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* Fix MASTER_SITESAntoine Brodin2014-09-051-1/+1
| | | | | | | Submitted by: tijl@ Notes: svn path=/head/; revision=367328
* Second run at cleaning out non staged ports without pending PRBaptiste Daroussin2014-09-025-69/+0
| | | | Notes: svn path=/head/; revision=366995
* Remove non staged ports without pending PR from b*Baptiste Daroussin2014-09-0115-1973/+0
| | | | Notes: svn path=/head/; revision=366862
* - Update Unipro UGENE and documentation to version 1.14.0Alexey Dokuchaev2014-09-017-226/+71
| | | | | | | | | | - Remove patches integrated upstream (it's nice to have direct contact) - Sort USES and pkg-plist, cleanup Makefile a bit while here Approved by: maintainer (implicit) Notes: svn path=/head/; revision=366842
* biology/crux: stage, modernize, add license (BSD[23]CLAUSE), cleanupsRene Ladan2014-08-264-46/+63
| | | | | | | | PR: 193026 Submitted by: Ports Fury Notes: svn path=/head/; revision=366266
* - StagifyDmitry Marakasov2014-08-258-3/+124
| | | | | | | - Fix build Notes: svn path=/head/; revision=366104
* update ports:Kurt Jaeger2014-08-2331-1187/+735
| | | | | | | | | | | | | | | biology/phrab biology/phred biology/consed Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to obtain the tarballs. PR: 191336 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) Notes: svn path=/head/; revision=365765
* Fix build. Hopefully it doesn't break the app.Adam Weinberger2014-08-221-0/+11
| | | | Notes: svn path=/head/; revision=365607
* Fix build on -current by un-clobbering LDFLAGS. Also, don'tAdam Weinberger2014-08-152-4/+13
| | | | | | | mute installation commands. Notes: svn path=/head/; revision=364996
* - Update to 5.10.2Wen Heping2014-08-104-270/+232
| | | | | | | | PR: 192198 Submitted by: tkato432@yahoo.com Notes: svn path=/head/; revision=364504
* Convert the Python framework bits to USES=python.Marcus von Appen2014-08-091-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Please use USES=python instead of USE_PYTHON. USE_PYTHON=yes becomes USES=python USE_PYTHON=2.7+ becomes USES=python:2.7+ USE_PYTHON_BUILD=3.3 becomes USES=python:3.3,build ... A new PYTHON_FEATURES variable was added, which enables certain features for a port and replaces some knobs at the same time; PYTHON_FEATURES=distutils replaces USE_PYDISTUTILS PYTHON_FEATURES=autoplist replaces PYDISTUTILS_AUTOPLIST PYTHON_FEATURES=py3kplist replaces PYTHON_PY3K_PLIST_HACK PYTHON_FEATURES=noegginfo replaces PYDISTUTILS_NOEGGINFO PYTHON_FEATURES=concurrent replaces PYTHON_CONCURRENT_INSTALL PYTHON_FEATURES=pythonprefix replaces USE_PYTHON_PREFIX Some knobs have been deprecated and are to be removed in the near future: PYTHON_MASTER_SITES - use MASTER_SITE_PYTHON instead PYTHON_PKGNAMESUFFIX - use PYTHON_PKGNAMEPREFIX instead PYDISTUTILS_INSTALLNOSINGLE - deprecated without replacement Some knobs have been removed completely: PYTHON_MASTER_SITE_SUBDIR PYTHON_DISTNAME PYTHON_WRKSRC Several variables specific to the Python framework are no longer passed to the build environment to avoid polluting dependency builds. PYTHON_VERSION is not passed to .MAKEFLAGS anymore PYTHON_DEFAULT_VERSION, PYTHON_DEFAULT_PORTVERSION and PYTHONBASE are not passed to the make environment anymore The conversion required a couple of ports to be updated to fit the changes and new requirements. Those included "bsd.python.mk" directly or contained checks in places, for which the USES framework would fail to provide correct values. Python modules directly using the upstream Python package (such as py-tkinter or py-sqlite3) were updated to avoid using the now unnecessary and remmoved knobs from "bsd.python.mk". Phabric: D399 exp-run: 167368 192357 PR: 167368 192357 Reviewed by: antoine, wg Exp-run award: antoine With hat: python@ Approved by: portmgr Notes: svn path=/head/; revision=364450
* - Switch to USES=libtool, drop .la filesDmitry Marakasov2014-08-062-4/+4
