*/*: sync with upstream

Taken from: HardenedBSD
2019-05-19 14:19:45 +02:00 · 2019-05-19 14:19:45 +02:00 · 4890cc86e6
parent 12c57e4469
commit 4890cc86e6
428 changed files with 4628 additions and 3738 deletions
--- a/archivers/Makefile
+++ b/archivers/Makefile
@ -173,6 +173,7 @@
    SUBDIR += py-backports.lzma
    SUBDIR += py-borgbackup
    SUBDIR += py-brotli
+    SUBDIR += py-brotlipy
    SUBDIR += py-bup
    SUBDIR += py-bz2file
    SUBDIR += py-czipfile
--- a/archivers/php-lz4/Makefile
+++ b/archivers/php-lz4/Makefile
@ -5,10 +5,11 @@ DISTVERSION=	0.3.5
 CATEGORIES=	archivers
 PKGNAMEPREFIX=	${PHP_PKGNAMEPREFIX}

-MAINTAINER=	pkaipila@gmail.com
+MAINTAINER=	pave@FreeBSD.org
 COMMENT=	This is the lz4 extension for PHP

 LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE

 LIB_DEPENDS=	liblz4.so:archivers/liblz4

@ -20,6 +21,4 @@ GH_PROJECT=	php-ext-lz4

 CONFIGURE_ARGS=	--with-lz4-includedir=${LOCALBASE}

-PHP_MODNAME=	lz4
-
 .include <bsd.port.mk>
--- a/archivers/php-zstd/Makefile
+++ b/archivers/php-zstd/Makefile
@ -1,11 +1,11 @@
 # $FreeBSD$

 PORTNAME=	zstd
-DISTVERSION=	0.6.1
+DISTVERSION=	0.7.3
 CATEGORIES=	archivers
 PKGNAMEPREFIX=	${PHP_PKGNAMEPREFIX}

-MAINTAINER=	pkaipila@gmail.com
+MAINTAINER=	pave@FreeBSD.org
 COMMENT=	This is the zstd extension for PHP

 LICENSE=	MIT
--- a/archivers/php-zstd/distinfo
+++ b/archivers/php-zstd/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1554397276
-SHA256 (kjdev-php-ext-zstd-0.6.1_GH0.tar.gz) = 0f68c060c0912d546a64c7aea687ff9d82f103b5dd87f35d16deb05ef629fd82
-SIZE (kjdev-php-ext-zstd-0.6.1_GH0.tar.gz) = 11395
+TIMESTAMP = 1558182324
+SHA256 (kjdev-php-ext-zstd-0.7.3_GH0.tar.gz) = 79a87a3f0a602942a08fd455535e5c00c435db9f33b8a4cb4c63907837a7c8bb
+SIZE (kjdev-php-ext-zstd-0.7.3_GH0.tar.gz) = 14902
--- a/archivers/py-brotlipy/Makefile
+++ b/archivers/py-brotlipy/Makefile
@ -0,0 +1,26 @@
+# $FreeBSD$
+
+PORTNAME=	brotlipy
+PORTVERSION=	0.7.0
+CATEGORIES=	archivers python
+MASTER_SITES=	CHEESESHOP
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	koobs@FreeBSD.org
+COMMENT=	Python binding to the Brotli library
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}cffi>=1.0.0:devel/py-cffi@${PY_FLAVOR}
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}cffi>=1.0.0:devel/py-cffi@${PY_FLAVOR}
+
+py27_RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}enum34>=1.0.4,<2.0:devel/py-enum34@${PY_FLAVOR}
+
+USES=		python
+USE_PYTHON=	autoplist distutils
+
+post-install:
+	${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/brotli/*.so
+
+.include <bsd.port.mk>
--- a/archivers/py-brotlipy/distinfo
+++ b/archivers/py-brotlipy/distinfo
@ -0,0 +1,3 @@
+TIMESTAMP = 1558091360
+SHA256 (brotlipy-0.7.0.tar.gz) = 36def0b859beaf21910157b4c33eb3b06d8ce459c942102f16988cca6ea164df
+SIZE (brotlipy-0.7.0.tar.gz) = 413338
--- a/archivers/py-brotlipy/pkg-descr
+++ b/archivers/py-brotlipy/pkg-descr
@ -0,0 +1,6 @@
+Brotlipy is a collection of CFFI-based bindings to the Brotli compression
+reference implementation as written by Google. This enables Python software
+to easily and quickly work with the Brotli compression algorithm,
+regardless of what interpreter is being used.
+
+WWW: https://github.com/python-hyper/brotlipy/
--- a/astro/R-cran-maptools/Makefile
+++ b/astro/R-cran-maptools/Makefile
@ -2,8 +2,7 @@
 # $FreeBSD$

 PORTNAME=	maptools
-DISTVERSION=	0.9-4
-PORTREVISION=	1
+DISTVERSION=	0.9-5
 CATEGORIES=	astro
 DISTNAME=	${PORTNAME}_${DISTVERSION}

--- a/astro/R-cran-maptools/distinfo
+++ b/astro/R-cran-maptools/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1537856753
-SHA256 (maptools_0.9-4.tar.gz) = 930875f598a516f0f9049fa2fae7391bc9bdf7e3e5db696059ab4ec2fc9ba39c
-SIZE (maptools_0.9-4.tar.gz) = 1580721
+TIMESTAMP = 1558269971
+SHA256 (maptools_0.9-5.tar.gz) = 5d9511f09fb49d57a51f28495b02239800596a4fcfad7b03ee1074d793657bdd
+SIZE (maptools_0.9-5.tar.gz) = 1581592
--- a/audio/Makefile
+++ b/audio/Makefile
@ -502,6 +502,7 @@
    SUBDIR += midipp
    SUBDIR += mikmod
    SUBDIR += milkytracker
+    SUBDIR += mio2jack
    SUBDIR += mixer.app
    SUBDIR += mixmos
    SUBDIR += mixxx
--- a/audio/fasttracker2/Makefile
+++ b/audio/fasttracker2/Makefile
@ -2,7 +2,7 @@
 # $FreeBSD$

 PORTNAME=	fasttracker2
-DISTVERSION=	0.1-b154
+DISTVERSION=	0.1-b156
 CATEGORIES=	audio
 MASTER_SITES=	https://16-bits.org/ \
 		LOCAL/ehaupt
--- a/audio/fasttracker2/distinfo
+++ b/audio/fasttracker2/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1557728684
-SHA256 (ft2clone-b154-code.zip) = dad244ae51b238f3c650be2724958f70d636d9e89ead57494ea87af63042145a
-SIZE (ft2clone-b154-code.zip) = 3425342
+TIMESTAMP = 1558273787
+SHA256 (ft2clone-b156-code.zip) = 35eef47873670c0f8c5e8a90d0cf007b961e881ecff71e94a4cdd15cb7bfb684
+SIZE (ft2clone-b156-code.zip) = 3459011
--- a/audio/gsequencer/Makefile
+++ b/audio/gsequencer/Makefile
@ -1,7 +1,7 @@
 # $FreeBSD$

 PORTNAME=	gsequencer
-DISTVERSION=	2.1.70
+DISTVERSION=	2.1.71
 CATEGORIES=	audio
 MASTER_SITES=	SAVANNAH/gsequencer/2.1.x

--- a/audio/gsequencer/distinfo
+++ b/audio/gsequencer/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1557107205
-SHA256 (gsequencer-2.1.70.tar.gz) = d167bdf245be8fa14549d999193bd088cfc01234fa228a30cd5906c45359a13c
-SIZE (gsequencer-2.1.70.tar.gz) = 5103227
+TIMESTAMP = 1558195505
+SHA256 (gsequencer-2.1.71.tar.gz) = 072181c4ba368caef313065d960187dda3598d421e1b37f2dec4eaa9fea02b51
+SIZE (gsequencer-2.1.71.tar.gz) = 5103439
--- a/audio/mio2jack/Makefile
+++ b/audio/mio2jack/Makefile
@ -0,0 +1,30 @@
+# $FreeBSD$
+
+PORTNAME=	mio2jack
+PORTVERSION=	g20180501
+CATEGORIES=	audio
+
+MAINTAINER=	tobik@FreeBSD.org
+COMMENT=	Expose Sndio MIDI ports to JACK
+
+LICENSE=	ISCL
+LICENSE_FILE=	${WRKSRC}/LICENSE.txt
+
+LIB_DEPENDS=	libjack.so:audio/jack \
+		libsndio.so:audio/sndio
+
+USES=		localbase:ldflags
+USE_GITHUB=	yes
+GH_ACCOUNT=	martingms
+GH_TAGNAME=	9d0de50b226539e3e61ad4f36aa74cfe160d2747
+
+MAKEFILE=	/dev/null
+ALL_TARGET=	mio2jack
+LDFLAGS+=	-ljack -lsndio
+
+PLIST_FILES=	bin/mio2jack
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/mio2jack ${STAGEDIR}${PREFIX}/bin
+
+.include <bsd.port.mk>
--- a/audio/mio2jack/distinfo
+++ b/audio/mio2jack/distinfo
@ -0,0 +1,3 @@
+TIMESTAMP = 1558244708
+SHA256 (martingms-mio2jack-g20180501-9d0de50b226539e3e61ad4f36aa74cfe160d2747_GH0.tar.gz) = 6a3161ecf360c2697c7c5d73ccee6a3a7fd6314b22f841b9a70f38ddf5e625f2
+SIZE (martingms-mio2jack-g20180501-9d0de50b226539e3e61ad4f36aa74cfe160d2747_GH0.tar.gz) = 2261
--- a/audio/mio2jack/pkg-descr
+++ b/audio/mio2jack/pkg-descr
@ -0,0 +1,6 @@
+Mio2jack is a tool to expose Sndio MIDI ports to JACK.
+
+For now it only handles one-way communication, that is MIDI events
+flowing in the Sndio to JACK direction.
+
+WWW: https://github.com/martingms/mio2jack
--- a/audio/moony-lv2/Makefile
+++ b/audio/moony-lv2/Makefile
@ -10,6 +10,8 @@ PKGNAMESUFFIX=	-lv2
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Realtime Lua as programmable glue in LV2

+BROKEN_FreeBSD_11=	undefined reference to `clog', see bug#237771
+
 LICENSE=	ART20
 LICENSE_FILE=	${WRKSRC}/COPYING

--- a/audio/pulseaudio-qt/Makefile
+++ b/audio/pulseaudio-qt/Makefile
@ -1,8 +1,7 @@
 # $FreeBSD$

 PORTNAME=	pulseaudio-qt
-DISTVERSION=	1.0.1
-PORTREVISION=	1
+DISTVERSION=	1.1.0
 MASTER_SITES=	KDE/stable/${PORTNAME}
 CATEGORIES=	audio kde

