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non port: biology/vcflib/Makefile

Number of commits found: 22

Monday, 1 Jan 2024
05:37 Jan Beich (jbeich) search for other commits by this committer Author: Nathan Fisher
lang/zig: update to 0.11.0

Changes:	https://ziglang.org/download/0.11.0/release-notes.html
PR:		273124
Approved by:	dch (maintainer)
commit hash: 8c1e3e605452d8181b2180dad180679d93aecbe3 commit hash: 8c1e3e605452d8181b2180dad180679d93aecbe3 commit hash: 8c1e3e605452d8181b2180dad180679d93aecbe3 commit hash: 8c1e3e605452d8181b2180dad180679d93aecbe3 8c1e3e6
Sunday, 30 Jul 2023
22:59 Robert Clausecker (fuz) search for other commits by this committer
biology/vcflib: not for armv6/7

Requires OpenMP which is not supported on armv6/armv7.

Approved by:	portmgr (build fix blanket)
MFH:		2023Q3
commit hash: 931dd7ad39c20013888e5427f78a0120cc2682e3 commit hash: 931dd7ad39c20013888e5427f78a0120cc2682e3 commit hash: 931dd7ad39c20013888e5427f78a0120cc2682e3 commit hash: 931dd7ad39c20013888e5427f78a0120cc2682e3 931dd7a
Thursday, 9 Feb 2023
15:35 Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Update to 1.0.7

Fixes regression in 1.0.6

Made Zig language support a default off option
Zig is experimental and problematic

Reported by:    portscout
commit hash: 5fee60fc3c922a534c2200372385de54590122a9 commit hash: 5fee60fc3c922a534c2200372385de54590122a9 commit hash: 5fee60fc3c922a534c2200372385de54590122a9 commit hash: 5fee60fc3c922a534c2200372385de54590122a9 5fee60f
Tuesday, 31 Jan 2023
16:25 Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Unbreak build on aarch64, probably others

Patch out hard-coded -march=native, not supported by clang aarch64
commit hash: 0d9ff1bcabfc0d026a6505fe7d9b2ccd7cf57c1f commit hash: 0d9ff1bcabfc0d026a6505fe7d9b2ccd7cf57c1f commit hash: 0d9ff1bcabfc0d026a6505fe7d9b2ccd7cf57c1f commit hash: 0d9ff1bcabfc0d026a6505fe7d9b2ccd7cf57c1f 0d9ff1b
Monday, 30 Jan 2023
22:05 Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Update to 1.0.6

A few minor upstream fixes
Unbundle WFA2-lib, which may be useful outside vcflib
Update some submodules to latest commit (no recent releases available)
commit hash: 4512fe6572782dda2df7fb1d3af56144f5d1c4a4 commit hash: 4512fe6572782dda2df7fb1d3af56144f5d1c4a4 commit hash: 4512fe6572782dda2df7fb1d3af56144f5d1c4a4 commit hash: 4512fe6572782dda2df7fb1d3af56144f5d1c4a4 4512fe6
Thursday, 26 Jan 2023
14:14 Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Patch in time.h for struct timespec

Forgot to add patch file to repo during upgrade
Needed on 12.3-RELEASE
commit hash: 62e06491dd1a548fb95ab05880b0d5a5d422534c commit hash: 62e06491dd1a548fb95ab05880b0d5a5d422534c commit hash: 62e06491dd1a548fb95ab05880b0d5a5d422534c commit hash: 62e06491dd1a548fb95ab05880b0d5a5d422534c 62e0649
Monday, 23 Jan 2023
23:51 Jan Beich (jbeich) search for other commits by this committer
lang/zig: rebuild consumers after 91552559ae79

Propagate standard library and miscompilation fixes into binary packages.
commit hash: ded326a4be6d267606a18e3bd6d1b5fba6eae55d commit hash: ded326a4be6d267606a18e3bd6d1b5fba6eae55d commit hash: ded326a4be6d267606a18e3bd6d1b5fba6eae55d commit hash: ded326a4be6d267606a18e3bd6d1b5fba6eae55d ded326a
Sunday, 22 Jan 2023
17:13 Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Update to 1.0.5

