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Two new features

Two new features were added on 2020-05-30:
  1. Repology links - each port now has a link to repology.org. See issue 148 for details.
  2. Ports I maintain report - port maintainers can now subscribe to a daily report of commits to the ports they maintain. See Watch ports I maintain at Report Subscriptions. Details at issue 138
non port: biology/kallisto/Makefile
SVNWeb

Number of commits found XX: 13

Mon, 3 Aug 2020
[ 15:45 jwb ] Original commit   Revision:544077
544077 biology/kallisto/Makefile
544077 biology/kallisto/distinfo
544077 biology/kallisto/files/patch-CMakeLists.txt
544077 biology/kallisto/files/patch-ext_htslib_configure.ac
544077 biology/kallisto/files/patch-src_CMakeLists.txt
biology/kallisto: Revert to 0.46.1

0.46.2 has long-standing regressions that are not being addressed, including
a seg fault when using --genomebam.
Also revert to bundled htslib in preparation for biology/htslib upgrade
to 1.10.  Kallisto source contains modified bits of htslib 1.4.1 that are
incompatible with htslib > 1.9.
Wed, 1 Apr 2020
[ 23:35 jwb ] Original commit   Revision:530250
530250 biology/kallisto/Makefile
530250 biology/kallisto/files/patch-src_Bootstrap.h
kallisto: Patch for build with GCC

PR:             ports/245240
Submitted by:   pkubaj
Sat, 15 Feb 2020
[ 23:09 jwb ] Original commit   Revision:526244
526244 biology/kallisto/Makefile
526244 biology/kallisto/distinfo
biology/kallisto: Upgrade to 0.46.2

Kallisto no longer builds in hdf5 by default, but it is still required
for some downstream tools like Sleuth.  Forcing it ON for now, but will
disable it in a future upgrade.

Reported by:    portscout
Wed, 6 Nov 2019
[ 00:18 jwb ] Original commit   Revision:516853
516853 biology/kallisto/Makefile
516853 biology/kallisto/distinfo
biology/kallisto: Upgrade to 0.46.1

Minor bug fixes and enhancements

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
Wed, 12 Jun 2019
[ 15:24 jwb ] Original commit   Revision:504011
504011 biology/kallisto/Makefile
504011 biology/kallisto/distinfo
biology/kallisto: Upgrade to 0.46.0

Reported by:    portscout
Sun, 24 Feb 2019
[ 20:32 jwb ] Original commit   Revision:493810
493810 biology/kallisto/Makefile
493810 biology/kallisto/distinfo
493810 biology/kallisto/files/kallisto-test.in
493810 biology/kallisto/files/patch-CMakeLists.txt
493810 biology/kallisto/files/patch-src_CMakeLists.txt
kallisto: Upgrade to 0.45.1, unbundle hstlib
Sat, 5 Jan 2019
[ 22:46 sunpoet ] Original commit   Revision:489412
489412 audio/csound/Makefile
489412 biology/kallisto/Makefile
489412 cad/freecad/Makefile
489412 cad/gmsh/Makefile
489412 devel/py-tables/Makefile
489412 graphics/alembic/Makefile
489412 graphics/blender/Makefile
489412 graphics/caffe/Makefile
489412 graphics/gdal/Makefile
489412 graphics/opencv/Makefile

(Only the first 10 of 61 ports in this commit are shown above. View all ports for this commit)
Update science/hdf5 to 1.10.4

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://portal.hdfgroup.org/display/support/HDF5%201.10.4#releasenotes
PR:		233070
Submitted by:	wen
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
Wed, 5 Sep 2018
[ 22:05 sunpoet ] Original commit   Revision:479046
479046 audio/csound6/Makefile
479046 biology/kallisto/Makefile
479046 cad/freecad/Makefile
479046 cad/gmsh/Makefile
479046 devel/py-tables/Makefile
479046 graphics/alembic/Makefile
479046 graphics/blender/Makefile
479046 graphics/caffe/Makefile
479046 graphics/opencv/Makefile
479046 graphics/openimageio/Makefile

(Only the first 10 of 50 ports in this commit are shown above. View all ports for this commit)
Update science/hdf5 to 1.10.2

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://portal.hdfgroup.org/display/support/HDF5%201.10.2#releasenotes
		https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.2/src/hdf5-1.10.2-RELEASE.txt
PR:		231009
Exp-run by:	antoine
Sun, 29 Jul 2018
[ 22:18 gerald ] Original commit   Revision:475857
475857 Mk/bsd.ruby.mk
475857 accessibility/atkmm/Makefile
475857 archivers/brotli/Makefile
475857 archivers/c-blosc/Makefile
475857 archivers/innoextract/Makefile
475857 archivers/kf5-karchive/Makefile
475857 archivers/lazperf/Makefile
475857 archivers/libpar2/Makefile
475857 archivers/paq/Makefile
475857 archivers/pxz/Makefile

(Only the first 10 of 1480 ports in this commit are shown above. View all ports for this commit)
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542
Sat, 2 Jun 2018
[ 19:40 linimon ] Original commit   Revision:471400
471400 archivers/lazperf/Makefile
471400 audio/libmusicxml/Makefile
471400 biology/kallisto/Makefile
471400 databases/xapian-core/Makefile
471400 deskutils/tasksh/Makefile
471400 deskutils/timewarrior/Makefile
471400 devel/courier-unicode/Makefile
471400 devel/easyloggingpp/Makefile
471400 devel/glibmm-reference/Makefile
471400 devel/hexd/Makefile

(Only the first 10 of 29 ports in this commit are shown above. View all ports for this commit)
Adjust USES to fix building on gcc-based archs (in particular, powerpc64).

On the clang architectures, these changes have no effect: the baser
compiler already includes the needed features.

While here, remove now-redundant CXXFLAGS statements and pet portlint
(no other content change).

Tested on both powerpc64 and amd64.

Approved by:	portmgr (tier-2 blanket)
Sat, 2 Dec 2017
[ 20:44 jwb ] Original commit   Revision:455382
455382 biology/Makefile
455382 biology/kallisto
455382 biology/kallisto/Makefile
455382 biology/kallisto/distinfo
455382 biology/kallisto/files
455382 biology/kallisto/files/kallisto-test.in
455382 biology/kallisto/pkg-descr
[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq
data

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13328

Number of commits found XX: 13

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