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* biology/diamond: Update to version 0.8.37jrm2017-04-022-5/+5
| | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.8.37 Approved by: swills (mentor, implicit)
* Bump PORTREVISIONs for ports depending on the canonical version of GCC andgerald2017-04-0116-11/+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
* Update devel/tbb to 2017.5martymac2017-03-071-0/+1
| | | | | | Also bring the following changes: - Fetch distfiles from Github - Bump dependent ports' PORTREVISIONs
* Mark the remaining ports depending on Google Code as DEPRECATED, with anmat2017-03-041-0/+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
* - Update to 1.42wen2017-03-012-4/+4
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* Fix USE_GITHUB's GH_TAGNAME usage.mat2017-02-282-5/+5
| | | | Sponsored by: Absolight
* biology/plinkseq: unbreak with clang 4.0jbeich2017-02-272-0/+12
| | | | | PR: 216618 Submitted by: Jason Bacon <bacon4000@gmail.com> (maintainer)
* biology/bowtie2: update to 2.3.0jbeich2017-02-274-6/+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)
* Mark a few more ports that create large logfiles broken on armv6.linimon2017-02-261-0/+2
| | | | Approved by: portmgr (tier-2 blanket)
* Mark various ports as broken on armv6: invokes x86 asm.linimon2017-02-262-0/+2
| | | | Approved by: portmgr (tier-2 blanket)
* - Update to 1.14.9danilo2017-02-253-6/+12
| | | | - Use github
* Move -fPIC to where Linux puts it so it is limited to a single library.tijl2017-02-142-4/+2
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* biology/diamond: Update to version 0.8.36.jrm2017-02-122-4/+4
| | | | Approved by: swills (mentor, implicit)
* biology/molden: Unbreak port, regenerate checksums, increment PORTREVISION.jmd2017-02-112-7/+5
| | | | | | Reviewed by: swills (mentor), pi (former maintainer) Approved by: swills (mentor), pi (former maintainer) Differential Revision: https://reviews.freebsd.org/D9501
* Add -fPIC to various ports to enable them to build on armv6.linimon2017-02-101-8/+3
| | | | Approved by: portmgr (tier-2 blanket)
* - Mark BROKEN: does not fetch, size/checksum mismatchamdmi32017-02-071-0/+2
| | | | Approved by: portmgr blanket
* Update to 1.5.1sunpoet2017-02-072-9/+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
* biology/diamond: Update to version 0.8.35.jrm2017-02-062-5/+5
| | | | | | Version 0.8.35 fixes a compiler error on i386. Approved by: swills (mentor, implicit)
* Move devel/rubygem-bio to biology/rubygem-biosunpoet2017-02-054-0/+36
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* Bump PORTREVISION for ports affected by the fix the last commit.mat2017-02-013-1/+3
| | | | | Done with: Tools/scripts/bump-revision.sh Sponsored by: Absolight
* Mark various ports broken on aarch64 and armv6.linimon2017-01-311-0/+2
| | | | Approved by: portmgr (tier-2 blanket)
* biology/diamond: Update to version 0.8.34.jrm2017-01-232-4/+4
| | | | | | | Upstream changelog: https://github.com/bbuchfink/diamond/releases Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D9288
* Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/sunpoet2017-01-213-3/+3
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* biology/diamond: Update to version 0.8.32.jrm2017-01-162-4/+4
| | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D9197
* biology/diamond: Update to version 0.8.31.jrm2017-01-132-4/+4
| | | | | | | | | | | | | | | | | | Upstream changelog: - Added compositional score adjustments (option --comp-based-stats (0,1)). This is a useful feature for filtering false positive hits and is enabled by default. - Removed --single-domain option and replaced by --max-hsps, to set the maximum number of Hsps per query/subject pair, to be consistent with BLAST. This option is set to 1 by default as getting more than 1 Hsp per subject seems to be confusing users. - Added option --no-self-hits to filter identical self-hits. Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D9134
* - Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOLamdmi32017-01-092-15/+3
| | | | Approved by: portmgr blanket
* devel/boost-*: update to 1.63.0jbeich2017-01-061-1/+1
| | | | | | | | Changes: http://www.boost.org/users/history/version_1_63_0.html PR: 215598 Exp-run by: antoine Approved by: office (bapt) MFH: 2017Q1
* Never set WRKSRC when using USE_GITHUB.mat2017-01-042-4/+0
| | | | | | | | | | If you want to set WRKSRC, set GH_PROJECT instead. - The GitHub URLs are case insensitive, but the distribution files you get out of them are not. - If the repository was renamed, the old URL will still work, but the distribution name will be ith the new name. Sponsored by: Absolight
* Assume "pkg-config zlib" works after 9.x reached EOLjbeich2017-01-041-3/+0
| | | | | | | Many ports passed ZLIB_CFLAGS="-I/usr/include" ZLIB_LIBS="-L/usr/lib -lz" which is unsafe at least with lang/gcc* that override some system headers and have newer libgcc_s.so that our old version in base may not be forward-compatible with.