--- a/audio/pulseaudio-qt/distinfo
+++ b/audio/pulseaudio-qt/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1553886892
-SHA256 (pulseaudio-qt-1.0.1.tar.xz) = bf571c642ac7b5d5e6a793654ce4a531efcdd89dd76da963ca547f4c1b5238ed
-SIZE (pulseaudio-qt-1.0.1.tar.xz) = 30360
+TIMESTAMP = 1558112808
+SHA256 (pulseaudio-qt-1.1.0.tar.xz) = 9c7cbc484dee6ab6bd6b479a5cca14c7f38a4d020f03e99ecfd047136da18662
+SIZE (pulseaudio-qt-1.1.0.tar.xz) = 30556
--- a/audio/pulseaudio-qt/pkg-plist
+++ b/audio/pulseaudio-qt/pkg-plist
@ -12,6 +12,7 @@ include/KF5/KF5PulseAudioQt/PulseAudioQt/Sink
 include/KF5/KF5PulseAudioQt/PulseAudioQt/SinkInput
 include/KF5/KF5PulseAudioQt/PulseAudioQt/Source
 include/KF5/KF5PulseAudioQt/PulseAudioQt/SourceOutput
+include/KF5/KF5PulseAudioQt/PulseAudioQt/Stream
 include/KF5/KF5PulseAudioQt/PulseAudioQt/StreamRestore
 include/KF5/KF5PulseAudioQt/PulseAudioQt/VolumeObject
 include/KF5/KF5PulseAudioQt/PulseAudioQt/card.h
@ -29,6 +30,7 @@ include/KF5/KF5PulseAudioQt/PulseAudioQt/sink.h
 include/KF5/KF5PulseAudioQt/PulseAudioQt/sinkinput.h
 include/KF5/KF5PulseAudioQt/PulseAudioQt/source.h
 include/KF5/KF5PulseAudioQt/PulseAudioQt/sourceoutput.h
+include/KF5/KF5PulseAudioQt/PulseAudioQt/stream.h
 include/KF5/KF5PulseAudioQt/PulseAudioQt/streamrestore.h
 include/KF5/KF5PulseAudioQt/PulseAudioQt/volumeobject.h
 include/KF5/pulseaudioqt_version.h
@ -37,5 +39,5 @@ lib/cmake/KF5PulseAudioQt/KF5PulseAudioQtConfigVersion.cmake
 lib/cmake/KF5PulseAudioQt/KF5PulseAudioQtTargets-%%CMAKE_BUILD_TYPE%%.cmake
 lib/cmake/KF5PulseAudioQt/KF5PulseAudioQtTargets.cmake
 lib/libKF5PulseAudioQt.so
-lib/libKF5PulseAudioQt.so.1
-lib/libKF5PulseAudioQt.so.1.0.1
+lib/libKF5PulseAudioQt.so.2
+lib/libKF5PulseAudioQt.so.1.1.0
--- a/biology/Makefile
+++ b/biology/Makefile
@ -42,12 +42,14 @@
    SUBDIR += freebayes
    SUBDIR += garlic
    SUBDIR += gatk
+    SUBDIR += gemma
    SUBDIR += gff2ps
    SUBDIR += gmap
    SUBDIR += gperiodic
    SUBDIR += graphlan
    SUBDIR += grappa
    SUBDIR += groopm
+    SUBDIR += hhsuite
    SUBDIR += hisat2
    SUBDIR += hmmer
    SUBDIR += htslib
--- a/biology/gemma/Makefile
+++ b/biology/gemma/Makefile
@ -0,0 +1,38 @@
+# $FreeBSD$
+
+PORTNAME=	gemma
+DISTVERSION=	0.98.1
+CATEGORIES=	biology
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Genome-wide Efficient Mixed Model Association
+
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+LIB_DEPENDS=	libcblas.so:math/cblas \
+		libgsl.so:math/gsl
+
+USES=		blaslapack:openblas compiler:c++11-lang eigen:3 gmake \
+		localbase:ldflags
+USE_GITHUB=	yes
+GH_ACCOUNT=	genetics-statistics
+GH_PROJECT=	GEMMA
+
+MAKEFILE=	${FILESDIR}/Makefile
+CXXFLAGS+=	-I${LOCALBASE}/include/eigen3 -DOPENBLAS -DOPENBLAS_LEGACY
+LDFLAGS+=	-lopenblas
+
+OPTIONS_DEFINE=	EXAMPLES
+
+pre-configure:
+	@${REINPLACE_CMD} -e 's|../bin/gemma|../gemma|' ${WRKSRC}/test/*.sh
+
+do-install-EXAMPLES-on:
+	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
+	(cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR})
+
+do-test:
+	(cd ${WRKSRC}/test && ${SH} test_suite.sh)
+
+.include <bsd.port.mk>
--- a/biology/gemma/distinfo
+++ b/biology/gemma/distinfo
@ -0,0 +1,3 @@
+TIMESTAMP = 1558018021
+SHA256 (genetics-statistics-GEMMA-0.98.1_GH0.tar.gz) = 6beeed4a9e727a96fdea9e86e39bbe9cbc9f0540ad3a1053814e95b0863a7e6b
+SIZE (genetics-statistics-GEMMA-0.98.1_GH0.tar.gz) = 49569015
--- a/biology/gemma/files/Makefile
+++ b/biology/gemma/files/Makefile
@ -0,0 +1,68 @@
+
+GEMMA_VERSION = $(shell cat ./VERSION)
+VGEN		= scripts/gen_version_info.sh
+CXXFLAGS	+= -DHAVE_INLINE -pthread -Wall -std=gnu++11
+CXXFLAGS 	+= -DNDEBUG -Icontrib/catch-1.9.7 -Isrc
+
+SRC_DIR		= ./src
+TEST_SRC_DIR	= ./test/src
+DESTDIR		?= .
+PREFIX		?= /usr/local
+MKDIR		?= mkdir
+INSTALL		?= install
+
+BIN		= gemma
+HDR		= $(wildcard src/*.h) ./src/version.h
+SOURCES		= $(wildcard src/*.cpp)
+OBJS		= $(SOURCES:.cpp=.o)
+LDFLAGS		+= -lgsl -lz
+
+.PHONY: all test
+
+all: $(BIN)
+
+./src/version.h: ./VERSION
+	$(shell bash $(VGEN) $(GUIX_PROFILE) > src/version.h)
+
+$(BIN): $(OBJS)
+	$(CXX) $(CXXFLAGS) -o $(BIN) $(OBJS) $(LDFLAGS)
+
+$(OBJS): $(HDR)
+
+install: all
+	$(MKDIR) -p $(DESTDIR)$(PREFIX)/bin
+	$(INSTALL) -s -c $(BIN) $(DESTDIR)$(PREFIX)/bin
+
+.SUFFIXES : .cpp .c .o $(SUFFIXES)
+
+./bin/unittests-gemma: contrib/catch-1.9.7/catch.hpp $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(OBJS)
+	$(CXX) $(CXXFLAGS) $(TEST_SRC_DIR)/unittests-main.o  $(TEST_SRC_DIR)/unittests-math.o $(filter-out src/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests-gemma
+
+unittests: all ./bin/unittests-gemma
+	./bin/unittests-gemma
+
+fast-check: all unittests
+	rm -vf test/output/*
+	cd test && ./dev_test_suite.sh | tee ../dev_test.log
+	grep -q 'success rate: 100%' dev_test.log
+
+slow-check: all
+	rm -vf test/output/*
+	cd test && ./test_suite.sh | tee ../test.log
+	grep -q 'success rate: 100%' test.log
+
+lengthy-check: all
+	rm -vf test/output/*
+	cd test && ./lengthy_test_suite.sh | tee ../lengthy_test.log
+	grep -q 'success rate: 100%' lengthy_test.log
+
+check: fast-check slow-check
+
+check-all: check lengthy-check
+
+clean:
+	rm -vf $(SRC_DIR)/*.o
+	rm -vf $(SRC_DIR)/*~
+	rm -vf $(TEST_SRC_DIR)/*.o
+	rm -vf $(BIN)
+	rm -vf ./bin/unittests-gemma
--- a/biology/gemma/files/patch-doc_manual.tex
+++ b/biology/gemma/files/patch-doc_manual.tex
@ -0,0 +1,124 @@
+--- doc/manual.tex.orig	2019-04-18 21:03:11 UTC
+++ doc/manual.tex
+@@ -767,8 +767,8 @@ of ``nan"s.
+ The basic usages for linear model association analysis with either the PLINK binary ped format or the BIMBAM format are:
+ 
+ \begin{verbatim}
+-./gemma -bfile [prefix] -lm [num] -o [prefix]
+-./gemma -g [filename] -p [filename] -a [filename] -lm [num] -o [prefix]
+gemma -bfile [prefix] -lm [num] -o [prefix]
+gemma -g [filename] -p [filename] -a [filename] -lm [num] -o [prefix]
+ \end{verbatim}
+ 
+ where the ``-lm [num]" option specifies which frequentist test to use,
+@@ -825,8 +825,8 @@ The basic usages to calculate an estimated relatedness
+ either the PLINK binary ped format or the BIMBAM format are:
+ %
+ \begin{verbatim}
+-./gemma -bfile [prefix] -gk [num] -o [prefix]
+-./gemma -g [filename] -p [filename] -gk [num] -o [prefix]
+gemma -bfile [prefix] -gk [num] -o [prefix]
+gemma -g [filename] -p [filename] -gk [num] -o [prefix]
+ \end{verbatim}
+ %
+ where the ``-gk [num]" option specifies which relatedness matrix to
+@@ -887,8 +887,8 @@ matrix with either the PLINK binary ped format or the 
+ are:
+ %
+ \begin{verbatim}
+-./gemma -bfile [prefix] -k [filename] -eigen -o [prefix]
+-./gemma -g [filename] -p [filename] -k [filename] -eigen -o [prefix]
+gemma -bfile [prefix] -k [filename] -eigen -o [prefix]
+gemma -g [filename] -p [filename] -k [filename] -eigen -o [prefix]
+ \end{verbatim}
+ %
+ where the ``-bfile [prefix]" specifies PLINK binary ped file prefix;
+@@ -923,8 +923,8 @@ The basic usages for association analysis with either 
+ ped format or the BIMBAM format are:
+ 
+ \begin{verbatim}
+-./gemma -bfile [prefix] -k [filename] -lmm [num] -o [prefix]
+-./gemma -g [filename] -p [filename] -a [filename] -k [filename] -lmm [num] -o [prefix]
+gemma -bfile [prefix] -k [filename] -lmm [num] -o [prefix]
+gemma -g [filename] -p [filename] -a [filename] -k [filename] -lmm [num] -o [prefix]
+ \end{verbatim}
+ 
+ where the ``-lmm [num]" option specifies which frequentist test to
+@@ -1037,8 +1037,8 @@ The basic usages for association analysis with either 
+ ped format or the BIMBAM format are:
+ 
+ \begin{verbatim}
+-./gemma -bfile [prefix] -k [filename] -lmm [num] -n [num1] [num2] [num3] -o [prefix]
+-./gemma -g [filename] -p [filename] -a [filename] -k [filename] -lmm [num]
+gemma -bfile [prefix] -k [filename] -lmm [num] -n [num1] [num2] [num3] -o [prefix]
+gemma -g [filename] -p [filename] -a [filename] -k [filename] -lmm [num]
+ -n [num1] [num2] [num3] -o [prefix]
+ \end{verbatim}
+ 
+@@ -1069,8 +1069,8 @@ In addition, when a small proportion of phenotypes are
+ missing, one can impute these missing values before association tests:
+ 
+ \begin{verbatim}
+-./gemma -bfile [prefix] -k [filename] -predict -n [num1] [num2] [num3] -o [prefix]
+-./gemma -g [filename] -p [filename] -a [filename] -k [filename] -predict
+gemma -bfile [prefix] -k [filename] -predict -n [num1] [num2] [num3] -o [prefix]
+gemma -g [filename] -p [filename] -a [filename] -k [filename] -predict
+ -n [num1] [num2] [num3] -o [prefix]
+ \end{verbatim}
+ 
+@@ -1099,8 +1099,8 @@ The basic usages for fitting a BSLMM with either the P
+ format or the BIMBAM format are:
+ 
+ \begin{verbatim}
+-./gemma -bfile [prefix] -bslmm [num] -o [prefix]
+-./gemma -g [filename] -p [filename] -a [filename] -bslmm [num] -o [prefix]
+gemma -bfile [prefix] -bslmm [num] -o [prefix]
+gemma -g [filename] -p [filename] -a [filename] -bslmm [num] -o [prefix]
+ \end{verbatim}
+ 
+ where the ``-bslmm [num]" option specifies which model to fit,
+@@ -1225,9 +1225,9 @@ The basic usages for association analysis with either 
+ ped format or the BIMBAM format are:
+ 
+ \begin{verbatim}
+-./gemma -bfile [prefix] -epm [filename] -emu [filename] -ebv [filename] -k [filename]
+gemma -bfile [prefix] -epm [filename] -emu [filename] -ebv [filename] -k [filename]
+ -predict [num] -o [prefix]
+-./gemma -g [filename] -p [filename] -epm [filename] -emu [filename] -ebv [filename]
+gemma -g [filename] -p [filename] -epm [filename] -emu [filename] -ebv [filename]
+ -k [filename] -predict [num] -o [prefix]
+ \end{verbatim}
+ 
+@@ -1300,8 +1300,8 @@ The basic usages for variance component estimation wit
+ matrices are:
+ 
+ \begin{verbatim}
+-./gemma -p [filename] -k [filename] -n [num] -vc [num] -o [prefix]
+-./gemma -p [filename] -mk [filename] -n [num] -vc [num] -o [prefix]
+gemma -p [filename] -k [filename] -n [num] -vc [num] -o [prefix]
+gemma -p [filename] -mk [filename] -n [num] -vc [num] -o [prefix]
+ \end{verbatim}
+ 
+ where the ``-vc [num]" option specifies which estimation to use, in
+@@ -1349,8 +1349,8 @@ binary ped format or the BIMBAM format. The basic usag
