*/*: sync with upstream

Taken from: HardenedBSD

accessibility/qt5-speech/Makefile

@@ -2,15 +2,31 @@
 
 PORTNAME=	speech
 DISTVERSION=	${QT5_VERSION}
+PORTREVISION=	1
 CATEGORIES=	accessibility
 PKGNAMEPREFIX=	qt5-
 
 MAINTAINER=	kde@FreeBSD.org
 COMMENT=	Accessibilty features for Qt5
 
-LIB_DEPENDS=	libspeechd.so:accessibility/speech-dispatcher
+USES=		compiler:c++11-lang gl pkgconfig qmake:outsource qt-dist:5,speech
-
+USE_GL=		gl
-USES=		compiler:c++11-lang pkgconfig qmake:outsource qt-dist:5,speech
 USE_QT=		core gui buildtools_build qmake_build
 
+OPTIONS_MULTI=		BACKEND
+OPTIONS_MULTI_BACKEND=	SPEECHD FLITE
+OPTIONS_DEFAULT=	SPEECHD
+OPTIONS_SUB=		yes
+
+SPEECHD_DESC=		Speech Dispatcher Backend
+SPEECHD_USES=		gettext-runtime gnome
+SPEECHD_USE=		GNOME=glib20
+SPEECHD_LIB_DEPENDS=	libspeechd.so:accessibility/speech-dispatcher
+SPEECHD_QMAKE_ON=	CONFIG+=with_speechd
+
+FLITE_DESC=		Festival Lite Backend
+FLITE_LIB_DEPENDS=	libflite.so:audio/flite
+FLITE_USE=		QT=multimedia,network
+FLITE_QMAKE_ON=		CONFIG+=with_flite
+
 .include <bsd.port.mk>

accessibility/qt5-speech/files/patch-qtspeech.pro

@@ -0,0 +1,18 @@
+--- qtspeech.pro.orig	2019-02-16 08:32:35 UTC
++++ qtspeech.pro
+@@ -1,7 +1,11 @@
+ load(configure)
+-qtCompileTest(flite)
+-qtCompileTest(flite_alsa)
+-!packagesExist(speech-dispatcher) {
+-    qtCompileTest(speechd)
++with_flite {
++	qtCompileTest(flite)
++	qtCompileTest(flite_alsa)
++}
++with_speechd {
++	!packagesExist(speech-dispatcher) {
++	    qtCompileTest(speechd)
++	}
+ }
+ load(qt_parts)

accessibility/qt5-speech/files/patch-src_plugins_tts_tts.pro

@@ -0,0 +1,31 @@
+--- src/plugins/tts/tts.pro.orig	2019-02-16 08:43:06 UTC
++++ src/plugins/tts/tts.pro
+@@ -1,10 +1,12 @@
+ TEMPLATE = subdirs
+ 
+-unix {
+-    CONFIG += link_pkgconfig
+-    config_speechd | packagesExist(speech-dispatcher) {
+-        SUBDIRS += speechdispatcher
+-    }
++with_speechd {
++	unix {
++	    CONFIG += link_pkgconfig
++	    config_speechd | packagesExist(speech-dispatcher) {
++	        SUBDIRS += speechdispatcher
++	    }
++	}
+ }
+ 
+ windows:!winrt: SUBDIRS += sapi
+@@ -15,6 +17,8 @@ uikit: SUBDIRS += ios
+ 
+ android: SUBDIRS += android
+ 
+-config_flite | config_flite_alsa {
+-    SUBDIRS += flite
++with_flite {
++	config_flite | config_flite_alsa {
++	    SUBDIRS += flite
++	}
+ }

accessibility/qt5-speech/pkg-plist

@@ -15,7 +15,8 @@
 %%QT_INCDIR%%/QtTextToSpeech/qvoice.h
 %%QT_CMAKEDIR%%/Qt5TextToSpeech/Qt5TextToSpeechConfig.cmake
 %%QT_CMAKEDIR%%/Qt5TextToSpeech/Qt5TextToSpeechConfigVersion.cmake
-%%QT_CMAKEDIR%%/Qt5TextToSpeech/Qt5TextToSpeech_QTextToSpeechPluginSpeechd.cmake
+%%FLITE%%%%QT_CMAKEDIR%%/Qt5TextToSpeech/Qt5TextToSpeech_QTextToSpeechEngineFlite.cmake
+%%SPEECHD%%%%QT_CMAKEDIR%%/Qt5TextToSpeech/Qt5TextToSpeech_QTextToSpeechPluginSpeechd.cmake
 %%QT_LIBDIR%%/libQt5TextToSpeech.prl
 %%QT_LIBDIR%%/libQt5TextToSpeech.so
 %%QT_LIBDIR%%/libQt5TextToSpeech.so.5
@@ -24,6 +25,8 @@
 %%DEBUG%%%%QT_LIBDIR%%/libQt5TextToSpeech.so.%%FULLVER%%.debug
 %%QT_MKSPECDIR%%/modules/qt_lib_texttospeech.pri
 %%QT_MKSPECDIR%%/modules/qt_lib_texttospeech_private.pri
-%%QT_PLUGINDIR%%/texttospeech/libqtexttospeech_speechd.so
+%%FLITE%%%%QT_PLUGINDIR%%/texttospeech/libqttexttospeech_flite.so
-%%DEBUG%%%%QT_PLUGINDIR%%/texttospeech/libqtexttospeech_speechd.so.debug
+%%FLITE%%%%DEBUG%%%%QT_PLUGINDIR%%/texttospeech/libqttexttospeech_flite.so.debug
+%%SPEECHD%%%%QT_PLUGINDIR%%/texttospeech/libqtexttospeech_speechd.so
+%%SPEECHD%%%%DEBUG%%%%QT_PLUGINDIR%%/texttospeech/libqtexttospeech_speechd.so.debug
 libdata/pkgconfig/Qt5TextToSpeech.pc

accessibility/rubygem-atk/Makefile

@@ -1,7 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	atk
-PORTVERSION=	3.3.1
+PORTVERSION=	3.3.2
 CATEGORIES=	accessibility rubygems
 MASTER_SITES=	RG
 

accessibility/rubygem-atk/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1547380579
+TIMESTAMP = 1550388827
-SHA256 (rubygem/atk-3.3.1.gem) = 3ca54d41d51af914a362f80844601e0028e8a007845fb6d47369f68b66ef7170
+SHA256 (rubygem/atk-3.3.2.gem) = 001cd0c39a4f1a66a3a9e607b6fbdca052a3dc99f98a1ee55ad484e7798f859d
-SIZE (rubygem/atk-3.3.1.gem) = 15872
+SIZE (rubygem/atk-3.3.2.gem) = 15872

archivers/py-brotli/Makefile

@@ -3,7 +3,7 @@
 
 PORTNAME=	brotli
 PORTVERSION=	1.0.7
-PORTREVISION=	1
+PORTREVISION=	2
 DISTVERSIONPREFIX=	v
 CATEGORIES=	archivers
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
@@ -17,15 +17,12 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 USES=		compiler:c++0x python shebangfix
 USE_PYTHON=	autoplist concurrent distutils
 
-PLIST_FILES=	bin/brotli
-
 GH_ACCOUNT=	google
 USE_GITHUB=	yes
 
 SHEBANG_FILES=	python/bro.py
 
 post-install:
-	${INSTALL_SCRIPT} ${WRKSRC}/python/bro.py ${STAGEDIR}${PREFIX}/bin/brotli
 	${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/_brotli.so
 
 .include <bsd.port.mk>

archivers/zip-ada/Makefile

@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	zip-ada
-PORTVERSION=	52
+DISTVERSION=	55
-PORTREVISION=	1
 CATEGORIES=	archivers
 MASTER_SITES=	SF/unzip-ada/
 DISTNAME=	zipada${PORTVERSION}
@@ -17,33 +16,11 @@ USES=		ada perl5 dos2unix zip
 USE_PERL5=	build
 WRKSRC=		${WRKDIR}/zip-ada
 MAKE_ENV+=	Build_Mode=Fast
-ZTOOLS=		zipada \
+
-		comp_zip \
+ZTOOLS=		bunzip bwt_dec bwt_enc comp_zip find_zip lzhuf \
-		find_zip \
+		lzma_dec lzma_enc rezip unzipada zipada
-		rezip \
+
-		za_gnat \
+DEMOS=		bwt_demo demo_csv_into_zip demo_unzip demo_zip
-		rz_gnat \
-		bunzip \
-		lz \
-		lzma_dec \
-		lzma_enc \
-		lz77_stats \
-		random_data \
-		several_sizes
-DEMOS=		demo_csv_into_zip \
-		demo_zip \
-		demo_unzip \
-		test_unz_streams \
-		test_chunk \
-		ziptest \
-		zip_with_many_files \
-		test_zip_info_timing \
-		test_stream_performance \
-		test_extract \
-		test_extract_tb \
-		test_lz_scramble \
-		test_llhc \
-		test_lz77
 
 OPTIONS_DEFINE=	EXAMPLES
 

archivers/zip-ada/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1475885730
+TIMESTAMP = 1550385910
-SHA256 (zipada52.zip) = f28ed2b99b70b095dc73b3cf4eab8c8ac4ae9bcb488992da36aa5b68d2dea719
+SHA256 (zipada55.zip) = 4309ba2677ca9e11ef29395f8cb569eab79bf63fd45d318fbe63d9fa976310c2
-SIZE (zipada52.zip) = 859223
+SIZE (zipada55.zip) = 1047285

archivers/zip-ada/pkg-plist

@@ -1,18 +1,18 @@
+bin/bwt_dec
+bin/bwt_enc
 bin/comp_zip
 bin/debzip2
 bin/find_zip
-bin/lz
+bin/lzhuf
-bin/lz77_stats
 bin/lzma_dec
 bin/lzma_enc
-bin/random_data
 bin/rezip
-bin/rz_gnat
+bin/unzipada
-bin/several_sizes
-bin/za_gnat
 bin/zipada
-include/zip-ada/bzip2_decoding.adb
+include/zip-ada/bzip2-decoding.adb
-include/zip-ada/bzip2_decoding.ads
+include/zip-ada/bzip2-decoding.ads
+include/zip-ada/bzip2.adb
+include/zip-ada/bzip2.ads
 include/zip-ada/length_limited_huffman_code_lengths.adb
 include/zip-ada/length_limited_huffman_code_lengths.ads
 include/zip-ada/lz77.adb
@@ -40,7 +40,6 @@ include/zip-ada/zip-compress-shrink.adb
 include/zip-ada/zip-compress-shrink.ads
 include/zip-ada/zip-compress.adb
 include/zip-ada/zip-compress.ads
-include/zip-ada/zip-compress__no_unsigned_64.adb
 include/zip-ada/zip-crc_crypto.adb
 include/zip-ada/zip-crc_crypto.ads
 include/zip-ada/zip-create.adb
@@ -52,23 +51,26 @@ include/zip-ada/zip.ads
 include/zip-ada/zip_streams.adb
 include/zip-ada/zip_streams.ads
 lib/gnat/zip-ada.gpr
-lib/zip-ada/bzip2_decoding.ali
+lib/zip-ada/bwt.ali
+lib/zip-ada/bzip2-decoding.ali
+lib/zip-ada/bzip2.ali
 lib/zip-ada/comp_zip_prc.ali
 lib/zip-ada/dual_io.ali
 lib/zip-ada/flexible_temp_files.ali
 lib/zip-ada/length_limited_huffman_code_lengths.ali
 lib/zip-ada/libzip-ada.a
 lib/zip-ada/lz77.ali
-lib/zip-ada/lz_scramble.ali
 lib/zip-ada/lzh.ali
 lib/zip-ada/lzma-decoding.ali
 lib/zip-ada/lzma-encoding.ali
 lib/zip-ada/lzma.ali
 lib/zip-ada/my_dots.ali
 lib/zip-ada/my_feedback.ali
+lib/zip-ada/my_get_password.ali
+lib/zip-ada/my_resolve_conflict.ali
+lib/zip-ada/my_tell_data.ali
 lib/zip-ada/rezip_lib.ali
-lib/zip-ada/rw_file.ali
+lib/zip-ada/summary.ali
-lib/zip-ada/tb_wrap.ali
 lib/zip-ada/unzip-decompress-huffman.ali
 lib/zip-ada/unzip-decompress.ali
 lib/zip-ada/unzip-streams.ali
@@ -83,17 +85,7 @@ lib/zip-ada/zip-create.ali
 lib/zip-ada/zip-headers.ali
 lib/zip-ada/zip.ali
 lib/zip-ada/zip_streams.ali
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bwt_demo
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/demo_csv_into_zip
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/demo_unzip
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/demo_zip
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test_chunk
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test_extract
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test_extract_tb
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test_llhc
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test_lz77
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test_lz_scramble
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test_stream_performance
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test_unz_streams
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test_zip_info_timing
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/zip_with_many_files
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ziptest

astro/mkgmap/Makefile

@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	mkgmap
-PORTVERSION=	r4271
+PORTVERSION=	r4278
 CATEGORIES=	astro converters java
 MASTER_SITES=	http://www.mkgmap.org.uk/download/ \
 		http://mirror.amdmi3.ru/distfiles/

astro/mkgmap/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1549989456
+TIMESTAMP = 1550501924
-SHA256 (mkgmap-r4271.tar.gz) = a1fa3bfca70a4740a2fad0a61cef902f2e38e7b9238b3ce41c27e57993b934b3
+SHA256 (mkgmap-r4278.tar.gz) = 2b024b31fc6df3a162c56a1e1b873bc4b78d1f0561fed9a1d0bc76b94af2b95e
-SIZE (mkgmap-r4271.tar.gz) = 3395854
+SIZE (mkgmap-r4278.tar.gz) = 3397001

astro/opencpn/Makefile

@@ -11,6 +11,8 @@ COMMENT=	Concise ChartPlotter/Navigator
 
 LICENSE=	GPLv2+
 
+BROKEN_aarch64=		Fails to compile: use of undeclared identifier rand
+
 LIB_DEPENDS=	libportaudio.so:audio/portaudio \
 		libcurl.so:ftp/curl \
 		libexpat.so:textproc/expat2 \
@@ -20,7 +22,7 @@ USE_GITHUB=	yes
 GH_ACCOUNT=	${GH_PROJECT}
 GH_PROJECT=	OpenCPN
 
-USES=		cmake compiler:c++11-lib gettext-tools localbase
+USES=		cmake compiler:c++11-lib gettext-tools gl gnome localbase
 USE_CXXSTD=	c++11
 USE_GL=		gl
 USE_GNOME=	cairo gdkpixbuf2 gtk20
@@ -32,8 +34,6 @@ CMAKE_ARGS=	-DBUNDLE_DOCS=ON -DBUNDLE_GSHHS=CRUDE -DBUNDLE_TCDATA=ON
 LDFLAGS+=	-Wl,-E # plugins
 LDFLAGS+=	-Wl,--as-needed # ICE, SM, Xext
 
-BROKEN_aarch64=		Fails to compile: use of undeclared identifier rand
-
 OPTIONS_DEFINE=	DOCS
 
 post-patch:
@@ -41,5 +41,9 @@ post-patch:
 		${WRKSRC}/src/mygdal/cpl_csv.cpp \
 		${WRKSRC}/src/mygdal/cpl_findfile.cpp \
 		${WRKSRC}/data/doc/help_en_US.html
+.if exists(/usr/lib/libstdc++.so)
+	@${REINPLACE_CMD} -e '/-msse/d' -e '/-mssse3/d' \
+		-e '/-mavx2/d' ${WRKSRC}/CMakeLists.txt
+.endif
 
 .include <bsd.port.mk>

astro/qmapshack/Makefile

@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	qmapshack
-PORTVERSION=	1.12.1
+PORTVERSION=	1.12.3
-PORTREVISION=	1
 CATEGORIES=	astro
 MASTER_SITES=	https://bitbucket.org/maproom/qmapshack/downloads/
 

astro/qmapshack/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1546180082
+TIMESTAMP = 1549642588
-SHA256 (qmapshack-1.12.1.tar.gz) = 6208e1fcb531a8b9580064e5314782c6f5b71158b4e841b80babeb09663fd6b4
+SHA256 (qmapshack-1.12.3.tar.gz) = 3d4ffbfa34c41d85d2a46d0d2a6c5254c305aa4ae137c253e6913f82097fe5fa
-SIZE (qmapshack-1.12.1.tar.gz) = 12033026
+SIZE (qmapshack-1.12.3.tar.gz) = 12029443

astro/viking/pkg-descr

@@ -5,4 +5,4 @@ Terraserver, Bing Aerial and other maps in it, download geocaches for
 an area on the map, make new tracks and waypoints, geotag images,
 see real-time GPS position, etc.
 