* Remove BROKEN_FreeBSD_9sunpoet2017-01-012-3/+0
| | | | Approved by: portmgr (blanket)
* biology/diamond: Update to version 0.8.30jrm2016-12-312-4/+4
| | | | | | | | | | | Upstream changes: - slightly improved sensitivity - added option to report unaligned queries: --unal (0=no, 1=yes) - pairwise, XML and SAM format will report unaligned queries by default - added option to filter alignments by subject cover (--subject-cover) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D9000
* biology/ncbi-blast+: Add MAKE_JOBS_UNSAFEjrm2016-12-231-0/+2
| | | | | | PR: 214997 Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D8882
* - Update to 1.007001sunpoet2016-12-212-4/+4
| | | | Changes: http://search.cpan.org/dist/BioPerl-Run/Changes
* biology/bowtie2: Update to version 2.2.9jrm2016-12-212-14/+18
| | | | | | | | | - Update license information. - Add python to USES (bowtie2-build bowtie2-inspect need python) - Add DOCS and EXAMPLES options Approved by: AMDmi3 (mentor) swills (mentor) Differential Revision: https://reviews.freebsd.org/D8182
* biology/cd-hit: Update to bug-fix release 4.6.6jrm2016-12-212-5/+4
| | | | | | | | | | | | | | Changes in version 4.6.6: Bug fix for cd-hit-dup in variable length input when write out R1 reads Changes in version 4.6.5: Add filter for -aL option so that short sequences will be skipped if not satisfy representative sequences' -aL requirement. This will make compute faster in clustering settings where sequences in the same cluster are required to have similar length using -aL -AL option (e.g. -aL 0.9). Approved by: AMDmi3 (mentor) swills (mentor) Differential Revision: https://reviews.freebsd.org/D8186
* biology/jellyfish: Update to version 2.2.6jrm2016-12-203-54/+56
| | | | | | | | | | | Upstream changes since version 2.2.4: - Fix compilation warnings/errors with newer version of gcc (5.3 & 6.1). - Fix bug in parsing function that made it stop on sequences that consist of only empty lines. - New methods in bindings to enumerate the mers of a string. Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8204
* - Update *_DEPENDS: Bio::Coordinate family has been moved from ↵sunpoet2016-12-191-2/+4
| | | | | | biology/p5-BioPerl into biology/p5-Bio-Coordinate - Bump PORTREVISION for dependency change
* - Add p5-Bio-Coordinate 1.007001sunpoet2016-12-195-0/+58
| | | | | | | Bio::Coordinate classes are used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples. WWW: http://search.cpan.org/dist/Bio-Coordinate/
* - Update to 1.007000sunpoet2016-12-194-20/+29
| | | | | | | | | | | | - Change MASTER_SITES back to CPAN - Update LICENSE - Add LICENSE_FILE - Use PORTDOCS - Convert to options target helper - Use INSTALL_SCRIPT - Pet portlint: fix diff header of patch file Changes: http://search.cpan.org/dist/BioPerl-Run/Changes
* - Update to 1.007001sunpoet2016-12-196-383/+180
| | | | | | | | - Update *_DEPENDS - Use TEST_DEPENDS: Test::Most and URI::Escape are test-only dependencies - Use PORTDATA, PORTDOCS and PORTEXAMPLES Changes: http://search.cpan.org/dist/BioPerl/Changes
* - Update to 2.5.0wen2016-12-195-68/+190
| | | | | | PR: 214997 Submitted by: mzaki@e-mail.ne.jp Approved by: maintainer(timeout, > 14 days)
* - Update to 2.40sunpoet2016-12-183-10/+22
| | | | | | | | - Update *_DEPENDS for biology/p5-bioperl renaming - Add NO_ARCH - Sort PLIST Changes: http://search.cpan.org/dist/Bio-Graphics/Changes
* - Move biology/p5-bioperl-run to biology/p5-BioPerl-Runsunpoet2016-12-186-8/+10
| | | | | | - Sort *_DEPENDS - Add NO_ARCH - Bump PORTREVISION for biology/p5-bioperl renaming
* - Add LICENSE_FILEsunpoet2016-12-181-2/+5
| | | | | - Add NO_ARCH - Bump PORTREVISION for biology/p5-bioperl renaming
* - Add LICENSEsunpoet2016-12-181-4/+8
| | | | | | - Add NO_ARCH - Sort *_DEPENDS - Bump PORTREVISION for biology/p5-bioperl renaming
* - Add LICENSEsunpoet2016-12-181-1/+7
| | | | | - Add NO_ARCH - Bump PORTREVISION for biology/p5-bioperl renaming
* - Move biology/p5-bioperl to biology/p5-BioPerlsunpoet2016-12-187-9/+7
| | | | | - Sort *_DEPENDS - Bump PORTREVISION for dependent ports
* biology/diamond: Update to version 0.8.29jrm2016-12-182-4/+4
| | | | | | | | Upstream change: fixed an issue that could cause a crash when using view on incomplete DAA files Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D8832
* biology/protomol: Support build with C++11 (taken from dports)marino2016-12-185-0/+48
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* biology/blat: Fix build on DF (taken from dports)marino2016-12-181-0/+14
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* biology/lamarc: Fix build on DF (taken from dports)marino2016-12-181-0/+11
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* biology/chemeq: fix build on GCC (taken from dports)marino2016-12-181-0/+11
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* Remove libintl.so.9 compatibility link that was added in r374303 totijl2016-12-093-2/+3
| | | | | prevent massive PORTREVISION bumps. Bump dependent ports that have not been bumped since.
* Remove libjpeg.so.11 compatibility link that was added in r374303 totijl2016-12-091-0/+1
| | | | | prevent massive PORTREVISION bumps. Bump dependent ports that have not been bumped since.
* Bump PORTREVISIONS for ports depending on the canonical version of GCC andgerald2016-12-077-5/+7
| | | | | | | | | | | | | | | lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some circumstances such as versions of FreeBSD or platforms), part II. The first part covered ports with USE_GCC=yes, USE_GCC=any, or one of gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang, c++11-lang, c++0x, c11 requested via USES=compiler. This adds ports with USES=fortran and ports using Mk/bsd.octave.mk which in turn has USES=fortran. PR: 214965 Reported by: thierry
* biology/molden: distfile was updated in xwin.cpi2016-12-042-4/+4
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* Do not use post-stage. Use post-install instead.mat2016-12-021-1/+1
| | | | | | | | | | | | The only reason to use post-stage is because the port needs to do "things" at a later time, like some plist manipulation. While there, fold post-install in do-install targets when they are defined. PR: 214780 Submitted by: mat Exp-run by: antoine Sponsored by: Absolight
* biology/njplot: Add site in MASTER_SITES because package builders arejrm2016-11-281-2/+4
| | | | | | | timing out during fetch. Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8651
* biology/diamond: Update to version 0.8.28jrm2016-11-282-5/+6
| | | | | | | | | | | | Correct LICENSE and set LICENSE_FILE Upstream changelog: - support for gzip compressed files containing multiple gzip streams - support for the BLAST pairwise format (option -f 0) - slightly improved sensitivity Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8652
* Fixup USE_GITHUB usage.mat2016-11-262-3/+3
| | | | | | | It already sets DISTNAME to a very nice unique name, do not set it yourself. Sponsored by: Absolight
* Replace USE_GCC=4.9+ by USE_GCC=yes, now that lang/gcc and the defaultgerald2016-11-261-1/+1
| | | | version for GCC in the Ports Collection have moved to GCC 4.9.
