*/*: sync with upstream

Taken from: FreeBSD

arabic/libreoffice/distinfo

@@ -1,2 +1,2 @@
-SHA256 (libreoffice/i18n/LibreOffice_5.0.5_Linux_x86_deb_langpack_ar.tar.gz) = d996fd3d2d23df769a69325c542b2450fa2f1b400b9a4543e4fe63b14c202098
-SIZE (libreoffice/i18n/LibreOffice_5.0.5_Linux_x86_deb_langpack_ar.tar.gz) = 2256147
+SHA256 (libreoffice/i18n/LibreOffice_5.0.6_Linux_x86_deb_langpack_ar.tar.gz) = a3b4aad49e5f7f041e7706817df65be7070c3d2ac209e932dee211c21eb48b1f
+SIZE (libreoffice/i18n/LibreOffice_5.0.6_Linux_x86_deb_langpack_ar.tar.gz) = 2256170

audio/calf/files/patch-src__calf__audio_fx.h

@@ -1,4 +1,4 @@
---- src/calf/audio_fx.h.orig
+--- src/calf/audio_fx.h.orig	2015-03-13 23:00:12 UTC
 +++ src/calf/audio_fx.h
 @@ -27,6 +27,7 @@
  #include "inertia.h"

audio/calf/files/patch-src__calf__osctl.h

@@ -1,4 +1,4 @@
---- src/calf/osctl.h.orig
+--- src/calf/osctl.h.orig	2014-01-26 21:24:40 UTC
 +++ src/calf/osctl.h
 @@ -26,7 +26,10 @@
  #include <vector>

audio/calf/files/patch-src_analyzer.cpp

@@ -0,0 +1,17 @@
+--- src/analyzer.cpp.orig	2014-10-14 18:53:15 UTC
++++ src/analyzer.cpp
+@@ -471,12 +471,12 @@ void analyzer::draw(int subindex, float 
+                                 //pumping up actual signal an erase surrounding
+                                 // sounds
+                                 fft_outL[_iter] = 0.25f * std::max(n * 0.6f * \
+-                                    fabs(fft_outL[_iter]) - var1L , 1e-20);
++                                    fabsf(fft_outL[_iter]) - var1L , 1e-20f);
+                                 if(_mode == 3 or _mode == 4) {
+                                     // do the same with R channel if needed
+                                     lastoutR = fft_outR[_iter];
+                                     fft_outR[_iter] = 0.25f * std::max(n * \
+-                                        0.6f * fabs(fft_outR[_iter]) - var1R , 1e-20);
++                                        0.6f * fabsf(fft_outR[_iter]) - var1R , 1e-20f);
+                                 }
+                                 break;
+                         }

audio/calf/files/patch-src_modules__dist.cpp

@@ -0,0 +1,13 @@
+--- src/modules_dist.cpp.orig	2015-03-13 23:00:12 UTC
++++ src/modules_dist.cpp
+@@ -794,8 +794,8 @@ uint32_t tapesimulator_audio_module::pro
+             lfo2.advance(1);
+
+             // dot
+-            rms = std::max((double)rms, (fabs(Lo) + fabs(Ro)) / 2);
+-            input = std::max((double)input, (fabs(Lc) + fabs(Rc)) / 2);
++            rms = std::max(rms, (fabsf(Lo) + fabsf(Ro)) / 2);
++            input = std::max(input, (fabsf(Lc) + fabsf(Rc)) / 2);
+
+             float values[] = {inL, inR, outs[0][i], outs[1][i]};
+             meters.process(values);

audio/calf/files/patch-src_modules__limit.cpp

@@ -0,0 +1,20 @@
+--- src/modules_limit.cpp.orig	2014-10-14 18:56:24 UTC
++++ src/modules_limit.cpp
+@@ -429,7 +429,7 @@ uint32_t multibandlimiter_audio_module::
+                 }
+
+                 // write multiband coefficient to buffer
+-                buffer[pos] = std::min(*params[param_limit] / std::max(fabs(tmpL), fabs(tmpR)), 1.0);
++                buffer[pos] = std::min(*params[param_limit] / std::max(fabsf(tmpL), fabsf(tmpR)), 1.0f);
+
+                 // step forward in multiband buffer
+                 pos = (pos + channels) % buffer_size;
+@@ -811,7 +811,7 @@ uint32_t sidechainlimiter_audio_module::
+                 }
+
+                 // write multiband coefficient to buffer
+-                buffer[pos] = std::min(*params[param_limit] / std::max(fabs(tmpL), fabs(tmpR)), 1.0);
++                buffer[pos] = std::min(*params[param_limit] / std::max(fabsf(tmpL), fabsf(tmpR)), 1.0f);
+
+                 // step forward in multiband buffer
+                 pos = (pos + channels) % buffer_size;