-WWW: http://sourceforge.net/apps/mediawiki/viking/index.php
+WWW: https://sourceforge.net/p/viking/wikiallura/Main_Page/

astro/xplanet/Makefile

@@ -7,7 +7,7 @@ PORTREVISION=	11
 CATEGORIES=	astro geography
 MASTER_SITES=	SF
 
-MAINTAINER=	novel@FreeBSD.org
+MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Draw pictures of the earth textured by an image
 
 GNU_CONFIGURE=	yes

audio/Makefile

@@ -906,6 +906,7 @@
     SUBDIR += zinf
     SUBDIR += zita-convolver
     SUBDIR += zita-resampler
+    SUBDIR += zrythm
     SUBDIR += zynaddsubfx
 
 .include <bsd.port.subdir.mk>

audio/amarok/Makefile

@@ -25,7 +25,7 @@ USES=		cmake compiler:c++11-lang desktop-file-utils \
 		kde:5 mysql:client,embedded pkgconfig qt:5 shebangfix ssl
 
 USE_QT=		core concurrent declarative dbus gui location network phonon4 \
-		quickcontrols2 script scripttools sql svg webchannel webengine \
+		quickcontrols2 script scripttools sql svg webchannel \
 		webkit widgets xml \
 		buildtools_build qmake_build
 
@@ -49,8 +49,10 @@ CMAKE_OFF=	WITH_FFmpeg
 
 BROKEN_sparc64=	does not build (GCC-related error)
 
-OPTIONS_DEFINE=		IPOD MP3TUNES MTP
+OPTIONS_DEFINE=		IPOD MP3TUNES MTP QTWEBENGINE
 OPTIONS_DEFAULT=	IPOD MP3TUNES MTP
+OPTIONS_DEFAULT_amd64=	QTWEBENGINE
+OPTIONS_DEFAULT_i386=	QTWEBENGINE
 OPTIONS_SUB=		yes
 
 IPOD_DESC=		Apple iPod support
@@ -73,6 +75,10 @@ MP3TUNES_CMAKE_BOOL_OFF=	WITH_Libgcrypt
 MTP_LIB_DEPENDS=	libmtp.so:multimedia/libmtp
 MTP_CMAKE_BOOL_OFF=	CMAKE_DISABLE_FIND_PACKAGE_Mtp
 
+QTWEBENGINE_DESC=	Add dependency on qt5-webengine
+QTWEBENGINE_USE=	qt=webengine
+QTWEBENGINE_CMAKE_BOOL_OFF=	CMAKE_DISABLE_FIND_PACKAGE_Qt5WebEngine
+
 post-patch:
 	@${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|' \
 		${WRKSRC}/cmake/modules/FindMySQL.cmake

audio/amarok/pkg-plist

@@ -56,12 +56,12 @@ lib/libampache_account_login.so
 %%QT_QMLDIR%%/org/kde/amarok/qml/AppletHeader.qml
 %%QT_QMLDIR%%/org/kde/amarok/qml/libqml_plugin.so
 %%QT_QMLDIR%%/org/kde/amarok/qml/qmldir
-%%QT_QMLDIR%%/org/kde/amarok/wikipedia/libamarok_context_applet_wikipedia.so
+%%QTWEBENGINE%%%%QT_QMLDIR%%/org/kde/amarok/wikipedia/libamarok_context_applet_wikipedia.so
-%%QT_QMLDIR%%/org/kde/amarok/wikipedia/qmldir
+%%QTWEBENGINE%%%%QT_QMLDIR%%/org/kde/amarok/wikipedia/qmldir
 %%DATADIR%%/data/DefaultPlaylistLayouts.xml
 %%DATADIR%%/data/InfoParserLoading.html
-%%DATADIR%%/data/WikipediaCustomStyle.css
+%%QTWEBENGINE%%%%DATADIR%%/data/WikipediaCustomStyle.css
-%%DATADIR%%/data/bullet.gif
+%%QTWEBENGINE%%%%DATADIR%%/data/bullet.gif
 %%DATADIR%%/data/first_run_jingle.ogg
 %%DATADIR%%/data/hover_info_template.html
 %%DATADIR%%/data/podcast_directory.opml
@@ -433,8 +433,8 @@ share/kpackage/amarok/org.kde.amarok.lyrics/contents.rcc
 share/kpackage/amarok/org.kde.amarok.lyrics/metadata.json
 share/kpackage/amarok/org.kde.amarok.photos/contents.rcc
 share/kpackage/amarok/org.kde.amarok.photos/metadata.json
-share/kpackage/amarok/org.kde.amarok.wikipedia/contents.rcc
+%%QTWEBENGINE%%share/kpackage/amarok/org.kde.amarok.wikipedia/contents.rcc
-share/kpackage/amarok/org.kde.amarok.wikipedia/metadata.json
+%%QTWEBENGINE%%share/kpackage/amarok/org.kde.amarok.wikipedia/metadata.json
 share/kpackage/genericqml/org.kde.amarok.context/contents.rcc
 share/kpackage/genericqml/org.kde.amarok.context/metadata.json
 share/kservices5/ServiceMenus/amarok_append.desktop

audio/beets/Makefile

@@ -3,7 +3,7 @@
 
 PORTNAME=	beets
 PORTVERSION=	1.4.7
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	audio python
 MASTER_SITES=	CHEESESHOP
 
@@ -14,7 +14,7 @@ LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}jellyfish>=0:devel/py-jellyfish@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}munkres>=0:math/py-munkres@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}munkres10>=0:math/py-munkres10@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}musicbrainzngs>=0.4:audio/py-musicbrainzngs@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}mutagen>=1.33:audio/py-mutagen@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}six>=1.9:devel/py-six@${PY_FLAVOR} \

audio/fmit/Makefile

@@ -4,43 +4,41 @@
 PORTNAME=	fmit
 PORTVERSION=	1.2.6
 DISTVERSIONPREFIX=	v
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	audio
 
 MAINTAINER=	danilo@FreeBSD.org
 COMMENT=	Free Music Instrument Tuner
 
-LICENSE=	GPLv2
+LICENSE=	GPLv2 LGPL21
+LICENSE_COMB=	multi
+LICENSE_FILE_GPLv2=	${WRKSRC}/COPYING_GPL.txt
+LICENSE_FILE_LGPL21=	${WRKSRC}/COPYING_LGPL.txt
 
 LIB_DEPENDS=	libfftw3.so:math/fftw3
 
 USES=		gl gnome pkgconfig qmake qt:5 tar:bzip2
 
-USE_QT=		buildtools core gui opengl qmake_build multimedia network svg widgets
+USE_QT=		buildtools_build core gui opengl qmake_build multimedia network svg widgets
 USE_GL=		gl glut
-QMAKE_ARGS+=	PREFIXSHORTCUT=${PREFIX}
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	gillesdegottex
 
-OPTIONS_DEFINE=	ALSA JACK OSS PORTAUDIO
+QMAKE_ARGS+=	PREFIXSHORTCUT=${PREFIX}
+
+OPTIONS_DEFINE=		ALSA JACK OSS PORTAUDIO
 OPTIONS_DEFAULT=	JACK OSS
 
-OPTIONS_SUB=	yes
+ALSA_LIB_DEPENDS=	libasound.so:audio/alsa-lib
+ALSA_QMAKE_ON=		CONFIG+=acs_alsa
 
-ALSA_LIB_DEPENDS=	libasound.so.2:audio/alsa-lib
+OSS_QMAKE_ON=		CONFIG+=acs_oss
-ALSA_CMAKE_ON=		-DSOUNDSYSTEM_USE_ALSA:BOOL=true
-ALSA_CMAKE_OFF=		-DSOUNDSYSTEM_USE_ALSA:BOOL=false
-
-OSS_CMAKE_ON=		-DSOUNDSYSTEM_USE_OSS:BOOL=true
-OSS_CMAKE_OFF=		-DSOUNDSYSTEM_USE_OSS:BOOL=false
 
 JACK_LIB_DEPENDS=	libjack.so:audio/jack
-JACK_CMAKE_ON=		-DSOUNDSYSTEM_USE_JACK:BOOL=true
+JACK_QMAKE_ON=		CONFIG+=acs_jack
-JACK_CMAKE_OFF=		-DSOUNDSYSTEM_USE_JACK:BOOL=false
 
 PORTAUDIO_LIB_DEPENDS=	libportaudio.so:audio/portaudio
-PORTAUDIO_CMAKE_ON=	-DSOUNDSYSTEM_USE_PORTAUDIO:BOOL=true
+PORTAUDIO_QMAKE_ON=	CONFIG+=acs_portaudio
-PORTAUDIO_CMAKE_OFF=	-DSOUNDSYSTEM_USE_PORTAUDIO:BOOL=false
 
 .include <bsd.port.mk>

audio/giada/Makefile

@@ -28,7 +28,7 @@ USES=		autoreconf compiler:c++11-lang gmake localbase
 USE_GITHUB=	yes
 GH_ACCOUNT=	monocasual
 GNU_CONFIGURE=	yes
-CONFIGURE_ARGS=	--target=freebsd
+CONFIGURE_ARGS=	--target=${OPSYS:tl}
 USE_XORG=	x11 xext xft xpm
 LDFLAGS+=	-lfltk
 

audio/giada/files/patch-src_core_init.cpp

@@ -0,0 +1,10 @@
+--- src/core/init.cpp.orig	2019-02-22 10:29:43 UTC
++++ src/core/init.cpp
+@@ -25,6 +25,7 @@
+  * -------------------------------------------------------------------------- */
+ 
+ 
++#include <atomic>
+ #include <thread>
+ #include <ctime>
+ #ifdef __APPLE__

audio/gsequencer/Makefile

@@ -1,7 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	gsequencer
-DISTVERSION=	2.1.53
+DISTVERSION=	2.1.60
 CATEGORIES=	audio
 MASTER_SITES=	SAVANNAH/gsequencer/2.1.x
 
@@ -36,6 +36,8 @@ LDFLAGS+=	-luuid
 
 INSTALLS_ICONS=	yes
 
+PLIST_SUB=	PORTVERSION=${PORTVERSION}
+
 OPTIONS_DEFINE=			JACK PULSEAUDIO
 
 JACK_CONFIGURE_ENABLE=		jack

audio/gsequencer/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1549941919
+TIMESTAMP = 1550819967
-SHA256 (gsequencer-2.1.53.tar.gz) = 0a0944912ef019b3a8bc64a0fc63465f69885a256f7200f4723cd4fc1de50fc2
+SHA256 (gsequencer-2.1.60.tar.gz) = 25824a7c2a1ccce470538faff1533623c38d9ca2ed1744e6eab08e803a86ea64
-SIZE (gsequencer-2.1.53.tar.gz) = 5082278
+SIZE (gsequencer-2.1.60.tar.gz) = 5096237

audio/gsequencer/files/patch-Makefile.in

@@ -0,0 +1,20 @@
+--- Makefile.in.orig	2019-02-17 01:56:10 UTC
++++ Makefile.in
+@@ -5957,7 +5957,7 @@ nobase_include_HEADERS = $(libags_la_HEA
+ 
+ # doc
+ # docdir = $(datadir)/doc/gsequencer
+-doc_DATA = README ags_example.xml
++#doc_DATA = README ags_example.xml
+ 
+ # documentation
+ manpages = \
+@@ -23930,7 +23930,7 @@ install-data-local:
+ 	install -c -p -m 644 $(top_srcdir)/application-x-gsequencer.xml $(DESTDIR)/$(datadir)/mime/packages/gsequencer.xml
+ 	install -c -p -m 644 $(top_srcdir)/gsequencer.appdata.xml $(DESTDIR)/$(datadir)/metainfo/
+ 	mkdir -p $(DESTDIR)/$(docdir)/
+-	gzip -9 -c $(top_srcdir)/ChangeLog > $(DESTDIR)/$(docdir)/changelog.gz
++	#gzip -9 -c $(top_srcdir)/ChangeLog > $(DESTDIR)/$(docdir)/changelog.gz
+ 
+ fix-local-html: html
+ 	find $(top_srcdir)/docs/reference/libags/libags-html -name "*.html" -type f -exec sed -i 's/\.\.\/gobject/\/usr\/share\/doc\/libglib2.0-doc\/gobject/g' {} \;

audio/gsequencer/pkg-plist

@@ -421,11 +421,11 @@ share/icons/hicolor/128x128/apps/gsequencer.png
 share/icons/hicolor/32x32/apps/gsequencer.png
 share/icons/hicolor/48x48/apps/gsequencer.png
 share/icons/hicolor/64x64/apps/gsequencer.png
-share/metainfo/gsequencer.appdata.xml
+share/metainfo/org.nongnu.gsequencer.gsequencer.appdata.xml
 share/mime/packages/gsequencer.xml
-share/xml/gsequencer/schema/dtd/2.1.53/ags_file.dtd
+share/xml/gsequencer/schema/dtd/%%PORTVERSION%%/ags_file.dtd
-share/xml/gsequencer/schema/dtd/2.1.53/ags_midi_file.dtd
+share/xml/gsequencer/schema/dtd/%%PORTVERSION%%/ags_midi_file.dtd
-share/xml/gsequencer/schema/dtd/2.1.53/ags_osc_file.dtd
+share/xml/gsequencer/schema/dtd/%%PORTVERSION%%/ags_osc_file.dtd
-share/xml/gsequencer/schema/dtd/2.1.53/ags_simple_file.dtd
+share/xml/gsequencer/schema/dtd/%%PORTVERSION%%/ags_simple_file.dtd
 share/xml/gsequencer/stylesheet/ags-xsl/midi-xml/ags-simple.xsl
 share/xml/gsequencer/stylesheet/ags-xsl/midi-xml/ags.xsl

audio/libcdaudio/Makefile

@@ -7,7 +7,7 @@ PORTREVISION=	3
 CATEGORIES=	audio
 MASTER_SITES=	SF
 
-MAINTAINER=	novel@FreeBSD.org
+MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Library for playing audio CDs
 
 USES=		libtool pathfix pkgconfig

audio/musicpd/Makefile

@@ -1,8 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	musicpd
-PORTVERSION=	0.21.4
+PORTVERSION=	0.21.5
-PORTREVISION=	1
 CATEGORIES=	audio ipv6
 MASTER_SITES=	https://www.musicpd.org/download/mpd/${PORTVERSION:R}/
 DISTNAME=	mpd-${PORTVERSION}

audio/musicpd/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1547301787
+TIMESTAMP = 1550922923
-SHA256 (mpd-0.21.4.tar.xz) = 247112eabf1b818a4052db7f0f5917ab00831ebc60a1ec3bf1154da4dc16a5c7
+SHA256 (mpd-0.21.5.tar.xz) = 2ea9f0eb3a7bdae5d705adf4e8ec45ef38b5b9ddf133f32b8926dd4e205b0ef9
-SIZE (mpd-0.21.4.tar.xz) = 663648
+SIZE (mpd-0.21.5.tar.xz) = 667624

audio/musicpd/files/patch-src_lib_cdio_Paranoia.hxx

@@ -0,0 +1,11 @@
+--- src/lib/cdio/Paranoia.hxx.orig	2019-02-22 14:23:33 UTC
++++ src/lib/cdio/Paranoia.hxx
+@@ -43,6 +43,8 @@
+ #include <stdexcept>
+ #include <utility>
+ 
++#include <cstdio>
++
+ class CdromDrive {
+ 	cdrom_drive_t *drv = nullptr;
+ 

audio/musicpd/files/patch-src_zeroconf_meson.build

@@ -1,20 +0,0 @@
---- src/zeroconf/meson.build.orig	2019-01-04 18:22:21 UTC
-+++ src/zeroconf/meson.build
-@@ -30,10 +30,14 @@ if zeroconf_option == 'bonjour'
-   if not compiler.has_header('dns_sd.h')
-     error('dns_sd.h not found')
-   endif
--  
--  bonjour_dep = declare_dependency(link_args: ['-framework', 'dnssd'])
-+
-+  if is_darwin
-+    bonjour_dep = declare_dependency(link_args: ['-framework', 'dnssd'])
-+  else
-+    bonjour_dep = declare_dependency(link_args: ['-ldns_sd'])
-+  endif
-   conf.set('HAVE_BONJOUR', true)
--  
-+
-   zeroconf = static_library(
-     'zeroconf_bonjour',
-     'ZeroconfGlue.cxx',

audio/nuvolaplayer/Makefile

@@ -5,7 +5,7 @@ PORTVERSION=	3.0.4
 PORTREVISION=	2
 CATEGORIES=	audio www
 
-MAINTAINER=	multimedia@FreeBSD.org
+MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Cloud music integration for your desktop
 
 LICENSE=	BSD2CLAUSE

audio/p5-MP3-Tag/Makefile

@@ -7,7 +7,7 @@ CATEGORIES=	audio perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
 
-MAINTAINER=	novel@FreeBSD.org
+MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Module for reading tags of MP3 audio files
 
 USES=		perl5

audio/paprefs/Makefile

@@ -2,23 +2,22 @@
 # $FreeBSD$
 
 PORTNAME=	paprefs
-PORTVERSION=	0.9.10
+PORTVERSION=	1.1
-PORTREVISION=	3
 CATEGORIES=	audio
 MASTER_SITES=	http://freedesktop.org/software/pulseaudio/${PORTNAME}/
 
 MAINTAINER=	romain@FreeBSD.org
 COMMENT=	GTK configuration dialog for PulseAudio
 
-LIB_DEPENDS=	libglademm-2.4.so:devel/libglademm24 \
+LICENSE=	GPLv2
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+LIB_DEPENDS=	libdbus-1.so:devel/dbus \
+		libdbus-glib-1.so:devel/dbus-glib \
 		libpulse.so:audio/pulseaudio
 
-GNU_CONFIGURE=	yes
+USES=		meson pkgconfig tar:xz
-USES=		compiler:c++11-lang localbase gmake pkgconfig
+USE_GNOME=	atkmm glib20 glibmm gtk30 gtkmm30 libsigc++20
-USE_CXXSTD=	c++11
-USE_GNOME=	gconfmm26 gnomeprefix intltool
-
-CONFIGURE_ARGS=	--disable-lynx
 
 OPTIONS_DEFINE=	PK NLS
 OPTIONS_SUB=	yes
@@ -27,6 +26,5 @@ PK_DESC=	Force dependency on PackageKit
 PK_LIB_DEPENDS=	libpackagekit-glib2.so:ports-mgmt/packagekit
 
 NLS_USES=		gettext
-NLS_CONFIGURE_ENABLE=	nls
 
 .include <bsd.port.mk>

audio/paprefs/distinfo

@@ -1,2 +1,3 @@
-SHA256 (paprefs-0.9.10.tar.gz) = 86f5c20d00c773993d5489ce94c4898e409d380986dc3afc5de20da6a1509e30
+TIMESTAMP = 1550185231
-SIZE (paprefs-0.9.10.tar.gz) = 224140
+SHA256 (paprefs-1.1.tar.xz) = 6ef243c17ebc19ca0e8569e23e00e597c801ca48a2facd77da1d4c08c42d3fa1
+SIZE (paprefs-1.1.tar.xz) = 69144

audio/paprefs/pkg-descr

@@ -2,7 +2,7 @@ PulseAudio Preferences (paprefs) is a simple GTK based configuration dialog for
 the PulseAudio sound server.
 
