-04-30 net-p2p/rtgui: Unfetchable for more than six months (google code has gone away) 2017-04-30 audio/xpi-musicpm: Unfetchable for more than six months (google code has gone away) 2017-04-30 audio/pidgin-musictracker: Unfetchable for more than six months (google code has gone away) 2017-04-30 audio/logitechmediaserver-superdatetime: Unfetchable for more than six months (google code has gone away) 2017-04-30 audio/last-cmus: Unfetchable for more than six months (google code has gone away) 2017-04-30 audio/mehdiaplayer: Unfetchable for more than six months (google code has gone away) 2017-04-30 japanese/nhocr: Unfetchable for more than six months (google code has gone away) 2017-04-30 misc/xsw: Unfetchable for more than six months (google code has gone away) 2017-04-30 dns/py-adns: Unfetchable for more than six months (google code has gone away) 2017-04-30 dns/py-bonjour: Unfetchable for more than six months (google code has gone away) 2017-04-30 games/robocalypto: Unfetchable for more than six months (google code has gone away) 2017-04-30 games/libfov: Unfetchable for more than six months (google code has gone away) 2017-04-30 games/dcross: Unfetchable for more than six months (google code has gone away) 2017-04-30 games/lostfeathers: Unfetchable for more than six months (google code has gone away) 2017-04-30 games/hexglass: Unfetchable for more than six months (google code has gone away) 2017-04-30 textproc/ibus-table: Unfetchable for more than six months (google code has gone away) 2017-04-30 textproc/chm2pdf: Unfetchable for more than six months (google code has gone away) 2017-04-30 textproc/dtdinst: Unfetchable for more than six months (google code has gone away) 2017-04-30 textproc/py-xmltv: Unfetchable for more than six months (google code has gone away) 2017-04-30 textproc/ibus-m17n: Unfetchable for more than six months (google code has gone away) 2017-04-30 textproc/libroxml: Unfetchable for more than six months (google code has gone away) 2017-04-30 mail/gnome-gmail-notifier: Unfetchable for more than six months (google code has gone away) 2017-04-30 irc/py-gozerbot: Unfetchable for more than six months (google code has gone away) 2017-04-30 irc/tircd: Unfetchable for more than six months (google code has gone away) 2017-04-30 graphics/qiviewer: Unfetchable for more than six months (google code has gone away) 2017-04-30 graphics/py-gchartwrapper: Unfetchable for more than six months (google code has gone away) 2017-04-30 graphics/svgfig: Unfetchable for more than six months (google code has gone away) 2017-04-30 graphics/iulib: Unfetchable for more than six months (google code has gone away) 2017-04-30 graphics/seam-carving-gui: Unfetchable for more than six months (google code has gone away) 2017-04-30 graphics/py-pyggel: Unfetchable for more than six months (google code has gone away) 2017-04-30 graphics/rubygem-gemojione2: Use graphics/rubygem-gemojione instead Notes: svn path=/head/; revision=439826
* biology/py-biom-format: Update to version 2.1.6Joseph Mingrone2017-04-292-4/+5
| | | | | | | | | Upstream changes: https://github.com/biocore/biom-format/releases/tag/2.1.6 Approved by: swills (mentor, implicit) Notes: svn path=/head/; revision=439751
* - Fix shebangsMartin Wilke2017-04-221-2/+3
| | | | Notes: svn path=/head/; revision=439170
* - Fix shebangsMartin Wilke2017-04-221-3/+4
| | | | Notes: svn path=/head/; revision=439143
* - Fix shebangsDmitry Marakasov2017-04-211-3/+7
| | | | | | | | - Add NO_ARCH - Switch to relative links Notes: svn path=/head/; revision=439093
* biology/diamond: Update to version 0.8.38Joseph Mingrone2017-04-212-6/+5
| | | | | | | | | | | | - The base compilers meet all of Diamond's requirements, so remove compiler:c++11-lang from USES definition. - Upstream release notes: https://github.com/bbuchfink/diamond/releases/tag/v0.8.38 Approved by: swills (mentor, implicit) Notes: svn path=/head/; revision=439081
* biology/seaview: Update version 4.6=>4.6.1Muhammad Moinur Rahman2017-04-112-4/+5
| | | | | | | - Add PORTSCOUT to ignore non-existent 4.6.1.3 version Notes: svn path=/head/; revision=438306
* biology/diamond: Update to version 0.8.37Joseph Mingrone2017-04-022-5/+5
| | | | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.8.37 Approved by: swills (mentor, implicit) Notes: svn path=/head/; revision=437552
