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non port: biology/jellyfish/Makefile
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Number of commits found: 26

Fri, 6 Jan 2023
[ 01:24 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:5ed1fc619eac271991f735f82aa77443899f992b  commit hash:5ed1fc619eac271991f735f82aa77443899f992b  commit hash:5ed1fc619eac271991f735f82aa77443899f992b  5ed1fc6 
biology/jellyfish: Bump PORTREVISION for biology/htslib update
Wed, 7 Sep 2022
[ 21:10 Stefan E├čer (se) search for other commits by this committer ]    commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52  commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52  commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52  b7f0544  (Only the first 10 of 27931 ports in this commit are shown above. View all ports for this commit)
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.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Tue, 12 Oct 2021
[ 15:01 Tobias Kortkamp (tobik) search for other commits by this committer ]    commit hash:ae22a7846afe2f4c0ac5bc88c5a63001c5eeafb1  commit hash:ae22a7846afe2f4c0ac5bc88c5a63001c5eeafb1  commit hash:ae22a7846afe2f4c0ac5bc88c5a63001c5eeafb1  ae22a78  (Only the first 10 of 70 ports in this commit are shown above. View all ports for this commit)
*: Clean up some things

- Fix typos
- Fix overwritten variables with focus on master/slave ports
- Remove unreferenced variables
- Sort categories
- Remove redundant option descriptions
- Clean up commented PORTREVISION
- Add missing USES

Reported by:	portscan
Fri, 17 Sep 2021
[ 18:01 Joseph Mingrone (jrm) search for other commits by this committer ]    commit hash:3b937ad738af5bdf96233d23bc6c1f7008085d85  commit hash:3b937ad738af5bdf96233d23bc6c1f7008085d85  commit hash:3b937ad738af5bdf96233d23bc6c1f7008085d85  3b937ad 
biology/jellyfish: Switch to static tarball and update license info

The GitHub-generated tarballs require reautoconf and more dependencies
including gettext, regardless whether the NLS knob is turned off.
https://github.com/gmarcais/Jellyfish/issues/138#issuecomment-463272029

This update also fixes a build issue when the NLS knob was turned off.
http://pkg.ftfl.ca/data/13amd64-default/2021-09-16_13h45m55s/logs/errors/Jellyfish-2.3.0_1.log

Differential Revision:	https://reviews.freebsd.org/D31984

Co-authored-by: Jason W. Bacon <jwb@FreeBSD.org>
Sat, 11 Sep 2021
[ 12:29 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:696f6acf5df455dddd38a7b023820f5eddcddc60  commit hash:696f6acf5df455dddd38a7b023820f5eddcddc60  commit hash:696f6acf5df455dddd38a7b023820f5eddcddc60  696f6ac 
biology/jellyfish: Fix unused open mode variable

PR:             258397
Reported by:    dim
Sun, 22 Aug 2021
[ 17:44 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:4952cf637ae51394337f4ec1c3df17417c171831  commit hash:4952cf637ae51394337f4ec1c3df17417c171831  commit hash:4952cf637ae51394337f4ec1c3df17417c171831  4952cf6 
biology/jellyfish: Update to 2.3.0

Changelog:      https://github.com/gmarcais/Jellyfish/releases/tag/v2.3.0
Wed, 7 Apr 2021
[ 08:09 Mathieu Arnold (mat) search for other commits by this committer ]    commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  cf118cc  (Only the first 10 of 8873 ports in this commit are shown above. View all ports for this commit)
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
Tue, 6 Apr 2021
[ 14:31 Mathieu Arnold (mat) search for other commits by this committer ]    commit hash:305f148f482daf30dcf728039d03d019f88344eb  commit hash:305f148f482daf30dcf728039d03d019f88344eb  commit hash:305f148f482daf30dcf728039d03d019f88344eb  305f148  (Only the first 10 of 29333 ports in this commit are shown above. View all ports for this commit)
Remove # $FreeBSD$ from Makefiles.
Mon, 3 Aug 2020
[ 17:40 jwb search for other commits by this committer ] Original commit   Revision:544090 (Only the first 10 of 12 ports in this commit are shown above. View all ports for this commit)
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
Sat, 7 Mar 2020
[ 19:25 jwb search for other commits by this committer ] Original commit   Revision:527971
biology/jellyfish: Patch for clang 10

Add cast to silence implicit conversion error

PR:             ports/244645
Submitted by:   dim
Sat, 14 Sep 2019
[ 22:01 jbeich search for other commits by this committer ] Original commit   Revision:512079 (Only the first 10 of 47 ports in this commit are shown above. View all ports for this commit)
Drop C++11 workaround for GCC < 6 after r449590

lang/gcc5 will expire in ~1 month. If someone still uses lang/gcc48
they should backport C++11 fix instead. QA on GCC architecuters is
currently limited to powerpc64 which uses GCC_DEFAULT.

