non port: biology/jellyfish/Makefile |
Number of commits found: 27 |
Saturday, 2 Mar 2024
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19:17 Nuno Teixeira (eduardo)
biology/jellyfish: Move man pages to share/man
Approved by: portmgr (blanket)
058e421 |
Friday, 6 Jan 2023
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01:24 Jason W. Bacon (jwb)
biology/jellyfish: Bump PORTREVISION for biology/htslib update
5ed1fc6 |
Wednesday, 7 Sep 2022
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21:10 Stefan Eßer (se)
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)
b7f0544 |
Tuesday, 12 Oct 2021
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15:01 Tobias Kortkamp (tobik)
*: 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
ae22a78 |
Friday, 17 Sep 2021
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18:01 Joseph Mingrone (jrm)
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>
3b937ad |
Saturday, 11 Sep 2021
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12:29 Jason W. Bacon (jwb)
biology/jellyfish: Fix unused open mode variable
PR: 258397
Reported by: dim
696f6ac |
Sunday, 22 Aug 2021
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17:44 Jason W. Bacon (jwb)
biology/jellyfish: Update to 2.3.0
Changelog: https://github.com/gmarcais/Jellyfish/releases/tag/v2.3.0
4952cf6 |
Wednesday, 7 Apr 2021
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08:09 Mathieu Arnold (mat)
One more small cleanup, forgotten yesterday.
Reported by: lwhsu
cf118cc |
Tuesday, 6 Apr 2021
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14:31 Mathieu Arnold (mat)
Remove # $FreeBSD$ from Makefiles.
305f148 |
Monday, 3 Aug 2020
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17:40 jwb
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
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Saturday, 7 Mar 2020
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19:25 jwb
biology/jellyfish: Patch for clang 10
Add cast to silence implicit conversion error
PR: ports/244645
Submitted by: dim
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Saturday, 14 Sep 2019
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22:01 jbeich
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
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Friday, 26 Jul 2019
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20:46 gerald
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
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Monday, 13 May 2019
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16:23 jwb
biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64
PR: 237868
Submitted by: pkubaj
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Friday, 3 May 2019
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21:06 linimon
These ports now build on aarch64.
Where necessary, pet portlint.
Approved by: portmgr
Obtained from: aarch64 TRYBROKEN run
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Wednesday, 12 Dec 2018
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01:35 gerald
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
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Sunday, 29 Jul 2018
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22:18 gerald
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
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Wednesday, 31 Jan 2018
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01:07 jwb
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
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Sunday, 10 Sep 2017
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20:55 gerald
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
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Saturday, 1 Apr 2017
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15:23 gerald
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
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Sunday, 1 Jan 2017
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03:45 sunpoet
Remove BROKEN_FreeBSD_9
Approved by: portmgr (blanket)
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Monday, 19 Dec 2016
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16:52 jrm
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
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Friday, 11 Nov 2016
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09:31 linimon
Mark various leaf ports broken on aarch64, and, where appropriate, other
tier-2 archs.
Approved by: portmgr (tier-2 blanket)
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Friday, 21 Oct 2016
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15:21 mat
Use USES=pathfix where applicable.
PR: 213195
Submitted by: mat
Exp-run by: antoine
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D8093
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Friday, 1 Apr 2016
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13:29 mat
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat: portmgr
Sponsored by: Absolight
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Tuesday, 29 Mar 2016
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20:55 amdmi3
- Use more appropriate BROKEN instead of IGNORE
PR: 208367
Submitted by: bacon4000@gmail.com (maintainer)
Suggested by: rakuco
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Thursday, 24 Mar 2016
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13:53 amdmi3
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
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Number of commits found: 27 |