*/*: sync with upstream

Taken from: HardenedBSD
2018-04-25 21:52:19 +02:00 · 2018-04-25 21:52:19 +02:00 · 5f1f285626
parent bb757dcd0e
commit 5f1f285626
969 changed files with 2538 additions and 1903 deletions
--- a/archivers/py-attic/Makefile
+++ b/archivers/py-attic/Makefile
@ -22,6 +22,10 @@ USES=		python:3.3+ ssl
 USE_PYTHON=	autoplist distutils

 PYDISTUTILS_BUILDPATH=${BUILD_WRKSRC}/build/lib.${OPSYS:tl}-${UNAMER}-${ARCH}-${PYTHON_VER}
+REINPLACE_ARGS=	-i ''
+
+post-patch:
+	@${REINPLACE_CMD} -e 's|msgpack-python|msgpack|' ${WRKSRC}/setup.py

 post-install:
 	@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/attic/*.so
--- a/archivers/py-borgbackup/pkg-descr
+++ b/archivers/py-borgbackup/pkg-descr
@ -8,4 +8,4 @@ The data deduplication technique used makes Borg suitable for daily backups
 since only changes are stored. The authenticated encryption technique makes it
 suitable for backups to not fully trusted targets.

-WWW: https://pypi.python.org/pypi/borgbackup
+WWW: https://pypi.org/project/borgbackup/
--- a/archivers/py-czipfile/pkg-descr
+++ b/archivers/py-czipfile/pkg-descr
@ -4,4 +4,4 @@ provides much faster, C-based zipfile decryption. The code is actually
 modifications to allow it to compile in Cython, and the _ZipDecrypter
 class adapted to take advantage of native C datatypes.

-WWW: https://pypi.python.org/pypi/czipfile
+WWW: https://pypi.org/project/czipfile/
--- a/archivers/py-python-lzo/pkg-descr
+++ b/archivers/py-python-lzo/pkg-descr
@ -7,4 +7,4 @@ requires no memory.
 In addition there are slower compression levels achieving a quite competitive
 compression ratio while still decompressing at this very high speed.

-WWW: https://pypi.python.org/pypi/python-lzo
+WWW: https://pypi.org/project/python-lzo/
--- a/archivers/py-warctools/pkg-descr
+++ b/archivers/py-warctools/pkg-descr
@ -1,4 +1,4 @@
 Command line tools and libraries for handling and manipulating ISO 28500
 WARC files and their HTTP contents.

-WWW: https://pypi.python.org/pypi/warctools
+WWW: https://pypi.org/project/warctools/
--- a/archivers/py-xopen/pkg-descr
+++ b/archivers/py-xopen/pkg-descr
@ -3,4 +3,4 @@ open function, but can also deal with compressed files. Supported compression
 formats are gzip, bzip2 and xz. They are automatically recognized by their file
 extensions .gz, .bz2 or .xz.

-WWW: https://pypi.python.org/pypi/xopen
+WWW: https://pypi.org/project/xopen/
--- a/astro/py-astLib/pkg-descr
+++ b/astro/py-astLib/pkg-descr
@ -4,4 +4,4 @@ coordinate conversions, and manipulating FITS images with World Coordinate
 System (WCS) information through PyWCSTools - a simple wrapping of WCSTools by
 Jessica Mink. PyWCSTools is distributed (and developed) as part of astLib.

-WWW: https://pypi.python.org/pypi/astLib
+WWW: https://pypi.org/project/astLib/
--- a/astro/py-pymetar/pkg-descr
+++ b/astro/py-pymetar/pkg-descr
@ -2,5 +2,5 @@ Pymetar is a python module and command line tool designed to fetch Metar
 reports from the NOAA (http://www.noaa.gov) and allow access to the
 included weather information.

-WWW: https://pypi.python.org/pypi/pymetar
+WWW: https://pypi.org/project/pymetar/
 WWW: https://github.com/klausman/pymetar
--- a/audio/py-mpd/pkg-descr
+++ b/audio/py-mpd/pkg-descr
@ -1,3 +1,3 @@
 An MPD (Music Player Daemon) client library written in pure Python.

