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* biology/py-pysam: Update to 0.14yuri2018-02-112-4/+4
| | | | | | | | Changelog: https://github.com/pysam-developers/pysam/releases/tag/v0.14 Reported by: portscout Approved by: tcberner (mentor, implicit)
* biology/py-bx-python: Update to 0.8.1yuri2018-02-102-8/+9
| | | | | | | | | | | | | | Additional port changes: * Changed to DISTVERSION. * Added USE_PYTHON=cython. * Added stripping. * Updated maintainer e-mail. Reported compiler warnings to the upstream. Reported by: portscout Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D14283
* Canonicalize PyPi WWWs:amdmi32018-02-091-1/+1
| | | | | | | - Switch to https:// - Remove trailing slashes Approved by: portmgr blanket
* biology/diamond: Update to version 0.9.17jrm2018-02-022-4/+4
| | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.17
* - Update to 3.3.20180129wen2018-02-012-5/+4
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* Multiple ports:jwb2018-01-3116-29/+16
| | | | | | | | Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org Remove Created by comments for same user Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14128
* devel/boost-*: update to 1.66.0jbeich2018-01-182-1/+2
| | | | | | | Changes: http://www.boost.org/users/history/version_1_66_0.html PR: 223922 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D13279
* - Convert to option helper install target (add OPTIONS_DEFINE=DOCSdanfe2018-01-121-2/+4
| | | | | | when it was missing) - Invoke INSTALL_DATA where appropriate instead of INSTALL_MAN - Fix some whitespace and formatting bugs along the way
* Update Qt5 ports to 5.9.3.rakuco2018-01-071-0/+10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This took quite a lot of time because Qt's own build system underwent several changes in 5.8.0 that took a while to adapt to. And, of course, qt5-webengine is a behemoth that we need to patch like crazy due to its bundling of Chromium. In fact, most of the Chromium patches in qt5-webengine have been imported with no changes from www/chromium@433510 ("www/chromium: update to 56.0.2924.87"). New port: accessibility/qt5-speech Bigger changes to Qt5 ports we had to make: - Qt now allows using a configure.json file to define configuration options and specify configuration checks that can be done when qmake is invoked. However, configure.json checks done in a subdirectory only propagates to subdirectories, and checks elsewhere will fail if all .pro files are being parsed at once (i.e. qmake -recursive), so several ports had to switch to USES=qmake:norecursive along with manual additional qmake invocations in subdirectories in order to work. It's been mentioned in a few places such as Qt's bug tracker that qmake's recursive mode is pretty much deprecated, so we might switch to non-recursive mode by default in the future. - Uses/qmake.mk: Introduce QMAKE_CONFIGURE_ARGS. qmake now accepts arbitrary options such as '-foo' and '-no-bar' at the end of the command-line. They can be specified in QMAKE_CONFIGURE_ARGS. - graphics/qt5-wayland: The port can only be built if graphics/mesa-libs is built with the WAYLAND option, so a corresponding option (off by default) was added to the port. - misc/qt5-doc: Switch to a pre-built documentation tarball. The existing port was not working with Qt 5.9. Instead of trying to fix it, switch to what Gentoo does and fetch a tarball that already contains all documentation so that we do not have to build anything at all. The tarball's name and location in download.qt.io look a bit weird, but it seems to work fine. - www/qt5-webengine: Use binutils from ports, Chromium's GN build system generates a build.ninja that uses ar(1) with the @file syntax that is not supported by BSD ar, so we need to use GNU ar from binutils. - x11-toolkits/qt5-declarative-render2d: This port was merged into the main Qt Declarative repository upstream, and into x11-toolkits/qt5-quick in the ports tree. Changes to other ports we had to make: - biology/ugene: Drop a '#define point "."' that is not present in more recent versions of the port. Defining a macro with such a common name causes build issues with Qt 5.9, which uses |point| as an argument name in methods. - cad/qelectrotech: Fix plist with Qt 5.9. Directories are no longer installed with `cp -f -R', but rather `qmake install qinstall', which does not install %%DATADIR%%/elements/10_electric/20_manufacturers_articles/bosch_rexroth/.directory That's a local file that should not even have been part of the tarball anyway. - chinese/gcin-qt5: Add additional private Qt directories (which should not be used in the first place) to get the port to build with Qt 5.9. - devel/qtcreator: Fix plist with Qt 5.9. Something changed in qdoc and some test classes no longer generate documentation files. - security/keepassx-devel: Import a patch sent upstream almost a year ago to fix the build with Qt 5.9. Thanks to antoine for the exp-run, and tcberner and Laurent Cimon <laurent@nuxi.ca> for landing changes in our qt-5.9 branch. PR: 224849