 Please note that this program can only configure local servers, and requires
-that a special module module-gconf is loaded in the sound server. (Since
+that a special module module-gsettings is loaded in the sound server. (This
-PulseAudio 0.9.5 this modules is loaded by default.)
+require to build the audio/pulseaudio port with option GSETTINGS).
 
-WWW: http://0pointer.de/lennart/projects/paprefs/
+WWW: https://freedesktop.org/software/pulseaudio/paprefs/

audio/paprefs/pkg-plist

@@ -13,6 +13,7 @@ share/locale/fi/LC_MESSAGES/paprefs.mo
 share/locale/fr/LC_MESSAGES/paprefs.mo
 share/locale/gu/LC_MESSAGES/paprefs.mo
 share/locale/hi/LC_MESSAGES/paprefs.mo
+share/locale/hr/LC_MESSAGES/paprefs.mo
 share/locale/hu/LC_MESSAGES/paprefs.mo
 share/locale/it/LC_MESSAGES/paprefs.mo
 share/locale/kn/LC_MESSAGES/paprefs.mo

audio/plasma5-plasma-pa/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1549993914
+TIMESTAMP = 1550686914
-SHA256 (KDE/plasma/5.15.0/plasma-pa-5.15.0.tar.xz) = 190a8d2d64227070082127cde98a2a3a91e30b7b16c8fd705b1e18d3cf13074f
+SHA256 (KDE/plasma/5.15.1/plasma-pa-5.15.1.tar.xz) = 206a7301e33e990a5efca379809c061961335e00fbfff252e0192f55a018b1dc
-SIZE (KDE/plasma/5.15.0/plasma-pa-5.15.0.tar.xz) = 94884
+SIZE (KDE/plasma/5.15.1/plasma-pa-5.15.1.tar.xz) = 95560

audio/py-pylast/Makefile

@@ -3,19 +3,20 @@
 
 PORTNAME=	pylast
 PORTVERSION=	3.0.0
+PORTREVISION=	1
 CATEGORIES=	audio python
 MASTER_SITES=	CHEESESHOP
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
-MAINTAINER=	ports@FreeBSD.org
+MAINTAINER=	sunpoet@FreeBSD.org
 COMMENT=	Python interface to Last.fm and Libre.fm
 
 LICENSE=	APACHE20
 LICENSE_FILE=	${WRKSRC}/COPYING
 
-RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR}
-
 USES=		python:3.5+
-USE_PYTHON=	distutils autoplist
+USE_PYTHON=	autoplist distutils
+
+NO_ARCH=	yes
 
 .include <bsd.port.mk>

audio/py-pylast/pkg-descr

@@ -1,3 +1,4 @@
-A Python interface to Last.fm (and other API compatible social networks).
+pyLast is a Python interface to Last.fm and other API-compatible websites such
+as Libre.fm.
 
 WWW: https://github.com/pylast/pylast

audio/tuxguitar/Makefile

@@ -18,7 +18,7 @@ MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Multitrack tablature editor and player
 
 LICENSE=	LGPL21
-LICENSE_FILE=	${WRKSRC}/../LICENSE
+LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	${JAVALIBDIR}/swt-devel.jar:x11-toolkits/swt-devel \
 		${JAVALIBDIR}/itext.jar:devel/itext \
@@ -38,7 +38,7 @@ USE_LDCONFIG=	yes
 JAVA_VERSION=	1.6+
 NOCCACHE=	yes
 
-WRKSRC_SUBDIR=	TuxGuitar
+BUILD_WRKSRC=	${WRKSRC}/TuxGuitar
 SF2_DIR=	${LOCALBASE}/share/sounds/sf2
 
 OPTIONS_DEFINE=	DOCS
@@ -56,11 +56,11 @@ post-extract:
 	@${CP} ${DISTDIR}/8MBGMSFX.SF2 ${WRKDIR}
 
 post-patch:
-	@${FIND} ${WRKSRC}/.. -name build.properties | ${XARGS} ${REINPLACE_CMD} -e '\
+	@${FIND} ${WRKSRC} -name build.properties | ${XARGS} ${REINPLACE_CMD} -e '\
 	    s|path\.swt=.*|path.swt=${JAVAJARDIR}/swt-devel.jar|; \
 	    s|path\.itext=.*|path.itext=${JAVAJARDIR}/itext.jar|; \
 	    s|path\.gervill=.*|path.gervill=${JAVAJARDIR}/gervill.jar|'
-	@${FIND} ${WRKSRC}/.. -name GNUmakefile | ${XARGS} ${REINPLACE_CMD} -e '\
+	@${FIND} ${WRKSRC} -name GNUmakefile | ${XARGS} ${REINPLACE_CMD} -e '\
 	    s|-I$$(shell gcj -print-file-name=include/)|-I${JAVA_HOME}/include \
 	    -I${JAVA_HOME}/include/freebsd -I${LOCALBASE}/include|; \
 	    s|-I $$(shell $$(GCJ) -print-file-name=include/)|-I${JAVA_HOME}/include \
@@ -73,38 +73,38 @@ post-patch:
 	    s|%%JAVASHAREDIR%%|${JAVASHAREDIR}|g; \
 	    s|%%DATADIR%%|${DATADIR}|g; \
 	    s|%%DOCSDIR%%|${DOCSDIR}|g' \
-	    ${WRKSRC}/build.properties
+	    ${WRKSRC}/TuxGuitar/build.properties
 
 post-build:
 .for p in ${PLUGINS}
-	(cd ${WRKSRC}/../TuxGuitar-${p}; \
+	(cd ${WRKSRC}/TuxGuitar-${p}; \
 	    ${SETENV} ${MAKE_ENV} ${ANT} ${MAKE_ARGS} ${ALL_TARGET})
 .endfor
-	cd ${WRKSRC}/../TuxGuitar-oss/jni && ${SETENV} ${MAKE_ENV} ${MAKE_CMD}
+	cd ${WRKSRC}/TuxGuitar-oss/jni && ${SETENV} ${MAKE_ENV} ${MAKE_CMD}
-	cd ${WRKSRC}/../TuxGuitar-fluidsynth/jni && ${SETENV} ${MAKE_ENV} ${MAKE_CMD}
+	cd ${WRKSRC}/TuxGuitar-fluidsynth/jni && ${SETENV} ${MAKE_ENV} ${MAKE_CMD}
-	cd ${WRKSRC}/../TuxGuitar-jack/jni && ${SETENV} ${MAKE_ENV} ${MAKE_CMD}
+	cd ${WRKSRC}/TuxGuitar-jack/jni && ${SETENV} ${MAKE_ENV} ${MAKE_CMD}
 
 do-install:
 	${INSTALL_SCRIPT} ${WRKDIR}/tuxguitar ${STAGEDIR}${PREFIX}/bin
-	${INSTALL_LIB} ${WRKSRC}/../TuxGuitar-oss/jni/libtuxguitar-oss-jni.so ${STAGEDIR}${PREFIX}/lib
+	${INSTALL_LIB} ${WRKSRC}/TuxGuitar-oss/jni/libtuxguitar-oss-jni.so ${STAGEDIR}${PREFIX}/lib
-	${INSTALL_LIB} ${WRKSRC}/../TuxGuitar-fluidsynth/jni/libtuxguitar-fluidsynth-jni.so ${STAGEDIR}${PREFIX}/lib
+	${INSTALL_LIB} ${WRKSRC}/TuxGuitar-fluidsynth/jni/libtuxguitar-fluidsynth-jni.so ${STAGEDIR}${PREFIX}/lib
 
 	@${MKDIR} ${STAGEDIR}${DATADIR}/plugins
-	${INSTALL_DATA} ${WRKSRC}/tuxguitar.jar ${STAGEDIR}${DATADIR}
+	${INSTALL_DATA} ${WRKSRC}/TuxGuitar/tuxguitar.jar ${STAGEDIR}${DATADIR}
-	${INSTALL_DATA} ${WRKSRC}/../misc/*.tg ${STAGEDIR}${DATADIR}
+	${INSTALL_DATA} ${WRKSRC}/misc/*.tg ${STAGEDIR}${DATADIR}
 	${INSTALL_DATA} ${WRKDIR}/8MBGMSFX.SF2 ${STAGEDIR}${DATADIR}
 .for p in ${PLUGINS}
-	${INSTALL_DATA} ${WRKSRC}/../TuxGuitar-${p}/tuxguitar-${p}.jar ${STAGEDIR}${DATADIR}/plugins
+	${INSTALL_DATA} ${WRKSRC}/TuxGuitar-${p}/tuxguitar-${p}.jar ${STAGEDIR}${DATADIR}/plugins
 .endfor
 	# Inline documentation
-	cd ${WRKSRC}/share/help &&   ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/help
+	cd ${WRKSRC}/TuxGuitar/share/help &&   ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/help
-	cd ${WRKSRC}/share/lang &&   ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/lang
+	cd ${WRKSRC}/TuxGuitar/share/lang &&   ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/lang
-	cd ${WRKSRC}/share/scales && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/scales
+	cd ${WRKSRC}/TuxGuitar/share/scales && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/scales
-	cd ${WRKSRC}/share/skins &&  ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/skins
+	cd ${WRKSRC}/TuxGuitar/share/skins &&  ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/skins
 
-	${INSTALL_DATA} ${WRKSRC}/../misc/tuxguitar.xpm ${STAGEDIR}${PREFIX}/share/pixmaps
+	${INSTALL_DATA} ${WRKSRC}/misc/tuxguitar.xpm ${STAGEDIR}${PREFIX}/share/pixmaps
-	${INSTALL_DATA} ${WRKSRC}/../misc/tuxguitar.desktop ${STAGEDIR}${PREFIX}/share/applications
+	${INSTALL_DATA} ${WRKSRC}/misc/tuxguitar.desktop ${STAGEDIR}${PREFIX}/share/applications
-	${INSTALL_MAN} ${WRKSRC}/../misc/tuxguitar.1 ${STAGEDIR}${MANPREFIX}/man/man1
+	${INSTALL_MAN} ${WRKSRC}/misc/tuxguitar.1 ${STAGEDIR}${MANPREFIX}/man/man1
 
 	# Share soundfont with FluidSynth
 	@${MKDIR} ${STAGEDIR}${SF2_DIR}
@@ -112,6 +112,6 @@ do-install:
 
 do-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
-	cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR}
+	cd ${WRKSRC}/TuxGuitar/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR}
 
 .include <bsd.port.mk>

audio/tuxguitar/files/patch-TuxGuitar-fluidsynth_jni_org__herac__tuxguitar__player__impl__midiport__fluidsynth__MidiSynth.c

@@ -0,0 +1,67 @@
+--- TuxGuitar-fluidsynth/jni/org_herac_tuxguitar_player_impl_midiport_fluidsynth_MidiSynth.c.orig	2009-10-31 14:34:13 UTC
++++ TuxGuitar-fluidsynth/jni/org_herac_tuxguitar_player_impl_midiport_fluidsynth_MidiSynth.c
+@@ -16,7 +16,11 @@ typedef struct{
+ 	jobject options;
+ }fluid_settings_foreach_option_data;
+ 
++#if FLUIDSYNTH_VERSION_MAJOR < 2
+ void fluid_settings_foreach_option_callback(void *data, char *name, char *option)
++#else
++void fluid_settings_foreach_option_callback(void *data, const char *name, const char *option)
++#endif
+ {
+ 	fluid_settings_foreach_option_data* handle = (fluid_settings_foreach_option_data *)data;
+ 	
+@@ -255,8 +259,12 @@ JNIEXPORT void JNICALL Java_org_herac_tuxguitar_player
+ 			jstring jvalue = NULL;
+ 			char *value = NULL;
+ 			const jbyte *jkey = (*env)->GetStringUTFChars(env, key, NULL);
+-			
++
++#if FLUIDSYNTH_VERSION_MAJOR < 2
+ 			fluid_settings_getstr(handle->settings,(char *)jkey, &value );
++#else
++			fluid_settings_dupstr(handle->settings,(char *)jkey, &value );
++#endif
+ 			jvalue = (*env)->NewStringUTF(env, value);
+ 			
+ 			(*env)->ReleaseStringUTFChars(env, key, jkey);
+@@ -274,7 +282,12 @@ JNIEXPORT void JNICALL Java_org_herac_tuxguitar_player
+ 		jmethodID mid = (*env)->GetMethodID(env, cl, "setValue", "(D)V");
+ 		if (mid != 0){
+ 			const jbyte *jkey = (*env)->GetStringUTFChars(env, key, NULL);
++#if FLUIDSYNTH_VERSION_MAJOR < 2
+ 			double value = fluid_settings_getnum_default(handle->settings,(char *)jkey);
++#else
++			double value = 0.0;
++			fluid_settings_getnum_default(handle->settings, (char*)jkey, &value);
++#endif
+ 			
+ 			(*env)->ReleaseStringUTFChars(env, key, jkey);
+ 			(*env)->CallVoidMethod( env, ref , mid , (jdouble)value );
+@@ -291,7 +304,12 @@ JNIEXPORT void JNICALL Java_org_herac_tuxguitar_player
+ 		jmethodID mid = (*env)->GetMethodID(env, cl, "setValue", "(I)V");
+ 		if (mid != 0){
+ 			const jbyte *jkey = (*env)->GetStringUTFChars(env, key, NULL);
++#if FLUIDSYNTH_VERSION_MAJOR < 2
+ 			int value = fluid_settings_getint_default(handle->settings,(char *)jkey);
++#else
++			int value = 0;
++			fluid_settings_getint_default(handle->settings,(char *)jkey, &value);
++#endif
+ 			
+ 			(*env)->ReleaseStringUTFChars(env, key, jkey);
+ 			(*env)->CallVoidMethod( env, ref , mid , (jint)value );
+@@ -308,7 +326,12 @@ JNIEXPORT void JNICALL Java_org_herac_tuxguitar_player
+ 		jmethodID mid = (*env)->GetMethodID(env, cl, "setValue", "(Ljava/lang/String;)V");
+ 		if (mid != 0){
+ 			const jbyte *jkey = (*env)->GetStringUTFChars(env, key, NULL);
++#if FLUIDSYNTH_VERSION_MAJOR < 2
+ 			char *value = fluid_settings_getstr_default(handle->settings,(char *)jkey);
++#else
++			char *value = NULL;
++			fluid_settings_getstr_default(handle->settings,(char *)jkey, &value);
++#endif
+ 			jstring jvalue = (*env)->NewStringUTF(env, value);
+ 			
+ 			(*env)->ReleaseStringUTFChars(env, key, jkey);

audio/tuxguitar/files/patch-TuxGuitar_build.properties

@@ -1,5 +1,5 @@
---- build.properties.orig	2009-10-31 14:32:52 UTC
+--- TuxGuitar/build.properties.orig	2009-10-31 14:32:52 UTC
-+++ build.properties
++++ TuxGuitar/build.properties
 @@ -5,15 +5,15 @@ ant.build.javac.source=1.4
  ant.build.javac.target=1.4
  
@@ -38,15 +38,15 @@
 -#dist.bin.path=/usr/local/bin/
 -#dist.share.path=/usr/local/share/TuxGuitar-${dist.version}/
 -#dist.doc.path=/usr/local/share/doc/TuxGuitar-${dist.version}/
-+lib.swt.jni=%%LOCALBASE%%/lib/
++lib.swt.jni=/usr/local/lib/
-+lib.swt.jar=%%JAVAJARDIR%%/swt-devel.jar
++lib.swt.jar=/usr/local/share/java/classes/swt-devel.jar
-+lib.itext.jar=%%JAVAJARDIR%%/itext.jar
++lib.itext.jar=/usr/local/share/java/classes/itext.jar
 +dist.file=xml/build-freebsd.xml
 +dist.version=1.2
-+dist.jar.path=%%JAVASHAREDIR%%/TuxGuitar-${dist.version}/
++dist.jar.path=/usr/local/share/java/TuxGuitar-${dist.version}/
-+dist.bin.path=%%PREFIX%%/bin
++dist.bin.path=/usr/local/bin
-+dist.share.path=%%DATADIR%%
++dist.share.path=/usr/local/share/tuxguitar
-+dist.doc.path=%%DOCSDIR%%
++dist.doc.path=/usr/local/share/doc/tuxguitar
  
  ########## DEFAULT MAC BUILD PROPERTIES ##########
  #lib.swt.jni=lib/

audio/wmix/Makefile

@@ -7,7 +7,7 @@ PORTREVISION=	3
 CATEGORIES=	audio windowmaker
 MASTER_SITES=	http://www.ne.jp/asahi/linux/timecop/software/
 
-MAINTAINER=	novel@FreeBSD.org
+MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Audio mixer for the WindowMaker dock with TV-like OSD
 