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=364198
* USES=execinfoBaptiste Daroussin2014-08-042-6/+2
| | | | Notes: svn path=/head/; revision=364067
* biology/p5-bioperl-run: 1.6.1 -> 1.6.901, unbreak, stagifyKurt Jaeger2014-08-045-217/+296
| | | | Notes: svn path=/head/; revision=363975
* biology/p5-bioperl: fix pkg-descr sidenote linkKurt Jaeger2014-08-041-1/+1
| | | | Notes: svn path=/head/; revision=363961
* Add a DOCS option.Adam Weinberger2014-08-032-5/+7
| | | | Notes: svn path=/head/; revision=363943
* biology/seqtools: 4.27 -> 4.28Kurt Jaeger2014-07-312-3/+3
| | | | Notes: svn path=/head/; revision=363530
* Convert a bunch of EXTRACT_SUFX=... into USES=tar:...Adam Weinberger2014-07-298-16/+8
| | | | | | | Approved by: portmgr (not really, but touches unstaged ports) Notes: svn path=/head/; revision=363374
* Convert a bunch of USE_BZIP2 to USES=tar:bzip2Adam Weinberger2014-07-292-4/+2
| | | | | | | Approved by: portmgr (not really, but touches unstaged ports) Notes: svn path=/head/; revision=363371
* Rename biology/ patch-xy patches to reflect the files they modify.Adam Weinberger2014-07-2811-13/+13
| | | | Notes: svn path=/head/; revision=363159
* - Update to 1.6.924 [1]Wen Heping2014-07-273-10/+11
| | | | | | | | | | - Reset maintainer to perl@ PR: 192088 [1] Submitted by: Kurt Jaeger<pi@FreeBSD.org> [1] Notes: svn path=/head/; revision=363015
* Really fix.Mathieu Arnold2014-07-251-2/+0
| | | | | | | Sponsored by: Absolight Notes: svn path=/head/; revision=362941
* Fix build.Mathieu Arnold2014-07-251-1/+1
| | | | | | | Sponsored by: Absolight Notes: svn path=/head/; revision=362915
* biology/p5-Bio-Graphics: 2.37 -> 2.38Kurt Jaeger2014-07-242-3/+3
| | | | Notes: svn path=/head/; revision=362773
* Reset maintainership for ports not staged with no pending PRBaptiste Daroussin2014-07-236-6/+6
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=362705
* - Switch to USES=libtool, drop .la filesDmitry Marakasov2014-07-222-3/+4
| | | | | | | | | - Fix shebangs Approved by: portmgr blanket Notes: svn path=/head/; revision=362596
* biology/mummer: Use OPSYS with OSVERSIONJohn Marino2014-07-191-1/+1
| | | | | | | | | I don't think selecting clang as a function of OSVERSION is generally desired, but if it's going to happen, make sure FreeBSD-specific conditions are limited to FreeBSD by comparing OPSYS first. Notes: svn path=/head/; revision=362284
* biology/garlic: Stage properly to unbreakJohn Marino2014-07-171-7/+5
| | | | | | | | | | | | The main problem was the WRKDIR is not within STAGEDIR. Fix this while moving all the directory creation steps into one. While here set TAR to use switches as outlined in its man page. Also, the permission setting in stagedir is not necessary, so it's simply been removed. Notes: svn path=/head/; revision=362131
* Add OPTIONS_DEFINE=DOCS for ports with %%PORTDOCS%% in the plist.Adam Weinberger2014-07-151-0/+2
| | | | | | | | | | Where possible, correct a few instances where PORTDOCS was being used to flag stuff in EXAMPLESDIR. For some ports, mostly those owned by ruby@, PORTDOCS is applied to pretty much everything whether it's documentation or example. Notes: svn path=/head/; revision=362014
* Add DOCS to OPTIONS_DEFINE to ports that check for PORT_OPTIONS:MDOCS.Adam Weinberger2014-07-152-14/+21
| | | | | | | While here, use OPTIONS helpers and re-enable manpage installation. Notes: svn path=/head/; revision=361934
* biology/platon: Unbreak by hosting known distfiles elsewhereJohn Marino2014-07-132-6/+9
| | | | | | | | | | | | The distfiles are regenerated often, too frequently to be suitable for ports. Fonz has decided to host the tarball of a known version to restore this unmaintained port. PR: 191685 Submitted by: Fonz Notes: svn path=/head/; revision=361671
* biology/seqtools: 4.26 -> 4.27Kurt Jaeger2014-07-122-4/+3
| | | | Notes: svn path=/head/; revision=361635
