| non port: biology/bedtools/Makefile |
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SVNWeb
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Number of commits found: 21 |
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Sat, 29 Apr 2023
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[ 01:03 Jason W. Bacon (jwb)  ]    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
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Wed, 7 Sep 2022
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[ 21:10 Stefan Eßer (se) ] b7f0544 (Only the first 10 of 27931 ports in this commit are shown above.  )
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 )
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Wed, 7 Apr 2021
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[ 08:09 Mathieu Arnold (mat) ] cf118cc (Only the first 10 of 8873 ports in this commit are shown above. )
One more small cleanup, forgotten yesterday.
Reported by: lwhsu
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Tue, 6 Apr 2021
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[ 14:31 Mathieu Arnold (mat) ] 305f148 (Only the first 10 of 29333 ports in this commit are shown above. )
Remove # $FreeBSD$ from Makefiles.
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Sun, 24 Jan 2021
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[ 18:25 jwb ]  
biology/bedtools: Upgrade to 2.30.0
Several bug fixes and performance enhancements
Reported by: portscout
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Fri, 22 Jan 2021
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[ 14:55 jwb ]
biology/bedtools: License changed upstream
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Thu, 19 Dec 2019
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[ 01:04 jwb ]
biology/bedtools: Upgrade to 2.29.2
Fixed a bug that mistakenly removed a BAM/CRAM header line
Reported by: portscout
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Wed, 11 Dec 2019
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[ 15:13 jwb ]
biology/bedtools: Upgrade to 2.29.1
Several important bug fixes.
Reported by: portscout
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Fri, 13 Sep 2019
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[ 13:21 jwb ]
biology/bedtools: Upgrade to 2.29.0
Add test target to run test scripts in dist
Reported by: portscout
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Fri, 26 Jul 2019
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[ 20:46 gerald ] (Only the first 10 of 3853 ports in this commit are shown above. )
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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Mon, 4 Mar 2019
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[ 06:55 jbeich ]
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
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Wed, 12 Dec 2018
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[ 01:35 gerald ] (Only the first 10 of 3168 ports in this commit are shown above. )
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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Sat, 22 Sep 2018
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[ 05:30 linimon ] (Only the first 10 of 34 ports in this commit are shown above. )
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)
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Sat, 16 Jun 2018
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[ 17:55 jwb ]
biology/bedtools: Fix Makefile to respect PREFIX
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D15851
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Thu, 19 Apr 2018
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[ 16:44 jwb ]
biology/bedtools: Upgrade to 2.27.1
PR: 227272
Submitted by: jwb
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D15137
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Fri, 22 Dec 2017
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[ 12:27 amdmi3 ]
- Fix build on 11+
Approved by: portmgr blanket
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Tue, 19 Dec 2017
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[ 14:41 linimon ] (Only the first 10 of 15 ports in this commit are shown above. )
Mark more recently failing ports broken on aarch64.
While here, pet portlint and reformat some other BROKEN statements.
Approved by: portmgr (tier-2 blanket)
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Thu, 30 Nov 2017
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[ 06:13 linimon ] (Only the first 10 of 189 ports in this commit are shown above. )
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
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Sat, 27 May 2017
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[ 15:07 linimon ] (Only the first 10 of 19 ports in this commit are shown above. )
Mark some ports failing on armv6, for errors classified as "clang".
While here, pet portlint.
Approved by: portmgr (tier-2 blanket)
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Mon, 22 Aug 2016
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[ 04:32 marino ]
biology/bedtools is not jobs safe
The version.o target tries to use version_git.h before that header is
created.
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Tue, 19 Jan 2016
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[ 08:56 wen ]
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
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Number of commits found: 21 |
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