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Code Issues Releases Wiki Activity

*/*: sync with upstream 

Taken from: HardenedBSD
This commit is contained in:
Franco Fichtner 2019-02-24 01:48:26 +01:00
parent b5b6c6e743
commit 6a73ac9889
1979 changed files with 18187 additions and 17402 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

22
accessibility/qt5-speech/Makefile
View File

@ -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 pkgconfig qmake:outsource qt-dist:5,speech
USES= compiler:c++11-lang gl pkgconfig qmake:outsource qt-dist:5,speech
USE_GL= gl
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>

18
accessibility/qt5-speech/files/patch-qtspeech.pro Normal file
View File

@ -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)

31
accessibility/qt5-speech/files/patch-src_plugins_tts_tts.pro Normal file
View File

@ -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
+ }
}

9
accessibility/qt5-speech/pkg-plist
View File

@ -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
%%DEBUG%%%%QT_PLUGINDIR%%/texttospeech/libqtexttospeech_speechd.so.debug
%%FLITE%%%%QT_PLUGINDIR%%/texttospeech/libqttexttospeech_flite.so
%%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

2
accessibility/rubygem-atk/Makefile
View File

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

6
accessibility/rubygem-atk/distinfo
View File

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

5
archivers/py-brotli/Makefile
View File

@ -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>

35
archivers/zip-ada/Makefile
View File

@ -2,8 +2,7 @@
# $FreeBSD$
PORTNAME= zip-ada
PORTVERSION= 52
PORTREVISION= 1
DISTVERSION= 55
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 \
find_zip \
rezip \
za_gnat \
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
ZTOOLS= bunzip bwt_dec bwt_enc comp_zip find_zip lzhuf \
lzma_dec lzma_enc rezip unzipada zipada
DEMOS= bwt_demo demo_csv_into_zip demo_unzip demo_zip
OPTIONS_DEFINE= EXAMPLES

6
archivers/zip-ada/distinfo
View File

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

40
archivers/zip-ada/pkg-plist
View File

@ -1,18 +1,18 @@
bin/bwt_dec
bin/bwt_enc
bin/comp_zip
bin/debzip2
bin/find_zip
bin/lz
bin/lz77_stats
bin/lzhuf
bin/lzma_dec
bin/lzma_enc
bin/random_data
bin/rezip
bin/rz_gnat
bin/several_sizes
bin/za_gnat
bin/unzipada
bin/zipada
include/zip-ada/bzip2_decoding.adb
include/zip-ada/bzip2_decoding.ads
include/zip-ada/bzip2-decoding.adb
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/tb_wrap.ali
lib/zip-ada/summary.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

2
astro/mkgmap/Makefile
View File

@ -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/

6
astro/mkgmap/distinfo
View File

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

10
astro/opencpn/Makefile
View File

@ -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>

3
astro/qmapshack/Makefile
View File

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

6
astro/qmapshack/distinfo
View File

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

2
astro/viking/pkg-descr
View File

@ -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/

2
astro/xplanet/Makefile
View File

@ -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

1
audio/Makefile
View File

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

10
audio/amarok/Makefile
View File

@ -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

12
audio/amarok/pkg-plist
View File

@ -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
%%QT_QMLDIR%%/org/kde/amarok/wikipedia/qmldir
%%QTWEBENGINE%%%%QT_QMLDIR%%/org/kde/amarok/wikipedia/libamarok_context_applet_wikipedia.so
%%QTWEBENGINE%%%%QT_QMLDIR%%/org/kde/amarok/wikipedia/qmldir
%%DATADIR%%/data/DefaultPlaylistLayouts.xml
%%DATADIR%%/data/InfoParserLoading.html
%%DATADIR%%/data/WikipediaCustomStyle.css
%%DATADIR%%/data/bullet.gif
%%QTWEBENGINE%%%%DATADIR%%/data/WikipediaCustomStyle.css
%%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
share/kpackage/amarok/org.kde.amarok.wikipedia/metadata.json
%%QTWEBENGINE%%share/kpackage/amarok/org.kde.amarok.wikipedia/contents.rcc
%%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