* Use gcc on all platforms.Adam Weinberger2014-07-101-6/+1
| | | | | | | | PR: 191692 Submitted by: maintainer Notes: svn path=/head/; revision=361497
* Stagify.Vanilla I. Shu2014-07-061-6/+5
| | | | | | | Approved by: portmgr@ (blanket) Notes: svn path=/head/; revision=360932
* Missed a NOPORTDOCS.Adam Weinberger2014-07-051-3/+4
| | | | Notes: svn path=/head/; revision=360705
* Remove NOPORTDOCS and NOPORTEXAMPLES from unstaged ports. Stage a couple whileAdam Weinberger2014-07-041-21/+19
| | | | | | | | | we're here. Remove any other references to NOPORT*. Approved by: portmgr (blanket for modernization) Notes: svn path=/head/; revision=360690
* - Chase database/sqlite3 slib bumpMartin Wilke2014-06-271-0/+1
| | | | | | | Approved by: portmgr (myself) Notes: svn path=/head/; revision=359586
* Fix compilation on 10+ (clang)Martin Wilke2014-06-272-2/+10
| | | | | | | | | Fix format of WWW entry in pkg-descr PR: 190798 Notes: svn path=/head/; revision=359532
* - Mark BROKENWen Heping2014-06-261-0/+2
| | | | | | | Approved by: portmgr@(implicit) Notes: svn path=/head/; revision=359364
* Put HOME in MAKE_ARGS to handle pverride of HOME in MAKE_ENV from bsd.port.mkAntoine Brodin2014-06-251-1/+2
| | | | Notes: svn path=/head/; revision=359207
* Use MAKE_CMD instead of GMAKEBaptiste Daroussin2014-06-241-2/+2
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=359138
* Mark as broken: no distinfo providedBaptiste Daroussin2014-06-221-2/+1
| | | | Notes: svn path=/head/; revision=358838
* Mark as broken: no distinfo providedBaptiste Daroussin2014-06-221-3/+1
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=358837
* Fix shebang line in Perl and Python scripts.Raphael Kubo da Costa2014-06-201-13/+6
| | | | | | | | PR: 191146 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) Notes: svn path=/head/; revision=358567
* Mark BROKEN: Fails to configureAntoine Brodin2014-06-191-0/+2
| | | | | | | | | | | | ===> Configuring for p5-bioperl-run-1.6.1_4 Invalid prerequisite condition '0/processing XML data/Bio::Tools::Run::EMBOSSacd' for XML::Twig at /usr/local/lib/perl5/site_perl/5.16/Module/Build/Base.pm line 1702. *** [do-configure] Error code 25 Reported by: pkg-fallout With hat: portmgr Notes: svn path=/head/; revision=358466
* biology/blast: Deprecate for removal after 4 September 2014John Marino2014-06-191-0/+3
| | | | | | | | | | | This unstaged port will be removed for legal reasons. PR: 190626 Submitted by: Muhammad Rahman Approved by: portmgr (implicit) Notes: svn path=/head/; revision=358383
* Update to 1.2.10.Raphael Kubo da Costa2014-06-173-35/+23
| | | | | | | | PR: 191129 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) Notes: svn path=/head/; revision=358183
* Update to 3.8.31.Raphael Kubo da Costa2014-06-175-89/+37
| | | | | | | | PR: 191130 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) Notes: svn path=/head/; revision=358182
* Reset the 99 ports still listed under sylvio@John Marino2014-06-111-1/+1
| | | | | | | | | | | | | | Sylvio's last commit was 17 months ago, a full 5 months after all of his ports could have been reset per policy. Given the push to complete staging (48 ports are still unstaged, something like 70+ have already been staged by other committers) and given that PRs are automatically assigned but never addressed, it's better just to reset all the ports and PRs so that it's clear to others that these ports are free to maintain. Approved by: portmgr (implicit) Notes: svn path=/head/; revision=357526
* Remove all the bootstrap files (.bs) from the plists.Mathieu Arnold2014-06-102-3/+0
| | | | | | | | | | | | | Starting with perl 5.20, they're not installed any more if empty, and on FreeBSD, they're (always ?) empty. PR: 190681 Submitted by: mat Exp-Run by: antoine Sponsored by: Absolight Notes: svn path=/head/; revision=357300
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