-WWW: https://pypi.python.org/pypi/python-mpd
+WWW: https://pypi.org/project/python-mpd/
--- a/audio/py-py-jack/pkg-descr
+++ b/audio/py-py-jack/pkg-descr
@ -3,4 +3,4 @@ For information about Jack see http://jackit.sourceforge.net. This
 enables a Python program to connect to and interact with pro-audio
 applications which use the Jack Audio Server.

-WWW: https://pypi.python.org/pypi/py-jack
+WWW: https://pypi.org/project/py-jack/
--- a/audio/py-pymad/pkg-descr
+++ b/audio/py-pymad/pkg-descr
@ -2,4 +2,4 @@ pymad is a Python module that allows Python programs to use the MPEG Audio
 Decoder library. pymad provides a high-level API, similar to the pyogg module,
 which makes reading PCM data from MPEG audio streams a piece of cake.

-WWW: https://pypi.python.org/pypi/pymad
+WWW: https://pypi.org/project/pymad/
--- a/audio/simon/Makefile
+++ b/audio/simon/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	simon
 PORTVERSION=	0.4.1
-PORTREVISION=	4
+PORTREVISION=	5
 CATEGORIES=	audio kde
 MASTER_SITES=	KDE/stable/${PORTNAME}/${PORTVERSION}/src
 DIST_SUBDIR=	KDE
@ -15,7 +15,7 @@ LIB_DEPENDS=	libasound.so:audio/alsa-lib \
 		libsamplerate.so:audio/libsamplerate \
 		libpocketsphinx.so:audio/pocketsphinx \
 		libsphinxad.so:audio/sphinxbase \
-		libqwt6.so:x11-toolkits/qwt6
+		libqwt6.so:x11-toolkits/qwt6@qt4

 USES=		cmake:outsource gettext kde:4 tar:bz2
 USE_KDE=	kdelibs automoc4 pimlibs
--- a/biology/paml/Makefile
+++ b/biology/paml/Makefile
@ -2,41 +2,30 @@
 # $FreeBSD$

 PORTNAME=	paml
-PORTVERSION=	4.9c
-PORTREVISION=	1
+DISTVERSION=	4.9h
 CATEGORIES=	biology
 MASTER_SITES=	http://abacus.gene.ucl.ac.uk/software/
-DISTNAME=	${PORTNAME}${PORTVERSION}
+DISTNAME=	${PORTNAME}${DISTVERSION}

 MAINTAINER=	jrm@FreeBSD.org
 COMMENT=	Phylogenetic Analysis by Maximum Likelihood (PAML)

 LICENSE=	GPLv3

-USES=		gmake tar:tgz
+USES=		dos2unix gmake tar:tgz
+DOS2UNIX_GLOB=	*.HKYG5 *.aa *.c *.ctl *.dat *.nexus *.nuc *.phy *.result *.tre \
+		*.trees *.txt *.xml paupblock paupend

 BINARIES=	baseml basemlg chi2 codeml evolver evolverNSbranches \
 		evolverNSbranchsites evolverNSsites pamp yn00

-PORTDOCS=	MCMCtree.Tutorials.pdf MCMCtreeDOC.pdf pamlDOC.pdf pamlFAQs.pdf \
-		pamlHistory.txt README.txt
+OPTIONS_DEFINE=	DOCS EXAMPLES

-DATA=		3s.trees 4s.trees 5s.trees 6s.trees GeneticCode.txt MCaa.dat	\
-		MCbase.dat MCbaseRandomTree.dat MCcodon.dat aaml.ctl baseml.ctl	\
-		brown.nuc brown.rooted.trees brown.trees codeml.ctl codonml.ctl	\
-		mcmctree.ctl pamp.ctl paupblock paupend paupstart stewart.aa	\
-		stewart.trees yn00.ctl
-PORTDATA=	${DATA} dat examples Technical
-
-OPTIONS_DEFINE=	DOCS
-
-# Remove Windows executables
 post-extract:
 	@${FIND} ${WRKSRC}/Technical -name "*.exe" -delete