 OPTIONS_DEFINE=	DOCS

audio/zrythm/Makefile

@@ -0,0 +1,52 @@
+# $FreeBSD$
+
+PORTNAME=	zrythm
+DISTVERSION=	g20190216
+PORTREVISION=	1
+CATEGORIES=	audio
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Modern music production system, also known as DAW
+
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/COPYING
+
+BUILD_DEPENDS=	kf5-breeze-icons>0:x11-themes/kf5-breeze-icons
+LIB_DEPENDS=	libavcodec.so:multimedia/ffmpeg \
+		libcyaml.so:textproc/libcyaml \
+		libdazzle-1.0.so:x11-toolkits/libdazzle \
+		libjack.so:audio/jack \
+		liblilv-0.so:audio/lilv \
+		libportaudio.so:audio/portaudio \
+		libsamplerate.so:audio/libsamplerate \
+		libserd-0.so:devel/serd \
+		libsmf.so:audio/libsmf \
+		libsndfile.so:audio/libsndfile \
+		libsord-0.so:devel/sord \
+		libasound.so:audio/alsa-lib \
+		libsratom-0.so:audio/sratom \
+		libsuil-0.so:audio/suil \
+		libyaml.so:textproc/libyaml
+RUN_DEPENDS=	gsettings-desktop-schemas>=0:devel/gsettings-desktop-schemas \
+		kf5-breeze-icons>0:x11-themes/kf5-breeze-icons
+
+USES=		autoreconf gettext-runtime gmake python:3.5+,build gettext-runtime gnome pkgconfig
+USE_GITLAB=	yes
+GL_SITE=	https://git.zrythm.org
+GL_COMMIT=	fd92153c1c2552b54ac9ea2b5981bbb880da04f8
+GNU_CONFIGURE=	yes
+USE_GNOME=	atk cairo gdkpixbuf2 glib20 gtk30 libxml2 pango
+GLIB_SCHEMAS=	org.zrythm.gschema.xml
+ALL_TARGET=	${PORTNAME}
+INSTALLS_ICONS=	yes
+
+BINARY_ALIAS=	python3=${PYTHON_CMD}
+
+MAKE_ARGS=	RELEASE=1
+
+PLIST_FILES=	bin/zrythm \
+		share/applications/zrythm.desktop \
+		share/fonts/zrythm/Segment7Standard/OFL.txt \
+		share/icons/hicolor/scalable/apps/z.svg
+
+.include <bsd.port.mk>

audio/zrythm/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1550345216
+SHA256 (zrythm-zrythm-fd92153c1c2552b54ac9ea2b5981bbb880da04f8_GL0.tar.gz) = 0769d2d6a007fc91878983173cada9cb305dbf0072ca9ca89b26c6f373e4dcf8
+SIZE (zrythm-zrythm-fd92153c1c2552b54ac9ea2b5981bbb880da04f8_GL0.tar.gz) = 602150

audio/zrythm/pkg-descr

@@ -0,0 +1,6 @@
+Zrythm is built using C and the GTK+3 toolkit and borrows ideas, concepts and
+code from other projects such as Ardour and Jalv. It is built with the intention
+to provide GNU/Linux and BSD users a full-featured alternative to proprietary
+DAWs and offers a unique approach to workflow that other GNU/Linux DAWs lack.
+
+WWW: https://www.zrythm.org/

benchmarks/Makefile

@@ -30,6 +30,7 @@
     SUBDIR += hs-criterion
     SUBDIR += hs-criterion-measurement
     SUBDIR += httperf
+    SUBDIR += hyperfine
     SUBDIR += imb
     SUBDIR += interbench
     SUBDIR += iorate

benchmarks/fio/Makefile

@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	fio
-PORTVERSION=	3.12
+PORTVERSION=	3.13
-PORTREVISION=	1
 CATEGORIES=	benchmarks
 MASTER_SITES=	http://brick.kernel.dk/snaps/
 

benchmarks/fio/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1541311888
+TIMESTAMP = 1550645470
-SHA256 (fio-3.12.tar.bz2) = f73ec0a84834a058adcaf9964eb7e9a7af0a6e41a4e5eff781438c12b99b3b9d
+SHA256 (fio-3.13.tar.bz2) = a21d1e50c18eecbd5ee6f7c3c0a8c8605bbe31b91e07c387b2144b02ea3fb235
-SIZE (fio-3.12.tar.bz2) = 864192
+SIZE (fio-3.13.tar.bz2) = 871425

benchmarks/hyperfine/Makefile

@@ -0,0 +1,105 @@
+# $FreeBSD$
+
+PORTNAME=	hyperfine
+DISTVERSIONPREFIX=	v
+DISTVERSION=	1.5.0
+CATEGORIES=	benchmarks
+
+MAINTAINER=	pizzamig@FreeBSD.org
+COMMENT=	Command-line benchmarking tool
+
+LICENSE=	APACHE20 MIT
+LICENSE_COMB=	dual
+LICENSE_FILE_APACHE20=	${WRKSRC}/LICENSE-APACHE
+LICENSE_FILE_MIT=	${WRKSRC}/LICENSE-MIT
+
+BROKEN_i386=	LLVM ERROR: No support for lowering a copy into EFLAGS when used by this instruction
+
+USES=	cargo
+USE_GITHUB=	yes
+GH_ACCOUNT=	sharkdp
+
+PLIST_FILES=	bin/hyperfine
+
+CARGO_CRATES=	aho-corasick-0.6.9 \
+		ansi_term-0.11.0 \
+		approx-0.3.0 \
+		atty-0.2.11 \
+		bitflags-1.0.4 \
+		cfg-if-0.1.6 \
+		clap-2.32.0 \
+		clicolors-control-0.2.0 \
+		cloudabi-0.0.3 \
+		colored-1.6.1 \
+		console-0.6.2 \
+		csv-1.0.2 \
+		csv-core-0.1.4 \
+		fuchsia-zircon-0.3.3 \
+		fuchsia-zircon-sys-0.3.3 \
+		indicatif-0.9.0 \
+		itoa-0.4.3 \
+		kernel32-sys-0.2.2 \
+		lazy_static-0.2.11 \
+		lazy_static-1.2.0 \
+		libc-0.2.43 \
+		lock_api-0.1.5 \
+		memchr-2.1.1 \
+		num-0.1.42 \
+		num-bigint-0.1.44 \
+		num-complex-0.1.43 \
+		num-integer-0.1.39 \
+		num-iter-0.1.37 \
+		num-rational-0.1.42 \
+		num-traits-0.2.6 \
+		owning_ref-0.4.0 \
+		parking_lot-0.6.4 \
+		parking_lot_core-0.3.1 \
+		proc-macro2-0.4.24 \
+		quote-0.6.10 \
+		rand-0.3.22 \
+		rand-0.4.3 \
+		rand-0.5.5 \
+		rand_core-0.2.2 \
+		rand_core-0.3.0 \
+		redox_syscall-0.1.42 \
+		redox_termios-0.1.1 \
+		regex-0.2.11 \
+		regex-1.0.6 \
+		regex-syntax-0.5.6 \
+		regex-syntax-0.6.3 \
+		rustc-serialize-0.3.24 \
+		rustc_version-0.2.3 \
+		ryu-0.2.7 \
+		scopeguard-0.3.3 \
+		semver-0.9.0 \
+		semver-parser-0.7.0 \
+		serde-1.0.82 \
+		serde_derive-1.0.82 \
+		serde_json-1.0.33 \
+		smallvec-0.6.6 \
+		stable_deref_trait-1.1.1 \
+		statistical-0.1.1 \
+		strsim-0.7.0 \
+		syn-0.15.22 \
+		term_size-0.3.1 \
+		termion-1.5.1 \
+		termios-0.3.1 \
+		textwrap-0.10.0 \
+		thread_local-0.3.6 \
+		ucd-util-0.1.3 \
+		unicode-width-0.1.5 \
+		unicode-xid-0.1.0 \
+		unreachable-1.0.0 \
+		utf8-ranges-1.0.2 \
+		version_check-0.1.5 \
+		void-1.0.2 \
+		winapi-0.2.8 \
+		winapi-0.3.6 \
+		winapi-build-0.1.1 \
+		winapi-i686-pc-windows-gnu-0.4.0 \
+		winapi-x86_64-pc-windows-gnu-0.4.0
+
+post-install:
+	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/hyperfine
+
+.include <bsd.port.mk>