4
audio/beets/Makefile
View File

@ -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} \

30
audio/fmit/Makefile
View File

@ -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
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
OSS_QMAKE_ON= CONFIG+=acs_oss
JACK_LIB_DEPENDS= libjack.so:audio/jack
JACK_CMAKE_ON= -DSOUNDSYSTEM_USE_JACK:BOOL=true
JACK_CMAKE_OFF= -DSOUNDSYSTEM_USE_JACK:BOOL=false
JACK_QMAKE_ON= CONFIG+=acs_jack
PORTAUDIO_LIB_DEPENDS= libportaudio.so:audio/portaudio
PORTAUDIO_CMAKE_ON= -DSOUNDSYSTEM_USE_PORTAUDIO:BOOL=true
PORTAUDIO_CMAKE_OFF= -DSOUNDSYSTEM_USE_PORTAUDIO:BOOL=false
PORTAUDIO_QMAKE_ON= CONFIG+=acs_portaudio
.include <bsd.port.mk>

2
audio/giada/Makefile
View File

@ -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

10
audio/giada/files/patch-src_core_init.cpp Normal file
View File

@ -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__

4
audio/gsequencer/Makefile
View File

@ -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

6
audio/gsequencer/distinfo
View File

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

20
audio/gsequencer/files/patch-Makefile.in Normal file
View File

@ -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' {} \;

10
audio/gsequencer/pkg-plist
View File

@ -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/2.1.53/ags_midi_file.dtd
share/xml/gsequencer/schema/dtd/2.1.53/ags_osc_file.dtd
share/xml/gsequencer/schema/dtd/2.1.53/ags_simple_file.dtd
share/xml/gsequencer/schema/dtd/%%PORTVERSION%%/ags_file.dtd
share/xml/gsequencer/schema/dtd/%%PORTVERSION%%/ags_midi_file.dtd
share/xml/gsequencer/schema/dtd/%%PORTVERSION%%/ags_osc_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

2
audio/libcdaudio/Makefile
View File

@ -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

3
audio/musicpd/Makefile
View File

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

6
audio/musicpd/distinfo
View File

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

11
audio/musicpd/files/patch-src_lib_cdio_Paranoia.hxx Normal file
View File

@ -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;

20
audio/musicpd/files/patch-src_zeroconf_meson.build
View File

@ -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',

2
audio/nuvolaplayer/Makefile
View File

@ -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

2
audio/p5-MP3-Tag/Makefile
View File

@ -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

18
audio/paprefs/Makefile
View File

@ -2,23 +2,22 @@
# $FreeBSD$
PORTNAME= paprefs
PORTVERSION= 0.9.10
PORTREVISION= 3
PORTVERSION= 1.1
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= compiler:c++11-lang localbase gmake pkgconfig
USE_CXXSTD= c++11
USE_GNOME= gconfmm26 gnomeprefix intltool
CONFIGURE_ARGS= --disable-lynx
USES= meson pkgconfig tar:xz
USE_GNOME= atkmm glib20 glibmm gtk30 gtkmm30 libsigc++20
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>

5
audio/paprefs/distinfo
View File

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

6
audio/paprefs/pkg-descr
View File

@ -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
PulseAudio 0.9.5 this modules is loaded by default.)
that a special module module-gsettings is loaded in the sound server. (This
require to build the audio/pulseaudio port with option GSETTINGS).
WWW: http://0pointer.de/lennart/projects/paprefs/
WWW: https://freedesktop.org/software/pulseaudio/paprefs/