* devel/boost-*: update to 1.62.0jbeich2016-11-231-0/+1
| | | | | | | | | | | | - Enable `long double` C99 math usage - Switch 9.x back to building with GCC Changes: http://www.boost.org/users/history/ PR: 199601 Submitted by: Chen Xu, bapt, amdmi3, truckman (based on) Reviewed by: rakuco (kde) (earlier version) Exp-run by: antoine (3 tries), truckman (consumers only, earlier versions) Approved by: bapt (office)
* - Remove unnecessary USES=shebangfixsunpoet2016-11-211-4/+8
| | | | - Convert to new options target helper
* Bump PORTREVISIONS for ports depending on the canonical version of GCC andgerald2016-11-205-2/+5
| | | | | | | | | lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some circumstances such as versions of FreeBSD or platforms). In particular that is ports with USE_GCC=yes, USE_GCC=any, or one of gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang, c++11-lang, c++0x, c11 requested via USES=compiler.
* biology/avida: Fix ncurses from ports supportmarino2016-11-191-1/+3
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* biology/njplot: Revive and update to version 2.4jrm2016-11-165-0/+109
| | | | | Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8518
* Mark various leaf ports broken on aarch64, and, where appropriate, otherlinimon2016-11-114-2/+8
| | | | | | tier-2 archs. Approved by: portmgr (tier-2 blanket)
* Attempt to fix build on non-x86 archs.linimon2016-11-111-3/+5
| | | | Approved by: portmgr (tier-2 blanket)
* biology/seqtools: update 4.43.0 -> 4.44.1pi2016-11-113-4/+14
| | | | | | - Blixem: Features can now be added to multiple different groups/filters. - Belvu: Fix a problem where column highlighting can get out of sync with the text.
* biology/molden: add missing LICENSE_NAMEpi2016-11-101-1/+2
| | | | Reported by: pkg-fallout
* biology/molden: fix distinfo, set LICENSEpi2016-11-102-7/+11
| | | | | | Submitted by: marino Reported by: Eduardo Lemos de Sa <eduardo.lemosdesa@gmail.com> MFH: 2016Q4
* The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.linimon2016-11-093-3/+3
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* Mark as broken on arm64.linimon2016-11-081-0/+2
| | | | Approved by: portmgr (tier-2 blanket)
* Mark broken on all tier-2 archs.linimon2016-11-081-0/+3
| | | | Approved by: portmgr (tier-2 blanket)
* Mark broken on the rest of the tier-2 archs: invokes x86 asm.linimon2016-11-081-1/+4
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* biology/diamond: Update to version 0.8.26jrm2016-11-062-4/+4
| | | | | | | Release notes: https://github.com/bbuchfink/diamond/releases/tag/v0.8.26 Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D8447
* Cleanup no longer needed CHMOD usage after r424898.mat2016-11-034-12/+5
| | | | | | | PR: 213743 Submitted by: mat Exp-run by: antoine Sponsored by: Absolight
* - Mark it BROKENwen2016-10-281-1/+3
| | | | - Reset maintainer to ports@
* Use USES=pathfix where applicable.mat2016-10-214-21/+11
| | | | | | | | PR: 213195 Submitted by: mat Exp-run by: antoine Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D8093
* ${RM} already has -f.mat2016-10-213-3/+3
| | | | | | | PR: 213570 Submitted by: mat Exp-run by: antoine Sponsored by: Absolight
* biology/diamond: update to version 0.8.24jrm2016-10-172-4/+4
| | | | | Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D8268
* biology/diamond: update to version 0.8.23jrm2016-10-102-4/+4
| | | | | | | | | | | Upstream release notes: Added option to change the genetic code used for translation of query in blastx mode (option --query-gencode, see here for a list of possible values: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi). Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8202
* Mark BROKEN: unfetchable, size mismatchantoine2016-10-011-0/+1
| | | | Reported by: pkg-fallout
* biology/blat: Fix build with non-base SSLmarino2016-10-011-4/+4
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* Update PORTREVISION and dinstinfo due to upstream tarball changejrm2016-09-302-3/+4
| | | | | | Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D8083
* biology/paml: update to version 4.9c and various improvementsjrm2016-09-284-33/+48
| | | | | | | | | | | | | | | | | - Update to version 4.9c - Set LICENSE=GPLv3 - Use the variable PORTDOCS to automate the generation of the DOCS plist (as suggested by mat@). - Install dat/ examples/ and Technical/ directories as well as files in the root directory of the distribution tarball. - Fix broken permissions. - Delete Windows executables. - Build and install useful binaries not built by upstream's Makefile. - Update pkg-descr. Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D8040
* Update email address to jrm@FreeBSD.org for ports that I maintainjrm2016-09-243-5/+3
| | | | | | Reviewed by: mat, swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D7995
* - Update to 1.68wen2016-09-232-3/+4
| | | | | | PR: 212874 Submitted by: wen@(myself) Approved by: maintainer
* - Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1]pawel2016-09-156-28/+39
| | | | | | | - Fix spelling in pkg-descr PR: 212682 [1] Submitted by: Hannes Hauswedell (maintainer) [1]
* GOOGLE_CODE has gone away.mat2016-09-141-0/+2
| | | | | | | | | | - If a port has another upstream, remove GOOGLE_CODE - If a port only has GOOGLE_CODE mark it BROKEN Some ports have a local mirror configured but for security reasons, it is not considered upstream. Sponsored by: Absolight
* - Update to 0.8.22amdmi32016-09-142-4/+4
| | | | | PR: 212603 Submitted by: jrm@ftfl.ca (maintainer)
* biology/ncbi-blast+: Remove redundant LIB_DEPENDS (bz2 libary)marino2016-09-111-3/+2
| | | | | | | All support platforms have libbz2.so in base, so this port will never pull in archivers/bzip2. Approved by: just-fix-it
* - Update to 1.72wen2016-09-112-4/+4
| | | | Changes: http://search.cpan.org/~cjfields/Bio-ASN1-EntrezGene-1.72/