* biology/seaview: Update version 4.6.2=>4.6.3bofh2018-01-063-7/+8
| | | | | | - Added pkg-plist to pet portlint Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES
* New USES=eigentcberner2018-01-031-5/+2
| | | | | | | | | | | | | | | | | | | | | | Usage: USES=eigen:<version>[,<type>] version: 2 or 3 (required) type: build (default), run For example: USES=eigen:2,build,run will add a BUILD- and RUN_DEPENDS on math/eigen2, and USES=eigen:3 will add a BUILD_DEPENDS on math/eigen3. * Convert the existing ports to use it - biology/iqtree: remove run time dependency (seemed not to be needed) - graphics/movit: remove run time dependency (seemed not to be needed) - science/avogadro: add run time dependeny (installed cmake file requires it to be present) Reviewed by: rakuco, mat Differential Revision: https://reviews.freebsd.org/D13702
* - Update to 3.697wen2018-01-012-3/+4
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* - Update to 5.16.0wen2018-01-013-4/+9
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* biology/iqtree: Fix distinfo after upstream re-released v1.6.1jrm2017-12-302-3/+4
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* biology/iqtree: Update to version 1.6.1jrm2017-12-292-9/+8
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases
* Disable the extra flag "-march=native" on arm to fix builds.linimon2017-12-271-3/+6
| | | | | Approved by: portmgr (tier-2 blanket) Obtained from: lonesome.com -exp run
* Update to 2.0.1sunpoet2017-12-273-5/+31
| | | | Changes: https://github.com/rvosa/bio-phylo/releases
* biology/canu: Replace += with = for dependsjwb2017-12-221-2/+2
| | | | | Approved by: jrm Differential Revision: https://reviews.freebsd.org/D13574
* - Fix build on 11+amdmi32017-12-222-4/+11
| | | | Approved by: portmgr blanket
* [new port] biology/canu: Single molecule sequence assemblerjwb2017-12-226-0/+167
| | | | | Approved by: jrm (mentor) or wen (mentor) Differential Revision: https://reviews.freebsd.org/D13574
* Try to bring some consistency to ports that have x86-specific pieces.linimon2017-12-212-12/+12
| | | | | | | | | | | | | | - in general, if we think that the code is not architecture-specific, and instead just enables x86 assembler by default, those should use BROKEN rather than IGNORE. This will allow them to be attempted with TRYBROKEN. - spell i386 as x86. - spell asm as assembler. - pet portlint. These changes should have no effect on tier-1 builds. Approved by: portmgr (tier-2 blanket)
* Switch from swig 2.0 to swig 3.0bapt2017-12-211-2/+4
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* Mark more recently failing ports broken on aarch64.linimon2017-12-191-2/+3
| | | | | | While here, pet portlint and reformat some other BROKEN statements. Approved by: portmgr (tier-2 blanket)
* Back out previous commits by jbeich demand.linimon2017-12-182-10/+2
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* Bah. Remove spare line from cut-and-paste.linimon2017-12-181-1/+0
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* Attempt to fix build on non-x86 archs. Untested, but does no harmlinimon2017-12-182-2/+11
| | | | | | on x86. Approved by: portmgr (tier-2 blanket)
* biology/diamond: Update to version 0.9.14jrm2017-12-142-4/+4
| | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.14
* biology/seqtools: re-try on powerpc* after r449590jbeich2017-12-121-2/+0
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* - Those ports fail to build with python3antoine2017-12-121-1/+1
| | | | - Add some explicit FLAVOR to dependencies where needed
* Mark several ports newly broken on arm.linimon2017-12-112-3/+9
| | | | | | While here, pet portlint. Approved by: portmgr (tier-2 blanket)
* biology/py-biom-format: Add required dependency on math/py-pandas and dojrm2017-12-101-3/+7
| | | | not install tests.