biology/Makefile

@@ -21,6 +21,7 @@
     SUBDIR += clustalw
     SUBDIR += consed
     SUBDIR += crux
+    SUBDIR += diamond
     SUBDIR += emboss
     SUBDIR += fasta
     SUBDIR += fasta3

biology/diamond/Makefile

@@ -0,0 +1,28 @@
+# Created by: [email protected]
+# $FreeBSD$
+
+PORTNAME=		diamond
+PORTVERSION=		0.7.12
+DISTVERSIONPREFIX=	v
+CATEGORIES=		biology
+
+MAINTAINER=		[email protected]
+COMMENT=		BLAST-compatible local sequence aligner
+
+LICENSE=		BSD2CLAUSE
+
+BUILD_DEPENDS=		${LOCALBASE}/include/boost:devel/boost-libs
+RUN_DEPENDS=		${LOCALBASE}/include/boost:devel/boost-libs
+
+ONLY_FOR_ARCHS=		amd64
+
+USES=			cmake:outsource
+
+CFLAGS+=		-DNDEBUG
+
+USE_GITHUB=		yes
+GH_ACCOUNT=		bbuchfink
+
+PLIST_FILES=		bin/diamond
+
+.include <bsd.port.mk>

biology/diamond/distinfo

@@ -0,0 +1,2 @@
+SHA256 (bbuchfink-diamond-v0.7.12_GH0.tar.gz) = 16f8f618e4e5e81071ef8b66dc39685a1e969434ddeff3d88fa01091971b662f
+SIZE (bbuchfink-diamond-v0.7.12_GH0.tar.gz) = 1826614

biology/diamond/files/patch-CMakeLists.txt

@@ -0,0 +1,33 @@
+--- CMakeLists.txt.orig	2016-03-29 09:23:52 UTC
++++ CMakeLists.txt
+@@ -9,6 +9,7 @@ if(BUILD_STATIC)
+     set(CMAKE_EXE_LINKER_FLAGS "-static")
+ endif()
+
++FIND_PACKAGE(Threads REQUIRED)
+ find_package(Boost
+   1.53.0 REQUIRED
+   COMPONENTS program_options timer iostreams thread
+@@ -16,9 +17,6 @@ find_package(Boost
+
+ find_package(ZLIB REQUIRED)
+
+-set(CMAKE_BUILD_TYPE Release)
+-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-uninitialized")
+-
+ add_subdirectory("src/algo/blast/core")
+ include_directories(
+   "${CMAKE_SOURCE_DIR}/src"
+@@ -29,6 +27,11 @@ add_executable(diamond src/main.cpp
+   src/basic/options.cpp
+   src/util/tinythread.cpp)
+
+-target_link_libraries(diamond blast_core ${Boost_LIBRARIES} ${ZLIB_LIBRARY})
++target_link_libraries(diamond blast_core ${Boost_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARY})
+
+ install(TARGETS diamond DESTINATION bin)
++
++get_cmake_property(_variableNames VARIABLES)
++foreach (_variableName ${_variableNames})
++    message(STATUS "${_variableName}=${${_variableName}}")
++endforeach()

biology/diamond/pkg-descr

@@ -0,0 +1,7 @@
+DIAMOND is a BLAST-compatible local aligner for mapping protein and translated
+DNA query sequences against a protein reference database (BLASTP and BLASTX
+alignment mode). The speedup over BLAST is up to 20,000 on short reads at a
+typical sensitivity of 90-99% relative to BLAST depending on the data and
+settings.
+
+WWW: http://ab.inf.uni-tuebingen.de/software/diamond/