Numerous new features and enhancements

Changes:    https://github.com/vcflib/vcflib/tags

Reported by:    portscout
commit hash: 459cb897f0423111cd4b55fac5caabeef7c81d77 commit hash: 459cb897f0423111cd4b55fac5caabeef7c81d77 commit hash: 459cb897f0423111cd4b55fac5caabeef7c81d77 commit hash: 459cb897f0423111cd4b55fac5caabeef7c81d77 459cb89
Friday, 6 Jan 2023
01:29 Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Bump PORTREVISION for biology/htslib update
commit hash: edf777d92b5bacec0fe48bf0c64349db0e344453 commit hash: edf777d92b5bacec0fe48bf0c64349db0e344453 commit hash: edf777d92b5bacec0fe48bf0c64349db0e344453 commit hash: edf777d92b5bacec0fe48bf0c64349db0e344453 edf777d
Wednesday, 7 Sep 2022
21:10 Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

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)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Wednesday, 29 Jun 2022
14:53 Stefan Eßer (se) search for other commits by this committer
Fix CONFLICTS_INSTALL in benchmarks and biology

Approved by:	portmgr (implicit)
commit hash: b52114270fb74b73a57ab9e58cfb84f4ac0271a3 commit hash: b52114270fb74b73a57ab9e58cfb84f4ac0271a3 commit hash: b52114270fb74b73a57ab9e58cfb84f4ac0271a3 commit hash: b52114270fb74b73a57ab9e58cfb84f4ac0271a3 b521142
Sunday, 6 Feb 2022
18:36 Stefan Eßer (se) search for other commits by this committer
Update CONFLICTS definitions in categories a* to c*

Update the CONFLICTS definitions of ports in the following categories:

- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters

An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.

There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.

Approved by:	portmgr (implicit)
commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e bdd2d4a
Friday, 28 Jan 2022
00:09 Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Update to 1.0.3

Several new commands
A few bug fixes and enhancements

Changes:        https://github.com/vcflib/vcflib/tags

Reported by:    portscout
commit hash: 8859320e5667960b2d8d21f1936a21e3e1f0ff3b commit hash: 8859320e5667960b2d8d21f1936a21e3e1f0ff3b commit hash: 8859320e5667960b2d8d21f1936a21e3e1f0ff3b commit hash: 8859320e5667960b2d8d21f1936a21e3e1f0ff3b 8859320
Thursday, 16 Dec 2021
21:49 Piotr Kubaj (pkubaj) search for other commits by this committer
biology/vcflib: unbreak on riscv64
commit hash: ed59e0d27e54065a2a9d5143fc39893ad6db9673 commit hash: ed59e0d27e54065a2a9d5143fc39893ad6db9673 commit hash: ed59e0d27e54065a2a9d5143fc39893ad6db9673 commit hash: ed59e0d27e54065a2a9d5143fc39893ad6db9673 ed59e0d
Thursday, 4 Nov 2021
14:23 Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Update to 1.0.2

Switch to github submodules for most deps rather than patch build system
Fixes build on powerpc64 and aarch64, possibly others

Changes:        https://github.com/vcflib/vcflib/tags

PR:             259622
Reported by:    pkubaj
commit hash: e02229c22ccbe188c405dcb5d81d14e5c809411e commit hash: e02229c22ccbe188c405dcb5d81d14e5c809411e commit hash: e02229c22ccbe188c405dcb5d81d14e5c809411e commit hash: e02229c22ccbe188c405dcb5d81d14e5c809411e e02229c
Wednesday, 7 Apr 2021
08:09 Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c cf118cc
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Sunday, 28 Mar 2021
16:39 pkubaj search for other commits by this committer
biology/vcflib: fix build on powerpc64le

Use GCC for its SSE -> AltiVec translation:
In file included from src/ssw.cpp:38:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:33:5: error: use of undeclared
identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
    __builtin_ia32_emms();
Original commitRevision:569399 
Saturday, 2 Jan 2021
01:46 linimon search for other commits by this committer
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
them BROKEN.

While here, pet portlint (Makevar order).

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:559904 
Monday, 3 Aug 2020
17:40 jwb search for other commits by this committer
biology/htslib: Upgrade to 1.10.2

Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/htslib/tags

Bump PORTREVISION on dependents that don't require additional patching

PR:             248089
Original commitRevision:544090 
Friday, 22 Jun 2018
00:03 linimon search for other commits by this committer
Mark these ports as broken on aarch64.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:473010 
Tuesday, 17 Apr 2018
03:11 jwb search for other commits by this committer
biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15109
Original commitRevision:467553 

Number of commits found: 22