1
audio/paprefs/pkg-plist
View File

@ -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

6
audio/plasma5-plasma-pa/distinfo
View File

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

9
audio/py-pylast/Makefile
View File

@ -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>

3
audio/py-pylast/pkg-descr
View File

@ -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

44
audio/tuxguitar/Makefile
View File

@ -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-fluidsynth/jni && ${SETENV} ${MAKE_ENV} ${MAKE_CMD}
cd ${WRKSRC}/../TuxGuitar-jack/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-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-fluidsynth/jni/libtuxguitar-fluidsynth-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
@${MKDIR} ${STAGEDIR}${DATADIR}/plugins
${INSTALL_DATA} ${WRKSRC}/tuxguitar.jar ${STAGEDIR}${DATADIR}
${INSTALL_DATA} ${WRKSRC}/../misc/*.tg ${STAGEDIR}${DATADIR}
${INSTALL_DATA} ${WRKSRC}/TuxGuitar/tuxguitar.jar ${STAGEDIR}${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}/share/lang && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/lang
cd ${WRKSRC}/share/scales && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/scales
cd ${WRKSRC}/share/skins && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/skins
cd ${WRKSRC}/TuxGuitar/share/help && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/help
cd ${WRKSRC}/TuxGuitar/share/lang && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/lang
cd ${WRKSRC}/TuxGuitar/share/scales && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/scales
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.desktop ${STAGEDIR}${PREFIX}/share/applications
${INSTALL_MAN} ${WRKSRC}/../misc/tuxguitar.1 ${STAGEDIR}${MANPREFIX}/man/man1
${INSTALL_DATA} ${WRKSRC}/misc/tuxguitar.xpm ${STAGEDIR}${PREFIX}/share/pixmaps
${INSTALL_DATA} ${WRKSRC}/misc/tuxguitar.desktop ${STAGEDIR}${PREFIX}/share/applications
${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>

67
audio/tuxguitar/files/patch-TuxGuitar-fluidsynth_jni_org__herac__tuxguitar__player__impl__midiport__fluidsynth__MidiSynth.c Normal file
View File

@ -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);

18
audio/tuxguitar/files/patch-build.properties → audio/tuxguitar/files/patch-TuxGuitar_build.properties
View File

@ -1,5 +1,5 @@
--- build.properties.orig 2009-10-31 14:32:52 UTC
+++ build.properties
--- TuxGuitar/build.properties.orig 2009-10-31 14:32:52 UTC
+++ 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.jar=%%JAVAJARDIR%%/swt-devel.jar
+lib.itext.jar=%%JAVAJARDIR%%/itext.jar
+lib.swt.jni=/usr/local/lib/
+lib.swt.jar=/usr/local/share/java/classes/swt-devel.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-${dist.version}/
+dist.bin.path=%%PREFIX%%/bin
+dist.share.path=%%DATADIR%%
+dist.doc.path=%%DOCSDIR%%
+dist.jar.path=/usr/local/share/java/TuxGuitar-${dist.version}/
+dist.bin.path=/usr/local/bin
+dist.share.path=/usr/local/share/tuxguitar
+dist.doc.path=/usr/local/share/doc/tuxguitar
########## DEFAULT MAC BUILD PROPERTIES ##########
#lib.swt.jni=lib/

2
audio/wmix/Makefile
View File

@ -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

52
audio/zrythm/Makefile Normal file
View File

@ -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>

3
audio/zrythm/distinfo Normal file
View File

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

6
audio/zrythm/pkg-descr Normal file
View File

@ -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/

1
benchmarks/Makefile
View File

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

3
benchmarks/fio/Makefile
View File

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

6
benchmarks/fio/distinfo
View File

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

105
benchmarks/hyperfine/Makefile Normal file
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@ -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>

157
benchmarks/hyperfine/distinfo Normal file
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@ -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