+ component estimation with summary statistics are:
+ 
+ \begin{verbatim}
+-./gemma -beta [filename] -bfile [prefix] -vc 1 -o [prefix]
+-./gemma -beta [filename] -g [filename] -p [filename] -a [filename] -vc 1 -o [prefix]
+gemma -beta [filename] -bfile [prefix] -vc 1 -o [prefix]
+gemma -beta [filename] -g [filename] -p [filename] -a [filename] -vc 1 -o [prefix]
+ \end{verbatim}
+ 
+ where the ``-vc 1" option specifies to use MQS-HEW; ``-beta
+@@ -1395,8 +1395,8 @@ previous MQS run. The basic usages for using the asymp
+ compute the confidence intervals are
+ 
+ \begin{verbatim}
+-./gemma -beta [filename] -bfile [prefix] -ref [prefix] -pve [num] -ci 1 -o [prefix]
+-./gemma -beta [filename] -g [filename] -p [filename] -ref [prefix] -pve [num] -ci 1 -o [prefix]
+gemma -beta [filename] -bfile [prefix] -ref [prefix] -pve [num] -ci 1 -o [prefix]
+gemma -beta [filename] -g [filename] -p [filename] -ref [prefix] -pve [num] -ci 1 -o [prefix]
+ \end{verbatim}
+ 
+ In the above usages, ``-ref [prefix]" specifies the prefix of the
--- a/biology/gemma/files/patch-src_gemma.cpp
+++ b/biology/gemma/files/patch-src_gemma.cpp
@ -0,0 +1,166 @@
+--- src/gemma.cpp.orig	2019-04-18 21:03:48 UTC
+++ src/gemma.cpp
+@@ -154,7 +154,7 @@ void GEMMA::PrintHelp(size_t option) {
+ 
+   if (option == 0) {
+     cout << endl;
+-    cout << " type ./gemma -h [num] for detailed help" << endl;
+    cout << " type gemma -h [num] for detailed help" << endl;
+     cout << " options: " << endl;
+     cout << "  1: quick guide" << endl;
+     cout << "  2: file I/O related" << endl;
+@@ -176,116 +176,116 @@ void GEMMA::PrintHelp(size_t option) {
+   if (option == 1) {
+     cout << " QUICK GUIDE" << endl;
+     cout << " to generate a relatedness matrix: " << endl;
+-    cout << "         ./gemma -bfile [prefix] -gk [num] -o [prefix]" << endl;
+-    cout << "         ./gemma -g [filename] -p [filename] -gk [num] -o [prefix]"
+    cout << "         gemma -bfile [prefix] -gk [num] -o [prefix]" << endl;
+    cout << "         gemma -g [filename] -p [filename] -gk [num] -o [prefix]"
+          << endl;
+     cout << " to generate the S matrix: " << endl;
+-    cout << "         ./gemma -bfile [prefix] -gs -o [prefix]" << endl;
+-    cout << "         ./gemma -p [filename] -g [filename] -gs -o [prefix]"
+    cout << "         gemma -bfile [prefix] -gs -o [prefix]" << endl;
+    cout << "         gemma -p [filename] -g [filename] -gs -o [prefix]"
+          << endl;
+-    cout << "         ./gemma -bfile [prefix] -cat [filename] -gs -o [prefix]"
+    cout << "         gemma -bfile [prefix] -cat [filename] -gs -o [prefix]"
+          << endl;
+-    cout << "         ./gemma -p [filename] -g [filename] -cat [filename] -gs "
+    cout << "         gemma -p [filename] -g [filename] -cat [filename] -gs "
+             "-o [prefix]"
+          << endl;
+-    cout << "         ./gemma -bfile [prefix] -sample [num] -gs -o [prefix]"
+    cout << "         gemma -bfile [prefix] -sample [num] -gs -o [prefix]"
+          << endl;
+-    cout << "         ./gemma -p [filename] -g [filename] -sample [num] -gs -o "
+    cout << "         gemma -p [filename] -g [filename] -sample [num] -gs -o "
+             "[prefix]"
+          << endl;
+     cout << " to generate the q vector: " << endl;
+-    cout << "         ./gemma -beta [filename] -gq -o [prefix]" << endl;
+-    cout << "         ./gemma -beta [filename] -cat [filename] -gq -o [prefix]"
+    cout << "         gemma -beta [filename] -gq -o [prefix]" << endl;
+    cout << "         gemma -beta [filename] -cat [filename] -gq -o [prefix]"
+          << endl;
+     cout << " to generate the ldsc weigthts: " << endl;
+-    cout << "         ./gemma -beta [filename] -gw -o [prefix]" << endl;
+-    cout << "         ./gemma -beta [filename] -cat [filename] -gw -o [prefix]"
+    cout << "         gemma -beta [filename] -gw -o [prefix]" << endl;
+    cout << "         gemma -beta [filename] -cat [filename] -gw -o [prefix]"
+          << endl;
+     cout << " to perform eigen decomposition of the relatedness matrix: "
+          << endl;
+-    cout << "         ./gemma -bfile [prefix] -k [filename] -eigen -o [prefix]"
+    cout << "         gemma -bfile [prefix] -k [filename] -eigen -o [prefix]"
+          << endl;
+-    cout << "         ./gemma -g [filename] -p [filename] -k [filename] -eigen "
+    cout << "         gemma -g [filename] -p [filename] -k [filename] -eigen "
+             "-o [prefix]"
+          << endl;
+     cout << " to estimate variance components: " << endl;
+-    cout << "         ./gemma -bfile [prefix] -k [filename] -vc [num] -o "
+    cout << "         gemma -bfile [prefix] -k [filename] -vc [num] -o "
+             "[prefix]"
+          << endl;
+-    cout << "         ./gemma -p [filename] -k [filename] -vc [num] -o [prefix]"
+    cout << "         gemma -p [filename] -k [filename] -vc [num] -o [prefix]"
+          << endl;
+-    cout << "         ./gemma -bfile [prefix] -mk [filename] -vc [num] -o "
+    cout << "         gemma -bfile [prefix] -mk [filename] -vc [num] -o "
+             "[prefix]"
+          << endl;
+     cout
+-        << "         ./gemma -p [filename] -mk [filename] -vc [num] -o [prefix]"
+-        << endl;
+-    cout << "         ./gemma -beta [filename] -cor [filename] -vc [num] -o "
+         << "         gemma -p [filename] -mk [filename] -vc [num] -o [prefix]"
+         << endl;
+    cout << "         gemma -beta [filename] -cor [filename] -vc [num] -o "
+             "[prefix]"
+          << endl;
+-    cout << "         ./gemma -beta [filename] -cor [filename] -cat [filename] "
+    cout << "         gemma -beta [filename] -cor [filename] -cat [filename] "
+             "-vc [num] -o [prefix]"
+          << endl;
+     cout << "         options for the above two commands: -crt -windowbp [num]"
+          << endl;
+-    cout << "         ./gemma -mq [filename] -ms [filename] -mv [filename] -vc "
+    cout << "         gemma -mq [filename] -ms [filename] -mv [filename] -vc "
+             "[num] -o [prefix]"
+          << endl;
+     cout << "         or with summary statistics, replace bfile with mbfile, "
+             "or g or mg; vc=1 for HE weights and vc=2 for LDSC weights"
+          << endl;
+-    cout << "         ./gemma -beta [filename] -bfile [filename] -cat "
+    cout << "         gemma -beta [filename] -bfile [filename] -cat "
+             "[filename] -wsnp [filename] -wcat [filename] -vc [num] -o [prefix]"
+          << endl;
+-    cout << "         ./gemma -beta [filename] -bfile [filename] -cat "
+    cout << "         gemma -beta [filename] -bfile [filename] -cat "
+             "[filename] -wsnp [filename] -wcat [filename] -ci [num] -o [prefix]"
+          << endl;
+     cout << " to fit a linear mixed model: " << endl;
+-    cout << "         ./gemma -bfile [prefix] -k [filename] -lmm [num] -o "
+    cout << "         gemma -bfile [prefix] -k [filename] -lmm [num] -o "
+             "[prefix]"
+          << endl;
+-    cout << "         ./gemma -g [filename] -p [filename] -a [filename] -k "
+    cout << "         gemma -g [filename] -p [filename] -a [filename] -k "
+             "[filename] -lmm [num] -o [prefix]"
+          << endl;
+     cout << " to fit a linear mixed model to test g by e effects: " << endl;
+-    cout << "         ./gemma -bfile [prefix] -gxe [filename] -k [filename] "
+    cout << "         gemma -bfile [prefix] -gxe [filename] -k [filename] "
+             "-lmm [num] -o [prefix]"
+          << endl;
+-    cout << "         ./gemma -g [filename] -p [filename] -a [filename] -gxe "
+    cout << "         gemma -g [filename] -p [filename] -a [filename] -gxe "
+             "[filename] -k [filename] -lmm [num] -o [prefix]"
+          << endl;
+     cout << " to fit a univariate linear mixed model with different residual "
+             "weights for different individuals: "
+          << endl;
+-    cout << "         ./gemma -bfile [prefix] -weight [filename] -k [filename] "
+    cout << "         gemma -bfile [prefix] -weight [filename] -k [filename] "
+             "-lmm [num] -o [prefix]"
+          << endl;
+-    cout << "         ./gemma -g [filename] -p [filename] -a [filename] "
+    cout << "         gemma -g [filename] -p [filename] -a [filename] "
+             "-weight [filename] -k [filename] -lmm [num] -o [prefix]"
+          << endl;
+     cout << " to fit a multivariate linear mixed model: " << endl;
+-    cout << "         ./gemma -bfile [prefix] -k [filename] -lmm [num] -n "
+    cout << "         gemma -bfile [prefix] -k [filename] -lmm [num] -n "
+             "[pheno cols...] -o [prefix]"
+          << endl;
+-    cout << "         ./gemma -g [filename] -p [filename] -a [filename] -k "
+    cout << "         gemma -g [filename] -p [filename] -a [filename] -k "
+             "[filename] -lmm [num] -n [pheno cols...] -o [prefix]"
+          << endl;
+     cout << " to fit a Bayesian sparse linear mixed model: " << endl;
+-    cout << "         ./gemma -bfile [prefix] -bslmm [num] -o [prefix]" << endl;
+-    cout << "         ./gemma -g [filename] -p [filename] -a [filename] -bslmm "
+    cout << "         gemma -bfile [prefix] -bslmm [num] -o [prefix]" << endl;
+    cout << "         gemma -g [filename] -p [filename] -a [filename] -bslmm "
+             "[num] -o [prefix]"
+          << endl;
+     cout << " to obtain predicted values: " << endl;
+-    cout << "         ./gemma -bfile [prefix] -epm [filename] -emu [filename] "
+    cout << "         gemma -bfile [prefix] -epm [filename] -emu [filename] "
+             "-ebv [filename] -k [filename] -predict [num] -o [prefix]"
+          << endl;
+-    cout << "         ./gemma -g [filename] -p [filename] -epm [filename] -emu "
+    cout << "         gemma -g [filename] -p [filename] -epm [filename] -emu "
+             "[filename] -ebv [filename] -k [filename] -predict [num] -o "
+             "[prefix]"
+          << endl;
+     cout << " to calculate correlations between SNPs: " << endl;
+-    cout << "         ./gemma -bfile [prefix] -calccor -o [prefix]" << endl;
