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2013-11-18Convert to USES=dos2unixBaptiste Daroussin
While here stagify some of the ports Modernize LIB_DEPENDS Extract zip with bsdtar when possible
2013-11-14biology/seqtools: update to 4.23William Grzybowski
PR: ports/183960 Submitted by: maintainer
2013-11-12Add stage supportBaptiste Daroussin
Use bsdtar to extract the distfile Rip out USE_GMAKE
2013-11-12Stage supportBaptiste Daroussin
drop USE_GMAKE
2013-11-10biology/seqtools: Tools for visualising sequence alignmentsWilliam Grzybowski
Blixem is an interactive browser of pairwise alignments that have been stacked up in a "master-slave" multiple alignment; it is not a 'true' multiple alignment but a 'one-to-many' alignment. Belvu is a multiple sequence alignment viewer and phylogenetic tool. Dotter is a graphical dot-matrix program for detailed comparison of two sequences. WWW: http://www.sanger.ac.uk/resources/software/seqtools/ PR: ports/183801 Submitted by: Kurt Jaeger <fbsd-ports opsec.eu>
2013-11-07. give maintainership to the submitter;Boris Samorodov
. add one month to DEPRACATION_DATE; while here: strip the indefinite article from COMMENT. PR: ports/183742 Submitted by: Kurt Jaeger <fbsd-ports@opsec.eu> (assigned maintainer)
2013-11-02- Update to 1.8Sunpoet Po-Chuan Hsieh
Changes: http://search.cpan.org/dist/Bio-GFF3/Changes
2013-11-01- Install official UGENE documentation (PDF)Alexey Dokuchaev
- Utilize DIST_SUBDIR as now it's more than one distfile
2013-10-31- Update to version 1.12.3Alexey Dokuchaev
- Conditionalize dependency on `devel/libexecinfo' - Try to detect SSE2 support - Convert to USES=qmake and stafigy - Improve grammar in port description while here Approved by: maintainer (implicit)
2013-10-29Update to version 36.3.6dPawel Pekala
PR: ports/181883 Submitted by: KATO Tsuguru <tkato432@yahoo.com>
2013-10-26Update to libmpc version 1.0.1 which brings the following fixes:Gerald Pfeifer
- Switched to automake 1.11.6, see CVE-2012-3386. - #14669: Fixed extraction of CC from gmp.h. - Fixed case of intermediate zero real or imaginary part in mpc_fma, found by hydra with GMP_CHECK_RANDOMIZE=1346362345. This is on top of the following changes from version 1.0 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no invariant sections) for the documentation. - 100% of all lines are covered by tests - Renamed functions . mpc_mul_2exp to mpc_mul_2ui . mpc_div_2exp to mpc_div_2ui - 0^0, which returned (NaN,NaN) previously, now returns (1,+0). - Removed compatibility with K&R compilers, which was untestable due to lack of such compilers. - New functions . mpc_log10 . mpc_mul_2si, mpc_div_2si - Speed-ups . mpc_fma - Bug fixes . mpc_div and mpc_norm now return a value indicating the effective rounding direction, as the other functions. . mpc_mul, mpc_sqr and mpc_norm now return correct results even if there are over- or underflows during the computation. . mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has infinite part and equals output variable is corrected. . mpc_fr_sub: Wrong return value for imaginary part is corrected. Convert to the new LIB_DEPENDS standard and remove hard-coded .so versions from a couple of dependent ports. Bump PORTREVISIONS of all dependent ports. PR: 183141 Approved by: portmgr (bdrewery)
2013-10-22- Remove manual creation and removal of share/applications, as it's now in ↵Dmitry Marakasov
the mtree (categories starting with [bce]) Approved by: portmgr (bdrewery)
2013-10-18Deprecated some ports broken for more than 6 monthBaptiste Daroussin
2013-10-10- Switch to build with lang/ruby19Thomas Abthorpe
- No PORTREVISION bump, option is off by default With hat: portmgr
2013-10-08Update BioCocoa to the latest release.David Chisnall
Approved by: bapt (mentor)
2013-10-04- Update to 0.5.1Wen Heping
2013-10-03- Update to 1.7Sunpoet Po-Chuan Hsieh
- Support STAGEDIR Changes: http://search.cpan.org/dist/Bio-GFF3/Changes
2013-10-01biology/avida: add <unistd.h>, <typoinfo> for modern compilersJohn Marino
2013-09-25- Remove NO_STAGE as these have been tested to be safeBryan Drewery
With hat: portmgr
2013-09-24Use value of BOINC_CLIENT_HOME in pkg-messageRene Ladan
2013-09-23- Add stagedir supportRene Ladan
- Rewrap lines
2013-09-23Respect 'make check-sanity' for this port too.Rene Ladan
2013-09-22Fix NO_STAGE attributionBaptiste Daroussin