* Most commonly used build systems support silent builds, when theyamdmi32016-09-101-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | hide actual commands executed and only show short summary line (like "CC foo.c"). CMake and ninja enable this by default, some autotools using ports do as well. This is unacceptable because we need complete build logs at any time, so we now switch to verbose build logs unconditionally. Note that this change deliberately affects ALL builds and not only package builds on cluster, because we need to be sure that user experiencing failure can always provide informative build log regardless of settings and without rerunning the build. Change summary: - Always do verbose builds for cmake, ninja and GNU configure (the latter includes check if --disable-silent-rules is actually supported by the configure script; there are isolated cases when it's not true) - Remove CMAKE_VERBOSE, NINJA_VERBOSE and CONFIGURE_ARGS=--disable-silent-rules from all ports which set them for this is no longer needed - Revert hacks for --disable-silent-rules support priorly committed to biology/ncbi-blast+ and net-p2p/mldonkey - no longer needed as well Submitted by: amdmi3 Reviewed by: mat Exp-run by: antoine Approved by: portmgr (mat, antoine) Differential Revision: D7534
* - Make configure script handle --disable-silent-rules gracefullyamdmi32016-09-061-1/+1
| | | | | PR: 212075 Approved by: portmgr blanket
* - Update to 0.8.20wen2016-09-062-4/+4
| | | | | PR: 212399 Submitted by: jrm@ftfl.ca(maintainer)
* - Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk withtijl2016-09-062-4/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Mk/Uses/linux.mk. - Replace USE_LINUX=yes with USES+=linux and USE_LINUX=(.*) with USES+=linux:\1 in all ports. - Replace USE_LINUX_APPS with USE_LINUX in all ports. - Use INSTALL_SCRIPT instead of INSTALL_PROGRAM to install scripts in some ports. - When USE_LINUX_RPM is defined, simplify the way DISTFILES and EXTRACT_ONLY are defined. - Remove BRANDELF_DIRS and BRANDELF_FILES handling. In the very rare cases that it is still necessary ports can run ${BRANDELF} from post-patch. - Remove AUTOMATIC_PLIST handling. Only one port used it. - Fix Linux MASTER_SITES. - Replace OVERRIDE_LINUX_BASE_PORT and OVERRIDE_LINUX_NONBASE_PORTS with default versions framework. - bsd.port.mk: - Move Linux related bits to Uses/linux.mk, except USE_LINUX_PREFIX. - Put USE_LINUX_PREFIX handling after USES processing. - Define DOCSDIR, DATADIR, etc. after handling USE_LINUX_PREFIX so it can give these variables a different default value. - When a package needs to run Linux ldconfig check before installation if Linux support is enabled. - emulators/linux_base-*: - Use USES=linux and remove duplication. - Remove files/lp. FreeBSD or CUPS lp(1) should work. - Remove files/yp.conf. No longer seems to be used. - Remove pkg-deinstall and move pkg-install into pkg-plist. - Update pkg-descr and pkg-message. - Fix handling of ldconfig cache in pkg-plist. - devel/fb-adb: Use a Linux shell to run a Linux script but patch the script to use FreeBSD mkdir so mkdir -p $path creates $path and not /compat/linux/$path. PR: 211645 Exp-run by: antoine Approved by: portmgr (antoine)
* biology/molden: 5.4 -> 5.7pi2016-08-262-6/+4
| | | | | | | | | | - Adds editable text fields that are longer than the visible string and introduces a new way of selecting a range of amino acids. - introduces interfaces to the open source packages openbabel and pharmer. Openbabel is used to create 2D images of the molecules in a .sdf file. It is also used to do 2D fingerprint searching. Pharmer is used to pharmacophore (3D) searching against indexed databases of .sdf files.
* Update to version 0.8.19pawel2016-08-262-4/+4
| | | | | PR: 212145 Submitted by: Joseph Mingrone (maintainer)
* - Mark BROKEN: does not fetch (distfile was removed from ftp)amdmi32016-08-221-0/+2
| | | | Approved by: portmgr blanket
* biology/bedtools is not jobs safemarino2016-08-221-0/+2
| | | | | The version.o target tries to use version_git.h before that header is created.
* - Switch to options helpersamdmi32016-08-183-16/+11
| | | | | - Regenerate patches with `make makepatch` - Mark WXGTK option broken: does not build: src/convErr/gc_errhandling.cpp:75:12: error: cannot initialize return object of type 'const char *' with an rvalue of type 'const wxChar *' (aka 'const wchar_t *')
* Update biology/diamond to 0.8.18.brd2016-08-152-4/+4
| | | | | | PR: 211845 Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer) Approved by: bdrewery (implicit)
* - Update to 1.9 [1]wen2016-08-082-10/+8
| | | | | | | | | | | - Moved to github [1] - Depend on newer sqlalchemy10 [1] - Update pkg-descr and WWW [1] - Limit python to -2.7 [2] - Reset maintainer to python@ for better maintain PR: 211621 Submitted by: pi@ [1], koobs@ [2]
* Update to version 0.8.17pawel2016-08-062-5/+5
| | | | | PR: 211582 Submitted by: Joseph Mingrone (maintainer)
* biology/seqtools: 4.42.1 -> 4.43.0pi2016-07-313-17/+227
| | | | | | ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/release_notes.html - Mark broken on 9.x: Fails to build due to C++ std issues
* Update to upstream release 0.8.16riggs2016-07-252-4/+4
| | | | | PR: 211335 Submitted by: jrm@ftfl.ca (maintainer)
* Cleanup $() variables in ports Makefiles.mat2016-07-201-1/+1
| | | | | | | Mostly replace with ${}, but sometime, replace with $$() because it is what was intended in the first place. (I think.) Sponsored by: Absolight
* - update libgd to 2.2.2dinoex2016-07-201-1/+1
| | | | | | | | | | | - new MASTER_SITES - add security patch PR: 210913 Submitted by: Piotr Kubaj MFH: 2016Q3 Security: CVE-2015-8874 Security: CVE-2016-3074 Security: http://www.openwall.com/lists/oss-security/2016/07/12/4
* When there is a do-install target, do not use a post-install target, domat2016-07-193-4/+5
| | | | | | | | | | | | everything at once. Sometime, rename post-install into a options helper target. I did not fix ports that were such a mess that I could not figure out what they really wanted to do. I also did not change ports that had some version of an auto-plist code in post-install, for the same reason. With hat: portmgr Sponsored by: Absolight
* Trim excess tabs, no-op changepawel2016-07-151-13/+13
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* Update to version 0.8.14pawel2016-07-152-4/+4
| | | | | PR: 211078 Submitted by: Joseph Mingrone (maintainer)
* - Update to 0.8.11amdmi32016-07-072-5/+5