+-    cout << "         ./gemma -g [filename] -p [filename] -calccor -o [prefix]"
+    cout << "         gemma -bfile [prefix] -calccor -o [prefix]" << endl;
+    cout << "         gemma -g [filename] -p [filename] -calccor -o [prefix]"
+          << endl;
+     cout << endl;
+   }
--- a/biology/gemma/pkg-descr
+++ b/biology/gemma/pkg-descr
@ -0,0 +1,5 @@
+GEMMA is a software toolkit for fast application of linear mixed models (LMMs)
+and related models to genome-wide association studies (GWAS) and other
+large-scale data sets.
+
+WWW: https://github.com/genetics-statistics/GEMMA
--- a/biology/gemma/pkg-plist
+++ b/biology/gemma/pkg-plist
@ -0,0 +1,20 @@
+bin/gemma
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/BXD_covariates.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/BXD_covariates2.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/BXD_geno.txt.gz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/BXD_pheno.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/BXD_snps.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HLC.bed
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HLC.bim
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HLC.fam
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HLC.simu.pheno.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HLC_covariates.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/demo.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940.anno.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940.bed
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940.bim
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940.fam
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940.geno.txt.gz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940.pheno.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940_snps.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mouse_hs1940_snps_anno.txt
--- a/biology/hhsuite/Makefile
+++ b/biology/hhsuite/Makefile
@ -0,0 +1,26 @@
+# $FreeBSD$
+
+PORTNAME=	hhsuite
+DISTVERSIONPREFIX=	v
+DISTVERSION=	3.2.0
+CATEGORIES=	biology science
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Remote protein homology detection suite
+
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	openmpi>0:net/openmpi
+LIB_DEPENDS=	libomp.so:devel/openmp
+RUN_DEPENDS=	openmpi>0:net/openmpi
+
+USES=		cmake perl5 python shebangfix
+SHEBANG_GLOB=	*.pl *.py
+USE_GITHUB=	yes
+GH_ACCOUNT=	soedinglab
+GH_PROJECT=	hh-suite
+
+LDFLAGS+=	-Wl,-rpath,${LOCALBASE}/mpi/openmpi/lib -L${LOCALBASE}/mpi/openmpi/lib -lmpi # force linking to openmpi, and not to mpich
+
+.include <bsd.port.mk>
--- a/biology/hhsuite/distinfo
+++ b/biology/hhsuite/distinfo
@ -0,0 +1,3 @@
+TIMESTAMP = 1558244086
+SHA256 (soedinglab-hh-suite-v3.2.0_GH0.tar.gz) = 6b870dcfbc1ffb9dd664a45415fcd13cf5970f49d1c7b824160c260fa138e6d6
+SIZE (soedinglab-hh-suite-v3.2.0_GH0.tar.gz) = 6273589
--- a/biology/hhsuite/files/patch-data_CMakeLists.txt
+++ b/biology/hhsuite/files/patch-data_CMakeLists.txt
@ -0,0 +1,11 @@
+--- data/CMakeLists.txt.orig	2019-05-19 05:46:02 UTC
+++ data/CMakeLists.txt
+@@ -7,7 +7,7 @@ INSTALL(FILES
+         do_not_delete.pin
+         do_not_delete.psq
+         PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
+-        DESTINATION data
+        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/hhsuite/data
+         )
+ 
+ include(ResourceCompiler)
--- a/biology/hhsuite/files/patch-scripts_CMakeLists.txt
+++ b/biology/hhsuite/files/patch-scripts_CMakeLists.txt
@ -0,0 +1,9 @@
+--- scripts/CMakeLists.txt.orig	2019-05-19 05:44:58 UTC
+++ scripts/CMakeLists.txt
+@@ -21,5 +21,5 @@ INSTALL(PROGRAMS
+         reformat.pl
+         renumberpdb.pl
+         splitfasta.pl
+-        DESTINATION scripts
+        DESTINATION ${CMAKE_INSTALL_PREFIX}/share/hhsuite/scripts
+         )
--- a/biology/hhsuite/files/patch-src_cs_getopt__pp.cc
+++ b/biology/hhsuite/files/patch-src_cs_getopt__pp.cc
@ -0,0 +1,11 @@
+--- src/cs/getopt_pp.cc.orig	2019-05-19 05:36:03 UTC
+++ src/cs/getopt_pp.cc
+@@ -21,7 +21,7 @@
+ #include <unistd.h>
+ #include "getopt_pp.h"
+ 
+-#ifdef __APPLE__
+#if defined(__APPLE__) || defined(__FreeBSD__)
+ extern char** environ;
+ #endif
+ 
--- a/biology/hhsuite/pkg-descr
+++ b/biology/hhsuite/pkg-descr
@ -0,0 +1,8 @@
+SIMD-vectorized implementation of the Viterbi algorithm for profile HMM
+alignment and introduced various other speed-ups. This accelerated HHsearch by a
+factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is
+~10x faster than PSI-BLAST and ~20x faster than HMMER3. Jobs to perform HHsearch
+and HHblits searches with many query profile HMMs can be parallelized over cores
+and over servers in a cluster using OpenMP and message passing interface (MPI).
+
+WWW: https://github.com/soedinglab/hh-suite
--- a/biology/hhsuite/pkg-plist
+++ b/biology/hhsuite/pkg-plist
@ -0,0 +1,59 @@
+bin/a3m_database_extract
+bin/a3m_database_filter
+bin/a3m_database_reduce
+bin/a3m_extract
+bin/a3m_reduce
+bin/cstranslate
+bin/cstranslate_mpi
+bin/ffindex_apply
+bin/ffindex_apply_mpi
+bin/ffindex_build
+bin/ffindex_from_fasta
+bin/ffindex_from_fasta_with_split
+bin/ffindex_get
+bin/ffindex_modify
+bin/ffindex_order
+bin/ffindex_reduce
+bin/ffindex_unpack
+bin/hhalign
+bin/hhalign_mpi
+bin/hhalign_omp
+bin/hhblits
+bin/hhblits_ca3m
+bin/hhblits_mpi
+bin/hhblits_omp
+bin/hhconsensus
+bin/hhfilter
+bin/hhmake
+bin/hhsearch
+bin/hhsearch_mpi
+bin/hhsearch_omp
+%%DATADIR%%/data/context_data.crf
+%%DATADIR%%/data/context_data.lib
+%%DATADIR%%/data/cs219.lib
+%%DATADIR%%/data/do_not_delete
+%%DATADIR%%/data/do_not_delete.phr
+%%DATADIR%%/data/do_not_delete.pin
+%%DATADIR%%/data/do_not_delete.psq
+%%DATADIR%%/scripts/Align.pm
+%%DATADIR%%/scripts/HHPaths.pm
+%%DATADIR%%/scripts/a3m.py
+%%DATADIR%%/scripts/addss.pl
+%%DATADIR%%/scripts/check_a3m.py
+%%DATADIR%%/scripts/cif2fasta.py
+%%DATADIR%%/scripts/create_profile_from_hhm.pl
+%%DATADIR%%/scripts/create_profile_from_hmmer.pl
+%%DATADIR%%/scripts/ffindex.py
+%%DATADIR%%/scripts/get_a3m_size.py
+%%DATADIR%%/scripts/hh_reader.py
+%%DATADIR%%/scripts/hhmakemodel.pl
+%%DATADIR%%/scripts/hhmakemodel.py
+%%DATADIR%%/scripts/hhsuitedb.py
+%%DATADIR%%/scripts/mergeali.pl
+%%DATADIR%%/scripts/multithread.pl
+%%DATADIR%%/scripts/pdb2fasta.pl
+%%DATADIR%%/scripts/pdbfilter.pl
+%%DATADIR%%/scripts/pdbfilter.py
+%%DATADIR%%/scripts/reformat.pl
+%%DATADIR%%/scripts/renumberpdb.pl
+%%DATADIR%%/scripts/splitfasta.pl
--- a/cad/Makefile
+++ b/cad/Makefile
@ -55,6 +55,7 @@
    SUBDIR += kicad-library-templates-devel
    SUBDIR += klayout
    SUBDIR += ldraw
+    SUBDIR += leocad
    SUBDIR += lepton-eda
    SUBDIR += libopencad
    SUBDIR += librecad
--- a/cad/leocad/Makefile
+++ b/cad/leocad/Makefile
@ -0,0 +1,34 @@
+# Created by: David Yeske <dyeske@gmail.com>
+# $FreeBSD$
+
+PORTNAME=	leocad
+DISTVERSIONPREFIX=	v
+DISTVERSION=	18.02.20190517
+CATEGORIES=	cad
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	CAD program for creating virtual LEGO models
+
+LICENSE=	GPLv2
+LICENSE_FILE=	${WRKSRC}/docs/COPYING.txt
+
+RUN_DEPENDS=	ldraw>0:cad/ldraw
+
+USES=		compiler:c++11-lang desktop-file-utils gl qmake qt:5 shared-mime-info
+USE_GITHUB=	yes
+GH_ACCOUNT=	leozide
+GH_TAGNAME=	f392e3c
+USE_QT=		core gui concurrent network opengl printsupport widgets xml buildtools_build linguisttools_build
+USE_GL=		gl
+
+QMAKE_ARGS=	INSTALL_PREFIX=${PREFIX} MAN_DIR=${PREFIX}/man/man1 LDRAW_LIBRARY_PATH=${PREFIX}/share/ldraw
+
+PLIST_FILES=	bin/leocad \
+		share/applications/leocad.desktop \
+		share/icons/hicolor/scalable/mimetypes/application-vnd.leocad.svg \
+		man/man1/leocad.1.gz \
+		share/metainfo/leocad.appdata.xml \
+		share/mime/packages/leocad.xml \
+		share/pixmaps/leocad.png
+
+.include <bsd.port.mk>
--- a/cad/leocad/distinfo
+++ b/cad/leocad/distinfo
@ -0,0 +1,3 @@
+TIMESTAMP = 1558142272
+SHA256 (leozide-leocad-v18.02.20190517-f392e3c_GH0.tar.gz) = 7b22858cbed34914b0100be7e3bfb4bd34e069dd7b57a99854482ffbefc1db0a
+SIZE (leozide-leocad-v18.02.20190517-f392e3c_GH0.tar.gz) = 5289474
--- a/cad/leocad/files/patch-common_lc__application.cpp
+++ b/cad/leocad/files/patch-common_lc__application.cpp
@ -0,0 +1,16 @@
+Remove the embedded build date and fix build with Clang 6
+
+common/lc_application.cpp:209:23: error: no matching literal operator for call to 'operator""__DATE__' with arguments of types 'const char *' and 'unsigned int', and no matching literal operator template
+                                printf("Compiled "__DATE__"\n");
+                                                  ^
+
+--- common/lc_application.cpp.orig	2019-05-17 23:24:38 UTC
+++ common/lc_application.cpp
+@@ -375,7 +375,6 @@ bool lcApplication::Initialize(QList<QPair<QString, bo
+ 			printf("LeoCAD Version " LC_VERSION_TEXT "\n");
+ #endif
+ 			printf("LeoCAD Version " LC_VERSION_TEXT "\n");
+-			printf("Compiled " __DATE__ "\n");
+ 
+ 			ShowWindow = false;
+ 			return true;
--- a/cad/leocad/files/patch-leocad.pro
+++ b/cad/leocad/files/patch-leocad.pro
@ -0,0 +1,11 @@
+--- leocad.pro.orig	2019-05-18 01:23:33 UTC
+++ leocad.pro
+@@ -108,7 +108,7 @@ unix:!macx {
+ 
+ 	target.path = $$BIN_DIR
+ 	docs.path = $$DOCS_DIR
+-	docs.files = docs/README.txt docs/CREDITS.txt docs/COPYING.txt
+	docs.files = 
+ 	man.path = $$MAN_DIR
+ 	man.files = docs/leocad.1
+ 	desktop.path = $$DESKTOP_DIR
--- a/cad/leocad/pkg-descr
+++ b/cad/leocad/pkg-descr
@ -0,0 +1,14 @@
+LeoCAD is a CAD program that can be used to create virtual LEGO models.
+
+LeoCAD has an intuitive interface that is designed to allow new users to start
+creating new models without having to spend too much time learning the
+application.
+
+LeoCAD is fully compatible with the LDraw Standard and related tools, and it
+reads and writes LDR and MPD files so that you can share and download models
+from the Internet.
+
+It currently features several thousand different pieces created by the LDraw
+community.
+
+WWW: https://www.leocad.org/
--- a/comms/chirp/Makefile
+++ b/comms/chirp/Makefile
@ -1,7 +1,7 @@
 # $FreeBSD$