2013-09-20Add NO_STAGE all over the place in preparation for the staging support (cat: ↵Baptiste Daroussin
biology)
2013-09-18Mark BROKEN, fails checksumBryan Drewery
With hat: portmgr
2013-09-08Add an explicit dependency on pkgconfAntoine Brodin
Approved by: portmgr (bapt)
2013-09-07- Use single space after WWW:Sunpoet Po-Chuan Hsieh
2013-09-07- convert to the new perl5 frameworkAndrej Zverev
Approved by: portmgr (bapt@, blanket)
2013-09-04- Make ports use the libc provided iconv implementation on 10-CURRENTGuido Falsi
after r254273 - Fix a bunch of ports to properly work after this - Mark converters/libiconv as IGNORE for systems with iconv in libc Reviewed by: bapt Approved by: portmgr (bapt) Discussed with: bapt, bsam (who both contributed ideas and code)
2013-08-29- Add WWWSunpoet Po-Chuan Hsieh
- Use single space after WWW: - Remove Author line
2013-08-29- Disconnect ports removed in r325546Bryan Drewery
2013-08-28Update to latest GNUstep core libraries.David Chisnall
Update dependent packages with more recent releases. Remove old and bit-rotted ones. Switch to using clang 3.3 and libobjc2 1.7 by default, so modern Objective-C features work out of the box and remove a lot of configurable options for sub-optimal (and, often, unsupported / deprecated upstream) configurations. Take maintainership of GNUstep-related ports. Several of the ports left in have scary warnings which mean that they are likely broken in lots of cases. Future commits will fix them. Approved by: bapt
2013-08-28Make sure to respect CC and CXX, this fixes the build on head without gccBaptiste Daroussin
2013-08-26Update math/gsl to 1.16 and adjust some dependent portsBrendan Fabeny
2013-08-20- Update to 2.3.5Wen Heping
- Add LICENSE - Remove pkg-message since license changed upstream - Do not install test files as example
2013-08-18biology/tinker: Regenerate distinfo to unbreak fetchJohn Marino
Apparently the distfile was rerolled. The sizes of the file are only a few bytes apart. Since the master site never changed, it's reasonable just to regenerate the distinfo and bump the PORTREVISION. PR: 180664 Approved by: bapt/culot (mentors, implicit)
2013-08-17Replace USE_GCC=4.6+ and USE_GCC=4.4+ by USE_GCC=yes.Gerald Pfeifer
Right now this is a noop in the former case and a noop in the latter case unless lang/gcc44 has been installed explicitly. This puts a bit more emphasis on standardizing on a canonical version "current" GCC and makes it easier to update that canonical version by changing the default in Mk/bsd.gcc.mk and updating the lang/gcc port. That is, USE_GCC=yes means "use a decent/modern version of GCC" without having to worry about details. Approved by: portmgr (bdrewery)
2013-08-14- Remove MAKE_JOBS_SAFE variableAlex Kozlov
Approved by: portmgr (bdrewery)
2013-08-14biology/libgenome: Mark jobs unsafeJohn Marino
Approved by: bapt/culot (mentors, implicit)
2013-08-09- update libdg to 2.1.0Dirk Meyer
2013-08-06- Pet portlint: remove blank line among *_DEPENDSSunpoet Po-Chuan Hsieh
2013-08-06- Convert to new perl frameworkAndrej Zverev
- Trim Makefile header Approved by: wen@ (maintainer)
2013-08-03- Convert to new perl frameworkMathieu Arnold
- Remove MAKE_JOBS_SAFE=yes, it's the default.
2013-08-03- Convert to new perl frameworkAndrej Zverev
- Trim Makefile header
2013-08-02- Convert to new perl frameworkMathieu Arnold
- Trim Makefile header - Remove MAKE_JOBS_SAFE=yes, it's the default.
2013-08-01- Update to 1.6Philippe Audeoud
- Convert to new perl5 framework - Changelog: http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-1.6/Changes
2013-07-26KDE3 and QT3 expired on 2013-07-01, remove these ports.Rene Ladan
Unfortunately, this also affects some ports using QT3 as a GUI toolkit. Changes to infrastructure files: - bsd.kde.mk : obsolete, remove - bsd.qt.mk : note that a CONFLICTS_BUILD line can probably go after a while - CHANGES : document the removals from bsd.port.mk - KNOBS : remove KDE and QT (KDE4 and QT4 should be used instead) - MOVED : add the removed ports PR: ports/180745 Submitted by: rene Approved by: portmgr (bapt) Exp-run by: bapt
2013-07-20- Update to 3.0Wen Heping
- Convert to optionsNG - Drop maintainership
2013-07-20- Update to 0.56Wen Heping
2013-07-20- Update to 2.37Wen Heping
Changes: http://cpansearch.perl.org/src/LDS/Bio-Graphics-2.37/Changes
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