benchmarks/hyperfine/distinfo

@@ -0,0 +1,157 @@
+TIMESTAMP = 1550141834
+SHA256 (rust/crates/aho-corasick-0.6.9.tar.gz) = 1e9a933f4e58658d7b12defcf96dc5c720f20832deebe3e0a19efd3b6aaeeb9e
+SIZE (rust/crates/aho-corasick-0.6.9.tar.gz) = 25979
+SHA256 (rust/crates/ansi_term-0.11.0.tar.gz) = ee49baf6cb617b853aa8d93bf420db2383fab46d314482ca2803b40d5fde979b
+SIZE (rust/crates/ansi_term-0.11.0.tar.gz) = 17087
+SHA256 (rust/crates/approx-0.3.0.tar.gz) = f71f10b5c4946a64aad7b8cf65e3406cd3da22fc448595991d22423cf6db67b4
+SIZE (rust/crates/approx-0.3.0.tar.gz) = 13937
+SHA256 (rust/crates/atty-0.2.11.tar.gz) = 9a7d5b8723950951411ee34d271d99dddcc2035a16ab25310ea2c8cfd4369652
+SIZE (rust/crates/atty-0.2.11.tar.gz) = 5916
+SHA256 (rust/crates/bitflags-1.0.4.tar.gz) = 228047a76f468627ca71776ecdebd732a3423081fcf5125585bcd7c49886ce12
+SIZE (rust/crates/bitflags-1.0.4.tar.gz) = 15282
+SHA256 (rust/crates/cfg-if-0.1.6.tar.gz) = 082bb9b28e00d3c9d39cc03e64ce4cea0f1bb9b3fde493f0cbc008472d22bdf4
+SIZE (rust/crates/cfg-if-0.1.6.tar.gz) = 7411
+SHA256 (rust/crates/clap-2.32.0.tar.gz) = b957d88f4b6a63b9d70d5f454ac8011819c6efa7727858f458ab71c756ce2d3e
+SIZE (rust/crates/clap-2.32.0.tar.gz) = 196073
+SHA256 (rust/crates/clicolors-control-0.2.0.tar.gz) = 1f84dec9bc083ce2503908cd305af98bd363da6f54bf8d4bf0ac14ee749ad5d1
+SIZE (rust/crates/clicolors-control-0.2.0.tar.gz) = 3029
+SHA256 (rust/crates/cloudabi-0.0.3.tar.gz) = ddfc5b9aa5d4507acaf872de71051dfd0e309860e88966e1051e462a077aac4f
+SIZE (rust/crates/cloudabi-0.0.3.tar.gz) = 22156
+SHA256 (rust/crates/colored-1.6.1.tar.gz) = dc0a60679001b62fb628c4da80e574b9645ab4646056d7c9018885efffe45533
+SIZE (rust/crates/colored-1.6.1.tar.gz) = 17671
+SHA256 (rust/crates/console-0.6.2.tar.gz) = ecd48adf136733979b49e15bc3b4c43cc0d3c85ece7bd08e6daa414c6fcb13e6
+SIZE (rust/crates/console-0.6.2.tar.gz) = 12487
+SHA256 (rust/crates/csv-1.0.2.tar.gz) = 6d54f6b0fd69128a2894b1a3e57af5849a0963c1cc77b165d30b896e40296452
+SIZE (rust/crates/csv-1.0.2.tar.gz) = 888793
+SHA256 (rust/crates/csv-core-0.1.4.tar.gz) = 4dd8e6d86f7ba48b4276ef1317edc8cc36167546d8972feb4a2b5fec0b374105
+SIZE (rust/crates/csv-core-0.1.4.tar.gz) = 25406
+SHA256 (rust/crates/fuchsia-zircon-0.3.3.tar.gz) = 2e9763c69ebaae630ba35f74888db465e49e259ba1bc0eda7d06f4a067615d82
+SIZE (rust/crates/fuchsia-zircon-0.3.3.tar.gz) = 22565
+SHA256 (rust/crates/fuchsia-zircon-sys-0.3.3.tar.gz) = 3dcaa9ae7725d12cdb85b3ad99a434db70b468c09ded17e012d86b5c1010f7a7
+SIZE (rust/crates/fuchsia-zircon-sys-0.3.3.tar.gz) = 7191
+SHA256 (rust/crates/indicatif-0.9.0.tar.gz) = a29b2fa6f00010c268bface64c18bb0310aaa70d46a195d5382d288c477fb016
+SIZE (rust/crates/indicatif-0.9.0.tar.gz) = 1355765
+SHA256 (rust/crates/itoa-0.4.3.tar.gz) = 1306f3464951f30e30d12373d31c79fbd52d236e5e896fd92f96ec7babbbe60b
+SIZE (rust/crates/itoa-0.4.3.tar.gz) = 11061
+SHA256 (rust/crates/kernel32-sys-0.2.2.tar.gz) = 7507624b29483431c0ba2d82aece8ca6cdba9382bff4ddd0f7490560c056098d
+SIZE (rust/crates/kernel32-sys-0.2.2.tar.gz) = 24537
+SHA256 (rust/crates/lazy_static-0.2.11.tar.gz) = 76f033c7ad61445c5b347c7382dd1237847eb1bce590fe50365dcb33d546be73
+SIZE (rust/crates/lazy_static-0.2.11.tar.gz) = 12361
+SHA256 (rust/crates/lazy_static-1.2.0.tar.gz) = a374c89b9db55895453a74c1e38861d9deec0b01b405a82516e9d5de4820dea1
+SIZE (rust/crates/lazy_static-1.2.0.tar.gz) = 10840
+SHA256 (rust/crates/libc-0.2.43.tar.gz) = 76e3a3ef172f1a0b9a9ff0dd1491ae5e6c948b94479a3021819ba7d860c8645d
+SIZE (rust/crates/libc-0.2.43.tar.gz) = 353810
+SHA256 (rust/crates/lock_api-0.1.5.tar.gz) = 62ebf1391f6acad60e5c8b43706dde4582df75c06698ab44511d15016bc2442c
+SIZE (rust/crates/lock_api-0.1.5.tar.gz) = 16967
+SHA256 (rust/crates/memchr-2.1.1.tar.gz) = 0a3eb002f0535929f1199681417029ebea04aadc0c7a4224b46be99c7f5d6a16
+SIZE (rust/crates/memchr-2.1.1.tar.gz) = 19591
+SHA256 (rust/crates/num-0.1.42.tar.gz) = 4703ad64153382334aa8db57c637364c322d3372e097840c72000dabdcf6156e
+SIZE (rust/crates/num-0.1.42.tar.gz) = 8323
+SHA256 (rust/crates/num-bigint-0.1.44.tar.gz) = e63899ad0da84ce718c14936262a41cee2c79c981fc0a0e7c7beb47d5a07e8c1
+SIZE (rust/crates/num-bigint-0.1.44.tar.gz) = 63732
+SHA256 (rust/crates/num-complex-0.1.43.tar.gz) = b288631d7878aaf59442cffd36910ea604ecd7745c36054328595114001c9656
+SIZE (rust/crates/num-complex-0.1.43.tar.gz) = 17731
+SHA256 (rust/crates/num-integer-0.1.39.tar.gz) = e83d528d2677f0518c570baf2b7abdcf0cd2d248860b68507bdcb3e91d4c0cea
+SIZE (rust/crates/num-integer-0.1.39.tar.gz) = 17881
+SHA256 (rust/crates/num-iter-0.1.37.tar.gz) = af3fdbbc3291a5464dc57b03860ec37ca6bf915ed6ee385e7c6c052c422b2124
+SIZE (rust/crates/num-iter-0.1.37.tar.gz) = 10201
+SHA256 (rust/crates/num-rational-0.1.42.tar.gz) = ee314c74bd753fc86b4780aa9475da469155f3848473a261d2d18e35245a784e
+SIZE (rust/crates/num-rational-0.1.42.tar.gz) = 17253
+SHA256 (rust/crates/num-traits-0.2.6.tar.gz) = 0b3a5d7cc97d6d30d8b9bc8fa19bf45349ffe46241e8816f50f62f6d6aaabee1
+SIZE (rust/crates/num-traits-0.2.6.tar.gz) = 39923
+SHA256 (rust/crates/owning_ref-0.4.0.tar.gz) = 49a4b8ea2179e6a2e27411d3bca09ca6dd630821cf6894c6c7c8467a8ee7ef13
+SIZE (rust/crates/owning_ref-0.4.0.tar.gz) = 12233
+SHA256 (rust/crates/parking_lot-0.6.4.tar.gz) = f0802bff09003b291ba756dc7e79313e51cc31667e94afbe847def490424cde5
+SIZE (rust/crates/parking_lot-0.6.4.tar.gz) = 31890
+SHA256 (rust/crates/parking_lot_core-0.3.1.tar.gz) = ad7f7e6ebdc79edff6fdcb87a55b620174f7a989e3eb31b65231f4af57f00b8c
+SIZE (rust/crates/parking_lot_core-0.3.1.tar.gz) = 26635
+SHA256 (rust/crates/proc-macro2-0.4.24.tar.gz) = 77619697826f31a02ae974457af0b29b723e5619e113e9397b8b82c6bd253f09
+SIZE (rust/crates/proc-macro2-0.4.24.tar.gz) = 30970
+SHA256 (rust/crates/quote-0.6.10.tar.gz) = 53fa22a1994bd0f9372d7a816207d8a2677ad0325b073f5c5332760f0fb62b5c
+SIZE (rust/crates/quote-0.6.10.tar.gz) = 15795
+SHA256 (rust/crates/rand-0.3.22.tar.gz) = 15a732abf9d20f0ad8eeb6f909bf6868722d9a06e1e50802b6a70351f40b4eb1
+SIZE (rust/crates/rand-0.3.22.tar.gz) = 11318
+SHA256 (rust/crates/rand-0.4.3.tar.gz) = 8356f47b32624fef5b3301c1be97e5944ecdd595409cc5da11d05f211db6cfbd
+SIZE (rust/crates/rand-0.4.3.tar.gz) = 76094
+SHA256 (rust/crates/rand-0.5.5.tar.gz) = e464cd887e869cddcae8792a4ee31d23c7edd516700695608f5b98c67ee0131c
+SIZE (rust/crates/rand-0.5.5.tar.gz) = 137359
+SHA256 (rust/crates/rand_core-0.2.2.tar.gz) = 1961a422c4d189dfb50ffa9320bf1f2a9bd54ecb92792fb9477f99a1045f3372
+SIZE (rust/crates/rand_core-0.2.2.tar.gz) = 15450
+SHA256 (rust/crates/rand_core-0.3.0.tar.gz) = 0905b6b7079ec73b314d4c748701f6931eb79fd97c668caa3f1899b22b32c6db
+SIZE (rust/crates/rand_core-0.3.0.tar.gz) = 20581
+SHA256 (rust/crates/redox_syscall-0.1.42.tar.gz) = cf8fb82a4d1c9b28f1c26c574a5b541f5ffb4315f6c9a791fa47b6a04438fe93
+SIZE (rust/crates/redox_syscall-0.1.42.tar.gz) = 14962
+SHA256 (rust/crates/redox_termios-0.1.1.tar.gz) = 7e891cfe48e9100a70a3b6eb652fef28920c117d366339687bd5576160db0f76
+SIZE (rust/crates/redox_termios-0.1.1.tar.gz) = 3227
+SHA256 (rust/crates/regex-0.2.11.tar.gz) = 9329abc99e39129fcceabd24cf5d85b4671ef7c29c50e972bc5afe32438ec384
+SIZE (rust/crates/regex-0.2.11.tar.gz) = 209507
+SHA256 (rust/crates/regex-1.0.6.tar.gz) = ee84f70c8c08744ea9641a731c7fadb475bf2ecc52d7f627feb833e0b3990467
+SIZE (rust/crates/regex-1.0.6.tar.gz) = 239455
+SHA256 (rust/crates/regex-syntax-0.5.6.tar.gz) = 7d707a4fa2637f2dca2ef9fd02225ec7661fe01a53623c1e6515b6916511f7a7
+SIZE (rust/crates/regex-syntax-0.5.6.tar.gz) = 233912
+SHA256 (rust/crates/regex-syntax-0.6.3.tar.gz) = fbc557aac2b708fe84121caf261346cc2eed71978024337e42eb46b8a252ac6e
+SIZE (rust/crates/regex-syntax-0.6.3.tar.gz) = 240173
+SHA256 (rust/crates/rustc-serialize-0.3.24.tar.gz) = dcf128d1287d2ea9d80910b5f1120d0b8eede3fbf1abe91c40d39ea7d51e6fda
+SIZE (rust/crates/rustc-serialize-0.3.24.tar.gz) = 45926
+SHA256 (rust/crates/rustc_version-0.2.3.tar.gz) = 138e3e0acb6c9fb258b19b67cb8abd63c00679d2851805ea151465464fe9030a
+SIZE (rust/crates/rustc_version-0.2.3.tar.gz) = 10210
+SHA256 (rust/crates/ryu-0.2.7.tar.gz) = eb9e9b8cde282a9fe6a42dd4681319bfb63f121b8a8ee9439c6f4107e58a46f7
+SIZE (rust/crates/ryu-0.2.7.tar.gz) = 41382
+SHA256 (rust/crates/scopeguard-0.3.3.tar.gz) = 94258f53601af11e6a49f722422f6e3425c52b06245a5cf9bc09908b174f5e27
+SIZE (rust/crates/scopeguard-0.3.3.tar.gz) = 9605
+SHA256 (rust/crates/semver-0.9.0.tar.gz) = 1d7eb9ef2c18661902cc47e535f9bc51b78acd254da71d375c2f6720d9a40403
+SIZE (rust/crates/semver-0.9.0.tar.gz) = 17344
+SHA256 (rust/crates/semver-parser-0.7.0.tar.gz) = 388a1df253eca08550bef6c72392cfe7c30914bf41df5269b68cbd6ff8f570a3
+SIZE (rust/crates/semver-parser-0.7.0.tar.gz) = 10268
+SHA256 (rust/crates/serde-1.0.82.tar.gz) = 6fa52f19aee12441d5ad11c9a00459122bd8f98707cadf9778c540674f1935b6
+SIZE (rust/crates/serde-1.0.82.tar.gz) = 71666
+SHA256 (rust/crates/serde_derive-1.0.82.tar.gz) = 96a7f9496ac65a2db5929afa087b54f8fc5008dcfbe48a8874ed20049b0d6154
+SIZE (rust/crates/serde_derive-1.0.82.tar.gz) = 47403
+SHA256 (rust/crates/serde_json-1.0.33.tar.gz) = c37ccd6be3ed1fdf419ee848f7c758eb31b054d7cd3ae3600e3bae0adf569811
+SIZE (rust/crates/serde_json-1.0.33.tar.gz) = 69738
+SHA256 (rust/crates/smallvec-0.6.6.tar.gz) = 622df2d454c29a4d89b30dc3b27b42d7d90d6b9e587dbf8f67652eb7514da484
+SIZE (rust/crates/smallvec-0.6.6.tar.gz) = 21395
+SHA256 (rust/crates/stable_deref_trait-1.1.1.tar.gz) = dba1a27d3efae4351c8051072d619e3ade2820635c3958d826bfea39d59b54c8
+SIZE (rust/crates/stable_deref_trait-1.1.1.tar.gz) = 8007
+SHA256 (rust/crates/statistical-0.1.1.tar.gz) = c139942f46d96c53b28420a2cdfb374629f122656bd9daef7fc221ed4d8ec228
+SIZE (rust/crates/statistical-0.1.1.tar.gz) = 5112
+SHA256 (rust/crates/strsim-0.7.0.tar.gz) = bb4f380125926a99e52bc279241539c018323fab05ad6368b56f93d9369ff550
+SIZE (rust/crates/strsim-0.7.0.tar.gz) = 8435
+SHA256 (rust/crates/syn-0.15.22.tar.gz) = ae8b29eb5210bc5cf63ed6149cbf9adfc82ac0be023d8735c176ee74a2db4da7
+SIZE (rust/crates/syn-0.15.22.tar.gz) = 146349
+SHA256 (rust/crates/term_size-0.3.1.tar.gz) = 9e5b9a66db815dcfd2da92db471106457082577c3c278d4138ab3e3b4e189327
+SIZE (rust/crates/term_size-0.3.1.tar.gz) = 10754
+SHA256 (rust/crates/termion-1.5.1.tar.gz) = 689a3bdfaab439fd92bc87df5c4c78417d3cbe537487274e9b0b2dce76e92096
+SIZE (rust/crates/termion-1.5.1.tar.gz) = 20659
+SHA256 (rust/crates/termios-0.3.1.tar.gz) = 72b620c5ea021d75a735c943269bb07d30c9b77d6ac6b236bc8b5c496ef05625
+SIZE (rust/crates/termios-0.3.1.tar.gz) = 9541
+SHA256 (rust/crates/textwrap-0.10.0.tar.gz) = 307686869c93e71f94da64286f9a9524c0f308a9e1c87a583de8e9c9039ad3f6
+SIZE (rust/crates/textwrap-0.10.0.tar.gz) = 15986
+SHA256 (rust/crates/thread_local-0.3.6.tar.gz) = c6b53e329000edc2b34dbe8545fd20e55a333362d0a321909685a19bd28c3f1b
+SIZE (rust/crates/thread_local-0.3.6.tar.gz) = 12388
+SHA256 (rust/crates/ucd-util-0.1.3.tar.gz) = 535c204ee4d8434478593480b8f86ab45ec9aae0e83c568ca81abf0fd0e88f86
+SIZE (rust/crates/ucd-util-0.1.3.tar.gz) = 25897
+SHA256 (rust/crates/unicode-width-0.1.5.tar.gz) = 882386231c45df4700b275c7ff55b6f3698780a650026380e72dabe76fa46526
+SIZE (rust/crates/unicode-width-0.1.5.tar.gz) = 15761
+SHA256 (rust/crates/unicode-xid-0.1.0.tar.gz) = fc72304796d0818e357ead4e000d19c9c174ab23dc11093ac919054d20a6a7fc
+SIZE (rust/crates/unicode-xid-0.1.0.tar.gz) = 16000
+SHA256 (rust/crates/unreachable-1.0.0.tar.gz) = 382810877fe448991dfc7f0dd6e3ae5d58088fd0ea5e35189655f84e6814fa56
+SIZE (rust/crates/unreachable-1.0.0.tar.gz) = 6355
+SHA256 (rust/crates/utf8-ranges-1.0.2.tar.gz) = 796f7e48bef87609f7ade7e06495a87d5cd06c7866e6a5cbfceffc558a243737
+SIZE (rust/crates/utf8-ranges-1.0.2.tar.gz) = 8510
+SHA256 (rust/crates/version_check-0.1.5.tar.gz) = 914b1a6776c4c929a602fafd8bc742e06365d4bcbe48c30f9cca5824f70dc9dd
+SIZE (rust/crates/version_check-0.1.5.tar.gz) = 8173
+SHA256 (rust/crates/void-1.0.2.tar.gz) = 6a02e4885ed3bc0f2de90ea6dd45ebcbb66dacffe03547fadbb0eeae2770887d
+SIZE (rust/crates/void-1.0.2.tar.gz) = 2356
+SHA256 (rust/crates/winapi-0.2.8.tar.gz) = 167dc9d6949a9b857f3451275e911c3f44255842c1f7a76f33c55103a909087a
+SIZE (rust/crates/winapi-0.2.8.tar.gz) = 455145
+SHA256 (rust/crates/winapi-0.3.6.tar.gz) = 92c1eb33641e276cfa214a0522acad57be5c56b10cb348b3c5117db75f3ac4b0
+SIZE (rust/crates/winapi-0.3.6.tar.gz) = 1029391
+SHA256 (rust/crates/winapi-build-0.1.1.tar.gz) = 2d315eee3b34aca4797b2da6b13ed88266e6d612562a0c46390af8299fc699bc
+SIZE (rust/crates/winapi-build-0.1.1.tar.gz) = 669
+SHA256 (rust/crates/winapi-i686-pc-windows-gnu-0.4.0.tar.gz) = ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6
+SIZE (rust/crates/winapi-i686-pc-windows-gnu-0.4.0.tar.gz) = 2918815
+SHA256 (rust/crates/winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz) = 712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f
+SIZE (rust/crates/winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz) = 2947998
+SHA256 (sharkdp-hyperfine-v1.5.0_GH0.tar.gz) = d5183611348e696e579dda846cee92b7b78c8ef18c00bfb9b0a62d0a63034823
+SIZE (sharkdp-hyperfine-v1.5.0_GH0.tar.gz) = 33024

benchmarks/hyperfine/pkg-descr

@@ -0,0 +1,14 @@
+A command-line benchmarking tool (inspired by bench).
+
+Features:
+* Statistical analysis across multiple runs.
+* Support for arbitrary shell commands.
+* Constant feedback about the benchmark progress and current estimates.
+* Warmup runs can be executed before the actual benchmark.
+* Cache-clearing commands can be set up before each timing run.
+* Statistical outlier detection.
+* Export results to various formats: CSV, JSON, Markdown.
+* Parameterized benchmarks.
+* Cross-platform
+
+WWW: https://github.com/sharkdp/hyperfine

benchmarks/phoronix-test-suite/Makefile

@@ -3,7 +3,7 @@
 
 PORTNAME=	phoronix-test-suite
 DISTVERSIONPREFIX=	v
-DISTVERSION=	8.4.1
+DISTVERSION=	8.6.0
 CATEGORIES=	benchmarks
 PKGNAMESUFFIX=	${PHP_PKGNAMESUFFIX}
 

benchmarks/phoronix-test-suite/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1544806187
+TIMESTAMP = 1550146462
-SHA256 (phoronix-test-suite-phoronix-test-suite-v8.4.1_GH0.tar.gz) = 29e2221ce0db9d11f98cbdab3f45c60e87868b366b00ad698e1a45fee8a96764
+SHA256 (phoronix-test-suite-phoronix-test-suite-v8.6.0_GH0.tar.gz) = 83d9299eb8b83be8092885dfeacaf849229c5bd2014aaded2299c37d81de4178
-SIZE (phoronix-test-suite-phoronix-test-suite-v8.4.1_GH0.tar.gz) = 863492
+SIZE (phoronix-test-suite-phoronix-test-suite-v8.6.0_GH0.tar.gz) = 875319

biology/Makefile

@@ -77,6 +77,7 @@
     SUBDIR += ngs-sdk
     SUBDIR += p5-AcePerl
     SUBDIR += p5-Bio-ASN1-EntrezGene
+    SUBDIR += p5-Bio-Cluster
     SUBDIR += p5-Bio-Coordinate
     SUBDIR += p5-Bio-Das
     SUBDIR += p5-Bio-Das-Lite

biology/hmmer/Makefile

@@ -12,10 +12,10 @@ COMMENT=	Profile hidden Markov models for biological sequence analysis
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-ONLY_FOR_ARCHS=	amd64 i386 ia64 powerpc powerpc64
+ONLY_FOR_ARCHS=	amd64 i386 powerpc powerpc64 powerpcspe
 ONLY_FOR_ARCHS_REASON=	requires SSE2 or AltiVec instructions
 
-USES=		gmake perl5 shebangfix
+USES=		compiler:c11 gmake perl5 shebangfix
 
 GNU_CONFIGURE=	yes
 MAKE_ARGS=	V=1

biology/igv/Makefile

@@ -2,7 +2,7 @@
 
 PORTNAME=	igv
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.4.16
+DISTVERSION=	2.4.19
 CATEGORIES=	biology java
 MASTER_SITES=	http://software.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img
 DISTFILES=	tools.png:img

biology/igv/distinfo

@@ -1,5 +1,5 @@
-TIMESTAMP = 1542564950
+TIMESTAMP = 1550956856
-SHA256 (igv-2.4.16/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c
+SHA256 (igv-2.4.19/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c
-SIZE (igv-2.4.16/tools.png) = 5139
+SIZE (igv-2.4.19/tools.png) = 5139
-SHA256 (igv-2.4.16/igvteam-igv-v2.4.16_GH0.tar.gz) = 3c8187d2a7e7991d1892417bf3880b050643a35c73af8e8b649de93feb05402b
+SHA256 (igv-2.4.19/igvteam-igv-v2.4.19_GH0.tar.gz) = 194dc530687f66cf1bdf3f9c317d5fbf9344725793e9b9c0f09cb6af70792ced
-SIZE (igv-2.4.16/igvteam-igv-v2.4.16_GH0.tar.gz) = 141291418
+SIZE (igv-2.4.19/igvteam-igv-v2.4.19_GH0.tar.gz) = 140831230

biology/iqtree/Makefile

@@ -2,8 +2,7 @@
 
 PORTNAME=	iqtree
 DISTVERSIONPREFIX=	v
-DISTVERSION=	1.6.9
+DISTVERSION=	1.6.10
-PORTREVISION=	1
 CATEGORIES=	biology
 
 MAINTAINER=	jrm@FreeBSD.org

biology/iqtree/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1545568930
+TIMESTAMP = 1550673203
-SHA256 (Cibiv-IQ-TREE-v1.6.9_GH0.tar.gz) = 35fb673474e2ec13b5bb70dc8e5639aae2f22cbc26161bb9d03efc9fe10129ad
+SHA256 (Cibiv-IQ-TREE-v1.6.10_GH0.tar.gz) = dcbf0753557855b851654b48e74943c7d6844072a201aa3059d28458569d92b6
-SIZE (Cibiv-IQ-TREE-v1.6.9_GH0.tar.gz) = 4865752
+SIZE (Cibiv-IQ-TREE-v1.6.10_GH0.tar.gz) = 4866628

biology/ngs-sdk/Makefile

@@ -1,7 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	ngs
-DISTVERSION=	2.9.3
+DISTVERSION=	2.9.4
 CATEGORIES=	biology
 PKGNAMESUFFIX=	-sdk
 

biology/ngs-sdk/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1539898469
+TIMESTAMP = 1550958847
-SHA256 (ncbi-ngs-2.9.3_GH0.tar.gz) = d16cdf340f4c66e449cc490a222e54e9074cd15fe0938cb75b951a72985f757d
+SHA256 (ncbi-ngs-2.9.4_GH0.tar.gz) = 04182f22324a49fa6b4fb7dbc38f718d3c9618dd468a4199fb9570f5ccfa388d
-SIZE (ncbi-ngs-2.9.3_GH0.tar.gz) = 1091640
+SIZE (ncbi-ngs-2.9.4_GH0.tar.gz) = 1092165

biology/ngs-sdk/pkg-plist

@@ -92,4 +92,4 @@ lib/libngs-adapt-c++.a
 lib/libngs-c++.a
 lib/libngs-sdk.so
 lib/libngs-sdk.so.2
-lib/libngs-sdk.so.2.9.3
+lib/libngs-sdk.so.2.9.4

biology/p5-Bio-Cluster/Makefile

@@ -0,0 +1,27 @@
+# Created by: Po-Chuan Hsieh <sunpoet@FreeBSD.org>
+# $FreeBSD$
+
+PORTNAME=	Bio-Cluster
+PORTVERSION=	1.7.3
+CATEGORIES=	biology perl5
+MASTER_SITES=	CPAN
+PKGNAMEPREFIX=	p5-
+
+MAINTAINER=	sunpoet@FreeBSD.org
+COMMENT=	BioPerl cluster modules
+
+LICENSE=	ART10 GPLv1+
+LICENSE_COMB=	dual
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+#TODO: Add Bio::Variation::SNP
+BUILD_DEPENDS=	${RUN_DEPENDS}
+RUN_DEPENDS=	p5-BioPerl>=0:biology/p5-BioPerl \
+		p5-XML-SAX>=0:textproc/p5-XML-SAX
+
+USES=		perl5
+USE_PERL5=	configure
+
+NO_ARCH=	yes
+
+.include <bsd.port.mk>