| | | | | PR: 210877 Submitted by: jrm@ftfl.ca (maintainer)
* Remove expired ports without open PRs:rene2016-07-057-161/+0
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* - LICENSEamdmi32016-07-022-10/+22
| | | | | - Optionalize NLS - Switch to options helpers
* biology/diamond: update 0.8.6 -> 0.8.9junovitch2016-06-302-4/+4
| | | | | PR: 210710 Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
* - Add missing dependency, fixing buildamdmi32016-06-241-1/+5
| | | | - Switch to options helpers
* - Switch to options helpersamdmi32016-06-212-7/+11
| | | | - Regenerate patches with `make makepatch`
* biology/diamond: update to 0.8.6rm2016-06-182-4/+4
| | | | | PR: 210345 Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
* - Fix run-time dependency issuesolivierd2016-06-111-2/+13
| | | | | | | - Bump PORTREVISION PR: 209767 Submitted by: Joseph Mingrone (maintainer)
* biology/seaview: Update version 4.5.4.8=>4.6bofh2016-06-102-7/+4
| | | | - UNBREAK
* Update to 0.8.5matthew2016-06-093-34/+18
| | | | | PR: 209611 Submitted by: jrm@ftfl.ca (maintainer)
* - Update to 1.35wen2016-06-082-3/+4
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* Remove unneeded usage of:mat2016-06-061-2/+1
| | | | | | | | - MASTER_SITE_SUBDIR - ${MASTER_SITES_FOO} - :DEFAULT (and use a default when appropriate) Sponsored by: Absolight
* Deprecate ports broken for more than 6 monthsantoine2016-06-042-0/+4
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* - Do install cmake and pkgconfig modulesamdmi32016-05-282-3/+8
| | | | | | | - While here, switch to options helpers PR: 209710 Submitted by: h2+fbsdports@fsfe.org (maintainer)
* biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1pi2016-05-278-20/+23
| | | | | | | | Changes: https://sourceforge.net/p/samtools/mailman/message/35033807/ PR: 209653 Submitted by: cartwright@asu.edu (maintainer)
* Remove useless WRKSRC definitions.mat2016-05-251-2/+0
| | | | | | While there, correct DEV_WARNINGS when they occur. Sponsored by: Absolight
* - Fix trailing whitespace in pkg-messagesamdmi32016-05-196-12/+12
| | | | Approved by: portmgr blanket
* - Fix trailing whitespace in pkg-descrs, categories [a-f]*amdmi32016-05-1921-36/+36
| | | | Approved by: portmgr blanket
* Fix DEPENDSantoine2016-05-191-2/+2
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* - Convert to USES=mysqlamdmi32016-05-171-8/+4
| | | | - Cosmetic fixes
* - Update to 4.9aamdmi32016-05-172-4/+7
| | | | | | | - While here, simplify WRKSRC and use options helpers PR: 209535 Submitted by: jrm@ftfl.ca (maintainer)
* biology/bowtie2: 2.2.7 -> 2.2.8pi2016-05-142-3/+3
| | | | | | | | | - Various website updates - Fixed the bowtie2-build issue that made TBB compilation fail PR: 208943 Submitted by: Joseph Mingrone <jrm@ftfl.ca> Approved by: Jason Bacon <bacon4000@gmail.com> (maintainer)
* Prevent collision with getline(3)bapt2016-05-141-0/+300
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* Prevent collision with getline(3)bapt2016-05-141-0/+291
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* Prevent collision with getline(3)bapt2016-05-124-6/+27
| | | | While here regen patches
* biology/seqan: update 1.3.1 -> 2.1.1junovitch2016-05-1012-1915/+3706
| | | | | | | | biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage UPDATING: document SeqAn updates and seqan1 port for legacy usage PR: 204127 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
* New port: biology/seqan-appsjunovitch2016-05-105-0/+220
| | | | | | | | | | | | | | | | | SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. This port contains applications built on SeqAn and developed within the SeqAn project. Among them are famous read mappers like RazerS and Yara, as well as many other tools. Some applications are packaged seperately and the library can be found at biology/seqan. WWW: http://www.seqan.de/ PR: 204127 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
* Add final slash in WWW entryolivierd2016-05-101-1/+1
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* The BIOM file format (canonically pronounced biome) is designed to be aolivierd2016-05-104-0/+48
| | | | | | | | | | | | | | | | | | | | | | | | general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project. The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome. WWW: http://biom-format.org/ PR: 209193 Submitted by: Joseph Mingrone
* During the exp-run in bug 208158, it was found that biology/ugene givesdim2016-05-084-0/+36
| | | | | | | | | | | | | | | | | | | | | | | | | | errors with libc++ 3.8.0: In file included from src/QScoreAdapter.cpp:1: In file included from src/QScoreAdapter.h:4: In file included from ../../include/U2Core/MAlignment.h:1: In file included from ../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignment.h:25: In file included from ../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignmentInfo.h:25: In file included from /usr/local/include/qt5/QtCore/QString:1: In file included from /usr/local/include/qt5/QtCore/qstring.h:41: In file included from /usr/local/include/qt5/QtCore/qchar.h:37: In file included from /usr/local/include/qt5/QtCore/qglobal.h:39: /usr/include/c++/v1/cstddef:43:15: fatal error: 'stddef.h' file not found #include_next <stddef.h> ^ This is because the port tries to add /usr/include as a system include directory, using -isystem, and this screws up the order of include directories. Fix it by patching up a number of .pri files to avoid using the -isystem flag. Approved by: h2+fbsdports@fsfe.org (maintainer) PR: 209366 MFH: 2016Q2
* DNA query sequences against a protein reference database (BLASTP and BLASTXwen2016-05-065-0/+71
| | | | | | | | | | | alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings. WWW: http://ab.inf.uni-tuebingen.de/software/diamond/ PR: 208998 Submitted by: jrm@ftfl.ca
* - Update to 1.14.8danilo2016-05-013-4/+4
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* biology/seqtools: 4.41.1 -> 4.42.1pi2016-04-232-5/+5
| | | | | | | - fixes build on 9.x - Added a feedback box to show the read depth at the selected coord. Hover over this box to see the specific base support (i.e. the number of A/C/G/Ts).