* Bump PORTREVISIONs for ports depending on the canonical version of GCC andGerald Pfeifer2017-04-0116-11/+16
| | | | | | | | | | | | | | | | | lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some circumstances such as versions of FreeBSD or platforms). This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using using Mk/bsd.octave.mk which in turn has USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang, c++11-lang, c++0x, c11, or gcc-c++11-lib. PR: 216707 Notes: svn path=/head/; revision=437439
* Update devel/tbb to 2017.5Ganael LAPLANCHE2017-03-071-0/+1
| | | | | | | | | Also bring the following changes: - Fetch distfiles from Github - Bump dependent ports' PORTREVISIONs Notes: svn path=/head/; revision=435599
* Mark the remaining ports depending on Google Code as DEPRECATED, with anMathieu Arnold2017-03-031-0/+2
| | | | | | | | | | | | | | EXPIRATION_DATE at the end of April 2017. In the past six months, about a third of the ports marked BROKEN because they were hosted on Google Code have been fixed. The remaining must not be of use to anyone. With hat: portmgr Sponsored by: Absolight Notes: svn path=/head/; revision=435349
* - Update to 1.42Wen Heping2017-03-012-4/+4
| | | | Notes: svn path=/head/; revision=435123
* Fix USE_GITHUB's GH_TAGNAME usage.Mathieu Arnold2017-02-282-5/+5
| | | | | | | Sponsored by: Absolight Notes: svn path=/head/; revision=435006
* biology/plinkseq: unbreak with clang 4.0Jan Beich2017-02-272-0/+12
| | | | | | | | PR: 216618 Submitted by: Jason Bacon <bacon4000@gmail.com> (maintainer) Notes: svn path=/head/; revision=434941
* biology/bowtie2: update to 2.3.0Jan Beich2017-02-274-6/+48
| | | | | | | | | | | - Unbreak with Clang 4.0 Changes: https://github.com/BenLangmead/bowtie2/releases/tag/v2.3.0 PR: 216619 Submitted by: Jason Bacon <bacon4000@gmail.com> (maintainer) Notes: svn path=/head/; revision=434940
* Mark a few more ports that create large logfiles broken on armv6.Mark Linimon2017-02-261-0/+2
| | | | | | | Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=434890
* Mark various ports as broken on armv6: invokes x86 asm.Mark Linimon2017-02-262-0/+2
| | | | | | | Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=434867
* - Update to 1.14.9Danilo Egea Gondolfo2017-02-243-6/+12
| | | | | | | - Use github Notes: svn path=/head/; revision=434741
* Move -fPIC to where Linux puts it so it is limited to a single library.Tijl Coosemans2017-02-132-4/+2
| | | | Notes: svn path=/head/; revision=434059
* biology/diamond: Update to version 0.8.36.Joseph Mingrone2017-02-122-4/+4
| | | | | | | Approved by: swills (mentor, implicit) Notes: svn path=/head/; revision=433945
* biology/molden: Unbreak port, regenerate checksums, increment PORTREVISION.Johannes M Dieterich2017-02-112-7/+5
| | | | | | | | | Reviewed by: swills (mentor), pi (former maintainer) Approved by: swills (mentor), pi (former maintainer) Differential Revision: https://reviews.freebsd.org/D9501 Notes: svn path=/head/; revision=433832
* Add -fPIC to various ports to enable them to build on armv6.Mark Linimon2017-02-091-8/+3
| | | | | | | Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=433767
* - Mark BROKEN: does not fetch, size/checksum mismatchDmitry Marakasov2017-02-071-0/+2
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=433554
* Update to 1.5.1Sunpoet Po-Chuan Hsieh2017-02-062-9/+8
| | | | | | | | | | | - Update LICENSE - Add LICENSE_FILE Changes: https://github.com/bioruby/bioruby/blob/bioruby-1.5/RELEASE_NOTES.rdoc https://github.com/bioruby/bioruby/blob/master/doc/RELEASE_NOTES-1.5.0.rdoc Notes: svn path=/head/; revision=433528
* biology/diamond: Update to version 0.8.35.Joseph Mingrone2017-02-052-5/+5
| | | | | | | | | Version 0.8.35 fixes a compiler error on i386. Approved by: swills (mentor, implicit) Notes: svn path=/head/; revision=433463
* Move devel/rubygem-bio to biology/rubygem-bioSunpoet Po-Chuan Hsieh2017-02-054-0/+36
| | | | Notes: svn path=/head/; revision=433348
* Bump PORTREVISION for ports affected by the fix the last commit.Mathieu Arnold2017-01-313-1/+3
| | | | | | | | Done with: Tools/scripts/bump-revision.sh Sponsored by: Absolight Notes: svn path=/head/; revision=432932
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