biology/p5-Bio-Cluster/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1549712664
+SHA256 (Bio-Cluster-1.7.3.tar.gz) = 1967fb3899b92f245b5bf6cb64ef076fc3f8427b1a96ca5f7b74d220b6191fbb
+SIZE (Bio-Cluster-1.7.3.tar.gz) = 58304

biology/p5-Bio-Cluster/pkg-descr

@@ -0,0 +1,4 @@
+Bio::Cluster is the BioPerl cluster modules. Classes and modules here describe
+the basic structure for a cluster of BioPerl objects.
+
+WWW: https://metacpan.org/release/Bio-Cluster

biology/p5-Bio-Cluster/pkg-plist

@@ -0,0 +1,20 @@
+%%SITE_PERL%%/Bio/Cluster.pm
+%%SITE_PERL%%/Bio/Cluster/ClusterFactory.pm
+%%SITE_PERL%%/Bio/Cluster/FamilyI.pm
+%%SITE_PERL%%/Bio/Cluster/SequenceFamily.pm
+%%SITE_PERL%%/Bio/Cluster/UniGene.pm
+%%SITE_PERL%%/Bio/Cluster/UniGeneI.pm
+%%SITE_PERL%%/Bio/ClusterI.pm
+%%SITE_PERL%%/Bio/ClusterIO.pm
+%%SITE_PERL%%/Bio/ClusterIO/dbsnp.pm
+%%SITE_PERL%%/Bio/ClusterIO/unigene.pm
+%%PERL5_MAN3%%/Bio::Cluster.3.gz
+%%PERL5_MAN3%%/Bio::Cluster::ClusterFactory.3.gz
+%%PERL5_MAN3%%/Bio::Cluster::FamilyI.3.gz
+%%PERL5_MAN3%%/Bio::Cluster::SequenceFamily.3.gz
+%%PERL5_MAN3%%/Bio::Cluster::UniGene.3.gz
+%%PERL5_MAN3%%/Bio::Cluster::UniGeneI.3.gz
+%%PERL5_MAN3%%/Bio::ClusterI.3.gz
+%%PERL5_MAN3%%/Bio::ClusterIO.3.gz
+%%PERL5_MAN3%%/Bio::ClusterIO::dbsnp.3.gz
+%%PERL5_MAN3%%/Bio::ClusterIO::unigene.3.gz

biology/p5-BioPerl-Run/Makefile

@@ -2,13 +2,13 @@
 # $FreeBSD$
 
 PORTNAME=	BioPerl-Run
-PORTVERSION=	1.007002
+PORTVERSION=	1.007003
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
 PKGNAMEPREFIX=	p5-
 
-MAINTAINER=	perl@FreeBSD.org
+MAINTAINER=	sunpoet@FreeBSD.org
 COMMENT=	Wrapper modules for common bioinformatics tools
 
 LICENSE=	ART10 GPLv1+
@@ -17,6 +17,7 @@ LICENSE_FILE_ART10=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	${RUN_DEPENDS}
 RUN_DEPENDS=	p5-Algorithm-Diff>=0:devel/p5-Algorithm-Diff \
+		p5-Bio-Cluster>=0:biology/p5-Bio-Cluster \
 		p5-Bio-FeatureIO>=0:biology/p5-Bio-FeatureIO \
 		p5-BioPerl>=1.007000:biology/p5-BioPerl \
 		p5-Config-Any>=0:devel/p5-Config-Any \
@@ -29,25 +30,20 @@ CONFLICTS=	p5-bioperl-run-1.[13579]*
 
 OPTIONS_DEFINE=	DOCS
 
-NO_ARCH=	yes
 USES=		perl5 shebangfix
 USE_PERL5=	modbuild
+
+NO_ARCH=	yes
+
 SHEBANG_FILES=	scripts/*
 
-PORTDOCS=	*
-
-post-build:
-	(cd ${WRKSRC} && ${PERL} ./Build manifest)
-
 post-install:
-.for i in bioperl_application_installer multi_hmmsearch panalysis papplmaker run_neighbor run_protdist
+.for i in multi_hmmsearch panalysis papplmaker run_neighbor run_protdist
 	${INSTALL_SCRIPT} ${WRKSRC}/scripts/${i}.PLS ${STAGEDIR}${PREFIX}/bin/bp_${i}
 .endfor
 
 post-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
-.for doc in AUTHORS Changes INSTALL.PROGRAMS README.md
+	cd ${WRKSRC} && ${INSTALL_DATA} AUTHORS Changes INSTALL.PROGRAMS README.md ${STAGEDIR}${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
-.endfor
 
 .include <bsd.port.mk>

biology/p5-BioPerl-Run/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1505487295
+TIMESTAMP = 1549711722
-SHA256 (BioPerl-Run-1.007002.tar.gz) = 29806fc407183a936897d49d01d227877f52c946e3ed96c0675ed1ed14e1ce07
+SHA256 (BioPerl-Run-1.007003.tar.gz) = e62e529352f0644bc26509065595d0a47fb6217e5f1301acad76182c2f062071
-SIZE (BioPerl-Run-1.007002.tar.gz) = 14493777
+SIZE (BioPerl-Run-1.007003.tar.gz) = 5138162

biology/p5-BioPerl-Run/files/patch-Build.PL

@@ -1,6 +1,6 @@
---- Build.PL.orig	2014-07-26 02:49:03 UTC
+--- Build.PL.orig	2019-02-08 19:53:38 UTC
 +++ Build.PL
-@@ -50,7 +50,8 @@ my $build = Module::Build->new(
+@@ -75,7 +75,8 @@ my $build = Module::Build->subclass(
      #create_makefile_pl  => 'passthrough'
  );
  

biology/p5-BioPerl-Run/pkg-plist

@@ -1,4 +1,3 @@
-bin/bp_bioperl_application_installer
 bin/bp_multi_hmmsearch
 bin/bp_panalysis
 bin/bp_papplmaker
@@ -15,12 +14,6 @@ bin/bp_run_protdist
 %%SITE_PERL%%/Bio/DB/SoapEUtilities/LinkAdaptor.pm
 %%SITE_PERL%%/Bio/DB/SoapEUtilities/Result.pm
 %%SITE_PERL%%/Bio/Factory/EMBOSS.pm
-%%SITE_PERL%%/Bio/Installer/EMBOSS.pm
-%%SITE_PERL%%/Bio/Installer/Generic.pm
-%%SITE_PERL%%/Bio/Installer/Hyphy.pm
-%%SITE_PERL%%/Bio/Installer/Muscle.pm
-%%SITE_PERL%%/Bio/Installer/Probcons.pm
-%%SITE_PERL%%/Bio/Installer/SLR.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Amap.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Blat.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/DBA.pm
@@ -37,20 +30,12 @@ bin/bp_run_protdist
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Proda.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/Sim4.pm
 %%SITE_PERL%%/Bio/Tools/Run/Alignment/StandAloneFasta.pm
-%%SITE_PERL%%/Bio/Tools/Run/Analysis.pm
 %%SITE_PERL%%/Bio/Tools/Run/Analysis/soap.pm
-%%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory.pm
 %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory/soap.pm
-%%SITE_PERL%%/Bio/Tools/Run/AssemblerBase.pm
 %%SITE_PERL%%/Bio/Tools/Run/BEDTools.pm
 %%SITE_PERL%%/Bio/Tools/Run/BEDTools/Config.pm
-%%SITE_PERL%%/Bio/Tools/Run/BWA.pm
-%%SITE_PERL%%/Bio/Tools/Run/BWA/Config.pm
 %%SITE_PERL%%/Bio/Tools/Run/BlastPlus.pm
 %%SITE_PERL%%/Bio/Tools/Run/BlastPlus/Config.pm
-%%SITE_PERL%%/Bio/Tools/Run/Bowtie.pm
-%%SITE_PERL%%/Bio/Tools/Run/Bowtie/Config.pm
-%%SITE_PERL%%/Bio/Tools/Run/Cap3.pm
 %%SITE_PERL%%/Bio/Tools/Run/Coil.pm
 %%SITE_PERL%%/Bio/Tools/Run/EMBOSSApplication.pm
 %%SITE_PERL%%/Bio/Tools/Run/EMBOSSacd.pm
@@ -65,17 +50,10 @@ bin/bp_run_protdist
 %%SITE_PERL%%/Bio/Tools/Run/Hmmer.pm
 %%SITE_PERL%%/Bio/Tools/Run/Infernal.pm
 %%SITE_PERL%%/Bio/Tools/Run/MCS.pm
-%%SITE_PERL%%/Bio/Tools/Run/Maq.pm
-%%SITE_PERL%%/Bio/Tools/Run/Maq/Config.pm
 %%SITE_PERL%%/Bio/Tools/Run/Match.pm
 %%SITE_PERL%%/Bio/Tools/Run/Mdust.pm
-%%SITE_PERL%%/Bio/Tools/Run/Meme.pm
-%%SITE_PERL%%/Bio/Tools/Run/Minimo.pm
-%%SITE_PERL%%/Bio/Tools/Run/Newbler.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phrap.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/FastTree.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Gerp.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/Gumby.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/Base.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
@@ -96,7 +74,6 @@ bin/bp_run_protdist
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
-%%SITE_PERL%%/Bio/Tools/Run/Phylo/PhyloBase.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phyml.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/QuickTree.pm
 %%SITE_PERL%%/Bio/Tools/Run/Phylo/Raxml.pm
@@ -120,12 +97,9 @@ bin/bp_run_protdist
 %%SITE_PERL%%/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm
 %%SITE_PERL%%/Bio/Tools/Run/StandAloneNCBIBlast.pm
 %%SITE_PERL%%/Bio/Tools/Run/StandAloneWUBlast.pm
-%%SITE_PERL%%/Bio/Tools/Run/TigrAssembler.pm
 %%SITE_PERL%%/Bio/Tools/Run/Tmhmm.pm
 %%SITE_PERL%%/Bio/Tools/Run/TribeMCL.pm
 %%SITE_PERL%%/Bio/Tools/Run/Vista.pm
-%%SITE_PERL%%/Bio/Tools/Run/WrapperBase.pm
-%%SITE_PERL%%/Bio/Tools/Run/WrapperBase/CommandExts.pm
 %%SITE_PERL%%/Bio/Tools/Run/tRNAscanSE.pm
 %%PERL5_MAN3%%/Bio::DB::ESoap.3.gz
 %%PERL5_MAN3%%/Bio::DB::ESoap::WSDL.3.gz
@@ -138,12 +112,6 @@ bin/bp_run_protdist
 %%PERL5_MAN3%%/Bio::DB::SoapEUtilities::LinkAdaptor.3.gz
 %%PERL5_MAN3%%/Bio::DB::SoapEUtilities::Result.3.gz
 %%PERL5_MAN3%%/Bio::Factory::EMBOSS.3.gz
-%%PERL5_MAN3%%/Bio::Installer::EMBOSS.3.gz
-%%PERL5_MAN3%%/Bio::Installer::Generic.3.gz
-%%PERL5_MAN3%%/Bio::Installer::Hyphy.3.gz
-%%PERL5_MAN3%%/Bio::Installer::Muscle.3.gz
-%%PERL5_MAN3%%/Bio::Installer::Probcons.3.gz
-%%PERL5_MAN3%%/Bio::Installer::SLR.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Amap.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Blat.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::DBA.3.gz
@@ -160,19 +128,11 @@ bin/bp_run_protdist
 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Proda.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::Sim4.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Alignment::StandAloneFasta.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Analysis.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Analysis::soap.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::AnalysisFactory.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::AnalysisFactory::soap.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::AssemblerBase.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::BEDTools.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::BEDTools::Config.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::BWA.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::BWA::Config.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::BlastPlus.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Bowtie.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Bowtie::Config.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Cap3.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Coil.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::EMBOSSApplication.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::EMBOSSacd.3.gz
@@ -187,17 +147,10 @@ bin/bp_run_protdist
 %%PERL5_MAN3%%/Bio::Tools::Run::Hmmer.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Infernal.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::MCS.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Maq.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Maq::Config.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Match.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Mdust.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Meme.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Minimo.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Newbler.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Phrap.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::FastTree.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Gerp.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Gumby.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Hyphy::Base.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Hyphy::BatchFile.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Hyphy::FEL.3.gz
@@ -218,7 +171,6 @@ bin/bp_run_protdist
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::ProtDist.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::ProtPars.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::Phylo::PhyloBase.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Phyml.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::QuickTree.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Phylo::Raxml.3.gz
@@ -242,10 +194,11 @@ bin/bp_run_protdist
 %%PERL5_MAN3%%/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::StandAloneNCBIBlast.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::StandAloneWUBlast.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::TigrAssembler.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Tmhmm.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::TribeMCL.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::Vista.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::WrapperBase.3.gz
-%%PERL5_MAN3%%/Bio::Tools::Run::WrapperBase::CommandExts.3.gz
 %%PERL5_MAN3%%/Bio::Tools::Run::tRNAscanSE.3.gz
+%%PORTDOCS%%%%DOCSDIR%%/AUTHORS
+%%PORTDOCS%%%%DOCSDIR%%/Changes
+%%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS
+%%PORTDOCS%%%%DOCSDIR%%/README.md

biology/p5-BioPerl/Makefile

@@ -2,94 +2,72 @@
 # $FreeBSD$
 
 PORTNAME=	BioPerl
-PORTVERSION=	1.007002
+PORTVERSION=	1.007005
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
-MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
+MASTER_SITE_SUBDIR=	CPAN:CDRAUG
 PKGNAMEPREFIX=	p5-
+DISTNAME=	${PORTNAME}-1.7.4
 
-MAINTAINER=	perl@FreeBSD.org
+MAINTAINER=	sunpoet@FreeBSD.org
 COMMENT=	Collection of Perl modules for bioinformatics
 
 LICENSE=	ART10 GPLv1+
 LICENSE_COMB=	dual
+LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	${RUN_DEPENDS}
-RUN_DEPENDS=	p5-Algorithm-Munkres>=0:math/p5-Algorithm-Munkres \
+RUN_DEPENDS=	p5-DBI>=0:databases/p5-DBI \
-		p5-Array-Compare>=0:misc/p5-Array-Compare \
+		p5-Data-Stag>=0:devel/p5-Data-Stag \
-		p5-CGI>=0:www/p5-CGI \
-		p5-Clone>=0:devel/p5-Clone \
-		p5-Convert-Binary-C>=0:converters/p5-Convert-Binary-C \
-		p5-DBD-mysql>=0:databases/p5-DBD-mysql \
-		p5-DBI>=0:databases/p5-DBI \
-		p5-Data-Stag>=0.11:devel/p5-Data-Stag \
 		p5-Error>=0:lang/p5-Error \
 		p5-GD>=0:graphics/p5-GD \
-		p5-Graph>=0.50:math/p5-Graph \
+		p5-Graph>=0:math/p5-Graph \
-		p5-GraphViz>=0:graphics/p5-GraphViz \
-		p5-HTML-Parser>=3:www/p5-HTML-Parser \
-		p5-HTML-TableExtract>=0:www/p5-HTML-TableExtract \
 		p5-HTTP-Message>=0:www/p5-HTTP-Message \
 		p5-IO-String>=0:devel/p5-IO-String \
 		p5-IO-stringy>=0:devel/p5-IO-stringy \
-		p5-Inline-C>=0.67:devel/p5-Inline-C \
+		p5-IPC-Run>=0:devel/p5-IPC-Run \
 		p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \
-		p5-PostScript>=0:print/p5-PostScript \
+		p5-Module-Build>=0:devel/p5-Module-Build \
-		p5-SVG>=2.26:textproc/p5-SVG \
-		p5-SVG-Graph>=0.01:graphics/p5-SVG-Graph \
 		p5-Set-Scalar>=0:devel/p5-Set-Scalar \
-		p5-Sort-Naturally>=0:textproc/p5-Sort-Naturally \
+		p5-Test-Most>=0:devel/p5-Test-Most \
-		p5-Spreadsheet-ParseExcel>=0:textproc/p5-Spreadsheet-ParseExcel \
+		p5-Test-RequiresInternet>=0:devel/p5-Test-RequiresInternet \
-		p5-XML-DOM>=0:textproc/p5-XML-DOM \
+		p5-URI>=0:net/p5-URI \
 		p5-XML-DOM-XPath>=0:textproc/p5-XML-DOM-XPath \
+		p5-XML-DOM>=0:textproc/p5-XML-DOM \
 		p5-XML-LibXML>=0:textproc/p5-XML-LibXML \
-		p5-XML-Parser>=0:textproc/p5-XML-Parser \
+		p5-XML-SAX-Base>=0:textproc/p5-XML-SAX-Base \
-		p5-XML-SAX>=0.15:textproc/p5-XML-SAX \
 		p5-XML-SAX-Writer>=0:textproc/p5-XML-SAX-Writer \
-		p5-XML-Simple>=0:textproc/p5-XML-Simple \
+		p5-XML-SAX>=0:textproc/p5-XML-SAX \
 		p5-XML-Twig>=0:textproc/p5-XML-Twig \
-		p5-XML-Writer>=0.400:textproc/p5-XML-Writer \
+		p5-XML-Writer>=0:textproc/p5-XML-Writer \
 		p5-YAML>=0:textproc/p5-YAML \
 		p5-libwww>=0:www/p5-libwww \
 		p5-libxml>=0:textproc/p5-libxml
-TEST_DEPENDS=	p5-Test-Most>=0:devel/p5-Test-Most \
+TEST_DEPENDS=	p5-Test-Memory-Cycle>=0:devel/p5-Test-Memory-Cycle \
-		p5-URI>=0:net/p5-URI
+		p5-Test-Weaken>=0:devel/p5-Test-Weaken
 