* many ports: mark broken on powerpc64swills2016-04-221-0/+2
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* - Switch to options helpersamdmi32016-04-173-16/+17
| | | | | - Regenerate patches with `make makepatch` - Simplify plist
* - Update to 1.66wen2016-04-172-4/+3
| | | | | | PR: 208825 Submitted by: wen@ Approved by: maintainer
* - Switch to options helpersamdmi32016-04-161-3/+8
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* Upgrade from 5.12.0 to 5.13.0. Release-announcement available here:mi2016-04-163-4/+5
| | | | | | https://groups.google.com/forum/#!topic/sbml-discuss/OEq_49c_X78 Notified by: portscout
* Update to version 1.22.0, which now unfortunately requires Qt 5.x. Alsodanfe2016-04-149-36/+204
| | | | | | | since around v1.18.0, UGENE is using Google's Breakpad library for crash reporting, which is very system-specific and does not support FreeBSD at the moment. Due to lack of resources and interest in porting it, simply disable crash reporting code for the time being.
* - Add LICENSEamdmi32016-04-101-1/+8
| | | | - Switch to options helpers
* Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.mat2016-04-0138-148/+148
| | | | | With hat: portmgr Sponsored by: Absolight
* - Update to 1.5.0amdmi32016-04-013-23/+11
| | | | | | PR: 208351 Submitted by: wen@FreeBSD.org Approved by: mauricio@arareko.net (maintainer)
* - Use more appropriate BROKEN instead of IGNOREamdmi32016-03-301-4/+2
| | | | | | PR: 208367 Submitted by: bacon4000@gmail.com (maintainer) Suggested by: rakuco
* - Update to 5.12.0wen2016-03-273-5/+7
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* - Clarify LICENSEamdmi32016-03-241-4/+3
| | | | | | | | - Add LICENSE_FILE - Remove USES=tar:bzip2 (incorrect and no-op with USE_GITHUB) - Drop unneeded (and incorrect anyway) PKG_CONFIG_PATH Approved by: portmgr blanket
* Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.amdmi32016-03-246-0/+146
| | | | | | | | | | | | A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. WWW: http://www.genome.umd.edu/jellyfish.html PR: 207929 Submitted by: bacon4000@gmail.com
* New port: biology/bowtie2.rakuco2016-03-236-0/+134
| | | | | | | | | | | | | | | Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. This is Bowtie version 2, which will need to coexists with Bowtie 1 for the foreseeable future. Both are required by certain genomics pipelines, in some cases (e.g. Trinity) by the same pipeline. WWW: https://github.com/BenLangmead/bowtie2 PR: 207908 Submitted by: Jason Bacon <bacon4000@gmail.com>
* New port: biology/slclust.rakuco2016-03-236-0/+85
| | | | | | | | | | | Slclust is a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters. WWW: http://sourceforge.net/projects/slclust/ PR: 207997 Submitted by: Jason Bacon <bacon4000@gmail.com>
* Trimmomatic performs a variety of useful trimming tasks for illuminawen2016-03-175-0/+41
| | | | | | | | | NGS paired-end and single ended data. WWW: http://www.usadellab.org/cms/?page=trimmomatic PR: 208044 Submitted by: bacon4000@gmail.com
* New port: biology/p5-transdecoderpi2016-03-175-0/+88
| | | | | | | | | | | | TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. WWW: http://transdecoder.github.io/ PR: 207993 Submitted by: Jason Bacon <bacon4000@gmail.com>
* biology/seqtools: 4.40.0 -> 4.41.1pi2016-03-153-4/+6
| | | | - mostly internal changes, some build fixes
* Always set the DEFAULT github DISTFILE with .tar.gz for EXTRACT_SUFX.mat2016-03-081-2/+2
| | | | | | | | | | | | Fix distinfo for the offending ports. lang/yorick's tag was moved, and the added patch was no longer needed. PR: 207644 Submitted by: mat Exp-run by by: antoine Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D4268
* New port: biology/bowtie.rakuco2016-03-056-0/+194
| | | | | | | | | | | Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. WWW: http://bowtie-bio.sourceforge.net/index.shtml PR: 206939 Submitted by: Jason Bacon <bacon4000@gmail.com>
* New port: biology/vcftools.rakuco2016-02-275-0/+59
| | | | | | | | | | A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project. WWW: https://github.com/vcftools/vcftools PR: 206926 Submitted by: Jason Bacon <bacon4000@gmail.com>
* - Update to 3.2.0wen2016-02-263-34/+62
| | | | | | | - Update pkg-descr PR: 205890 Submitted by: tkato432@yahoo.com
* - Update to 1.14.7danilo2016-02-212-3/+3
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* - Update to 1.34wen2016-02-122-3/+3
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* biology/seqtools: 4.39.3 -> 4.40.0pi2016-02-062-3/+3
| | | | | | | - Blixem can now accept a 'command' tag in a gff line for a region feature. The given command should return gff and will be run by blixem on the given region. - Blixem now supports fetching sequence data over https.