14
benchmarks/hyperfine/pkg-descr Normal file
View File

@ -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

2
benchmarks/phoronix-test-suite/Makefile
View File

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

6
benchmarks/phoronix-test-suite/distinfo
View File

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

1
biology/Makefile
View File

@ -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

4
biology/hmmer/Makefile
View File

@ -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

2
biology/igv/Makefile
View File

@ -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

10
biology/igv/distinfo
View File

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

3
biology/iqtree/Makefile
View File

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

6
biology/iqtree/distinfo
View File

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

2
biology/ngs-sdk/Makefile
View File

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

6
biology/ngs-sdk/distinfo
View File

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

2
biology/ngs-sdk/pkg-plist
View File

@ -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

27
biology/p5-Bio-Cluster/Makefile Normal file
View File

@ -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>

3
biology/p5-Bio-Cluster/distinfo Normal file
View File

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

4
biology/p5-Bio-Cluster/pkg-descr Normal file
View File

@ -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

20
biology/p5-Bio-Cluster/pkg-plist Normal file
View File

@ -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

20
biology/p5-BioPerl-Run/Makefile
View File

@ -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
${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
.endfor
cd ${WRKSRC} && ${INSTALL_DATA} AUTHORS Changes INSTALL.PROGRAMS README.md ${STAGEDIR}${DOCSDIR}
.include <bsd.port.mk>

6
biology/p5-BioPerl-Run/distinfo
View File

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

4
biology/p5-BioPerl-Run/files/patch-Build.PL
View File

@ -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'
);

55
biology/p5-BioPerl-Run/pkg-plist
View File

@ -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

74
biology/p5-BioPerl/Makefile
View File

@ -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 \
p5-Array-Compare>=0:misc/p5-Array-Compare \
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 \
RUN_DEPENDS= p5-DBI>=0:databases/p5-DBI \
p5-Data-Stag>=0:devel/p5-Data-Stag \
p5-Error>=0:lang/p5-Error \
p5-GD>=0:graphics/p5-GD \
p5-Graph>=0.50: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-Graph>=0:math/p5-Graph \
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-SVG>=2.26:textproc/p5-SVG \
p5-SVG-Graph>=0.01:graphics/p5-SVG-Graph \
p5-Module-Build>=0:devel/p5-Module-Build \
p5-Set-Scalar>=0:devel/p5-Set-Scalar \
p5-Sort-Naturally>=0:textproc/p5-Sort-Naturally \
p5-Spreadsheet-ParseExcel>=0:textproc/p5-Spreadsheet-ParseExcel \
p5-XML-DOM>=0:textproc/p5-XML-DOM \
p5-Test-Most>=0:devel/p5-Test-Most \
p5-Test-RequiresInternet>=0:devel/p5-Test-RequiresInternet \
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>=0.15:textproc/p5-XML-SAX \
p5-XML-SAX-Base>=0:textproc/p5-XML-SAX-Base \
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 \
p5-URI>=0:net/p5-URI
TEST_DEPENDS= p5-Test-Memory-Cycle>=0:devel/p5-Test-Memory-Cycle \
p5-Test-Weaken>=0:devel/p5-Test-Weaken
USES= perl5 shebangfix
USE_PERL5= modbuild
NO_ARCH= yes
SHEBANG_FILES= scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
USE_PERL5= configure
PORTDATA= *
PORTDOCS= *
PORTEXAMPLES= *
NO_ARCH= yes
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:
@${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}
SHEBANG_FILES= examples/*.pl examples/*/*.pl
post-install-DOCS-on:
@${MKDIR} ${STAGEDIR}${DOCSDIR}
.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL.md MANIFEST README.md
${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR}
.endfor
${CP} -R ${WRKSRC}/deobfuscator ${STAGEDIR}${DOCSDIR}
cd ${WRKSRC} && ${INSTALL_DATA} AUTHORS Changes MANIFEST README.md ${STAGEDIR}${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>