* [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for ↵jwb2017-12-095-0/+47
| | | | | | | adapter and quality trimming Approved by: jrm (mentor) Differential Revision: D13400
* These are also broken on aarch64 in the same way as armv6/7.linimon2017-12-091-0/+1
| | | | Approved by: portmgr (tier-2 blanket)
* Mark more ports broken that fail on both armv6 and armv7.linimon2017-12-091-0/+3
| | | | Approved by: portmgr (tier-2 blanket)
* Revert previous fat-fingered commit. These are the error messages fromlinimon2017-12-081-2/+2
| | | | | | | benchmarks/libmicro. Pointy hat to: self Approved by: portmgr (tier-2 blanket)
* Update errror message on armvX.linimon2017-12-081-2/+2
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* biology/fasttree: update to version 2.1.10jwb2017-12-054-19/+45
| | | | | Approved by: jrm Differential Revision: https://reviews.freebsd.org/D8187
* biology/py-macs2: Restrict to python 2.7.jwb2017-12-051-2/+2
| | | | | | | Use ${PYNUMPY} per mat suggestion. Approved by: jrm Differential Revision: https://reviews.freebsd.org/D13350
* Add a USES=python:env, that will not add a dependency on Python.mat2017-12-042-4/+2
| | | | | | | It has the same effect than setting PYTHON_NO_DEPENDS, but in a more compact way. Sponsored by: Absolight
* Fix configure options for gnustep-maketheraven2017-12-031-1/+1
| | | | | | | We were not setting the flag to select the GNUstep ABI, so were defaulting to using the GCC-compatible version, which was likely to trigger a lot of subtle bugs. This was noticed when C++ exceptions thrown through Objective-C stack frames caused segfaults.
* [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation ↵jwb2017-12-034-0/+41
| | | | | | | (ChIP) sequences Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13322
* [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq ↵jwb2017-12-035-0/+91
| | | | | | | data Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13328
* Fix packaging with python3antoine2017-12-012-14/+14
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* [unbreak] biology/bwa: Remove old patch filesjwb2017-12-013-37/+0
| | | | | Approved by: jrm Differential Revision: https://reviews.freebsd.org/D13314
* [new port] biology/fastqc: Quality control tool for high throughput sequence ↵jwb2017-12-015-0/+260
| | | | | | | data Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13304
* biology/py-cutadapt: Remove MASTER_SITE_SUBDIR per mentor commentjwb2017-12-011-1/+0
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13303
* Convert Python ports to FLAVORS.mat2017-11-309-17/+15
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Ports using USE_PYTHON=distutils are now flavored. They will automatically get flavors (py27, py34, py35, py36) depending on what versions they support. There is also a USE_PYTHON=flavors for ports that do not use distutils but need FLAVORS to be set. A USE_PYTHON=noflavors can be set if using distutils but flavors are not wanted. A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been added to cope with Python ports that did not have the Python PKGNAMEPREFIX but are flavored. USES=python now also exports a PY_FLAVOR variable that contains the current python flavor. It can be used in dependency lines when the port itself is not python flavored. For example, deskutils/calibre. By default, all the flavors are generated. To only generate flavors for the versions in PYTHON2_DEFAULT and PYTHON3_DEFAULT, define BUILD_DEFAULT_PYTHON_FLAVORS in your make.conf. In all the ports with Python dependencies, the *_DEPENDS entries MUST end with the flavor so that the framework knows which to build/use. This is done by appending '@${PY_FLAVOR}' after the origin (or @${FLAVOR} if in a Python module with Python flavors, as the content will be the same). For example: RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} PR: 223071 Reviewed by: portmgr, python Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D12464
* For ports that are marked BROKEN on armv6, and also fail to build onlinimon2017-11-305-0/+5
| | | | | | | | | | armv7, mark them so. This is part two of a multipart commit to bring armv7 ports to parity with armv6. Approved by: portmgr (tier-2 blanket) Obtained from: lonesome.com -exp run
* biology/bowtie2: Upgrade to 2.3.3.1jwb2017-11-305-50/+19