 PORTNAME=	chirp
-DISTVERSION=	0.4.1.2018.09.06
+DISTVERSION=	0.4.1.2019.05.11
 CATEGORIES=	comms hamradio
 MASTER_SITES=	https://trac.chirp.danplanet.com/chirp_daily/daily-${PORTVERSION:C/[0-9]+\.[0-9]+\.[0-9]+\.//:C/\.//g}/
 DISTNAME=	${PORTNAME}-daily-${PORTVERSION:C/[0-9]+\.[0-9]+\.[0-9]+\.//:C/\.//g}
@ -17,8 +17,10 @@ BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}libxml2>0:textproc/py-libxml2@${PY_FLAVOR}
 		${PYTHON_PKGNAMEPREFIX}gtk2>0:x11-toolkits/py-gtk2@${PY_FLAVOR}
 RUN_DEPENDS:=	${BUILD_DEPENDS}

-USES=		desktop-file-utils gettext python:2.7
+USES=		desktop-file-utils python:2.7
 USE_PYTHON=	distutils autoplist
+
+NLS_USES=	gettext
 NO_ARCH=	yes

 .include <bsd.port.mk>
--- a/comms/chirp/distinfo
+++ b/comms/chirp/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1537546528
-SHA256 (chirp-daily-20180906.tar.gz) = 553db776ee505743c8eaea9def986199cce34f6857501764f8865c9150099801
-SIZE (chirp-daily-20180906.tar.gz) = 777421
+TIMESTAMP = 1557955924
+SHA256 (chirp-daily-20190511.tar.gz) = f24b62917fecc3e7a8e5f5a268e69b2df71285fbcc07ba1e6a24af3dffacbacc
+SIZE (chirp-daily-20190511.tar.gz) = 865361
--- a/databases/galera/Makefile
+++ b/databases/galera/Makefile
@ -14,7 +14,6 @@ LICENSE=	GPLv2
 BROKEN_aarch64=		fails to compile: gu_int128.h: use of undeclared identifier '__bswap64_var'
 BROKEN_armv6=		fails to compile: gu_int128.h: use of undeclared identifier '__bswap64_var'
 BROKEN_armv7=		fails to compile: gu_int128.h: use of undeclared identifier '__bswap64_var'
-BROKEN_powerpc64=	fails to configure: Checking for C library pthread... no
 NOT_FOR_ARCHS=		i386
 # On i386 older versions of clang produce:
 #   cannot compile this atomic library call yet ... __atomic_add_fetch
@ -30,7 +29,7 @@ BUILD_DEPENDS=	checkmk:devel/check \
 		${LOCALBASE}/include/boost/shared_ptr.hpp:devel/boost-libs
 LIB_DEPENDS=	libboost_date_time.so:devel/boost-libs

-USES=		python:build scons ssl
+USES=		compiler:c++11-lang python:build scons ssl

 USE_LDCONFIG=	yes

--- a/databases/pgpool-II-35/Makefile
+++ b/databases/pgpool-II-35/Makefile
@ -2,7 +2,7 @@
 # $FreeBSD$

 PORTNAME=	pgpool-II
-PORTVERSION=	3.5.20
+PORTVERSION=	3.5.21
 CATEGORIES=	databases
 MASTER_SITES=	http://www.pgpool.net/mediawiki/images/
 PKGNAMESUFFIX=	35
--- a/databases/pgpool-II-35/distinfo
+++ b/databases/pgpool-II-35/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1554556296
-SHA256 (pgpool-II-3.5.20.tar.gz) = c1f3288bcf60d1a21e2071e767cf2ba92d5421945376a700f05bc140c05de735
-SIZE (pgpool-II-3.5.20.tar.gz) = 2278264
+TIMESTAMP = 1558014268
+SHA256 (pgpool-II-3.5.21.tar.gz) = af35cc101e04513f5fb98d4a64040a9de7035eff09cbb2482cd438b8e37c8d87
+SIZE (pgpool-II-3.5.21.tar.gz) = 2284652
--- a/databases/pgpool-II-36/Makefile
+++ b/databases/pgpool-II-36/Makefile
@ -1,7 +1,7 @@
 # $FreeBSD$

 PORTNAME=	pgpool-II
-PORTVERSION=	3.6.16
+PORTVERSION=	3.6.17
 CATEGORIES=	databases
 MASTER_SITES=	http://www.pgpool.net/mediawiki/images/
 PKGNAMESUFFIX=	36
--- a/databases/pgpool-II-36/distinfo
+++ b/databases/pgpool-II-36/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1554556578
-SHA256 (pgpool-II-3.6.16.tar.gz) = 2bcc4cc19b9ab9e6f666dd9538834c83f7bb22d2fdcf41336f36c33dbe7c363c
-SIZE (pgpool-II-3.6.16.tar.gz) = 3296415
+TIMESTAMP = 1558014337
+SHA256 (pgpool-II-3.6.17.tar.gz) = cbe239d193a1c3f7cb9839b0e1a2500e0d9ec5d8f763cd9dcc094770e845ef73
+SIZE (pgpool-II-3.6.17.tar.gz) = 3315365
--- a/databases/pgpool-II-37/Makefile
+++ b/databases/pgpool-II-37/Makefile
@ -1,7 +1,7 @@
 # $FreeBSD$

 PORTNAME=	pgpool-II
-PORTVERSION=	3.7.9
+PORTVERSION=	3.7.10
 CATEGORIES=	databases
 MASTER_SITES=	http://www.pgpool.net/mediawiki/images/
 PKGNAMESUFFIX=	37
--- a/databases/pgpool-II-37/distinfo
+++ b/databases/pgpool-II-37/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1554556566
-SHA256 (pgpool-II-3.7.9.tar.gz) = ff255c1270bca564b7775b90dd1f598eacd33b4ca4dfc02fcd430a514679d977
-SIZE (pgpool-II-3.7.9.tar.gz) = 3352257
+TIMESTAMP = 1558014430
+SHA256 (pgpool-II-3.7.10.tar.gz) = ff4c2ad146d62aafc22c8ae10f592f7a6e924e93823755d51b120b213b91d8d6
+SIZE (pgpool-II-3.7.10.tar.gz) = 3375419
--- a/databases/pgpool-II-40/Makefile
+++ b/databases/pgpool-II-40/Makefile
@ -1,7 +1,7 @@
 # $FreeBSD$

 PORTNAME=	pgpool-II
-PORTVERSION=	4.0.4
+PORTVERSION=	4.0.5
 CATEGORIES=	databases
 MASTER_SITES=	http://www.pgpool.net/mediawiki/images/
 PKGNAMESUFFIX=	40
--- a/databases/pgpool-II-40/distinfo
+++ b/databases/pgpool-II-40/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1554556646
-SHA256 (pgpool-II-4.0.4.tar.gz) = 1b399568d049fb3c1802329a477fc65679e1db7c3ee7ffff51eae36605b9ee39
-SIZE (pgpool-II-4.0.4.tar.gz) = 3736577
+TIMESTAMP = 1558015937
+SHA256 (pgpool-II-4.0.5.tar.gz) = 84450766c04214a7d850bf35ba99d699ce35c17e8744a4749f20d819f5144f6c
+SIZE (pgpool-II-4.0.5.tar.gz) = 3768842
--- a/databases/pgpool/Makefile
+++ b/databases/pgpool/Makefile
@ -2,7 +2,7 @@
 # $FreeBSD$

 PORTNAME=	pgpool
-PORTVERSION=	3.4.23
+PORTVERSION=	3.4.24
 CATEGORIES=	databases
 MASTER_SITES=	http://www.pgpool.net/mediawiki/images/
 DISTNAME=	${PORTNAME}-II-${PORTVERSION}
--- a/databases/pgpool/distinfo
+++ b/databases/pgpool/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1554556131
-SHA256 (pgpool-II-3.4.23.tar.gz) = f8371a3e7eddea83d309a20c0907a61348284eab9d8674f6de2d7edb2173af6c
-SIZE (pgpool-II-3.4.23.tar.gz) = 2182309
+TIMESTAMP = 1558014223
+SHA256 (pgpool-II-3.4.24.tar.gz) = be4ca23e77ebb70fe06e83dc1d6ab80839be612913720962f103523eb38f735e
+SIZE (pgpool-II-3.4.24.tar.gz) = 2184878
--- a/databases/tiledb/Makefile
+++ b/databases/tiledb/Makefile
@ -2,7 +2,7 @@
 # $FreeBSD$