chinese/libreoffice-zh_CN/distinfo

@@ -1,4 +1,4 @@
-SHA256 (libreoffice/i18n/LibreOffice_5.0.5_Linux_x86_deb_langpack_zh-CN.tar.gz) = 5417cb66c3697857a1a8d096725cfe239e45e3be7de8c165f1e8a61dc3b39cd8
-SIZE (libreoffice/i18n/LibreOffice_5.0.5_Linux_x86_deb_langpack_zh-CN.tar.gz) = 567927
-SHA256 (libreoffice/i18n/LibreOffice_5.0.5_Linux_x86_deb_helppack_zh-CN.tar.gz) = 27f7cc581da2ad46ace96bee168aab585b36921f68eb2b7a26ad3ceeceaa99f0
-SIZE (libreoffice/i18n/LibreOffice_5.0.5_Linux_x86_deb_helppack_zh-CN.tar.gz) = 10640847
+SHA256 (libreoffice/i18n/LibreOffice_5.0.6_Linux_x86_deb_langpack_zh-CN.tar.gz) = 06697ee5a200808d36816f19060057e33c0876afd71329d820bdc2842e0ab8db
+SIZE (libreoffice/i18n/LibreOffice_5.0.6_Linux_x86_deb_langpack_zh-CN.tar.gz) = 567869
+SHA256 (libreoffice/i18n/LibreOffice_5.0.6_Linux_x86_deb_helppack_zh-CN.tar.gz) = 0dbfd1ecf21c12cfc229a875c463862a0528f198138f66bb92d06ae815a9b538
+SIZE (libreoffice/i18n/LibreOffice_5.0.6_Linux_x86_deb_helppack_zh-CN.tar.gz) = 10640861

chinese/libreoffice-zh_TW/distinfo

@@ -1,4 +1,4 @@
-SHA256 (libreoffice/i18n/LibreOffice_5.0.5_Linux_x86_deb_langpack_zh-TW.tar.gz) = 0ba7f350135dee30a03b60198b3e76b6f1b8144c5a86e4afec4a7b8532fe9be7
-SIZE (libreoffice/i18n/LibreOffice_5.0.5_Linux_x86_deb_langpack_zh-TW.tar.gz) = 565116
-SHA256 (libreoffice/i18n/LibreOffice_5.0.5_Linux_x86_deb_helppack_zh-TW.tar.gz) = 963019456a1bc963db1670a2c55bed152b5da72ed058e6cf9ab088a3d5bf2d87
-SIZE (libreoffice/i18n/LibreOffice_5.0.5_Linux_x86_deb_helppack_zh-TW.tar.gz) = 10697230
+SHA256 (libreoffice/i18n/LibreOffice_5.0.6_Linux_x86_deb_langpack_zh-TW.tar.gz) = 6cb04c177f0fe68f5288a0d644a192e2a01ba6c550caef11f4c8d353f9741cfc
+SIZE (libreoffice/i18n/LibreOffice_5.0.6_Linux_x86_deb_langpack_zh-TW.tar.gz) = 565073
+SHA256 (libreoffice/i18n/LibreOffice_5.0.6_Linux_x86_deb_helppack_zh-TW.tar.gz) = 66624f4c8f622bbb3563997e47408257aba6cc5e814cdf714cb8977fedf095eb
+SIZE (libreoffice/i18n/LibreOffice_5.0.6_Linux_x86_deb_helppack_zh-TW.tar.gz) = 10697555

databases/Makefile

@@ -937,6 +937,8 @@
     SUBDIR += sqldeveloper
     SUBDIR += sqlite-ext-miscfuncs
     SUBDIR += sqlite-ext-pcre
+    SUBDIR += sqlite-ext-regexp
+    SUBDIR += sqlite-ext-spellfix
     SUBDIR += sqlite2
     SUBDIR += sqlite3
     SUBDIR += sqlitebrowser

databases/mariadb100-server/Makefile

@@ -1,7 +1,7 @@
 # $FreeBSD$
 
 PORTNAME?=	mariadb
-PORTVERSION=	10.0.23
+PORTVERSION=	10.0.25
 CATEGORIES=	databases ipv6
 MASTER_SITES=	http://ftp.osuosl.org/pub/${SITESDIR}/ \
 		http://mirrors.supportex.net/${SITESDIR}/ \
@@ -24,23 +24,18 @@ SUB_FILES=	pkg-message
 PKGMESSAGE=	${WRKDIR}/pkg-message
 