6
biology/p5-BioPerl/distinfo
View File

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

80
biology/p5-BioPerl/files/patch-Bio-Root-Build.pm
View File

@ -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

114
biology/p5-BioPerl/files/patch-Build.PL
View File

@ -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;
}

904
biology/p5-BioPerl/pkg-plist
View File

File diff suppressed because it is too large Load Diff

29
biology/pbbam/Makefile
View File

@ -1,8 +1,7 @@
# $FreeBSD$
PORTNAME= pbbam
DISTVERSION= g20180416
PORTREVISION= 3
DISTVERSION= 0.18.0 # Test with biology/unanimity before upgrading!
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.
CMAKE_ARGS+= -DHTSLIB_INCLUDE_DIRS:STRING=${LOCALBASE}/include/htslib \
-DHTSLIB_LIBRARIES:STRING="-L${LOCALBASE}/lib -lhts" \
-DPacBioBAM_build_tests:BOOL=OFF \
-DPacBioBAM_build_docs:BOOL=OFF
pre-configure:
@${REINPLACE_CMD} -e "s|'python'|'${PYTHON_VERSION}'|g" \
${WRKSRC}/meson.build
do-install:
${INSTALL_PROGRAM} ${BUILD_WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin
${INSTALL_DATA} ${BUILD_WRKSRC}/lib/* ${STAGEDIR}${PREFIX}/lib
cd ${WRKSRC}/include && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include
${MV} ${STAGEDIR}${PREFIX}/include/meson.build \
${STAGEDIR}${PREFIX}/include/pbbam
post-install:
${RLN} ${STAGEDIR}${PREFIX}/lib/libpbbam.so.${PORTVERSION} \
${STAGEDIR}${PREFIX}/lib/libpbbam.so.0.18
${RLN} ${STAGEDIR}${PREFIX}/lib/libpbbam.so.${PORTVERSION} \
${STAGEDIR}${PREFIX}/lib/libpbbam.so.0
.include <bsd.port.mk>

6
biology/pbbam/distinfo
View File

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

11
biology/pbbam/files/patch-meson__options.txt Normal file
View File

@ -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',

20
biology/pbbam/pkg-plist
View File

@ -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

21
biology/pbcopper/Makefile
View File

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

6
biology/pbcopper/distinfo
View File

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

21
biology/pbcopper/files/patch-cmake_pbcopper-gitsha1.cmake
View File

@ -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()

7
biology/pbcopper/files/patch-meson__options.txt Normal file
View File

@ -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')

9
biology/pbcopper/pkg-plist
View File

@ -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

8
biology/pbseqan/Makefile
View File

@ -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

6
biology/pbseqan/distinfo
View File

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

38
biology/unanimity/Makefile
View File

@ -2,8 +2,7 @@
PORTNAME= unanimity
DISTVERSIONPREFIX= v
DISTVERSION= 3.1.0
PORTREVISION= 2
DISTVERSION= 3.4.1
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
BUILD_DEPENDS= pbseqan>=g20171002:biology/pbseqan \
pbbam>=g20180416:biology/pbbam \
pbcopper>=g20180413:biology/pbcopper
# Very sensitive to pbbam and pbcopper versions!
# Fully test new combinations and upgrade them together.
BUILD_DEPENDS= seqan>=2.4.0:biology/seqan \
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
PLIST_FILES= bin/arrow bin/ccs bin/gcpp lib/libcc2.a lib/libunanimity.a
LDFLAGS+= -lexecinfo
post-install:
${INSTALL_DATA} ${WRKSRC}/src/libcc2.a ${WRKSRC}/src/libunanimity.a \
${STAGEDIR}${PREFIX}/lib
${RLN} ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0.0 \
${STAGEDIR}${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>

6
biology/unanimity/distinfo
View File

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

11
biology/unanimity/files/patch-CMakeLists.txt
View File

@ -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

10
biology/unanimity/files/patch-cmake_uny-config.cmake
View File

@ -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)

11
biology/unanimity/files/patch-cmake_uny-gitsha1.cmake
View File

@ -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

11
biology/unanimity/files/patch-meson.build Normal file
View File

@ -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)

8
biology/unanimity/files/patch-meson__options.txt Normal file
View File

@ -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')

15
biology/unanimity/files/patch-src_CMakeLists.txt
View File

@ -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}

9
biology/unanimity/files/patch-src_variantCaller_variantCaller.cpp Normal file
View File

@ -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>

82
biology/unanimity/pkg-plist Normal file
View File

@ -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

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