Commit History - (may be incomplete: see SVNWeb link above for full details) |
Date | By | Description |
22 Jan 2021 14:55:02
2.29.2

|
jwb  |
biology/bedtools: License changed upstream |
19 Dec 2019 01:04:11
2.29.2

|
jwb  |
biology/bedtools: Upgrade to 2.29.2
Fixed a bug that mistakenly removed a BAM/CRAM header line
Reported by: portscout |
11 Dec 2019 15:13:20
2.29.1

|
jwb  |
biology/bedtools: Upgrade to 2.29.1
Several important bug fixes.
Reported by: portscout |
13 Sep 2019 13:21:59
2.29.0

|
jwb  |
biology/bedtools: Upgrade to 2.29.0
Add test target to run test scripts in dist
Reported by: portscout |
26 Jul 2019 20:46:57
2.27.1_3

|
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 |
04 Mar 2019 06:55:09
2.27.1_2

|
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 |
12 Dec 2018 01:35:36
2.27.1_2

|
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 |
22 Sep 2018 05:30:32
2.27.1_1

|
linimon  |
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) |
16 Jun 2018 17:55:02
2.27.1_1

|
jwb  |
biology/bedtools: Fix Makefile to respect PREFIX
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D15851 |
19 Apr 2018 16:44:59
2.27.1

|
jwb  |
biology/bedtools: Upgrade to 2.27.1
PR: 227272
Submitted by: jwb
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D15137 |
22 Dec 2017 12:27:14
2.25.0

|
amdmi3  |
- Fix build on 11+
Approved by: portmgr blanket |
19 Dec 2017 14:41:29
2.25.0

|
linimon  |
Mark more recently failing ports broken on aarch64.
While here, pet portlint and reformat some other BROKEN statements.
Approved by: portmgr (tier-2 blanket) |
30 Nov 2017 06:13:35
2.25.0

|
linimon  |
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 |
27 May 2017 15:07:12
2.25.0

|
linimon  |
Mark some ports failing on armv6, for errors classified as "clang".
While here, pet portlint.
Approved by: portmgr (tier-2 blanket) |
22 Aug 2016 04:32:18
2.25.0

|
marino  |
biology/bedtools is not jobs safe
The version.o target tries to use version_git.h before that header is
created. |
19 Jan 2016 08:56:34
2.25.0

|
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 |