 SLAVEDIRS=	databases/mariadb100-client
-USES=		bison:build cmake cpe execinfo gmake shebangfix
+USES=		bison:build cmake compiler:c++11-lib cpe execinfo gmake shebangfix
 USE_LDCONFIG=	${PREFIX}/lib/mysql ${PREFIX}/lib/mysql/plugin
 SHEBANG_FILES=	scripts/*.sh
 SITESDIR=	mariadb/mariadb-${PORTVERSION}/source
 
 OPTIONS_DEFINE=		FASTMTX
-OPTIONS_RADIO=		SSL
-OPTIONS_RADIO_SSL=	BUNDLED_SSL OPENSSL WITHOUT_SSL
-OPTIONS_DEFAULT+=	OPENSSL
 NO_OPTIONS_SORT=	yes
 
-BUNDLED_SSL_DESC=	SSL/TLS support via (bundled) CyaSSL
 FASTMTX_DESC=		Replace mutexes with spinlocks
-WITHOUT_SSL_DESC=	No SSL/TLS support
 
-CMAKE_ARGS+=	-DINSTALL_DOCDIR="share/doc/mysql" \
-		-DINSTALL_DOCREADMEDIR="share/doc/mysql" \
+CMAKE_ARGS+=	-DINSTALL_DOCDIR="share/doc/mariadb" \
+		-DINSTALL_DOCREADMEDIR="share/doc/mariadb" \
 		-DINSTALL_INCLUDEDIR="include/mysql" \
 		-DINSTALL_INFODIR="info" \
 		-DINSTALL_LIBDIR="lib/mysql" \
@@ -56,6 +51,7 @@ CMAKE_ARGS+=	-DINSTALL_DOCDIR="share/doc/mysql" \
 		-DINSTALL_SUPPORTFILESDIR="share/mysql" \
 		-DWITH_UNIT_TESTS=0 \
 		-DWITH_LIBEDIT=0 \
+		-DWITH_SSL=${OPENSSLBASE} \
 		-DWITH_LIBWRAP=1 \
 		-DEXECINFO_ROOT=${LOCALBASE} \
 		-DCOMPILATION_COMMENT="FreeBSD Ports"
@@ -73,47 +69,55 @@ CONFLICTS_INSTALL=	mariadb5*-${PKGNAMESUFFIX:C/^[0-9]*-//}-* \
 
 .if !defined(CLIENT_ONLY)
 # MySQL-Server options
-USE_MYSQL=		yes
 USE_LDCONFIG+=		${PREFIX}/lib/mysql/plugin
-OPTIONS_DEFINE+=	INNODB MAXKEY MROONGA OQGRAPH
+OPTIONS_DEFINE+=	MAXKEY
 OPTIONS_DEFAULT+=	MAXKEY
-OPTIONS_SUB=		yes
+OPTIONS_GROUP=		ENGINES
+OPTIONS_GROUP_ENGINES=	INNOBASE MROONGA OQGRAPH SPHINX SPIDER TOKUDB
+
+ENGINES_DESC=	Optional MariaDB storage engines
+INNOBASE_DESC=	Build InnoDB engine next to XtraDB
+MAXKEY_DESC=	Change max key length from 1000 to 4000
+MROONGA_DESC=	Mroonga Full Text Search engine
+OQGRAPH_DESC=	Open Query Graph Computation engine (Requires GCC)
+SPHINX_DESC=	SphinxSE engine
+SPIDER_DESC=	Partitioning and XA-transactions engine
+TOKUDB_DESC=	Fractal tree index tree data structure engine
+
+OPTIONS_SUB=	yes
+
+TOKUDB_PORTDOCS=	PATENTS README.md
 
-INNODB_DESC=		Build InnoDB engine next to XtraDB
-MAXKEY_DESC=		Change max key length from 1000 to 4000
-MROONGA_DESC=		Mroonga Full Text Search engine (gcc)
-OQGRAPH_DESC=		Open Query Graph Computation engine (gcc)
 .endif
 
