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* biology/abyss: Move man pages to share/manNuno Teixeira2024-03-032-2/+3
| | | | Approved by: portmgr (blanket)
* */*: bump PORTREVISION after the upgrade of MPICH to 4.1.2Thierry Thomas2023-12-101-0/+1
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* biology/abyss: Update 2.3.5 → 2.3.7Yuri Victorovich2023-07-223-17/+6
| | | | Reported by: portscout
* biology/abyss: Fix build with llvm15Muhammad Moinur Rahman2023-06-071-1/+7
| | | | Approved by: portmgr (blanket)
* *: Bump PORTREVISIONs for math/mpc update to 1.3.1Gerald Pfeifer2023-04-231-1/+1
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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)
* */*: bump all consumers after recent boost upgradeDima Panov2022-08-121-0/+1
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* biology/abyss: Add test targetYuri Victorovich2022-07-301-0/+2
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* biology/abyss: Update 2.3.1 -> 2.3.5Yuri Victorovich2022-07-295-13/+22
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* devel/libffi: Bump deps PORTREVISION for shlib changeKevin Bowling2022-05-091-0/+1
| | | | | PR: 263764 Reported by: VVD <vvd@unislabs.com>
* cleanup: drop support for EOL FreeBSD 11.XRene Ladan2021-09-301-1/+0
| | | | | | | | | | | | | | | | | Search criteria used: - 11.4 - OSREL* - OSVER* - *_FreeBSD_11 Input from: - adridg: devel/qca-legacy - jbeich: _WITH_DPRINTF, _WITH_GETLINE, GNU bfd workarounds - sunpoet: security/p5-*OpenSSL* Reviewed by: doceng, kde, multimedia, perl, python, ruby, rust Differential Revision: https://reviews.freebsd.org/D32008 Test Plan: make index
* biology/abyss: Broken on 11Yuri Victorovich2021-08-211-0/+1
| | | | Reported by: fallout
* biology/abyss: Update 2.3.0-3 -> 2.3.1Yuri Victorovich2021-04-222-5/+4
| | | | Reported by: portscout
* biology/abyss: Update 2.2.5 -> 2.3.0-3Yuri Victorovich2021-04-183-6/+11
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* 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/abyss: Add PORTSCOUT lineYuri Victorovich2021-03-141-0/+2
| | | | Notes: svn path=/head/; revision=568329
* biology/abyss: Update 2.2.4 -> 2.2.5Yuri Victorovich2020-09-273-6/+5
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=550242
* Chanse update of devel/libffiNiclas Zeising2020-07-041-0/+1
| | | | | | | | | | | | | Chase the devel/libffi update Bump portrevision of all dependent ports to chace shard library version bump in libffi. Update LIB_DEPENDS lines where needed to not require a specific version of libffi.so. PR: 247028 (for tracking) Notes: svn path=/head/; revision=541232
* biology/abyss: Update 2.2.3 -> 2.2.4Yuri Victorovich2020-05-302-5/+4
| | | | Notes: svn path=/head/; revision=537064
* Drop dependency on devel/openmpJan Beich2020-03-081-2/+2
| | | | | | | | | | - Drop if devel/llvm* was used as a substitute Approved by: yuri, rene (earlier version) Differential Revision: https://reviews.freebsd.org/D23020 Notes: svn path=/head/; revision=528082
* biology/abyss: Broken on i386Yuri Victorovich2020-01-181-0/+2
| | | | | | | Reported by: fallout Notes: svn path=/head/; revision=523491
* biology/abyss: Update 2.1.5 -> 2.2.3Yuri Victorovich2020-01-133-14/+8
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=522851
* devel/boost-*: update to 1.72.0Jan Beich2019-12-111-1/+1
| | | | | | | | | | Changes: http://www.boost.org/users/history/version_1_72_0.html PR: 241449 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D22136 Notes: svn path=/head/; revision=519824
* devel/openmp: update to 9.0.0Jan Beich2019-09-211-1/+1
| | | | | | | | | | | - Connect tests to the framework to help QA remaining patches - Force rebuild all consumers after https://reviews.llvm.org/D59783 Changes: http://llvm.org/viewvc/llvm-project/openmp/tags/RELEASE_900/final/?view=log ABI: https://abi-laboratory.pro/tracker/timeline/llvm_openmp/ Notes: svn path=/head/; revision=512535
* devel/boost-*: update to 1.71.0Jan Beich2019-08-191-1/+1
| | | | | | | | | | Changes: http://www.boost.org/users/history/version_1_71_0.html PR: 238827 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D20774 Notes: svn path=/head/; revision=509290
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2019-07-261-1/+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/abyss: fix build on big-endian architecturesPiotr Kubaj2019-06-213-2/+20
| | | | | | | | | | | | | | | Use new GCC from ports on GCC architectures. Merge 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5, fixes build on GCC architectures. Also include sys/endian.h and use bswap32 and bswap64 for byte-swapping (PR at https://github.com/bcgsc/abyss/pull/287 ). PR: 238737 Approved by: yuri (maintainer), mat (mentor) Differential Revision: https://reviews.freebsd.org/D20717 Notes: svn path=/head/; revision=504788
* devel/openmp: phase outJan Beich2019-05-081-1/+1
| | | | | | | | | | | | - Expire after the last version without /usr/lib/libomp.so - Drop SOVERSION for seamless transition (i.e., avoid conditionals) PR: 236907 Approved by: bapt (maintainer) Differential Revision: https://reviews.freebsd.org/D19767 Notes: svn path=/head/; revision=501030
* devel/boost-*: update to 1.70.0Jan Beich2019-04-121-0/+1
| | | | | | | | | | Changes: http://www.boost.org/users/history/version_1_70_0.html PR: 235956 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D19303 Notes: svn path=/head/; revision=498698
* New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end ↵Yuri Victorovich2019-02-255-0/+115
sequence assembler Notes: svn path=/head/; revision=493842
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