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non port: biology/bedtools/Makefile

Number of commits found: 22

Wednesday, 8 Nov 2023
16:42 Jason W. Bacon (jwb) search for other commits by this committer
biology/bedtools: Update to 2.31.1

Code updates for modern compilers

Changes: https://github.com/arq5x/bedtools2/releases
commit hash: 1e46f94e3f92c12e7b0696d62410edd490c0d86a commit hash: 1e46f94e3f92c12e7b0696d62410edd490c0d86a commit hash: 1e46f94e3f92c12e7b0696d62410edd490c0d86a commit hash: 1e46f94e3f92c12e7b0696d62410edd490c0d86a 1e46f94
Saturday, 29 Apr 2023
01:03 Jason W. Bacon (jwb) search for other commits by this committer
biology/bedtools: Update to 2.31.0

New summary tool
Numerous minor fixes and enhancements
Changes: https://github.com/arq5x/bedtools2/releases

Reported by:    portscout
commit hash: 44171f2c6a245e722e47ae30ef692591210435bf commit hash: 44171f2c6a245e722e47ae30ef692591210435bf commit hash: 44171f2c6a245e722e47ae30ef692591210435bf commit hash: 44171f2c6a245e722e47ae30ef692591210435bf 44171f2
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
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, 24 Jan 2021
18:25 jwb search for other commits by this committer
biology/bedtools: Upgrade to 2.30.0

Several bug fixes and performance enhancements

Reported by:    portscout
Original commitRevision:562501 
Friday, 22 Jan 2021
14:55 jwb search for other commits by this committer
biology/bedtools: License changed upstream
Original commitRevision:562312 
Thursday, 19 Dec 2019
01:04 jwb search for other commits by this committer
biology/bedtools: Upgrade to 2.29.2

Fixed a bug that mistakenly removed a BAM/CRAM header line

Reported by:    portscout
Original commitRevision:520414 
Wednesday, 11 Dec 2019
15:13 jwb search for other commits by this committer
biology/bedtools: Upgrade to 2.29.1

Several important bug fixes.

Reported by:    portscout
Original commitRevision:519810 
Friday, 13 Sep 2019
13:21 jwb search for other commits by this committer
biology/bedtools: Upgrade to 2.29.0

Add test target to run test scripts in dist

Reported by:    portscout
Original commitRevision:511958 
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, 4 Mar 2019
06:55 jbeich search for other commits by this committer
biology/bedtools: unbreak with libc++ 8

In file included from FileReader.cpp:1:
In file included from /usr/include/c++/v1/iostream:38:
In file included from /usr/include/c++/v1/ios:216:
In file included from /usr/include/c++/v1/__locale:15:
In file included from /usr/include/c++/v1/string:505:
In file included from /usr/include/c++/v1/string_view:176:
In file included from /usr/include/c++/v1/__string:57:
In file included from /usr/include/c++/v1/algorithm:640:
In file included from /usr/include/c++/v1/initializer_list:47:
In file included from /usr/include/c++/v1/cstddef:38:
../../../utils//gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^

PR:		236192
Approved by:	portmgr blanket
Original commitRevision:494554 
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 
Saturday, 22 Sep 2018
05:30 linimon search for other commits by this committer
Fix build on gcc-based archs by updating USES.

Tested on powerpc64 and amd64 (for no regression).

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:480340 
Saturday, 16 Jun 2018
17:55 jwb search for other commits by this committer
biology/bedtools: Fix Makefile to respect PREFIX

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15851
Original commitRevision:472560 
Thursday, 19 Apr 2018
16:44 jwb search for other commits by this committer
biology/bedtools: Upgrade to 2.27.1

PR:             227272
Submitted by:   jwb
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15137
Original commitRevision:467783 
Friday, 22 Dec 2017
12:27 amdmi3 search for other commits by this committer
- Fix build on 11+

Approved by:	portmgr blanket
Original commitRevision:456976 
Tuesday, 19 Dec 2017
14:41 linimon search for other commits by this committer
Mark more recently failing ports broken on aarch64.

While here, pet portlint and reformat some other BROKEN statements.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:456719 
Thursday, 30 Nov 2017
06:13 linimon search for other commits by this committer
For ports that are marked BROKEN on armv6, and also fail to build on
armv7, mark them so.

This is part two of a multipart commit to bring armv7 ports to parity
with armv6.

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run
Original commitRevision:455167 
Saturday, 27 May 2017
15:07 linimon search for other commits by this committer
Mark some ports failing on armv6, for errors classified as "clang".

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:441847 
Monday, 22 Aug 2016
04:32 marino search for other commits by this committer
biology/bedtools is not jobs safe

The version.o target tries to use version_git.h before that header is
created.
Original commitRevision:420587 
Tuesday, 19 Jan 2016
08:56 wen search for other commits by this committer
The bedtools utilities are a suite of tools for performing a wide range of
genomics analysis tasks.  The most widely-used of these tools enable genome
arithmetic, i.e., set theory on the genome.  For example, with bedtools one
can intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.

Although each individual utility is designed to do a relatively simple task,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.

WWW: http://bedtools.readthedocs.org/

PR:		204536
Submitted by:	scottcheloha@gmail.com
Original commitRevision:406676 

Number of commits found: 22