-BUNDLED_SSL_CMAKE_ON=	-DWITH_SSL=bundled
 FASTMTX_CMAKE_ON=	-DWITH_FAST_MUTEXES=1
-OPENSSL_CMAKE_ON=	-DWITH_SSL=yes
-OPENSSL_USE=	OPENSSL=yes
-WITHOUT_SSL_CMAKE_ON=	-DWITH_SSL=no
+USE_OPENSSL=		yes
 
 .if defined(CLIENT_ONLY)
 # MySQL-Client part
 USES+=		readline
 .else
 # MySQL-Server part
-USE_MYSQL=	yes
-WANT_MYSQL_VER=	100m
+USES+=		mysql:100m
 USE_RC_SUBR=	mysql-server
 USERS=		mysql
 GROUPS=		mysql
 CMAKE_ARGS+=	-DWITH_EMBEDDED_SERVER="ON" \
 		-DCMAKE_SKIP_BUILD_RPATH:BOOL=YES \
 		-DWITHOUT_EXAMPLE_STORAGE_ENGINE=1
 
-INNODB_CMAKE_OFF=	-DWITHOUT_INNOBASE=1
+.for ENGINE in ${OPTIONS_GROUP_ENGINES}
+${ENGINE}_CMAKE_OFF=    -DWITHOUT_${ENGINE}=1
+.endfor
+
 MAXKEY_EXTRA_PATCHES+=	${FILESDIR}/extra-patch-include_my__compare.h
 MROONGA_CMAKE_OFF=	-DWITHOUT_MROONGA=1
 OQGRAPH_LIB_DEPENDS=	libboost_system.so:devel/boost-libs \
 			libJudy.so:devel/judy
 # Currently OQGraph does not build using clang.
 # See See https://mariadb.atlassian.net/browse/MDEV-8051.
 OQGRAPH_USE=		gcc
-OQGRAPH_BROKEN=		does not build
+OQGRAPH_BROKEN=		OQGraph does not build
 
 post-install:
 	# Remove programs to avoid conflict with mariadb100-client
@@ -122,7 +126,9 @@ post-install:
 	${RM} ${STAGEDIR}${PREFIX}/bin/msql2mysql \
 		${STAGEDIR}${PREFIX}/bin/mysql_config \
 		${STAGEDIR}${PREFIX}/bin/mysql_find_rows \
-		${STAGEDIR}${PREFIX}/bin/mysqlaccess
+		${STAGEDIR}${PREFIX}/bin/mysqlaccess \
+		${STAGEDIR}${DOCSDIR}/COPYING.AGPLv3 \
+		${STAGEDIR}${DOCSDIR}/COPYING.GPLv2
 .endif
 
 .include <bsd.port.pre.mk>
@@ -133,8 +139,14 @@ CMAKE_ARGS+=	-DWITH_JEMALLOC="system"
 CMAKE_ARGS+=	-DWITH_JEMALLOC="no"
 .endif
 
-# Server segfaults on i386 when built with clang >= 3.4
+.if ${PORT_OPTIONS:MTOKUDB}
+NOT_FOR_ARCHS=  i386
+NOT_FOR_ARCHS_REASON=   TokuDB not supported on 32-bit platforms, see \
+                        https://github.com/percona/PerconaFT/blob/master/README.md
+.endif
+
 .if ${ARCH} == 'i386' && ${OSVERSION} >= 1001000
+# Server segfaults on i386 when built with clang >= 3.4
 USE_GCC=	yes
 .endif
 

databases/mariadb100-server/distinfo

@@ -1,2 +1,2 @@
-SHA256 (mariadb-10.0.23.tar.gz) = 156eed69892834be66736aebe0a17a76d5031fd1c2f481a82228ff33bb7ba274
-SIZE (mariadb-10.0.23.tar.gz) = 57394548
+SHA256 (mariadb-10.0.25.tar.gz) = 4540832c18112a332f61f4eeb57140890c4e2188ae12b312f4e2e8a0363553e4
+SIZE (mariadb-10.0.25.tar.gz) = 57459461