 do-build:
-	@cd ${WRKSRC}/src && \
-	${SETENV} ${MAKE_ENV} ${MAKE_CMD}
+	@cd ${WRKSRC}/src && ${SETENV} ${MAKE_ENV} ${MAKE_CMD}
 .for f in NSbranches NSsites NSbranchsites
 	@cd ${WRKSRC}/src && \
 	${CC} ${CFLAGS} -DCodon${f} -o evolver${f} evolver.c tools.c -lm
@ -46,16 +35,19 @@ do-install:
 .for f in ${BINARIES}
 	${INSTALL_PROGRAM} ${WRKSRC}/src/${f} ${STAGEDIR}${PREFIX}/bin
 .endfor
-	@${MKDIR} ${STAGEDIR}${DATADIR}
-.for f in ${DATA}
-	${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}/${DATADIR}
-.endfor
-	(cd ${WRKSRC} && ${COPYTREE_SHARE} "dat examples Technical" \
-	${STAGEDIR}/${DATADIR})

 do-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 	${INSTALL_DATA} ${WRKSRC}/doc/* ${STAGEDIR}${DOCSDIR}
 	${INSTALL_DATA} ${WRKSRC}/README.txt ${STAGEDIR}${DOCSDIR}

+do-install-EXAMPLES-on:
+	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
+	(cd ${WRKSRC} && ${COPYTREE_SHARE} "dat Technical" \
+		${STAGEDIR}${EXAMPLESDIR})
+	(cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR})
+.for f in *.aa *.ctl *.dat *.nuc *.trees *.txt paup*
+	${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${EXAMPLESDIR}
+.endfor
+
 .include <bsd.port.mk>
--- a/biology/paml/distinfo
+++ b/biology/paml/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1475182775
-SHA256 (paml4.9c.tgz) = 8be4250399f3daaf22b0b643fa1a1fd5fddb892d54ce330bfe77ea9dbed577b9
-SIZE (paml4.9c.tgz) = 5409741
+TIMESTAMP = 1524675240
+SHA256 (paml4.9h.tgz) = 623bf6cf4a018a4e7b4dbba189c41d6c0c25fdca3a0ae24703b82965c772edb3
+SIZE (paml4.9h.tgz) = 6241149
--- a/biology/paml/pkg-plist
+++ b/biology/paml/pkg-plist
@ -1,3 +1,165 @@
+%%PORTDOCS%%%%DOCSDIR%%/MCMCtree.Tutorials.pdf
+%%PORTDOCS%%%%DOCSDIR%%/README.txt
+%%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf
+%%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf
+%%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3s.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/4s.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/5s.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/6s.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/9s.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/ECP_EDN_15.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/PAMLCladeModelCDnotes.pdf
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/codeml.CladeC.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/codeml.CladeD.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/tree.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/BF.Clock23.xlsx
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/BFdriverDOC.pdf
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/FixedDsClock23.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/README.BayesFactor.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/bf1/mcmctree.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/bf2/mcmctree.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mcmctree.Infinitesites.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mcmctree.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mtCDNApri.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mtCDNApri123.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/GeneticCode.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden4s.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden4s.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/codeml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCaa.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbase.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbaseRandomTree.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCcodon.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.phy
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/codeml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs123.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/README2.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/aaml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/aaml2.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/baseml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/baseml2.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codeml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codonml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codonml2.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/mtmam.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Pt/eigenQREV.pdf
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Pt/testPMat.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSbranches.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSbranchsites.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSclade.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSsites.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/PositiveSites.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/codeml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/multiruns.c
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/multiruns.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.Beast.Nulldata.xml
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.Beast.xml
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.NodeNumbers.tre
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.nexus
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.tre
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/baseml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/commands.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/in.BV.HKYG5
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock1.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock2.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock3.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.tre
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/baseml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/in.BV.HKYG5
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ExactlnL.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/YN00abglobin.result
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/aaml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/baseml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.rooted.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/codeml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/codonml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dNdSGene1.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/MtZoa.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/cpREV10.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/cpREV64.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/dayhoff-dcmut.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/dayhoff.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974a.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974c.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974p.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974v.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/grantham.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/jones-dcmut.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/jones.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/lg.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/miyata.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtArt.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtREV24.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtmam.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/wag.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/RasMol.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/SiteNumbering.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/codeml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/codemlYangSwanson2002.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysin.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysin.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysinYangSwanson2002.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/codeml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mcmctree.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/AAcodon.result.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/codeml.AAcodon.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/codeml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/miyata.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNAmam.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNAmam.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/2s.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/OmegaAA.dat
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/codeml.HC.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/codeml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNA.HC.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtprim9.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pamp.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupblock
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupend
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupstart
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.aa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/yn00.ctl
 bin/baseml
 bin/basemlg
 bin/chi2
--- a/biology/py-cutadapt/pkg-descr
+++ b/biology/py-cutadapt/pkg-descr
@ -1,4 +1,4 @@
 Cutadapt finds and removes adapter sequences, primers, poly-A tails and other
 types of unwanted sequences from your high-throughput sequencing reads.