 PORTNAME=	tiledb
-PORTVERSION=	1.5.0
+PORTVERSION=	1.5.1
 CATEGORIES=	databases

 MAINTAINER=	sunpoet@FreeBSD.org
--- a/databases/tiledb/distinfo
+++ b/databases/tiledb/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1557532072
-SHA256 (TileDB-Inc-TileDB-1.5.0_GH0.tar.gz) = 6c7021f0aa403f0b6351bf850a79c13f4ab3c4a00456144092eb8e9dbd2ee366
-SIZE (TileDB-Inc-TileDB-1.5.0_GH0.tar.gz) = 17248673
+TIMESTAMP = 1558105437
+SHA256 (TileDB-Inc-TileDB-1.5.1_GH0.tar.gz) = f31fc3a6d1511e88ead38b2ab9938e16a68fdca4e47ce41e3a068d60115a93d7
+SIZE (TileDB-Inc-TileDB-1.5.1_GH0.tar.gz) = 17250631
--- a/deskutils/xfce4-tumbler/Makefile
+++ b/deskutils/xfce4-tumbler/Makefile
@ -2,8 +2,7 @@
 # $FreeBSD$

 PORTNAME=	tumbler
-PORTVERSION=	0.2.3
-PORTREVISION=	2
+PORTVERSION=	0.2.4
 CATEGORIES=	deskutils xfce
 MASTER_SITES=	XFCE/src/xfce/${PORTNAME}/${PORTVERSION:R}/
 PKGNAMEPREFIX=	xfce4-
--- a/deskutils/xfce4-tumbler/distinfo
+++ b/deskutils/xfce4-tumbler/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1536858933
-SHA256 (xfce4/tumbler-0.2.3.tar.bz2) = d022e1bd1559fba33e4bf20fb053b219eca17676ebffb1ceb214fcd58a187d40
-SIZE (xfce4/tumbler-0.2.3.tar.bz2) = 538109
+TIMESTAMP = 1558125774
+SHA256 (xfce4/tumbler-0.2.4.tar.bz2) = 0ff497e13f9f9322112cb7707918dd8970e405447f0c92dac40ec3d659e5b6a6
+SIZE (xfce4/tumbler-0.2.4.tar.bz2) = 560604
--- a/devel/Makefile
+++ b/devel/Makefile
@ -435,6 +435,7 @@
    SUBDIR += darts
    SUBDIR += dash.el
    SUBDIR += datadraw
+    SUBDIR += date
    SUBDIR += dbus
    SUBDIR += dbus-c++
    SUBDIR += dbus-glib
@ -492,6 +493,7 @@
    SUBDIR += dsymbol
    SUBDIR += dub
    SUBDIR += dulwich
+    SUBDIR += dupl
    SUBDIR += duplo
    SUBDIR += dwarfdump
    SUBDIR += dxa65
@ -561,6 +563,7 @@
    SUBDIR += elixir-unsafe
    SUBDIR += embb
    SUBDIR += emscripten
+    SUBDIR += entt
    SUBDIR += epl.el
    SUBDIR += epm
    SUBDIR += epydoc
@ -609,6 +612,7 @@
    SUBDIR += erlang-syslog
    SUBDIR += erlang-unicode_util_compat
    SUBDIR += es-eric6
+    SUBDIR += estd
    SUBDIR += etcd
    SUBDIR += etcd31
    SUBDIR += etcd32
@ -5214,6 +5218,7 @@
    SUBDIR += qtcreator
    SUBDIR += quickcheck++
    SUBDIR += quilt
+    SUBDIR += rabs
    SUBDIR += racer
    SUBDIR += racerd
    SUBDIR += radare2
@ -5305,6 +5310,7 @@
    SUBDIR += rubygem-attic
    SUBDIR += rubygem-attr_required
    SUBDIR += rubygem-authlogic
+    SUBDIR += rubygem-avro
    SUBDIR += rubygem-awesome_print
    SUBDIR += rubygem-aws-eventstream
    SUBDIR += rubygem-aws-sdk
@ -5499,6 +5505,7 @@
    SUBDIR += rubygem-git-version-bump
    SUBDIR += rubygem-github_api
    SUBDIR += rubygem-gitlab-default_value_for
+    SUBDIR += rubygem-gitlab-labkit
    SUBDIR += rubygem-gitlab-pygments.rb
    SUBDIR += rubygem-gitlab-sidekiq-fetcher
    SUBDIR += rubygem-gitlab_git
@ -5927,6 +5934,8 @@
    SUBDIR += rubygem-uuid
    SUBDIR += rubygem-uuidtools
    SUBDIR += rubygem-validatable
+    SUBDIR += rubygem-validate_email
+    SUBDIR += rubygem-validate_url
    SUBDIR += rubygem-versionomy
    SUBDIR += rubygem-virtus
    SUBDIR += rubygem-warbler
@ -5936,6 +5945,7 @@
    SUBDIR += rubygem-web-console-rails50
    SUBDIR += rubygem-web-console2
    SUBDIR += rubygem-webby
+    SUBDIR += rubygem-webfinger
    SUBDIR += rubygem-webpacker-rails5
    SUBDIR += rubygem-webpacker-rails50
    SUBDIR += rubygem-will_paginate
--- a/devel/avro-c/Makefile
+++ b/devel/avro-c/Makefile
@ -2,9 +2,8 @@
 # $FreeBSD$

 PORTNAME=	avro
-PORTVERSION=	1.8.2
+PORTVERSION=	1.9.0
 DISTVERSIONPREFIX=	release-
-PORTREVISION=	1
 CATEGORIES=	devel
 PKGNAMESUFFIX=	-c

--- a/devel/avro-c/distinfo
+++ b/devel/avro-c/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1519473626
-SHA256 (apache-avro-release-1.8.2_GH0.tar.gz) = 19040889f2c822445b6ccf14e6f13ccf2d7851458790ae1539a2688d21c76ae0
-SIZE (apache-avro-release-1.8.2_GH0.tar.gz) = 2141779
+TIMESTAMP = 1558166522
+SHA256 (apache-avro-release-1.9.0_GH0.tar.gz) = 832558e90c97c9305bff37de1146a1fa8acbb83dfa022e8f174b348fd27f8510
+SIZE (apache-avro-release-1.9.0_GH0.tar.gz) = 1823945
--- a/devel/avro-c/files/patch-src_CMakeLists.txt
+++ b/devel/avro-c/files/patch-src_CMakeLists.txt
@ -1,11 +0,0 @@
--- src/CMakeLists.txt.orig	2017-04-17 23:56:17 UTC
-+++ src/CMakeLists.txt
-@@ -82,7 +82,7 @@ source_group(Avro FILES ${AVRO_SRC})
- # The version.sh script gives us a SOVERSION that uses colon as a
- # separator; we need periods.
- 
-string(REPLACE ":" "." LIBAVRO_DOT_VERSION ${LIBAVRO_VERSION})
-+set(LIBAVRO_DOT_VERSION 0)
- 
- add_library(avro-static STATIC ${AVRO_SRC})
- target_link_libraries(avro-static ${JANSSON_LIBRARIES} ${CODEC_LIBRARIES} ${THREADS_LIBRARIES})
--- a/devel/avro-c/files/patch-src_avro_refcount.h
+++ b/devel/avro-c/files/patch-src_avro_refcount.h
@ -1,11 +0,0 @@
--- src/avro/refcount.h.orig	2017-04-17 23:56:17 UTC
-+++ src/avro/refcount.h
-@@ -118,7 +118,7 @@ avro_refcount_dec(volatile int *refcount
-  * GCC intrinsics
-  */
- 
-#elif (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__) > 40500
-+#elif (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__) > 40500 || defined(__clang__)
- 
- static inline void
- avro_refcount_set(volatile int *refcount, int value)
--- a/devel/avro-c/files/patch-src_codec.c
+++ b/devel/avro-c/files/patch-src_codec.c
@ -1,12 +0,0 @@
--- src/codec.c.orig	2016-05-15 00:38:52 UTC
-+++ src/codec.c
-@@ -21,6 +21,9 @@
- #  if defined(__APPLE__)
- #    include <libkern/OSByteOrder.h>
- #    define __bswap_32 OSSwapInt32
-+#  elif defined(__FreeBSD__)
-+#    include <sys/endian.h>
-+#    define __bswap_32 bswap32
- #  else
- #    include <byteswap.h>
- #  endif
--- a/devel/avro-c/pkg-plist
+++ b/devel/avro-c/pkg-plist
@ -20,5 +20,6 @@ include/avro/schema.h
 include/avro/value.h
 lib/libavro.a
 lib/libavro.so
-lib/libavro.so.0
+lib/libavro.so.23
+lib/libavro.so.23.0.0
 libdata/pkgconfig/avro-c.pc
--- a/devel/avro-cpp/Makefile
+++ b/devel/avro-cpp/Makefile
@ -2,9 +2,8 @@
 # $FreeBSD$

 PORTNAME=	avro
-PORTVERSION=	1.8.2
+PORTVERSION=	1.9.0
 DISTVERSIONPREFIX=	release-
-PORTREVISION=	5
 CATEGORIES=	devel
 PKGNAMESUFFIX=	-cpp

--- a/devel/avro-cpp/distinfo
+++ b/devel/avro-cpp/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1519473626
-SHA256 (apache-avro-release-1.8.2_GH0.tar.gz) = 19040889f2c822445b6ccf14e6f13ccf2d7851458790ae1539a2688d21c76ae0
-SIZE (apache-avro-release-1.8.2_GH0.tar.gz) = 2141779
+TIMESTAMP = 1558166524
+SHA256 (apache-avro-release-1.9.0_GH0.tar.gz) = 832558e90c97c9305bff37de1146a1fa8acbb83dfa022e8f174b348fd27f8510
+SIZE (apache-avro-release-1.9.0_GH0.tar.gz) = 1823945
--- a/devel/avro-cpp/files/patch-impl_json_JsonIO.hh
+++ b/devel/avro-cpp/files/patch-impl_json_JsonIO.hh
@ -1,11 +0,0 @@
--- impl/json/JsonIO.hh.orig	2015-12-02 18:53:55 UTC
-+++ impl/json/JsonIO.hh
-@@ -159,7 +159,7 @@ class AVRO_DECL JsonGenerator {
- 
-     void escapeCtl(char c) {
-         out_.write('\\');
-        out_.write('U');
-+        out_.write('u'); // https://issues.apache.org/jira/browse/AVRO-1191
-         out_.write('0');
-         out_.write('0');
-         out_.write(toHex((static_cast<unsigned char>(c)) / 16));
--- a/devel/avro-cpp/pkg-plist
+++ b/devel/avro-cpp/pkg-plist
@ -2,7 +2,6 @@ bin/avrogencpp
 include/avro/AvroParse.hh
 include/avro/AvroSerialize.hh
 include/avro/AvroTraits.hh
-include/avro/Boost.hh
 include/avro/Compiler.hh
 include/avro/Config.hh
 include/avro/DataFile.hh
@ -12,6 +11,7 @@ include/avro/Exception.hh
 include/avro/Generic.hh
 include/avro/GenericDatum.hh
 include/avro/Layout.hh
+include/avro/LogicalType.hh
 include/avro/Node.hh
 include/avro/NodeConcepts.hh
 include/avro/NodeImpl.hh
--- a/devel/avro/Makefile
+++ b/devel/avro/Makefile
@ -3,6 +3,7 @@

 PORTNAME=	avro
 PORTVERSION=	1.8.2
+PORTREVISION=	1
 CATEGORIES=	devel

 MAINTAINER=	sunpoet@FreeBSD.org
@ -12,15 +13,17 @@ LICENSE=	APACHE20

 USES=		metaport

-OPTIONS_DEFINE=	C CPP PYTHON
-OPTIONS_DEFAULT=C CPP PYTHON
+OPTIONS_DEFINE=	C CPP PYTHON RUBY
+OPTIONS_DEFAULT=C CPP PYTHON RUBY
 C_DESC=		Install C library
 CPP_DESC=	Install C++ library
 PYTHON_DESC=	Install Python library
+RUBY_DESC=	Install Ruby library

