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non port: biology/bedtools/Makefile
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Number of commits found XX: 15

Thu, 19 Dec 2019
[ 01:04 jwb ] Original commit   Revision:520414
520414 biology/bedtools/Makefile
520414 biology/bedtools/distinfo
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 ] Original commit   Revision:519810
519810 biology/bedtools/Makefile
519810 biology/bedtools/distinfo
biology/bedtools: Upgrade to 2.29.1

Several important bug fixes.

Reported by:    portscout
Fri, 13 Sep 2019
[ 13:21 jwb ] Original commit   Revision:511958
511958 biology/bedtools/Makefile
511958 biology/bedtools/distinfo
511958 biology/bedtools/files/patch-Makefile
511958 biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h
511958 biology/bedtools/files/patch-src_utils_htslib_Makefile
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 ] Original commit   Revision:507372
507372 Mk/bsd.ruby.mk
507372 accessibility/atkmm/Makefile
507372 accessibility/kmag/Makefile
507372 accessibility/kmousetool/Makefile
507372 accessibility/kmouth/Makefile
507372 accessibility/libqaccessibilityclient/Makefile
507372 accessibility/qt5-speech/Makefile
507372 archivers/R-cran-zip/Makefile
507372 archivers/ark/Makefile
507372 archivers/brotli/Makefile

(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 ] Original commit   Revision:494554
494554 biology/bedtools/Makefile
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 ] Original commit   Revision:487272
487272 Mk/bsd.ruby.mk
487272 accessibility/atkmm/Makefile
487272 accessibility/kmag/Makefile
487272 accessibility/kmousetool/Makefile
487272 accessibility/kmouth/Makefile
487272 accessibility/qt5-speech/Makefile
487272 archivers/R-cran-zip/Makefile
487272 archivers/ark/Makefile
487272 archivers/brotli/Makefile
487272 archivers/c-blosc/Makefile

(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 ] Original commit   Revision:480340
480340 audio/beatslash-lv2/Makefile
480340 audio/eq10q-lv2/Makefile
480340 audio/midi-matrix-lv2/Makefile
480340 audio/oaml/Makefile
480340 biology/bedtools/Makefile
480340 databases/lua-xapian/Makefile
480340 databases/mysql-connector-c++/Makefile
480340 databases/p5-Xapian/Makefile
480340 databases/postgis23/Makefile
480340 databases/postgis24/Makefile

(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 ] Original commit   Revision:472560
472560 biology/bedtools/Makefile
472560 biology/bedtools/files/patch-Makefile
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 ] Original commit   Revision:467783
467783 biology/bedtools/Makefile
467783 biology/bedtools/distinfo
467783 biology/bedtools/files/patch-Makefile
467783 biology/bedtools/files/patch-src_utils_FileRecordTools_Records_StrandQueue.h
467783 biology/bedtools/pkg-descr
467783 biology/bedtools/pkg-plist
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 ] Original commit   Revision:456976
456976 biology/bedtools/Makefile
456976 biology/bedtools/files/patch-src_utils_FileRecordTools_Records_StrandQueue.h
- Fix build on 11+

Approved by:	portmgr blanket
Tue, 19 Dec 2017
[ 14:41 linimon ] Original commit   Revision:456719
456719 biology/bedtools/Makefile
456719 comms/gnuradio/Makefile
456719 editors/libreoffice/Makefile
456719 emulators/stella/Makefile
456719 games/armagetron/Makefile
456719 graphics/gsculpt/Makefile
456719 net/linknx/Makefile
456719 net/rsplib/Makefile
456719 science/afni/Makefile
456719 security/botan2/Makefile

(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 ] Original commit   Revision:455167
455167 archivers/snappy-java/Makefile
455167 astro/tkgeomap/Makefile
455167 audio/beast/Makefile
455167 audio/bristol/Makefile
455167 audio/deadbeef/Makefile
455167 audio/funktrackergold/Makefile
455167 audio/gervill/Makefile
455167 audio/gstreamer-plugins-taglib/Makefile
455167 audio/gstreamer1-plugins-taglib/Makefile
455167 audio/xmcd/Makefile

(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 ] Original commit   Revision:441847
441847 audio/vsound/Makefile
441847 biology/bedtools/Makefile
441847 cad/layouteditor/Makefile
441847 databases/sqliteodbc-sqlite2/Makefile
441847 databases/tarantool/Makefile
441847 databases/xtrabackup/Makefile
441847 devel/dmucs/Makefile
441847 devel/dyncall/Makefile
441847 devel/lpc21isp/Makefile
441847 devel/obby/Makefile

(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 ] Original commit   Revision:420587
420587 biology/bedtools/Makefile
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 ] Original commit   Revision:406676
406676 biology/Makefile
406676 biology/bedtools
406676 biology/bedtools/Makefile
406676 biology/bedtools/distinfo
406676 biology/bedtools/files
406676 biology/bedtools/files/patch-Makefile
406676 biology/bedtools/pkg-descr
406676 biology/bedtools/pkg-plist
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 XX: 15

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