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13300
* [new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, pojwb2017-11-305-0/+74
| | | | | | ly-A tails, etc Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13294
* biology/bwa: Upgrade to 0.7.17jwb2017-11-282-5/+10
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13283
* biology/vcftools: Upgrade to latest release 0.1.15jwb2017-11-282-4/+4
| | | | | Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D13276
* - Switch to options helpersamdmi32017-11-261-1/+5
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* biology/diamond: Update to version 0.9.13jrm2017-11-182-4/+4
| | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.13
* - Update to 3.1b2wen2017-11-115-39/+69
| | | | | | | | - Pass maintainership to submitter PR: 223561 Submitted by: mzaki@niid.go.jp Approved by: bacon4000@gmail.com(previous maintainer)
* Fix the context of some patches so that they apply with stricter patch(1)antoine2017-11-102-6/+6
| | | | | PR: 223545 With hat: portmgr
* biology/diamond: Update to version 0.9.12jrm2017-11-092-7/+5
| | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.12
* Fix USE_GITHUB usage.mat2017-11-062-5/+4
| | | | Sponsored by: Absolight
* biology/py-pysam: Update to 0.13yuri2017-11-062-6/+8
| | | | | Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D12967
* biology/diamond: Update to 0.9.11jrm2017-11-033-10/+14
| | | | Upstream changes: https://github.com/bbuchfink/diamond/releases
* biology/molden: chase another intransparent upstream distfile upgrade.jmd2017-11-012-4/+4
| | | | | | Reviewed by: swills (mentor), mat Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D12829
* - Fix installing scripts and support binarieswen2017-10-304-8/+39
| | | | | | | - Add LICENSE PR: 223098 Submitted by: mzaki@niid.go.jp
* Update biology/py-pysam to 0.12.0.1tcberner2017-10-262-4/+4
| | | | | PR: 223254 Submitted by: Yuri Victorovich <yuri@rawbw.com> (maintainer)
* biology/htslib biology/bcftools biology/samtools: Update to 1.6pizzamig2017-10-2525-897/+171
| | | | | | | | PR: 223094 Submitted by: mzaki@niid.go.jp Approved by: cartwright@asu.edu (maintainer) Approved by: olivier (mentor) Differential Revision: https://reviews.freebsd.org/D12768
* biology/iqtree: Add EXAMPLES option and fix mess with installation ofjrm2017-10-221-1/+13
| | | | example files in first commit
* New port, biology/iqtree: Efficient phylogenomic softwarejrm2017-10-224-0/+43
| | | | WWW: http://www.iqtree.org/
* Mark as broken ports with no public distfilesbapt2017-10-136-1/+10
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* Remove dead master sitesbapt2017-10-132-2/+3
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* biology/molden: unbreak by chasing latest intransparent distfile update.jmd2017-09-282-4/+4
| | | | | | Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D12521
* devel/boost-*: update to 1.65.1jbeich2017-09-251-1/+1
| | | | | | | | | Changes: http://www.boost.org/users/history/version_1_65_1.html PR: 218835 Approved by: maintainer timeout (1.65.1: 2 weeks; 1.65.0: 1 month) Tested by: jhibbits (on powerpc64, earlier version) Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D11582
* devel/boost-*: enable C++11 featuresjbeich2017-09-251-1/+1
| | | | | | | | PR: 218835 Obtained from: https://github.com/DragonFlyBSD/DeltaPorts/pull/690 Approved by: maintainer timeout (2 months) Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D11582
* biology/ssaha: unbreak with gcc7jbeich2017-09-251-0/+9
| | | | | | | | | | In file included from Binary/..//Global/SSAHAMain.cpp:51:0: Binary/..//Global/SSAHAMain.cpp: In function 'void processQuery(QueryParameterStruct&)': Binary/..//Global/SSAHAMain.cpp:968:23: error: ISO C++ forbids comparison between pointer and integer [-fpermissive] assert( pAligner!=false); ^ PR: 222542
* Remove USES=execinfo.mat2017-09-222-2/+2
| | | | | | | PR: 220271 Submitted by: mat (review), Yasuhiro KIMURA (PR) Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D11488
* Update tbb to 2018 and bump dependent ports' revisionsmartymac2017-09-171-1/+1
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* Update to 1.007002sunpoet2017-09-163-23/+5
| | | | Changes: http://search.cpan.org/dist/BioPerl-Run/Changes
* Add p5-Bio-FeatureIO 1.6.905sunpoet2017-09-165-0/+67
