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* biology/cd-hit: allow to build without GCC on libomp-less systemsPiotr Kubaj2023-08-121-4/+4
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* Remove WWW entries moved into port MakefilesStefan Eßer2022-09-071-2/+0
| | | | | | | | | | Commit b7f05445c00f has added WWW entries to port Makefiles based on WWW: lines in pkg-descr files. This commit removes the WWW: lines of moved-over URLs from these pkg-descr files. Approved by: portmgr (tcberner)
* Add WWW entries to port MakefilesStefan Eßer2022-09-071-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | It has been common practice to have one or more URLs at the end of the ports' pkg-descr files, one per line and prefixed with "WWW:". These URLs should point at a project website or other relevant resources. Access to these URLs required processing of the pkg-descr files, and they have often become stale over time. If more than one such URL was present in a pkg-descr file, only the first one was tarnsfered into the port INDEX, but for many ports only the last line did contain the port specific URL to further information. There have been several proposals to make a project URL available as a macro in the ports' Makefiles, over time. This commit implements such a proposal and moves one of the WWW: entries of each pkg-descr file into the respective port's Makefile. A heuristic attempts to identify the most relevant URL in case there is more than one WWW: entry in some pkg-descr file. URLs that are not moved into the Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr files in order to preserve them. There are 1256 ports that had no WWW: entries in pkg-descr files. These ports will not be touched in this commit. The portlint port has been adjusted to expect a WWW entry in each port Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as deprecated. Approved by: portmgr (tcberner)
* biology/cd-hit: check for omp.h on all architecturesPiotr Kubaj2022-04-271-3/+1
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* biology/cd-hit: fix build on armv7Piotr Kubaj2021-11-211-1/+1
| | | | Same issue as on powerpc.
* biology/cd-hit: fix build on powerpcPiotr Kubaj2021-06-101-0/+6
| | | | | LLVM on powerpc doesn't have libomp: cdhit-common.c++:36:9: fatal error: 'omp.h' file not found
* One more small cleanup, forgotten yesterday.Mathieu Arnold2021-04-071-1/+0
| | | | Reported by: lwhsu
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* biology/cd-hit: Drop dependency on gccJason W. Bacon2021-01-111-2/+2
| | | | | | | | | | Simply remove compiler:openmp Builds with base compiler on amd64, i386, and powerpc64 PR: port/247753, ports/252379 Notes: svn path=/head/; revision=561228
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2019-07-261-0/+1
| | | | | | | | | | | | | | | | | | as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3 to GCC 9.1 under most circumstances now after revision 507371. 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, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, everything INDEX-11 shows with a dependency on lang/gcc9 now. PR: 238330 Notes: svn path=/head/; revision=507372
* biology/cd-hit: Upgrade to 4.8.1Jason W. Bacon2019-03-144-14/+106
| | | | | | | Convert Makefile REINPLACE to patch for sending upstream Notes: svn path=/head/; revision=495746
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-12-121-1/+1
| | | | | | | | | | | | | | | | | | defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t GCC 8.2 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, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, as a double check, everything INDEX-11 showed depending on lang/gcc7. PR: 231590 Notes: svn path=/head/; revision=487272
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-07-291-1/+1
| | | | | | | | | | | | | | | | | in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which has now moved from GCC 6 to GCC 7 by default. This includes ports - featuring USE_GCC=yes or USE_GCC=any, - featuring USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and those - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x, c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib. PR: 222542 Notes: svn path=/head/; revision=475857
* Bump PORTREVISIONs of all users of math/mpc that we just updated toGerald Pfeifer2018-03-101-1/+1
| | | | | | | version 1.1.0 (via revision 464079). Notes: svn path=/head/; revision=464084
* Multiple ports:Jason W. Bacon2018-01-311-2/+1
| | | | | | | | | | | 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 Notes: svn path=/head/; revision=460452
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2017-09-101-1/+1
| | | | | | | | | | | | | | | | | (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 Notes: svn path=/head/; revision=449591
* Bump PORTREVISIONs for ports depending on the canonical version of GCC andGerald Pfeifer2017-04-011-0/+1
| | | | | | | | | | | | | | | | | lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some circumstances such as versions of FreeBSD or platforms). This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using using Mk/bsd.octave.mk which in turn has USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang, c++11-lang, c++0x, c11, or gcc-c++11-lib. PR: 216707 Notes: svn path=/head/; revision=437439
* biology/cd-hit: Update to bug-fix release 4.6.6Joseph Mingrone2016-12-202-5/+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 Notes: svn path=/head/; revision=429002
* Do not use post-stage. Use post-install instead.Mathieu Arnold2016-12-021-1/+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 Notes: svn path=/head/; revision=427552
* Bump PORTREVISIONS for ports depending on the canonical version of GCC andGerald Pfeifer2016-11-201-0/+1
| | | | | | | | | | | | 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. Notes: svn path=/head/; revision=426566
* - Update maintainer mail addressMartin Wilke2015-12-111-2/+2
| | | | | | | | | | | | - Update/Remove MASTER_SITE PR: 204755 Submitted by: jwbacon@tds.net (maintainer) Approved by: mat (mentor) Differential Revision: D4493 Notes: svn path=/head/; revision=403506
* - Use compiler:openmp instead of gccWen Heping2015-09-191-4/+1
| | | | | | | | | - Minor cleanup Reported by: danfe@ Notes: svn path=/head/; revision=397322
* CD-HIT is a very widely used program for clustering and comparing protein orWen Heping2015-09-194-0/+80
nucleotide sequences. WWW: http://weizhong-lab.ucsd.edu/cd-hit/ PR: 203183 Submitted by: jwbacon@tds.net Notes: svn path=/head/; revision=397318
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