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non port: biology/jellyfish/Makefile

Number of commits found: 27

Saturday, 2 Mar 2024
19:17 Nuno Teixeira (eduardo) search for other commits by this committer
biology/jellyfish: Move man pages to share/man

Approved by:	portmgr (blanket)
commit hash: 058e4213c94833fea79a8ba280f0b6b54023a5a9 commit hash: 058e4213c94833fea79a8ba280f0b6b54023a5a9 commit hash: 058e4213c94833fea79a8ba280f0b6b54023a5a9 commit hash: 058e4213c94833fea79a8ba280f0b6b54023a5a9 058e421
Friday, 6 Jan 2023
01:24 Jason W. Bacon (jwb) search for other commits by this committer
biology/jellyfish: Bump PORTREVISION for biology/htslib update
commit hash: 5ed1fc619eac271991f735f82aa77443899f992b commit hash: 5ed1fc619eac271991f735f82aa77443899f992b commit hash: 5ed1fc619eac271991f735f82aa77443899f992b commit hash: 5ed1fc619eac271991f735f82aa77443899f992b 5ed1fc6
Wednesday, 7 Sep 2022
21:10 Stefan E├čer (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
Tuesday, 12 Oct 2021
15:01 Tobias Kortkamp (tobik) search for other commits by this committer
*: 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
commit hash: ae22a7846afe2f4c0ac5bc88c5a63001c5eeafb1 commit hash: ae22a7846afe2f4c0ac5bc88c5a63001c5eeafb1 commit hash: ae22a7846afe2f4c0ac5bc88c5a63001c5eeafb1 commit hash: ae22a7846afe2f4c0ac5bc88c5a63001c5eeafb1 ae22a78
Friday, 17 Sep 2021
18:01 Joseph Mingrone (jrm) search for other commits by this committer
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>
commit hash: 3b937ad738af5bdf96233d23bc6c1f7008085d85 commit hash: 3b937ad738af5bdf96233d23bc6c1f7008085d85 commit hash: 3b937ad738af5bdf96233d23bc6c1f7008085d85 commit hash: 3b937ad738af5bdf96233d23bc6c1f7008085d85 3b937ad
Saturday, 11 Sep 2021
12:29 Jason W. Bacon (jwb) search for other commits by this committer
biology/jellyfish: Fix unused open mode variable

PR:             258397
Reported by:    dim
commit hash: 696f6acf5df455dddd38a7b023820f5eddcddc60 commit hash: 696f6acf5df455dddd38a7b023820f5eddcddc60 commit hash: 696f6acf5df455dddd38a7b023820f5eddcddc60 commit hash: 696f6acf5df455dddd38a7b023820f5eddcddc60 696f6ac
Sunday, 22 Aug 2021
17:44 Jason W. Bacon (jwb) search for other commits by this committer
biology/jellyfish: Update to 2.3.0

Changelog:      https://github.com/gmarcais/Jellyfish/releases/tag/v2.3.0
commit hash: 4952cf637ae51394337f4ec1c3df17417c171831 commit hash: 4952cf637ae51394337f4ec1c3df17417c171831 commit hash: 4952cf637ae51394337f4ec1c3df17417c171831 commit hash: 4952cf637ae51394337f4ec1c3df17417c171831 4952cf6
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
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 
Saturday, 7 Mar 2020
19:25 jwb search for other commits by this committer
biology/jellyfish: Patch for clang 10

Add cast to silence implicit conversion error

PR:             ports/244645
Submitted by:   dim
Original commitRevision:527971 
Saturday, 14 Sep 2019
22:01 jbeich search for other commits by this committer
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
Original commitRevision:512079 
Friday, 26 Jul 2019
20:46 gerald search for other commits by this committer
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
Original commitRevision:507372 
Monday, 13 May 2019
16:23 jwb search for other commits by this committer
biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64

PR:             237868
Submitted by:   pkubaj
Original commitRevision:501578 
Friday, 3 May 2019
21:06 linimon search for other commits by this committer
These ports now build on aarch64.

Where necessary, pet portlint.

Approved by:	portmgr
Obtained from:	aarch64 TRYBROKEN run
Original commitRevision:500752 
Wednesday, 12 Dec 2018
01:35 gerald search for other commits by this committer
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
Original commitRevision:487272 
Sunday, 29 Jul 2018
22:18 gerald search for other commits by this committer
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
Original commitRevision:475857 
Wednesday, 31 Jan 2018
01:07 jwb search for other commits by this committer
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
Original commitRevision:460452 
Sunday, 10 Sep 2017
20:55 gerald search for other commits by this committer
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
Original commitRevision:449591 
Saturday, 1 Apr 2017
15:23 gerald search for other commits by this committer
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
Original commitRevision:437439 
Sunday, 1 Jan 2017
03:45 sunpoet search for other commits by this committer
Remove BROKEN_FreeBSD_9

Approved by:	portmgr (blanket)
Original commitRevision:430235 
Monday, 19 Dec 2016
16:52 jrm search for other commits by this committer
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
Original commitRevision:428954 
Friday, 11 Nov 2016
09:31 linimon search for other commits by this committer
Mark various leaf ports broken on aarch64, and, where appropriate, other
tier-2 archs.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:425879 
Friday, 21 Oct 2016
15:21 mat search for other commits by this committer
Use USES=pathfix where applicable.

PR:		213195
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D8093
Original commitRevision:424427 
Friday, 1 Apr 2016
13:29 mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
Original commitRevision:412344 
Tuesday, 29 Mar 2016
20:55 amdmi3 search for other commits by this committer
- Use more appropriate BROKEN instead of IGNORE

PR:		208367
Submitted by:	bacon4000@gmail.com (maintainer)
Suggested by:	rakuco
Original commitRevision:412137 
Thursday, 24 Mar 2016
13:53 amdmi3 search for other commits by this committer
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
Original commitRevision:411785 

Number of commits found: 27