 C_LIB_DEPENDS=		libavro.so:devel/avro-c
 CPP_LIB_DEPENDS=	libavrocpp.so:devel/avro-cpp
 PYTHON_RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}avro>=0:devel/py-avro@${PY_FLAVOR}
 PYTHON_USES=		python:env
+RUBY_RUN_DEPENDS=	rubygem-avro>=0:devel/rubygem-avro

 .include <bsd.port.mk>
--- a/devel/benchmark/Makefile
+++ b/devel/benchmark/Makefile
@ -2,9 +2,7 @@

 PORTNAME=	benchmark
 DISTVERSIONPREFIX=	v
-DISTVERSION=	1.4.1-25
-PORTREVISION=	1
-DISTVERSIONSUFFIX=	-gaf441fc
+DISTVERSION=	1.5
 CATEGORIES=	devel

 MAINTAINER=	yuri@FreeBSD.org
--- a/devel/benchmark/distinfo
+++ b/devel/benchmark/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1534606759
-SHA256 (google-benchmark-v1.4.1-25-gaf441fc_GH0.tar.gz) = 87da8e5803dda1e92c8db7b3bff37e3a79b9e4b0623383ea16ecc63d63a53882
-SIZE (google-benchmark-v1.4.1-25-gaf441fc_GH0.tar.gz) = 131207
+TIMESTAMP = 1558189367
+SHA256 (google-benchmark-v1.5_GH0.tar.gz) = feba1c44cbace01627435a675aa271f4b012068dbea9922443c58fedd56eb5eb
+SIZE (google-benchmark-v1.5_GH0.tar.gz) = 150159
--- a/devel/ccache/Makefile
+++ b/devel/ccache/Makefile
@ -3,9 +3,9 @@

 PORTNAME=	ccache
 #PORTVERSION must be set later due to depending on PORT_OPTIONS.
-PORTREVISION=	1
+PORTREVISION=	0
 CATEGORIES=	devel
-MASTER_SITES=	https://www.samba.org/ftp/ccache/ \
+MASTER_SITES=	https://github.com/ccache/ccache/releases/download/v${DISTVERSION}/ \
 		LOCAL/bdrewery

 MAINTAINER=	bdrewery@FreeBSD.org
@ -35,13 +35,13 @@ LLVMLINK_DESC=	Create llvm compiler links if llvm is installed
 TINDERBOX_DESC=	Create tarball for tinderbox usage
 MEMCACHED_DESC=	Build in experimental Memcached support

-USES=		compiler
+USES=		compiler gmake

 MEMCACHED_EXTRA_PATCHES=	\
 				${FILESDIR}/extra-patch-memcached-configure.ac \
 				${FILESDIR}/extra-patch-memcached-Makefile.in
 MEMCACHED_CONFIGURE_ENABLE=	memcached
-MEMCACHED_USES=			autoreconf gmake pkgconfig
+MEMCACHED_USES=			autoreconf pkgconfig
 MEMCACHED_LIB_DEPENDS=		libmemcached.so:databases/libmemcached
 MEMCACHED_LDFLAGS=		-L${LOCALBASE}/lib
 MEMCACHED_CFLAGS=		-I${LOCALBASE}/include
@ -82,9 +82,7 @@ ALL_TARGET=	all docs
 PLIST_FILES+=	man/man1/ccache.1.gz
 .endif
 .else
-PORTVERSION=	3.4.3
-# Only needed pre-3.5
-EXTRA_PATCHES+=	${FILESDIR}/extra-patch-configure.ac
+PORTVERSION=	3.7.1
 .endif

 .include <bsd.port.pre.mk>
--- a/devel/ccache/distinfo
+++ b/devel/ccache/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1538593366
-SHA256 (ccache-3.4.3.tar.gz) = 6ee63d919274da937cbcb2870da16a3b386e100f7f942ea8b7f081652df3d00b
-SIZE (ccache-3.4.3.tar.gz) = 466575
+TIMESTAMP = 1558214189
+SHA256 (ccache-3.7.1.tar.gz) = e562fcdbe766406b6fe4bf97ce5c001d2be8a17465f33bcddefc9499bbb057d8
+SIZE (ccache-3.7.1.tar.gz) = 498581
--- a/devel/ccache/files/extra-patch-configure.ac
+++ b/devel/ccache/files/extra-patch-configure.ac
@ -1,19 +0,0 @@
--- m4/feature_macros.m4.orig	2017-02-13 15:05:54.405968000 -0800
-+++ m4/feature_macros.m4	2017-02-13 15:16:32.931104000 -0800
-@@ -120,7 +120,7 @@
-                 Define to the level of X/Open that your system supports)
-       ;;
-     *)
-      AC_DEFINE(_XOPEN_SOURCE, 600,
-+      AC_DEFINE(_XOPEN_SOURCE, 700,
-                 Define to the level of X/Open that your system supports)
-       ;;
-   esac
-@@ -142,6 +142,6 @@
-       ;;
-   esac
- 
-  AC_DEFINE(_POSIX_C_SOURCE, 200112L, Define to activate features from IEEE Stds 1003.1-2001)
-+  AC_DEFINE(_POSIX_C_SOURCE, 200809L, Define to activate features from IEEE Stds 1003.1-2001)
- 
- fi
--- a/devel/cmake-doc/Makefile
+++ b/devel/cmake-doc/Makefile
@ -1,7 +1,7 @@
 # $FreeBSD$

 PORTNAME=	cmake
-DISTVERSION=	3.14.3
+DISTVERSION=	3.14.4
 CATEGORIES=	devel
 MASTER_SITES=	https://www.cmake.org/files/v${PORTVERSION:R}/
 PKGNAMESUFFIX=	-doc
--- a/devel/cmake-gui/Makefile
+++ b/devel/cmake-gui/Makefile
@ -1,7 +1,7 @@
 # $FreeBSD$