 USES=		perl5 shebangfix
-USE_PERL5=	modbuild
+USE_PERL5=	configure
-NO_ARCH=	yes
-SHEBANG_FILES=	scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
 
-PORTDATA=	*
+NO_ARCH=	yes
-PORTDOCS=	*
-PORTEXAMPLES=	*
 
 OPTIONS_DEFINE=	DOCS EXAMPLES PGTEST SQLITETEST
 PGTEST_DESC=	Test PostGreSQL
-SQLITETEST_DESC=	Test SQLite
+SQLITETEST_DESC=Test SQLite
+
 PGTEST_RUN_DEPENDS=	p5-DBD-Pg>=3:databases/p5-DBD-Pg
 PGTEST_BUILD_DEPENDS=	p5-DBD-Pg>=3:databases/p5-DBD-Pg
 SQLITETEST_RUN_DEPENDS=	p5-DBD-SQLite>=1:databases/p5-DBD-SQLite
 SQLITETEST_BUILD_DEPENDS=	p5-DBD-SQLite>=1:databases/p5-DBD-SQLite
 
-post-patch:
+SHEBANG_FILES=	examples/*.pl examples/*/*.pl
-	@${FIND} ${WRKSRC}/examples ${WRKSRC}/deobfuscator -name "*.pl" -o -name "*.cgi" \
-		-o -name "*.PL" | ${XARGS} ${REINPLACE_CMD} -i '' -Ee \
-		'1s|(/usr)?/bin/perl|${PERL}|'
-
-post-install:
-	@${MKDIR} ${STAGEDIR}${DATADIR}
-	${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${STAGEDIR}${DATADIR}
 
 post-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
-.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL.md MANIFEST README.md
+	cd ${WRKSRC} && ${INSTALL_DATA} AUTHORS Changes MANIFEST README.md ${STAGEDIR}${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
-.endfor
-	${CP} -R ${WRKSRC}/deobfuscator ${STAGEDIR}${DOCSDIR}
 
 post-install-EXAMPLES-on:
 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
-	${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR}
+	cd ${WRKSRC}/examples/ && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
 
 .include <bsd.port.mk>

biology/p5-BioPerl/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1505232617
+TIMESTAMP = 1550843244
-SHA256 (BioPerl-1.007002.tar.gz) = 17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1
+SHA256 (BioPerl-1.7.4.tar.gz) = 5a074947bba299cdb47cbf1c66689502db02c022fc138459e3393da45d7c707b
-SIZE (BioPerl-1.007002.tar.gz) = 12362741
+SIZE (BioPerl-1.7.4.tar.gz) = 7642013

biology/p5-BioPerl/files/patch-Bio-Root-Build.pm

@@ -1,80 +0,0 @@
---- Bio/Root/Build.pm.orig	2014-07-10 20:13:23 UTC
-+++ Bio/Root/Build.pm
-@@ -83,49 +83,9 @@
-         }
-     }
-     closedir($scripts_dir);
--    my $question = $int_ok ? "Install [a]ll BioPerl scripts, [n]one, ".
--        "or choose groups [i]nteractively?" : "Install [a]ll BioPerl scripts ".
--        "or [n]one?";
--
--    my $prompt = $accept ? 'a' : $self->prompt($question, 'a');
--
--    if ($prompt =~ /^[aA]/) {
--        $self->log_info("  - will install all scripts\n");
--        $self->notes(chosen_scripts => 'all');
--    }
--    elsif ($prompt =~ /^[iI]/) {
--        $self->log_info("  - will install interactively:\n");
--
--        my @chosen_scripts;
--        foreach my $group_dir (@group_dirs) {
--            my $group = File::Basename::basename($group_dir);
--            print "    * group '$group' has:\n";
--
--            my @script_files = @{$self->rscan_dir($group_dir, qr/\.PLS$|\.pl$/)};
--            foreach my $script_file (@script_files) {
--                my $script = File::Basename::basename($script_file);
--                print "      $script\n";
--            }
--
--            my $result = $self->prompt("    Install scripts for group '$group'? [y]es [n]o [q]uit", 'n');
--            die if $result =~ /^[qQ]/;
--            if ($result =~ /^[yY]/) {
--                $self->log_info("      + will install group '$group'\n");
--                push(@chosen_scripts, @script_files);
--            }
--            else {
--                $self->log_info("      - will not install group '$group'\n");
--            }
--        }
- 
--        my $chosen_scripts = @chosen_scripts ? join("|", @chosen_scripts) : 'none';
--
--        $self->notes(chosen_scripts => $chosen_scripts);
--    }
--    else {
--        $self->log_info("  - won't install any scripts\n");
--        $self->notes(chosen_scripts => 'none');
--    }
-+    $self->log_info("  - willt install all scripts\n");
-+    $self->notes(chosen_scripts => 'all');
- 
-     print "\n";
- }
-@@ -1153,22 +1113,9 @@
- sub prompt_for_network {
-     my ($self, $accept) = @_;
- 
--    my $proceed = $accept ? 0 : $self->y_n(  "Do you want to run tests that require connection to servers across the internet\n"
--                                           . "(likely to cause some failures)? y/n", 'n');
--
--    if ($proceed) {
--        $self->notes('network' => 1);
--        $self->log_info("  - will run internet-requiring tests\n");
--        my $use_email = $self->y_n("Do you want to run tests requiring a valid email address? y/n",'n');
--        if ($use_email) {
--            my $address = $self->prompt("Enter email address:");
--            $self->notes(email => $address);
--        }
--    }
--    else {
--        $self->notes(network => 0);
--        $self->log_info("  - will not run internet-requiring tests\n");
--    }
-+    my $proceed = 0;
-+    $self->notes(network => 0);
-+    $self->log_info("  - will not run internet-requiring tests\n");
- }
- 
- =head2 print_build_script

biology/p5-BioPerl/files/patch-Build.PL

@@ -1,114 +0,0 @@
---- Build.PL.orig	2016-11-06 03:59:41 UTC
-+++ Build.PL
-@@ -226,7 +226,6 @@ my $build = Bio::Root::Build->new(
- 
-     build_requires => {
-         'Module::Build' => 0.42,
--        'CPAN'          => 1.81,
-         'Test::Harness' => 2.62,
-         'Test::Most'    => 0,
-         'URI::Escape'   => 0
-@@ -413,101 +412,8 @@ sub test_biodbgff {
- 
- sub prompt_for_biodb {
-     my $accept = shift;
--    my $proceed = $accept ? 0 : $build->y_n(
--        "Do you want to run the Bio::DB::GFF or "
--            . "Bio::DB::SeqFeature::Store live database tests? " . "y/n",
--        'n'
--    );
--
--    if ($proceed) {
--        my @driver_choices;
--        foreach my $poss ( 'SQLite', 'mysql', 'Pg', 'Oracle' ) {
--            if ( grep {/$poss/i} @drivers ) {
--                my $choice = $poss;
--                $choice =~ s/^(.)/[$1]/;
--                push( @driver_choices, $choice );
--            }
--        }
--
--        my $driver;
--        if ( @driver_choices > 1 ) {
--            my ($default) = $driver_choices[0] =~ /\[(.)/;
--            $driver = $build->prompt(
--                "Which database driver should be used? "
--                    . join( " ", @driver_choices ),
--                $default
--            );
--        } else {
--            ($driver) = $driver_choices[0] =~ /\[(.)/;
--        }
--        if ( $driver =~ /^[mM]/ ) {
--            $driver = 'mysql';
--        } elsif ( $driver =~ /^[pP]/ ) {
--            $driver = 'Pg';
--        } elsif ( $driver =~ /^[oO]/ ) {
--            $driver = 'Oracle';
--        } elsif ( $driver =~ /^[sS]/ ) {
--            $driver = 'SQLite';
--        }
--
--        my $test_db = $build->prompt(
--            "Which database should I use for testing the $driver driver?\n"
--                . "This database should already be present but doesn't have to "
--                . "be preloaded for any schema",
--            'test'
--        );
--        my $test_host = $build->prompt(
--            "On which host is database '$test_db' running (hostname, ip address or host:port)",
--            'localhost'
--        );
--        my $test_user = $build->prompt(
--            "User name for connecting to database '$test_db'?", 'undef' );
--        my $test_pass = $build->prompt(
--            "Password for connecting to database '$test_db'?", 'undef' );
--
--        my $use_host = 1;
--        if ( $test_host eq 'undef' || $test_host eq 'localhost' ) {
--            $use_host = 0;
--        }
--
--        my $test_dsn;
--        if ( $driver eq 'Pg' || $driver eq 'SQLite' ) {
--            $test_dsn = "dbi:$driver:dbname=$test_db";
--            $mysql_ok = 0;
--        } else {
--            $test_dsn = "dbi:$driver:database=$test_db";
--            $mysql_ok = 0;
--        }
--        if ($use_host) {
--            $test_dsn .= ";host=$test_host";
--        }
--
--        $build->notes( dbd_driver => $driver );
--        $build->notes( test_db    => $test_db );
--        $build->notes( test_host  => $test_host );
--        $build->notes(
--            test_user => $test_user eq 'undef' ? undef : $test_user );
--        $build->notes(
--            test_pass => $test_pass eq 'undef' ? undef : $test_pass );
--        $build->notes( test_dsn => $test_dsn );
--
--        $build->log_info(
--            "  - will run tests with database driver '$driver' and these settings:\n",
--            "    Database $test_db\n",
--            "    Host     $test_host\n",
--            "    DSN      $test_dsn\n",
--            "    User     $test_user\n",
--            "    Password $test_pass\n"
--        );
--        $build->log_info( "  - will not run the BioDBSeqFeature live "
--                . "database tests (requires MySQL or Pg driver)\n" )
--            unless ( $driver eq 'mysql' or $driver eq 'Pg' );
--    } else {
--        $build->log_info(
--            "  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"
--        );
--    }
--
-+    my $proceed = 0;
-+    $build->log_info("  - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
-     $build->log_info("\n");
-     return $proceed;
- }

biology/pbbam/Makefile

@@ -1,8 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	pbbam
-DISTVERSION=	g20180416
+DISTVERSION=	0.18.0 # Test with biology/unanimity before upgrading!
-PORTREVISION=	3
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -11,26 +10,24 @@ COMMENT=	PacBio BAM C++ library, with SWIG bindings
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
-BUILD_DEPENDS=	boost-libs>=1.60.0:devel/boost-libs
 LIB_DEPENDS=	libhts.so:biology/htslib \
 		libboost_regex.so:devel/boost-libs
 
-USES=		cmake compiler:c++14-lang pkgconfig
+# Meson needs BOOST_ROOT=${LOCALBASE}
+# https://github.com/mesonbuild/meson/issues/2239
+USES=		compiler:c++14-lang localbase meson pkgconfig python
+USE_LDCONFIG=	yes
 USE_GITHUB=	yes
 GH_ACCOUNT=	PacificBiosciences
-GH_TAGNAME=	c6b8113adb5104948879e9ff69f739121f12a09f
 
-# Disable tests for now.  Bound to bundled googletest.
+pre-configure:
-CMAKE_ARGS+=	-DHTSLIB_INCLUDE_DIRS:STRING=${LOCALBASE}/include/htslib \
+	@${REINPLACE_CMD} -e "s|'python'|'${PYTHON_VERSION}'|g" \
-		-DHTSLIB_LIBRARIES:STRING="-L${LOCALBASE}/lib -lhts" \
+		${WRKSRC}/meson.build
-		-DPacBioBAM_build_tests:BOOL=OFF \
-		-DPacBioBAM_build_docs:BOOL=OFF
 
-do-install:
+post-install:
-	${INSTALL_PROGRAM} ${BUILD_WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin
+	${RLN} ${STAGEDIR}${PREFIX}/lib/libpbbam.so.${PORTVERSION} \
-	${INSTALL_DATA} ${BUILD_WRKSRC}/lib/* ${STAGEDIR}${PREFIX}/lib
+		${STAGEDIR}${PREFIX}/lib/libpbbam.so.0.18
-	cd ${WRKSRC}/include && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include
+	${RLN} ${STAGEDIR}${PREFIX}/lib/libpbbam.so.${PORTVERSION} \
-	${MV} ${STAGEDIR}${PREFIX}/include/meson.build \
+		${STAGEDIR}${PREFIX}/lib/libpbbam.so.0
-		${STAGEDIR}${PREFIX}/include/pbbam
 
 .include <bsd.port.mk>

biology/pbbam/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1524331626
+TIMESTAMP = 1550453627
-SHA256 (PacificBiosciences-pbbam-g20180416-c6b8113adb5104948879e9ff69f739121f12a09f_GH0.tar.gz) = f7ede42417110db4fcc3fbc4b837911a0e2242e541a88c8ac34b4c26b4e5aad4
+SHA256 (PacificBiosciences-pbbam-0.18.0_GH0.tar.gz) = 45286e5f7deb7ff629e0643c8a416155915aec7b85d54c60b5cdc07f4d7b234a
-SIZE (PacificBiosciences-pbbam-g20180416-c6b8113adb5104948879e9ff69f739121f12a09f_GH0.tar.gz) = 8105156
+SIZE (PacificBiosciences-pbbam-0.18.0_GH0.tar.gz) = 8136503

biology/pbbam/files/patch-meson__options.txt

@@ -0,0 +1,11 @@
+--- meson_options.txt.orig	2019-02-17 01:55:33 UTC
++++ meson_options.txt
+@@ -15,7 +15,7 @@ option('auto-validate',
+ 
+ option('tests',
+     type : 'boolean',
+-    value : true,
++    value : false,
+     description : 'Enable dependencies required for testing')
+ 
+ option('permissive-cigar',

biology/pbbam/pkg-plist

@@ -118,7 +118,19 @@ include/pbbam/internal/ReadGroupInfo.inl
 include/pbbam/internal/SequenceInfo.inl
 include/pbbam/internal/Tag.inl
 include/pbbam/internal/Validator.inl
-include/pbbam/meson.build
+include/pbbam/vcf/VcfFile.h
+include/pbbam/vcf/VcfFormat.h
+include/pbbam/vcf/VcfHeader.h
+include/pbbam/vcf/VcfHeaderTypes.h
+include/pbbam/vcf/VcfQuery.h
+include/pbbam/vcf/VcfReader.h
+include/pbbam/vcf/VcfSort.h
+include/pbbam/vcf/VcfVariant.h
+include/pbbam/vcf/VcfWriter.h
+include/pbbam/vcf/internal/VcfFile.inl
+include/pbbam/vcf/internal/VcfHeader.inl
+include/pbbam/vcf/internal/VcfHeaderTypes.inl
+include/pbbam/vcf/internal/VcfVariant.inl
 include/pbbam/virtual/VirtualPolymeraseBamRecord.h
 include/pbbam/virtual/VirtualPolymeraseCompositeReader.h
 include/pbbam/virtual/VirtualPolymeraseReader.h
@@ -129,4 +141,8 @@ include/pbbam/virtual/VirtualZmwBamRecord.h
 include/pbbam/virtual/WhitelistedZmwReadStitcher.h
 include/pbbam/virtual/ZmwReadStitcher.h
 include/pbbam/virtual/ZmwWhitelistVirtualReader.h
-lib/libpbbam.a
+lib/libpbbam.so
+lib/libpbbam.so.0
+lib/libpbbam.so.0.18
+lib/libpbbam.so.0.18.0
+libdata/pkgconfig/pbbam.pc

biology/pbcopper/Makefile

@@ -1,8 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	pbcopper
-DISTVERSION=	g20180413
+DISTVERSION=	0.4.1 # Test with biology/unanimity before upgrading!
-PORTREVISION=	3
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -13,17 +12,17 @@ LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
 LIB_DEPENDS=	libboost_regex.so:devel/boost-libs
 
-USES=		cmake compiler:c++14-lang
+# Meson needs BOOST_ROOT=${LOCALBASE}
-# Although there are a couple releases, git describe --tags does not work
+# https://github.com/mesonbuild/meson/issues/2239
-# so we cannot use the usual USE_GITHUB tools here.
+USES=		compiler:c++14-lang localbase meson
+USE_LDCONFIG=	yes
 USE_GITHUB=	yes
 GH_ACCOUNT=	PacificBiosciences
-GH_TAGNAME=	17ef457a0dbe1894a8d17af7ddba01a6261bf117
 
-do-install:
+post-install:
-	${INSTALL_DATA} ${BUILD_WRKSRC}/lib/*.a ${STAGEDIR}${PREFIX}/lib
+	${RLN} ${STAGEDIR}${PREFIX}/lib/libpbcopper.so.${PORTVERSION} \
-	cd ${WRKSRC}/include && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include
+		${STAGEDIR}${PREFIX}/lib/libpbcopper.so.0.4
-	${MV} ${STAGEDIR}${PREFIX}/include/meson.build \
+	${RLN} ${STAGEDIR}${PREFIX}/lib/libpbcopper.so.${PORTVERSION} \
-		${STAGEDIR}${PREFIX}/include/pbcopper
+		${STAGEDIR}${PREFIX}/lib/libpbcopper.so.0
 