| | | | | | | | | | | | | | | | | | | | | | Bio::FeatureIO is an iterator subsystem for genomic sequence features. Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg, Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the format objects, which most people should use. The Bio::FeatureIO system can be thought of like biological file handles. They are attached to filehandles with smart formatting rules (eg, GFF format, or BED format) and can either read or write feature objects (Bio::SeqFeature objects, or more correctly, Bio::FeatureHolderI implementing objects, of which Bio::SeqFeature is one such object). If you want to know what to do with a Bio::SeqFeatureI object, read Bio::SeqFeatureI. The idea is that you request a stream object for a particular format. All the stream objects have a notion of an internal file that is read from or written to. A particular FeatureIO object instance is configured for either input or output. A specific example of a stream object is the Bio::FeatureIO::gff object. WWW: http://search.cpan.org/dist/Bio-FeatureIO/
* Fix license information for portgs that use "the same license as Perl".mat2017-09-1510-10/+10
| | | | Sponsored by: Absolight
* - Update to 1.007002wen2017-09-133-15/+4
| | | | Changes: http://search.cpan.org/src/CJFIELDS/BioPerl-1.007002/Changes
* Bump PORTREVISION for ports depending on the canonical version of GCCgerald2017-09-1115-15/+15
| | | | | | | | | | | | | | (via Mk/bsd.default-versions.mk and lang/gcc) which has moved from GCC 5.4 to GCC 6.4 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang, c++14-lang, c++0x, c11, or gcc-c++11-lib. PR: 219275
* Update to 3.3.20170530sunpoet2017-09-042-3/+5
| | | | Changes: https://github.com/stephaneguindon/phyml/releases
* Remove expired ports:rene2017-08-235-87/+0
| | | | | | | | | | | | | | | | | | 2017-08-23 games/plee-the-bear: Broken for more than 6 months 2017-08-23 x11-themes/kde-icons-umicons: Broken for more than 6 months 2017-08-23 lang/bigloo: Broken for more than 6 months 2017-08-23 audio/linux-neroaaccodec: Broken for more than 6 months 2017-08-23 x11-themes/kde-icons-dark-glass: Broken for more than 6 months 2017-08-23 misc/fortune-mod-ferengi_rules_of_acquisition: Broken for more than 6 months 2017-08-23 misc/fortune-mod-culmea-culmilor: Broken for more than 6 months 2017-08-23 misc/xyzcmd: Broken for more than 6 months 2017-08-23 russian/fortuneru: Broken for more than 6 months 2017-08-23 security/bdc: Broken for more than 6 months 2017-08-23 x11-themes/kde-icons-icosx: Broken for more than 6 months 2017-08-23 devel/insight: Broken for more than 6 months 2017-08-23 devel/gdb66: Broken for more than 6 months 2017-08-23 biology/biojava: Broken for more than 6 months 2017-08-23 games/xroach: Broken for more than 6 months
* Update GNUstep core libraries.theraven2017-08-211-1/+1
| | | | | | | | | | Update the default Objective-C compiler. Fix various build failures in GNUstep ports from newer versions of the GNUstep core libraries and from changes to GNUstep Make. Update various ports that use GNUstep and bump the portrevision of the ones that haven't had a new release.
* - update to 1.70wen2017-08-182-4/+4
| | | | | | PR: 221443 Submitted by: wen@(myself) Approved by: maintainer
* biology/diamond: Update to version 0.9.10jrm2017-08-162-4/+4
| | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.10
* - Update to 1.53wen2017-07-232-4/+4
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* Deprecate ports BROKEN for more than 6 monthsantoine2017-07-221-0/+2
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* biology/seaview: Update version 4.6.1=>4.6.2bofh2017-07-222-4/+4
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* Chase next distfile update. Upstream contacted whether we would be allowed ↵jmd2017-07-142-4/+4
| | | | | | | | to host a distfile copy. Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D11586
* biology/molden: Unbreak by chasing their latest opaque update to the ↵jmd2017-07-122-7/+5
| | | | | | | | distribution. Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D11338
* Update math/gsl to 2.4tcberner2017-07-041-1/+1
| | | | | Exp-Run by: antoine PR: 220408
* biology/diamond: Update to version 0.9.9jrm2017-07-042-4/+4
| | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.9