 PORTNAME=	cmake
-DISTVERSION=	3.14.3
+DISTVERSION=	3.14.4
 CATEGORIES=	devel
 MASTER_SITES=	https://www.cmake.org/files/v${PORTVERSION:R}/
 PKGNAMESUFFIX=	-gui
--- a/devel/date/Makefile
+++ b/devel/date/Makefile
@ -0,0 +1,34 @@
+# $FreeBSD$
+
+PORTNAME=	date
+DISTVERSIONPREFIX=	v
+DISTVERSION=	2.4.1-80
+DISTVERSIONSUFFIX=	-ged0368f
+CATEGORIES=	devel
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Date and time library based on the C++11/14/17 <chrono> header
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE.txt
+
+RUN_DEPENDS=	${LOCALBASE}/include/boost/chrono/typeof/boost/chrono/chrono.hpp:devel/boost-libs
+LIB_DEPENDS=	libcurl.so:ftp/curl
+TEST_DEPENDS=	bash:shells/bash
+
+USES=		cmake compiler:c++17-lang
+USE_GITHUB=	yes
+GH_ACCOUNT=	HowardHinnant
+USE_LDCONFIG=	yes
+
+CMAKE_ON=	BUILD_SHARED_LIBS
+CMAKE_OFF=	ENABLE_DATE_TESTING
+
+do-test:
+	@cd ${WRKSRC} && ${REINPLACE_CMD} 's|!/bin/bash|!${LOCALBASE}/bin/bash|' compile_fail.sh test_fail.sh
+	@cd ${BUILD_WRKSRC} && \
+		${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DENABLE_DATE_TESTING:BOOL=ON ${CMAKE_SOURCE_PATH} && \
+		${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \
+		${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} testit
+
+.include <bsd.port.mk>
--- a/devel/date/distinfo
+++ b/devel/date/distinfo
@ -0,0 +1,3 @@
+TIMESTAMP = 1558125722
+SHA256 (HowardHinnant-date-v2.4.1-80-ged0368f_GH0.tar.gz) = 4b8f053e9ba717b66829ca0aa4df03eeed68996416bbef17353716cebdf09156
+SIZE (HowardHinnant-date-v2.4.1-80-ged0368f_GH0.tar.gz) = 804032
--- a/devel/date/pkg-descr
+++ b/devel/date/pkg-descr
@ -0,0 +1,22 @@
+This is actually several separate C++11/C++14/C++17 libraries:
+* "date.h" is a header-only library which builds upon <chrono>. It adds some new
+  duration types, and new time_point types. It also adds "field" types such as
+  year_month_day which is a struct {year, month, day}. And it provides
+  convenient means to convert between the "field" types and the time_point
+  types.
+* "tz.h" / "tz.cpp" are a timezone library built on top of the "date.h" library.
+  This timezone library is a complete parser of the IANA timezone database. It
+  provides for an easy way to access all of the data in this database, using the
+  types from "date.h" and <chrono>. The IANA database also includes data on leap
+  seconds, and this library provides utilities to compute with that information
+  as well.
+* "iso_week.h" is a header-only library built on top of the "date.h" library
+  which implements the ISO week date calendar.
+* "julian.h" is a header-only library built on top of the "date.h" library which
+  implements a proleptic Julian calendar which is fully interoperable with
+  everything above.
+* "islamic.h" is a header-only library built on top of the "date.h" library
+  which implements a proleptic Islamic calendar which is fully interoperable
+  with everything above.
+
+WWW: https://github.com/HowardHinnant/date
--- a/devel/date/pkg-plist
+++ b/devel/date/pkg-plist
@ -0,0 +1,11 @@
+include/date/chrono_io.h
+include/date/date.h
+include/date/ios.h
+include/date/islamic.h
+include/date/iso_week.h
+include/date/julian.h
+include/date/ptz.h
+include/date/tz.h
+include/date/tz_private.h
+lib/cmake/date/dateConfig.cmake
+lib/libtz.so
--- a/devel/dupl/Makefile
+++ b/devel/dupl/Makefile
@ -0,0 +1,23 @@
+# $FreeBSD$
+
+PORTNAME=	dupl
+DISTVERSIONPREFIX=	v
+DISTVERSION=	1.0.0-11
+DISTVERSIONSUFFIX=	-g28d787e
+CATEGORIES=	devel
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Tool for code clone detection
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+USES=		go
+USE_GITHUB=	yes
+GH_ACCOUNT=	mibk
+
+GO_PKGNAME=	github.com/${GH_ACCOUNT}/${PORTNAME}
+
+PLIST_FILES=	bin/${PORTNAME}
+
+.include <bsd.port.mk>
--- a/devel/dupl/distinfo
+++ b/devel/dupl/distinfo
@ -0,0 +1,3 @@
+TIMESTAMP = 1558228845
+SHA256 (mibk-dupl-v1.0.0-11-g28d787e_GH0.tar.gz) = fb205c0b9fc93bcacc834b1e367d493bf187af098c05c2a60fb298520a7e036b
+SIZE (mibk-dupl-v1.0.0-11-g28d787e_GH0.tar.gz) = 19213
--- a/devel/dupl/pkg-descr
+++ b/devel/dupl/pkg-descr
@ -0,0 +1,11 @@
+dupl is a tool written in Go for finding code clones. So far it can find clones
+only in the Go source files. The method uses suffix tree for serialized ASTs. It
+ignores values of AST nodes. It just operates with their types (e.g.
+if a == 13 {} and if x == 100 {} are considered the same provided it exceeds the
+minimal token sequence size).
+
+Due to the used method dupl can report so called "false positives" on the
+output.  These are the ones we do not consider clones (whether they are too
+small, or the values of the matched tokens are completely different).
+
+WWW: https://github.com/mibk/dupl
--- a/devel/entt/Makefile
+++ b/devel/entt/Makefile
@ -0,0 +1,26 @@
+# $FreeBSD$
+
+PORTNAME=	entt
+DISTVERSIONPREFIX=	v
+DISTVERSION=	3.0.0
+CATEGORIES=	devel
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Fast and reliable entity-component system (ECS) and much more
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+USES=		cmake
+USE_GITHUB=	yes
+GH_ACCOUNT=	skypjack
+
+NO_ARCH=	yes
+
+do-test:
+	@cd ${BUILD_WRKSRC} && \
+		${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DBUILD_TESTING:BOOL=ON ${CMAKE_SOURCE_PATH} && \
+		${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \
+		${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test
+
+.include <bsd.port.mk>
--- a/devel/entt/distinfo
+++ b/devel/entt/distinfo
@ -0,0 +1,3 @@
+TIMESTAMP = 1558116593
+SHA256 (skypjack-entt-v3.0.0_GH0.tar.gz) = f8928314a18f1fabda5398efdef7a001d09de43c2ffda90c1b77e56f5d41574b
+SIZE (skypjack-entt-v3.0.0_GH0.tar.gz) = 266513
--- a/devel/entt/pkg-descr
+++ b/devel/entt/pkg-descr
@ -0,0 +1,7 @@
+EnTT is a header-only, tiny and easy to use library for game programming and
+much more written in modern C++, mainly known for its innovative
+entity-component-system (ECS) model.
+Among others, it's used in Minecraft by Mojang, the ArcGIS Runtime SDKs by Esri
+and The Forge by Confetti.
+
+WWW: https://github.com/skypjack/entt/wiki
--- a/devel/entt/pkg-plist
+++ b/devel/entt/pkg-plist
@ -0,0 +1,40 @@
+include/entt/config/config.h
+include/entt/config/version.h
+include/entt/core/algorithm.hpp
+include/entt/core/family.hpp
+include/entt/core/hashed_string.hpp
+include/entt/core/ident.hpp
+include/entt/core/monostate.hpp
+include/entt/core/type_traits.hpp
+include/entt/core/utility.hpp
+include/entt/entity/actor.hpp
+include/entt/entity/entity.hpp
+include/entt/entity/fwd.hpp
+include/entt/entity/group.hpp
+include/entt/entity/helper.hpp
+include/entt/entity/prototype.hpp
+include/entt/entity/registry.hpp
+include/entt/entity/runtime_view.hpp
+include/entt/entity/snapshot.hpp
+include/entt/entity/sparse_set.hpp
+include/entt/entity/storage.hpp
+include/entt/entity/view.hpp
+include/entt/entt.hpp
+include/entt/fwd.hpp
+include/entt/locator/locator.hpp
+include/entt/meta/factory.hpp
+include/entt/meta/meta.hpp
+include/entt/process/process.hpp
+include/entt/process/scheduler.hpp
+include/entt/resource/cache.hpp
+include/entt/resource/fwd.hpp
+include/entt/resource/handle.hpp
+include/entt/resource/loader.hpp
+include/entt/signal/delegate.hpp
+include/entt/signal/dispatcher.hpp
+include/entt/signal/emitter.hpp
+include/entt/signal/fwd.hpp
+include/entt/signal/sigh.hpp
+lib/cmake/entt/EnTTConfig.cmake
+lib/cmake/entt/EnTTConfigVersion.cmake
+lib/cmake/entt/EnTTTargets.cmake
--- a/devel/estd/Makefile
+++ b/devel/estd/Makefile
@ -0,0 +1,25 @@
+# $FreeBSD$
+
+PORTNAME=	estd
+DISTVERSION=	0.3.2
+CATEGORIES=	devel
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Header-only C++ utilities in the style of the standard library
+
+LICENSE=	BSD3CLAUSE
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+USES=		cmake
+USE_GITHUB=	yes
+GH_ACCOUNT=	fizyr
+
+NO_ARCH=	yes
+
+do-test:
+	@cd ${BUILD_WRKSRC} && \
+		${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DBUILD_TESTS:BOOL=ON ${CMAKE_SOURCE_PATH} && \
+		${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \
+		${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} check
+
+.include <bsd.port.mk>
--- a/devel/estd/distinfo
+++ b/devel/estd/distinfo
@ -0,0 +1,3 @@
+TIMESTAMP = 1558195191
+SHA256 (fizyr-estd-0.3.2_GH0.tar.gz) = a6250518230c43ccc7becaa9f061fe52a6faab21d221f604be9db019ebcce72a
+SIZE (fizyr-estd-0.3.2_GH0.tar.gz) = 127922
--- a/devel/estd/pkg-descr
+++ b/devel/estd/pkg-descr
@ -0,0 +1,8 @@
+estd is a header-only C++ library providing some additional utilities in the
+style of the standard library.
+
+The include files are ordered hierarchically in the style of Boost. You can
+include a whole sublibrary with a single header, or pick only the bits you want
+to use.
+
+WWW: https://github.com/fizyr/estd
--- a/devel/estd/pkg-plist
+++ b/devel/estd/pkg-plist
@ -0,0 +1,72 @@
+include/estd/any.hpp
+include/estd/any/any.hpp
+include/estd/convert.hpp
+include/estd/convert/conversion.hpp
+include/estd/convert/convert.hpp
+include/estd/convert/numerical.hpp
+include/estd/convert/stl.hpp
+include/estd/convert/stl/array.hpp
+include/estd/convert/stl/deque.hpp
+include/estd/convert/stl/forward_list.hpp
+include/estd/convert/stl/list.hpp
+include/estd/convert/stl/map.hpp
+include/estd/convert/stl/set.hpp
+include/estd/convert/stl/unordered_map.hpp
+include/estd/convert/stl/unordered_set.hpp
+include/estd/convert/stl/vector.hpp
+include/estd/convert/traits.hpp
+include/estd/heap_array.hpp
+include/estd/heap_array/heap_array.hpp
+include/estd/range.hpp
+include/estd/range/detail/deref_proxy.hpp
+include/estd/range/enumerate.hpp
+include/estd/range/range.hpp
+include/estd/result.hpp
+include/estd/result/detail/copyable.hpp
+include/estd/result/detail/map.hpp
+include/estd/result/detail/result_storage.hpp
+include/estd/result/error.hpp
+include/estd/result/in_place.hpp
+include/estd/result/result.hpp
+include/estd/result/traits.hpp
+include/estd/result/unspecified_category.hpp
+include/estd/scope_guard.hpp
+include/estd/scope_guard/scope_guard.hpp
+include/estd/traits.hpp
+include/estd/traits/containers.hpp
+include/estd/traits/decay_if.hpp
+include/estd/traits/is_comparible.hpp
+include/estd/traits/is_integer_sequence.hpp
+include/estd/traits/is_tuple.hpp
+include/estd/traits/iterator.hpp
+include/estd/traits/replace_type.hpp
+include/estd/traits/type_traits.hpp
+include/estd/tuple.hpp
+include/estd/tuple/fold.hpp
+include/estd/tuple/for_each.hpp
+include/estd/tuple/transform.hpp
+include/estd/tuple/tuple.hpp
+include/estd/tuple/zip.hpp
+include/estd/type_name.hpp
+include/estd/type_name/demangle.hpp
+include/estd/type_name/std.hpp
+include/estd/type_name/std/containers.hpp
+include/estd/type_name/std/containers/array.hpp
+include/estd/type_name/std/containers/deque.hpp
+include/estd/type_name/std/containers/forward_list.hpp
+include/estd/type_name/std/containers/list.hpp
+include/estd/type_name/std/containers/map.hpp
+include/estd/type_name/std/containers/set.hpp
+include/estd/type_name/std/containers/string.hpp
+include/estd/type_name/std/containers/vector.hpp
+include/estd/type_name/type_name.hpp
+include/estd/utility.hpp
+include/estd/utility/integer_sequence.hpp
+include/estd/utility/make_ref.hpp
+include/estd/utility/move_marker.hpp
+include/estd/utility/parameter_pack.hpp
+include/estd/view.hpp
+include/estd/view/view.hpp
+lib/cmake/estd/estd-config-version.cmake
+lib/cmake/estd/estd-config.cmake
+lib/cmake/estd/targets.cmake
--- a/devel/libcjson/Makefile
+++ b/devel/libcjson/Makefile
@ -2,7 +2,7 @@
 # $FreeBSD$

 PORTNAME=	libcjson
-PORTVERSION=	1.7.11
+PORTVERSION=	1.7.12
 DISTVERSIONPREFIX=	v
 CATEGORIES=	devel

--- a/devel/libcjson/distinfo
+++ b/devel/libcjson/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1555338922
-SHA256 (DaveGamble-cJSON-v1.7.11_GH0.tar.gz) = 17ace0e31ebd639906983b05fe1d51576b948ca5411c2162f55dd34c122162ca
-SIZE (DaveGamble-cJSON-v1.7.11_GH0.tar.gz) = 348097
+TIMESTAMP = 1558105464
+SHA256 (DaveGamble-cJSON-v1.7.12_GH0.tar.gz) = 760687665ab41a5cff9c40b1053c19572bcdaadef1194e5cba1b5e6f824686e7
+SIZE (DaveGamble-cJSON-v1.7.12_GH0.tar.gz) = 348294
--- a/devel/libzim/Makefile
+++ b/devel/libzim/Makefile
@ -7,6 +7,9 @@ CATEGORIES=	devel
 MAINTAINER=	swills@FreeBSD.org
 COMMENT=	Reference implementation of the ZIM specification

+LICENSE=	GPLv2+
+LICENSE_FILE=	${WRKSRC}/COPYING
+
 LIB_DEPENDS=	libicui18n.so:devel/icu \
 		libxapian.so:databases/xapian-core

--- a/devel/libzim/pkg-descr
+++ b/devel/libzim/pkg-descr
@ -1,4 +1,4 @@
 The openZIM project proposes offline storage solutions for content coming from
 the Web.

-WWW: http://www.openzim.org/wiki/OpenZIM
+WWW: https://www.openzim.org/wiki/OpenZIM
--- a/devel/p5-CPAN-Perl-Releases/Makefile
+++ b/devel/p5-CPAN-Perl-Releases/Makefile
@ -2,7 +2,7 @@
 # $FreeBSD$

 PORTNAME=	CPAN-Perl-Releases
-PORTVERSION=	4.00
+PORTVERSION=	4.02
 CATEGORIES=	devel perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
--- a/devel/p5-CPAN-Perl-Releases/distinfo
+++ b/devel/p5-CPAN-Perl-Releases/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1557679328
-SHA256 (CPAN-Perl-Releases-4.00.tar.gz) = 55a8f221890abc659a0e285c0e62a184fbd39cd048d11615e6fa867bd207c45c
-SIZE (CPAN-Perl-Releases-4.00.tar.gz) = 23745
+TIMESTAMP = 1558166528
+SHA256 (CPAN-Perl-Releases-4.02.tar.gz) = cb37d4725f098247b93bc3988931cd1b8d856a18a9e7b7afc065ba2e2994abfc
+SIZE (CPAN-Perl-Releases-4.02.tar.gz) = 23801
--- a/devel/php-composer/Makefile
+++ b/devel/php-composer/Makefile
@ -2,7 +2,7 @@
 # $FreeBSD$

 PORTNAME=	composer
-DISTVERSION=	1.8.4
+DISTVERSION=	1.8.5
 CATEGORIES=	devel
 MASTER_SITES=	https://getcomposer.org/download/${DISTVERSION}/
 PKGNAMEPREFIX=	${PHP_PKGNAMEPREFIX}
--- a/Show More
+++ b/Show More