 .include <bsd.port.mk>

biology/pbcopper/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1524500014
+TIMESTAMP = 1550453144
-SHA256 (PacificBiosciences-pbcopper-g20180413-17ef457a0dbe1894a8d17af7ddba01a6261bf117_GH0.tar.gz) = 13f006d53334a0538657e0ba5c6e02f811f1901cd25fce220fc9011726ffe23f
+SHA256 (PacificBiosciences-pbcopper-0.4.1_GH0.tar.gz) = 4c8daf6c1a6efe3860a16fb5b6111ebe65221423254819f3a68a400d0a984fcd
-SIZE (PacificBiosciences-pbcopper-g20180413-17ef457a0dbe1894a8d17af7ddba01a6261bf117_GH0.tar.gz) = 3033636
+SIZE (PacificBiosciences-pbcopper-0.4.1_GH0.tar.gz) = 3095846

biology/pbcopper/files/patch-cmake_pbcopper-gitsha1.cmake

@@ -1,21 +0,0 @@
---- cmake/pbcopper-gitsha1.cmake.orig	2018-03-16 16:16:38 UTC
-+++ cmake/pbcopper-gitsha1.cmake
-@@ -5,16 +5,15 @@ endif()
- set(__find_git_sha1 YES)
- 
- function(find_git_sha1 _GIT_SHA1)
--    find_package(Git QUIET REQUIRED)
-     execute_process(COMMAND
--        "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=*"
-+        echo ce9a4b6
-         WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
-         RESULT_VARIABLE res
-         OUTPUT_VARIABLE out
-         ERROR_QUIET
-         OUTPUT_STRIP_TRAILING_WHITESPACE)
-     if (NOT res EQUAL 0)
--        message(FATAL_ERROR "Could not determine git sha1 via `git describe --always --dirty=*`")
-+        message(FATAL_ERROR "Could not determine git sha1")
-     endif()
-     set(${_GIT_SHA1} "${out}" PARENT_SCOPE)
- endfunction()

biology/pbcopper/files/patch-meson__options.txt

@@ -0,0 +1,7 @@
+--- meson_options.txt.orig	2019-02-17 22:34:29 UTC
++++ meson_options.txt
+@@ -1,3 +1,3 @@
+ option('build-examples', type : 'boolean', value : true,  description : 'Build pbcopper examples')
+ option('build-docs',     type : 'boolean', value : false, description : 'Build pbcopper docs')
+-option('tests',          type : 'boolean', value : true,  description : 'Enable dependencies required for testing')
++option('tests',          type : 'boolean', value : false,  description : 'Enable dependencies required for testing')

biology/pbcopper/pkg-plist

@@ -1,4 +1,5 @@
 include/pbcopper/PbcopperConfig.h
+include/pbcopper/PbcopperMakeUnique.h
 include/pbcopper/align/Seed.h
 include/pbcopper/align/Seeds.h
 include/pbcopper/align/internal/Seed-inl.h
@@ -23,7 +24,6 @@ include/pbcopper/cli/toolcontract/ResolvedToolContract.h
 include/pbcopper/cli/toolcontract/ResourceType.h
 include/pbcopper/cli/toolcontract/Task.h
 include/pbcopper/cli/toolcontract/TaskType.h
-include/pbcopper/cli/toolcontract/internal/Config-inl.h
 include/pbcopper/cli/toolcontract/internal/Driver-inl.h
 include/pbcopper/cli/toolcontract/internal/InputFileType-inl.h
 include/pbcopper/cli/toolcontract/internal/OutputFileType-inl.h
@@ -48,7 +48,6 @@ include/pbcopper/json/JSON.h
 include/pbcopper/json/internal/json.hpp
 include/pbcopper/logging/Logging.h
 include/pbcopper/logging/internal/Logging-inl.h
-include/pbcopper/meson.build
 include/pbcopper/parallel/FireAndForget.h
 include/pbcopper/parallel/WorkQueue.h
 include/pbcopper/qgram/Index.h
@@ -72,4 +71,8 @@ include/pbcopper/utility/internal/FileUtils-inl.h
 include/pbcopper/utility/internal/Stopwatch-inl.h
 include/pbcopper/utility/internal/StringUtils-inl.h
 include/pbcopper/utility/internal/SystemInfo-inl.h
-lib/libpbcopper.a
+lib/libpbcopper.so
+lib/libpbcopper.so.0
+lib/libpbcopper.so.0.4
+lib/libpbcopper.so.0.4.1
+libdata/pkgconfig/pbcopper.pc

biology/pbseqan/Makefile

@@ -1,7 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	pbseqan
-DISTVERSION=	g20171002
+DISTVERSION=	g20171011
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -10,16 +10,18 @@ COMMENT=	Pacific Biosciences patched and stripped down SeqAn
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
+DEPRECATED=	Upstream merged into SeqAn project: Use biology/seqan
+
 USE_GITHUB=	yes
 GH_ACCOUNT=	PacificBiosciences
 GH_PROJECT=	seqan
-GH_TAGNAME=	d01138731be5d54ef4948053493408075f19e0b1
+GH_TAGNAME=	21d95d737d8decb5cc3693b9065d81e831e7f57d
 
 NO_BUILD=	yes
 NO_ARCH=	yes
 
 do-install:
-	${MKDIR} ${STAGEDIR}${PREFIX}/include/PacBio
+	@${MKDIR} ${STAGEDIR}${PREFIX}/include/PacBio
 	cd ${WRKSRC}/include/seqan && \
 		${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include/PacBio/seqan
 

biology/pbseqan/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1524324484
+TIMESTAMP = 1550366556
-SHA256 (PacificBiosciences-seqan-g20171002-d01138731be5d54ef4948053493408075f19e0b1_GH0.tar.gz) = c17d3935405a3282b59ae30e4bcc8e1e690342318aa8e46257a52b2704b92460
+SHA256 (PacificBiosciences-seqan-g20171011-21d95d737d8decb5cc3693b9065d81e831e7f57d_GH0.tar.gz) = dcdc564c877190089bd691ab4097164266e675217645613426fb1ff44029da8c
-SIZE (PacificBiosciences-seqan-g20171002-d01138731be5d54ef4948053493408075f19e0b1_GH0.tar.gz) = 1527074
+SIZE (PacificBiosciences-seqan-g20171011-21d95d737d8decb5cc3693b9065d81e831e7f57d_GH0.tar.gz) = 1527033

biology/unanimity/Makefile

@@ -2,8 +2,7 @@
 
 PORTNAME=		unanimity
 DISTVERSIONPREFIX=	v
-DISTVERSION=		3.1.0
+DISTVERSION=		3.4.1
-PORTREVISION=		2
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -14,30 +13,31 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BROKEN_aarch64=		fails to compile: mmintrin.h:47:5: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
 
-# Sensitive to dependency versions, use latest commit for everything
+# Very sensitive to pbbam and pbcopper versions!
-BUILD_DEPENDS=	pbseqan>=g20171002:biology/pbseqan \
+# Fully test new combinations and upgrade them together.
-		pbbam>=g20180416:biology/pbbam \
+BUILD_DEPENDS=	seqan>=2.4.0:biology/seqan \
-		pbcopper>=g20180413:biology/pbcopper
+		swig30>=3.0:devel/swig30 \
+		${PYNUMPY}
 LIB_DEPENDS=	libhts.so:biology/htslib \
-		libboost_regex.so:devel/boost-libs
+		libboost_regex.so:devel/boost-libs \
+		libpbbam.so.0.18.0:biology/pbbam \
+		libpbcopper.so.0.4.1:biology/pbcopper
+RUN_DEPENDS=	${PYNUMPY}
 
-USES=		cmake:insource compiler:c++14-lang pkgconfig python
+# Meson needs BOOST_ROOT=${LOCALBASE}
+# https://github.com/mesonbuild/meson/issues/2239
+USES=		compiler:c++14-lang localbase meson pkgconfig python:2.7
+USE_LDCONFIG=	yes
 USE_GITHUB=	yes
 GH_ACCOUNT=	PacificBiosciences
 
-CMAKE_ARGS+=	-DHTSLIB_INCLUDE_DIRS:STRING=${LOCALBASE}/include/htslib \
-		-DHTSLIB_LIBRARIES:STRING="-L${LOCALBASE}/lib -lhts" \
-		-DPacBioBAM_INCLUDE_DIRS:STRING=${LOCALBASE}/include/pbbam \
-		-DPacBioBAM_LIBRARIES:STRING="-L${LOCALBASE}/lib -lpbbam" \
-		-DSEQAN_INCLUDE_DIRS:STRING=${LOCALBASE}/include/PacBio \
-		-Dpbcopper_INCLUDE_DIRS=${LOCALBASE}/include \
-		-Dpbcopper_LIBRARIES="-L${LOCALBASE}/lib -lpbcopper"
 CFLAGS_i386=	-msse2 -Wno-c++11-narrowing
-
+LDFLAGS+=	-lexecinfo
-PLIST_FILES=	bin/arrow bin/ccs bin/gcpp lib/libcc2.a lib/libunanimity.a
 
 post-install:
-	${INSTALL_DATA} ${WRKSRC}/src/libcc2.a ${WRKSRC}/src/libunanimity.a \
+	${RLN} ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0.0 \
-		${STAGEDIR}${PREFIX}/lib
+		${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0
+	${RLN} ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0.0 \
+		${STAGEDIR}${PREFIX}/lib/libunanimity.so.3
 
 .include <bsd.port.mk>

biology/unanimity/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1534907295
+TIMESTAMP = 1551014614
-SHA256 (PacificBiosciences-unanimity-v3.1.0_GH0.tar.gz) = 355866bd3f83bf1f7c322269c01d3c2f943e30942455741d6e802b0ad3f89912
+SHA256 (PacificBiosciences-unanimity-v3.4.1_GH0.tar.gz) = fccb2cf14cdc324592724df5699a113a04ce6d4f40f00c68ca3df541e17b4f35
-SIZE (PacificBiosciences-unanimity-v3.1.0_GH0.tar.gz) = 6493202
+SIZE (PacificBiosciences-unanimity-v3.4.1_GH0.tar.gz) = 6493661

biology/unanimity/files/patch-CMakeLists.txt

@@ -1,11 +0,0 @@
---- CMakeLists.txt.orig	2018-03-07 23:10:34 UTC
-+++ CMakeLists.txt
-@@ -37,7 +37,7 @@ include(uny-ccache)
- include(uny-releasewithassert)
- include(uny-dependencies)
- include(uny-compilerflags)
--include(uny-gitsha1)
-+# include(uny-gitsha1)
- include(uny-config)
- 
- # Build library

biology/unanimity/files/patch-cmake_uny-config.cmake

@@ -1,10 +0,0 @@
---- cmake/uny-config.cmake.orig	2016-09-12 19:55:43 UTC
-+++ cmake/uny-config.cmake
-@@ -1,6 +1,6 @@
- # Config generation
- 
--find_git_sha1(UNANIMITY_GIT_SHA1)
-+# find_git_sha1(UNANIMITY_GIT_SHA1)
- 
- file (STRINGS "${UNY_RootDir}/CHANGELOG.md" UNANIMITY_CHANGELOG)
- 

biology/unanimity/files/patch-cmake_uny-gitsha1.cmake

@@ -1,11 +0,0 @@
---- cmake/uny-gitsha1.cmake.orig	2018-03-07 23:10:34 UTC
-+++ cmake/uny-gitsha1.cmake
-@@ -7,7 +7,7 @@ set(__find_git_sha1 YES)
- function(find_git_sha1 _GIT_SHA1)
-     find_package(Git QUIET REQUIRED)
-     execute_process(COMMAND
--        "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=-dirty"
-+        echo 6f11a13e1472b8c00337ba8c5e94bf83bdab31d6
-         WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
-         RESULT_VARIABLE res
-         OUTPUT_VARIABLE out

biology/unanimity/files/patch-meson.build

@@ -0,0 +1,11 @@
+--- meson.build.orig	2019-02-17 22:59:57 UTC
++++ meson.build
+@@ -90,7 +90,7 @@ subdir('src')
+ 
+ if (not meson.is_subproject()) and get_option('swig')
+   uny_python_interp = find_program(get_option('PYTHON'), required : true)
+-  uny_swig = find_program('swig', required : true)
++  uny_swig = find_program('swig3.0', required : true)
+ 
+   uny_pv_ver = run_command(uny_python_interp, ['-c', 'import sys; sys.stdout.write(sys.version[:3])']).stdout()
+   message('Python version: ' + uny_pv_ver)

biology/unanimity/files/patch-meson__options.txt

@@ -0,0 +1,8 @@
+--- meson_options.txt.orig	2019-02-17 22:53:47 UTC
++++ meson_options.txt
+@@ -1,4 +1,4 @@
+-option('tests',            type : 'boolean', value : true,  description : 'Enable dependencies required for testing')
++option('tests',            type : 'boolean', value : false,  description : 'Enable dependencies required for testing')
+ 
+ # python:
+ option('swig',             type : 'boolean', value : true,        description : 'Build UNANMITIY\'s SWIG interfacing code')

biology/unanimity/files/patch-src_CMakeLists.txt

@@ -1,15 +0,0 @@
---- src/CMakeLists.txt.orig	2018-03-07 23:10:34 UTC
-+++ src/CMakeLists.txt
-@@ -53,11 +53,11 @@ configure_file(
- 
- # includes
- set(UNY_INCLUDE_DIRS
-+    ${SEQAN_INCLUDE_DIRS}
-     ${UNY_IncludeDir}
-     ${CMAKE_BINARY_DIR}/generated
-     ${Boost_INCLUDE_DIRS}
-     ${HTSLIB_INCLUDE_DIRS}
--    ${SEQAN_INCLUDE_DIRS}
-     ${CPPOPTPARSE_IncludeDir}
-     ${PacBioBAM_INCLUDE_DIRS}
-     ${pbcopper_INCLUDE_DIRS}

biology/unanimity/files/patch-src_variantCaller_variantCaller.cpp

@@ -0,0 +1,9 @@
+--- src/variantCaller/variantCaller.cpp.orig	2019-02-17 23:15:10 UTC
++++ src/variantCaller/variantCaller.cpp
+@@ -1,5 +1,6 @@
+ // Author: David Seifert
+ 
++#include <iostream>
+ #include <fstream>
+ #include <string>
+ 

biology/unanimity/pkg-plist

@@ -0,0 +1,82 @@
+bin/ChimeraLabeler
+bin/arrow
+bin/ccs
+bin/ccs_sim
+bin/gcpp
+bin/genomic_sim
+bin/variantCaller
+include/pacbio/UnanimityConfig.h
+include/pacbio/UnanimityVersion.h
+include/pacbio/align/AffineAlignment.h
+include/pacbio/align/AlignConfig.h
+include/pacbio/align/BandedAligner.h
+include/pacbio/align/BandedChainAlignment.h
+include/pacbio/align/ChainScorer.h
+include/pacbio/align/ChainSeeds.h
+include/pacbio/align/ChainSeedsConfig.h
+include/pacbio/align/FilterSeeds.h
+include/pacbio/align/FindSeeds.h
+include/pacbio/align/FindSeedsConfig.h
+include/pacbio/align/HomopolymerHasher.h
+include/pacbio/align/LinearAlignment.h
+include/pacbio/align/LocalAlignment.h
+include/pacbio/align/PairwiseAlignment.h
+include/pacbio/align/SeedScorer.h
+include/pacbio/align/SparseAlignment.h
+include/pacbio/align/internal/BCAlignBlocks.h
+include/pacbio/align/internal/BCAlignImpl.h
+include/pacbio/ccs/Consensus.h
+include/pacbio/ccs/ConsensusSettings.h
+include/pacbio/ccs/SparseAlignment.h
+include/pacbio/ccs/Whitelist.h
+include/pacbio/chimera/ChimeraLabel.h
+include/pacbio/chimera/ChimeraLabeler.h
+include/pacbio/chimera/ChimeraResultWriter.h
+include/pacbio/consensus/AbstractMatrix.h
+include/pacbio/consensus/Coverage.h
+include/pacbio/consensus/EasyReadScorer.h
+include/pacbio/consensus/Evaluator.h
+include/pacbio/consensus/Integrator.h
+include/pacbio/consensus/IntervalMask.h
+include/pacbio/consensus/MatrixViewConvention.h
+include/pacbio/consensus/ModelConfig.h
+include/pacbio/consensus/ModelSelection.h
+include/pacbio/consensus/Mutation.h
+include/pacbio/consensus/Polish.h
+include/pacbio/consensus/PolishResult.h
+include/pacbio/consensus/Template.h
+include/pacbio/consensus/internal/ModelInternalInitializer.h
+include/pacbio/data/ChemistryMapping.h
+include/pacbio/data/ChemistryTriple.h
+include/pacbio/data/Interval.h
+include/pacbio/data/IntervalTree.h
+include/pacbio/data/PlainOption.h
+include/pacbio/data/Read.h
+include/pacbio/data/ReadId.h
+include/pacbio/data/Sequence.h
+include/pacbio/data/State.h
+include/pacbio/data/StrandType.h
+include/pacbio/data/SubreadResultCounter.h
+include/pacbio/data/internal/BaseEncoding.h
+include/pacbio/data/internal/ConversionFunctions.h
+include/pacbio/denovo/PoaConsensus.h
+include/pacbio/denovo/PoaGraph.h
+include/pacbio/denovo/RangeFinder.h
+include/pacbio/denovo/SparsePoa.h
+include/pacbio/exception/CCSExceptions.h
+include/pacbio/exception/InvalidEvaluatorException.h
+include/pacbio/exception/ModelError.h
+include/pacbio/exception/StateError.h
+include/pacbio/io/Utility.h
+include/pacbio/parallel/WorkQueue.h
+include/pacbio/util/ExecUtils.h
+include/pacbio/util/Timer.h
+lib/libunanimity.so
+lib/libunanimity.so.3
+lib/libunanimity.so.3.0
+lib/libunanimity.so.3.0.0
+%%PYTHON_SITELIBDIR%%/ConsensusCore2.py
+%%PYTHON_SITELIBDIR%%/ConsensusCore2.pyc
+%%PYTHON_SITELIBDIR%%/ConsensusCore2.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/_ConsensusCore2.so
+libdata/pkgconfig/unanimity.pc