* biology/mapm3: document ncurses rqmt (USES+=ncurses), respect LDFLAGSmarino2016-02-021-0/+2
| | | | | | Also link with libncurses, not libtermcap approved by: infrastructure blanket
* biology/samtools: document ncurses requirement (USES+=ncurses)marino2016-02-021-1/+1
| | | | approved by: infrastructure blanket
* biology/molden: updated distfile, take maintainerpi2016-01-212-4/+4
| | | | | | - upstream distfile is moving target with same version number Submitted by: antoine
* Mark BROKEN: checksum and size mismatchantoine2016-01-211-0/+1
| | | | Reported by: pkg-fallout
* The bedtools utilities are a suite of tools for performing a wide range ofwen2016-01-196-0/+135
| | | | | | | | | | | | | | | | | genomics analysis tasks. The most widely-used of these tools enable genome arithmetic, i.e., set theory on the genome. For example, with bedtools one can intersect, merge, count, complement, and shuffle genomic intervals from multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF. Although each individual utility is designed to do a relatively simple task, e.g., intersect two interval files, more sophisticated analyses can be conducted by stringing together multiple bedtools operations on the command line or in shell scripts. WWW: http://bedtools.readthedocs.org/ PR: 204536 Submitted by: scottcheloha@gmail.com
* biology/molden: 5.0.7 -> 5.4pi2016-01-195-192/+799
| | | | | | | | | | | | | | Changes: - Missing hydrogens atoms of HETATM molecules (pdb files) are stored locally. - Pdb files can now be clipped. - Fixes missing residues. Introduces an alternative way of generating rotamers, without using z-matrices. This potentially a faster algorithm. - Supports Movie making through avconv/ffmpeg. - calculates the Electron Localization Function (ELF). - Updated code of ambfor/ambmd to speed up optimisations/MD of proteins solvated in water (Jan, 2014). PR: 204341
* mark ports that don't work with Ruby 2.3swills2016-01-171-0/+1
| | | | PR: 205774
* Convert LICENSE= "GPLxx # or later" to "GPLxx+"amdmi32016-01-134-4/+4
| | | | Approved by: portmgr blanket
* Add Public Domain support to ports license framework. You can now useamdmi32016-01-121-3/+1
| | | | | | | | | | | | | LICENSE= PD Note that although Public Domain is not technically a license, it's handled in the same way as licenses here, which is a common practice (Arch, Gentoo, Fedora, Debian, even FOSSology do the same). Convert all ports which redefine Public Domain LICENSE to LICENSE=PD. Approved by: portmgr (bapt) Differential Revision: D4149
* Remove deprecated PLIST_DIRSTRY and also no longer needed PLIST_DIRSpawel2016-01-101-2/+0
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* biology/crux is not jobs safemarino2015-12-311-0/+2
| | | | | This cython-based port has failed on me a couple of times in a bulk build. I'm not sure what the actual problem is but the issue is itermittent.
* biology/htslib: Replace FreeBSD-specific fix with a generic onemarino2015-12-291-5/+4
| | | | | | | This port will not build if ENOTRECOVERABLE is not defined, period. It's not necessary to check OPSYS and version, just apply the fallback definition if it's not defined. This unbreaks DragonFly after last commit.
* Cleanup GH_* and variables order.mat2015-12-293-3/+1
| | | | Sponsored by: Absolight
* biology/consed: undeprecate, it presumably builds fine but it is restricted.rene2015-12-261-5/+1
| | | | Add a note to ports/LEGAL
* - Update to 7.266wen2015-12-255-42/+133
| | | | | PR: 205558 Submitted by: cartwright@asu.edu(maintainer)
* biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3junovitch2015-12-2527-173/+930
| | | | | | | | | | | | | - Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require version 1.3 of htslib. - Add CURL option to htslib - Add TEST_TARGET with perl and bash dependencies for testing - Tidy up spacing and pkg-message's PR: 205524 PR: 205525 PR: 205526 Submitted by: cartwright@asu.edu (maintainer)
* mark some of the ports that don't build on powerpc64 for meswills2015-12-144-0/+7
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* - Update maintainer mail addressmiwi2015-12-1112-23/+22
| | | | | | | | | - Update/Remove MASTER_SITE PR: 204755 Submitted by: jwbacon@tds.net (maintainer) Approved by: mat (mentor) Differential Revision: D4493
* - Update to 1.32wen2015-12-113-6/+8
| | | | | - Add LICENSE - Pet portlint
* biology/seqtools: 4.39.2 -> 4.39.3pi2015-12-052-3/+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.
* biology/seqtools: 4.39.1 -> 4.39.2pi2015-12-022-3/+3
| | | | | | - Blixem: Improve the display of features in the detail view when they have transparent fill.
* - Mark BROKEN: checksum mismatch:amdmi32015-11-291-0/+2
| | | | fetch: http://www.platonsoft.nl/spek/xraysoft/unix/platon.tar.gz: size mismatch: expected 12080181, actual 12080357
* Remove expired ports:rene2015-11-2915-933/+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
* biology/platon: fix fetchingrm2015-11-203-6/+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>
* - Switch to options helpersamdmi32015-11-191-1/+1
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* biology/seqtools: Fix distinfo, WWWpi2015-11-182-3/+3
| | | | | | - Side effect of the seqtools automated build system Submitted by: pkg-fallout
* biology/seqtools: 4.39.0 -> 4.39.1pi2015-11-142-3/+3
| | | | | - Fix a bug in Belvu where the display was being initialised in command-line-only modes.
* - Update to 1.14.6danilo2015-11-103-4/+4
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* Mark a few ports BROKEN: unfetchableantoine2015-11-091-0/+2
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* biology/seqtools: 4.36 -> 4.39.0pi2015-11-092-3/+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.