* Update devel/readline to 7.0 patch 3sunpoet2017-06-271-1/+1
| | | | | | | | | | | - Bump PORTREVISION for shlib change Changes: https://cnswww.cns.cwru.edu/php/chet/readline/CHANGES https://lists.gnu.org/archive/html/bug-bash/2016-09/msg00107.html https://lists.gnu.org/archive/html/bug-readline/2017-01/msg00002.html Differential Revision: https://reviews.freebsd.org/D11172 PR: 219947 Exp-run by: antoine
* Begin deorbit burn of ia64. We have not attempted to build packages forlinimon2017-06-251-1/+1
| | | | | | | | it for many years. While here, alphabetize ARCHs, pet portlint, and modernize usages. Approved by: portmgr (tier-2 blanket)
* Mark BROKEN.mat2017-06-221-0/+2
| | | | | | | | => Attempting to fetch ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden5.7.tar.gz fetch: ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden5.7.tar.gz: size mismatch: expected 5339411, actual 5339467 => Couldn't fetch it - please try to retrieve this Sponsored by: Absolight
* biology/diamond: Update to version 0.9.8jrm2017-06-162-4/+4
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* - Update WWWamdmi32017-06-102-8/+7
| | | | | - Add LICENSE - Simplify installation
* - Update to 0.11.2.2wen2017-06-102-4/+4
| | | | | PR: 219892 Submitted by: yuri@rawbw.com(maintainer)
* Previous commit unbroke the port.linimon2017-06-031-2/+0
| | | | Reported by: xmj
* biology/diamond: Update to version 0.9.4jrm2017-06-032-4/+4
| | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.4
* Remove outdated PERL_LEVEL checksunpoet2017-06-021-8/+2
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* Remove outdated PERL_LEVEL checksunpoet2017-06-021-8/+2
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* Update WWWsunpoet2017-05-301-1/+1
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* biology/diamond: Update to version 0.9.3jrm2017-05-292-4/+4
| | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases Approved by: swills (mentor, implicit)
* Mark some ports failing on armv6, for errors classified as "clang".linimon2017-05-271-0/+2
| | | | | | While here, pet portlint. Approved by: portmgr (tier-2 blanket)
* Mark some ports failing on armv6, for errors classified as "???".linimon2017-05-272-3/+6
| | | | | | While here, pet portlint. Approved by: portmgr (tier-2 blanket)
* biology/molden: Chase recent upstream change of molden distfile.jmd2017-05-242-4/+4
| | | | | | Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D10864
* - Update to 0.11.2.1joneum2017-05-242-5/+5
| | | | | | | PR: 219396 Submitted by: Yuri Victorovich (Maintainer) <yuri@rawbw.com> Approved by: rene (mentor) Differential Revision: https://reviews.freebsd.org/D10856
* biology/diamond: Update to version 0.9.1jrm2017-05-232-6/+6
| | | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases - License has changed to AGPLv3 Approved by: swills (mentor, implicit)
* Revision bump of all ports with USE_GL after consolidation of mesa-libsrezny2017-05-233-3/+3
| | | | | Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D10845
* It is possible that r441426 will fix the build problem on armv6. Givelinimon2017-05-221-1/+0
| | | | | | it a try. Approved by: portmgr (tier-2 blanket)
* Mark some ports failing on power64. In cases where the error messagelinimon2017-05-221-0/+2
| | | | | | | | | was a stub, provide a real one. While here, pet portlint. Approved by: portmgr (tier-2 blanket) Reported by: swills
* Mark BROKEN: checksum and size mismatchantoine2017-05-201-0/+2
| | | | Reported by: pkg-fallout
* - Update to 5.15.0wen2017-05-183-3/+14
|
* Mark some ports failing on power64. In cases where the error messagelinimon2017-05-135-3/+6
| | | | | | | | was a stub, provide a real one. While here, pet portlint. Approved by: portmgr (tier-2 blanket)
* - Update to 0.11.1miwi2017-05-082-4/+4
| | | | | PR: 219122 Submitted by: maintainer
* - Update to 1.5.1miwi2017-05-072-6/+4
|
* bx-python is a python library and associated set of scripts to allow for rapidmiwi2017-05-064-0/+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>
* pysam is a lightweight wrapper of the htslib C-API and provides facilities tomiwi2017-05-065-0/+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>
* - Update to 1.69wen2017-05-032-4/+4
| | | | | | PR: 218903 Submitted by: wen@ Approved by: maintainer
