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non port: biology/bedtools/Makefile
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Number of commits found: 21

Sat, 29 Apr 2023
[ 01:03 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:44171f2c6a245e722e47ae30ef692591210435bf  commit hash:44171f2c6a245e722e47ae30ef692591210435bf  commit hash:44171f2c6a245e722e47ae30ef692591210435bf  44171f2 
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
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)
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.
Sun, 24 Jan 2021
[ 18:25 jwb search for other commits by this committer ] Original commit   Revision:562501
biology/bedtools: Upgrade to 2.30.0

Several bug fixes and performance enhancements

Reported by:    portscout
Fri, 22 Jan 2021
[ 14:55 jwb search for other commits by this committer ] Original commit   Revision:562312
biology/bedtools: License changed upstream
Thu, 19 Dec 2019
[ 01:04 jwb search for other commits by this committer ] Original commit   Revision:520414
biology/bedtools: Upgrade to 2.29.2

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

Reported by:    portscout
Wed, 11 Dec 2019
[ 15:13 jwb search for other commits by this committer ] Original commit   Revision:519810
biology/bedtools: Upgrade to 2.29.1

Several important bug fixes.

Reported by:    portscout
Fri, 13 Sep 2019
[ 13:21 jwb search for other commits by this committer ] Original commit   Revision:511958
biology/bedtools: Upgrade to 2.29.0

Add test target to run test scripts in dist

Reported by:    portscout
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, 4 Mar 2019
[ 06:55 jbeich search for other commits by this committer ] Original commit   Revision:494554
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
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
Sat, 22 Sep 2018
[ 05:30 linimon search for other commits by this committer ] Original commit   Revision:480340 (Only the first 10 of 34 ports in this commit are shown above. View all ports for this commit)
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)
Sat, 16 Jun 2018
[ 17:55 jwb search for other commits by this committer ] Original commit   Revision:472560
biology/bedtools: Fix Makefile to respect PREFIX

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15851
Thu, 19 Apr 2018
[ 16:44 jwb search for other commits by this committer ] Original commit   Revision:467783
biology/bedtools: Upgrade to 2.27.1

PR:             227272
Submitted by:   jwb
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15137
Fri, 22 Dec 2017
[ 12:27 amdmi3 search for other commits by this committer ] Original commit   Revision:456976
- Fix build on 11+

Approved by:	portmgr blanket
Tue, 19 Dec 2017
[ 14:41 linimon search for other commits by this committer ] Original commit   Revision:456719 (Only the first 10 of 15 ports in this commit are shown above. View all ports for this commit)
Mark more recently failing ports broken on aarch64.

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

Approved by:	portmgr (tier-2 blanket)
Thu, 30 Nov 2017
[ 06:13 linimon search for other commits by this committer ] Original commit   Revision:455167 (Only the first 10 of 189 ports in this commit are shown above. View all ports for this commit)
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
Sat, 27 May 2017
[ 15:07 linimon search for other commits by this committer ] Original commit   Revision:441847 (Only the first 10 of 19 ports in this commit are shown above. View all ports for this commit)
Mark some ports failing on armv6, for errors classified as "clang".

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
Mon, 22 Aug 2016
[ 04:32 marino search for other commits by this committer ] Original commit   Revision:420587
biology/bedtools is not jobs safe

The version.o target tries to use version_git.h before that header is
created.
Tue, 19 Jan 2016
[ 08:56 wen search for other commits by this committer ] Original commit   Revision:406676
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

Number of commits found: 21