* - Update to 1.14.5danilo2015-11-063-4/+4
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* Fix ports that confused the meaning of WRKDIR and WRKSRC.mat2015-11-051-5/+5
| | | | | | | | PR: 204056 Submitted by: mat Reviewed by: bapt Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D2735
* biology/seaview: Broken, Does not fetch (checksum mismatch)marino2015-11-021-0/+2
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* - Update to 2015.09.21madpilot2015-10-285-25/+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
* Deprecate ports broken for more than 6 monthsantoine2015-10-264-0/+8
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* biology/seaview: Update version 4.5.4.7=>4.5.4.8bofh2015-10-202-3/+3
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* - Update to 36.3.8danilo2015-10-162-4/+4
| | | | | | | - Pass maintainership to submitter PR: 203817 Submitted by: Wendell Borges <wendell@bsd.com.br>
* - Add LICENSE_FILEamdmi32015-10-151-1/+2
| | | | - Switch to options helpers
* - Pet portlintamdmi32015-10-151-4/+5
| | | | | - Add LICENSE - Drop unneeded WX_UNICODE
* - Fix typosunpoet2015-10-111-1/+1
| | | | Approved by: portmgr (blanket)
* - Update to 1.14.4danilo2015-10-073-4/+4
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* - Update to 1.14.3danilo2015-10-023-4/+4
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* biology/seaview: Update version 4.5.4.6=>4.5.4.7bofh2015-10-012-4/+3
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* biology/grappa: define license (GPLv2)rm2015-09-261-0/+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>
* BWA is a program for aligning sequencing reads against a large referencerm2015-09-268-0/+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>
* Fast indexing and retrieval of FASTA records from flat file data bases.rm2015-09-265-0/+85
| | | | | | | WWW: http://sourceforge.net/projects/cdbfasta/ PR: 203233 Submitted by: Jason Bacon <jwbacon@tds.net>
* Simple and quick FastQ and FastA tool for file reading and conversion.rm2015-09-264-0/+39
| | | | | | | WWW: https://github.com/fstrozzi/Fastool PR: 203293 Submitted by: Jason Bacon <jwbacon@tds.net>
* FastTree infers approximately-maximum-likelihood phylogenetic trees fromrm2015-09-264-0/+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>
* The FASTX-Toolkit is a collection of command line tools for Short-Readsrm2015-09-265-0/+57
| | | | | | | | | FASTA/FASTQ files preprocessing. WWW: http://hannonlab.cshl.edu/fastx_toolkit/ PR: 203318 Submitted by: Jason Bacon <jwbacon@tds.net>
* Gordon's text utilities.rm2015-09-265-0/+50
| | | | | | | WWW: https://github.com/agordon/libgtextutils PR: 203309 Submitted by: Jason Bacon <jwbacon@tds.net>
* Typos, whitespace and capitalization fixes (A-F).olgeni2015-09-211-1/+1
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* - Use compiler:openmp instead of gccwen2015-09-191-4/+1
| | | | | | - Minor cleanup Reported by: danfe@
* CD-HIT is a very widely used program for clustering and comparing protein orwen2015-09-195-0/+81
| | | | | | | | | nucleotide sequences. WWW: http://weizhong-lab.ucsd.edu/cd-hit/ PR: 203183 Submitted by: jwbacon@tds.net
* Make all GNUstep ports install into the System domain so that the Local ↵theraven2015-09-192-66/+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
* - Update to 1.14.2danilo2015-09-173-4/+5
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* Remove ansi version fo wxGTK 2.8 and only keep the unicode versionbapt2015-09-172-1/+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
* biology/seaview: Update version 4.5.4.4=>4.5.4.6bofh2015-09-152-5/+5
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* Make it so that the default Perl is always called perl5.mat2015-09-145-72/+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
* Enfoce unicode version of wxGTKbapt2015-09-141-0/+1
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* - Update to 1.14.1danilo2015-09-143-5/+5
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* - Add LICENSEsunpoet2015-09-042-8/+8
| | | | | | | | | - Add NO_ARCH - Use BROKEN_RUBY22 - While I'm here, use single space after WWW: Approved by: portmgr (blanket) With hat: ruby
* - Unbreak on PowerPC by using atomicops implementation for Linux and GCCdanfe2015-09-022-12/+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
* - Do not falsely advertise that PowerPC build runs out of space and failsdanfe2015-09-021-11/+5
| | | | - Remove redundant PKGMESSAGE assignment and sanitize symlinks while here
* Unbreak the build on PowerPC (at least) by always using va_copy() macro fordanfe2015-09-022-20/+7
| | | | copying variable argument lists, not just on AMD64.
* Unbreak the build on PowerPC, it had nothing to do with "error in pthreads":danfe2015-09-022-2/+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.
* - Switch to options helpersamdmi32015-09-021-6/+2
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* Switch to USES=iconv:build.rakuco2015-08-251-1/+2
| | | | | The port does not use iconv on its own, the only dependency comes via libxml2, which has one header that includes iconv.h.
* Fix previous commit.mat2015-08-191-1/+0
| | | | | Pointy hat to: mat Sponsored by: Absolight
* Convert ports to use the options helpers in categories [abc]*, and minor fixes.mat2015-08-197-41/+17
| | | | | Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D3412?
* biology/ugene: qt4-linguist -> qt4-linguisttoolspgollucci2015-08-191-2/+3
| | | | | | | | - add USES=desktop-file-utils PR: 202138 Submitted by: s3erios@gmail.com Approved by: h2+fbsdports@fsfe.org
* Remove UNIQUENAME and LATEST_LINK.mat2015-08-171-2/+0
| | | | | | | | | | | | | | | | | UNIQUENAME was never unique, it was only used by USE_LDCONFIG and now, we won't have conflicts there. Use PKGBASE instead of LATEST_LINK in PKGLATESTFILE, the *only* consumer is pkg-devel, and it works just fine without LATEST_LINK as pkg-devel has the correct PKGNAME anyway. Now that UNIQUENAME is gone, OPTIONSFILE is too. (it's been called OPTIONS_FILE now.) Reviewed by: antoine, bapt Exp-run by: antoine Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D3336
* biology/seqtools: 4.35 -> 4.36pi2015-08-082-3/+3
| | | | Minor under-the-hood changes
* Fix build on mips by properly respecting compiler and flagsamdmi32015-08-052-9/+20
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* Update to 1.65.mat2015-08-052-4/+4
| | | | | | | PR: 201888 Submitted by: brueffer Approved by: maintainer Sponsored by: Absolight
* Unbreakantoine2015-07-291-1/+1
| | | | Reported by: pkg-fallout
* - Fix four cases of an obvious typo: LICENSE_FILES -> LICENSE_FILEdanfe2015-07-251-2/+2
| | | | | | - While here: move knobs to their expected location, remove useless check for ${PORT_OPTIONS:MDOCS} when installing documentation, standardize Makefile headers
* - Update Unipro UGENE to version 1.17.0 (documentation was also rerolled)danfe2015-07-152-16/+11
| | | | - Remove no longer required local source code tweaks (picked up upstream)
* - Update to 1.14.0danilo2015-07-133-4/+5
| | | | - Use install-strip
* biology/seqtools: 4.34.1 -> 4.35pi2015-07-072-5/+5
| | | | | | | - Blixem bug fix in sorting features, RT 473624 - Compilation of the seqtools in parallel, RT 467905 - Fix bug with sorting by similarity/identity to first sequence (RT:473624) - Fix an error compiling with multiple threads (RT:467905)
* After r390893, chmod u+w/u-w for stripping perl XS modules is unnecessary,adamw2015-06-291-5/+2
| | | | | | and in fact now leads to incorrect permissions. Remove all instances of it from perl@ ports.
generated by cgit (git 2.34.1) at 2024-11-26 19:05:07 +0800