* devel/boost-*: update to 1.64.0jbeich2017-05-021-1/+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
* Update math/gsl to 2.3tcberner2017-05-021-0/+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
* Provide error messages for some ports failing on aarch64, and, in alinimon2017-05-022-0/+5
| | | | | | | | few cases, other tier-2 archs. While here, pet portlint. Approved by: portmgr (tier-2 blanket)
* 2017-04-30 devel/stormlib-ghost++: Unfetchable for more than six months ↵ler2017-04-305-79/+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
* biology/py-biom-format: Update to version 2.1.6jrm2017-04-292-4/+5
| | | | | | Upstream changes: https://github.com/biocore/biom-format/releases/tag/2.1.6 Approved by: swills (mentor, implicit)
* - Fix shebangsmiwi2017-04-221-2/+3
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* - Fix shebangsmiwi2017-04-221-3/+4
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* - Fix shebangsamdmi32017-04-221-3/+7
| | | | | - Add NO_ARCH - Switch to relative links
* biology/diamond: Update to version 0.8.38jrm2017-04-212-6/+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)
* biology/seaview: Update version 4.6=>4.6.1bofh2017-04-122-4/+5
| | | | - Add PORTSCOUT to ignore non-existent 4.6.1.3 version
* 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
|
* 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
|
* 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
|
* 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
|
* 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
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2016-07-04 security/openpgpsdk: Broken for more than 6 months 2016-07-04 security/radiusniff: Broken for more than 6 months 2016-07-04 security/pear-Auth_OpenID: Broken for more than 6 months 2016-07-04 security/sshit: Broken for more than 6 months 2016-07-04 security/ifd-slb_rf60: Broken for more than 6 months 2016-07-04 security/rainbowcrack: Broken for more than 6 months 2016-07-04 security/vlog: Broken for more than 6 months 2016-07-04 security/cryptstring: Broken for more than 6 months 2016-07-04 x11/libdnd: Broken for more than 6 months 2016-07-04 x11/xlupe: Broken for more than 6 months 2016-07-04 x11/xco: Broken for more than 6 months 2016-07-04 x11/xclick: Broken for more than 6 months 2016-07-04 devel/ocfpcsc: Broken for more than 6 months 2016-07-04 devel/dits: Broken for more than 6 months 2016-07-04 devel/ruby-cache: Broken for more than 6 months 2016-07-04 devel/rapidsvn: Broken for more than 6 months 2016-07-04 devel/svnkit: Broken for more than 6 months 2016-07-04 devel/py-EnthoughtBase: Broken for more than 6 months 2016-07-04 devel/cl-uffi: Broken for more than 6 months 2016-07-04 devel/ruby-event-loop: Broken for more than 6 months 2016-07-04 devel/libqxt: Broken for more than 6 months 2016-07-04 devel/dasm: Broken for more than 6 months 2016-07-04 devel/libopendaap: Broken for more than 6 months 2016-07-04 devel/cl-uffi-sbcl: Depends on expiring devel/cl-uffi 2016-07-04 devel/cvs2p4: Broken for more than 6 months 2016-07-04 devel/bufferpool: Broken for more than 6 months 2016-07-04 devel/ifd-test: Broken for more than 6 months 2016-07-04 devel/eric4: Broken for more than 6 months 2016-07-04 devel/uclmmbase: Broken for more than 6 months 2016-07-04 devel/obfuscatejs: Broken for more than 6 months 2016-07-04 devel/oniguruma: Broken for more than 6 months 2016-07-04 devel/libbnr: Broken for more than 6 months 2016-07-04 devel/c4: Broken for more than 6 months 2016-07-04 devel/memcheck: Broken for more than 6 months 2016-07-04 devel/liblcfg: Broken for more than 6 months 2016-07-04 devel/omake: Broken for more than 6 months 2016-07-04 devel/svndelta: Broken for more than 6 months 2016-07-04 devel/papp: Broken for more than 6 months 2016-07-04 devel/mk: Broken for more than 6 months 2016-07-04 devel/avltree: Broken for more than 6 months 2016-07-04 devel/cbind: Broken for more than 6 months 2016-07-04 devel/tclgetopts: Broken for more than 6 months 2016-07-04 devel/antlrworks: Broken for more than 6 months 2016-07-04 devel/acme: Broken for more than 6 months 2016-07-04 devel/libopensync022: Broken for more 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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
generated by cgit (git 2.34.1) at 2025-02-18 16:52:09 +0800