PR:		193528
Fri, 26 Jul 2019
[ 20:46 gerald search for other commits by this committer ] Original commit   Revision:507372 (Only the first 10 of 3853 ports in this commit are shown above. View all ports for this commit)
Bump PORTREVISION for ports depending on the canonical version of GCC
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
Mon, 13 May 2019
[ 16:23 jwb search for other commits by this committer ] Original commit   Revision:501578
biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64

PR:             237868
Submitted by:   pkubaj
Fri, 3 May 2019
[ 21:06 linimon search for other commits by this committer ] Original commit   Revision:500752 (Only the first 10 of 30 ports in this commit are shown above. View all ports for this commit)
These ports now build on aarch64.

Where necessary, pet portlint.

Approved by:	portmgr
Obtained from:	aarch64 TRYBROKEN run
Wed, 12 Dec 2018
[ 01:35 gerald search for other commits by this committer ] Original commit   Revision:487272 (Only the first 10 of 3168 ports in this commit are shown above. View all ports for this commit)
Bump PORTREVISION for ports depending on the canonical version of GCC
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
Sun, 29 Jul 2018
[ 22:18 gerald search for other commits by this committer ] Original commit   Revision:475857 (Only the first 10 of 1480 ports in this commit are shown above. View all ports for this commit)
Bump PORTREVISION for ports depending on the canonical version of GCC
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
Wed, 31 Jan 2018
[ 01:07 jwb search for other commits by this committer ] Original commit   Revision:460452 (Only the first 10 of 56 ports in this commit are shown above. View all ports for this commit)
Multiple ports:
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
Sun, 10 Sep 2017
[ 20:55 gerald search for other commits by this committer ] Original commit   Revision:449591 (Only the first 10 of 1201 ports in this commit are shown above. View all ports for this commit)
Bump PORTREVISION for ports depending on the canonical version of GCC
(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
Sat, 1 Apr 2017
[ 15:23 gerald search for other commits by this committer ] Original commit   Revision:437439 (Only the first 10 of 1118 ports in this commit are shown above. View all ports for this commit)
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
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
Sun, 1 Jan 2017
[ 03:45 sunpoet search for other commits by this committer ] Original commit   Revision:430235 (Only the first 10 of 161 ports in this commit are shown above. View all ports for this commit)
Remove BROKEN_FreeBSD_9

Approved by:	portmgr (blanket)
Mon, 19 Dec 2016
[ 16:52 jrm search for other commits by this committer ] Original commit   Revision:428954
biology/jellyfish: Update to version 2.2.6

Upstream changes since version 2.2.4:
- Fix compilation warnings/errors with newer version of gcc (5.3 & 6.1).
- Fix bug in parsing function that made it stop on sequences that consist
  of only empty lines.
- New methods in bindings to enumerate the mers of a string.

Approved by:	AMDmi3 (mentor)
Differential Revision:	https://reviews.freebsd.org/D8204
Fri, 11 Nov 2016
[ 09:31 linimon search for other commits by this committer ] Original commit   Revision:425879
Mark various leaf ports broken on aarch64, and, where appropriate, other
tier-2 archs.

Approved by:	portmgr (tier-2 blanket)
Fri, 21 Oct 2016
[ 15:21 mat search for other commits by this committer ] Original commit   Revision:424427 (Only the first 10 of 354 ports in this commit are shown above. View all ports for this commit)
Use USES=pathfix where applicable.

PR:		213195
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D8093
Fri, 1 Apr 2016
[ 13:29 mat search for other commits by this committer ] Original commit   Revision:412344 (Only the first 10 of 1009 ports in this commit are shown above. View all ports for this commit)
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
Tue, 29 Mar 2016
[ 20:55 amdmi3 search for other commits by this committer ] Original commit   Revision:412137
- Use more appropriate BROKEN instead of IGNORE

PR:		208367
Submitted by:	bacon4000@gmail.com (maintainer)
Suggested by:	rakuco
Thu, 24 Mar 2016
[ 13:53 amdmi3 search for other commits by this committer ] Original commit   Revision:411785
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
A k-mer is a substring of length k, and counting the occurrences of all such
substrings is a central step in many analyses of DNA sequence. JELLYFISH can
count k-mers quickly by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase parallelism.

WWW: http://www.genome.umd.edu/jellyfish.html

PR:		207929
Submitted by:	bacon4000@gmail.com

Number of commits found: 26