-WWW: https://pypi.python.org/pypi/cutadapt
+WWW: https://pypi.org/project/cutadapt/
--- a/biology/py-pysam/pkg-descr
+++ b/biology/py-pysam/pkg-descr
@ -7,4 +7,4 @@ This module provides a low-level wrapper around the htslib C-API as using
 cython and a high-level API for convenient access to the data within standard
 genomic file formats.

-WWW: https://pypi.python.org/pypi/pysam
+WWW: https://pypi.org/project/pysam/
--- a/cad/openscad-devel/Makefile
+++ b/cad/openscad-devel/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	openscad
 PORTVERSION=	2018.04.19
-#PORTREVISION=	1
+PORTREVISION=	1
 CATEGORIES=	cad
 PKGNAMESUFFIX=  -devel
 DIST_SUBDIR=            ${PORTNAME}
@ -14,6 +14,8 @@ COMMENT=	Programmer's solid 3D CAD modeller
 LICENSE=	GPLv2+
 LICENSE_FILE=	${WRKSRC}/COPYING

+BROKEN_FreeBSD_10=      Missing __cxa_thread_atexit
+
 BUILD_DEPENDS=	${LOCALBASE}/bin/flex:textproc/flex \
 		${LOCALBASE}/include/boost/tuple/tuple.hpp:devel/boost-libs
 LIB_DEPENDS=	libgmp.so:math/gmp \
@ -26,19 +28,20 @@ LIB_DEPENDS=	libgmp.so:math/gmp \

 CONFLICTS=	openscad

+USES=		bison compiler:c++11-lang desktop-file-utils eigen:3 gettext-tools \
+		pkgconfig python:run qmake shebangfix
 USE_GITHUB=     yes
 GH_ACCOUNT=     openscad
 GH_PROJECT=     openscad
 GH_TAGNAME=	179074dff8c23cbc0e651ce8463737df0006f4ca

-USES=		bison compiler:c++11-lang desktop-file-utils eigen:3 gettext-tools \
-		pkgconfig python:run qmake shebangfix
 #SHEBANG_FILES=	libraries/MCAD/get_submodules.py
 USE_GL=		glu glew
 USE_QT4=	corelib gui opengl moc_build uic_build rcc_build
 PLIST_SUB=	PORTVERSION=${PORTVERSION}
 QMAKE_ENV=	EIGENDIR=${LOCALBASE}/include/eigen3
 QMAKE_ARGS+=	VERSION=${PORTVERSION} \
+		EXPERIMENTAL=yes \
 		QMAKE_LEX=${LOCALBASE}/bin/flex \
 		QMAKE_YAC=${LOCALBASE}/bin/bison

@ -46,10 +49,4 @@ post-patch:
 	@${REINPLACE_CMD} -e 's,share/man,man,' \
 		${WRKSRC}/openscad.pro

-#.include <bsd.port.options.mk>
-#
-#.if ${ARCH} == i386 && ${OSVERSION} >= 1100000
-#USE_GCC=        yes
-#.endif
-
 .include <bsd.port.mk>
--- a/cad/openscad-devel/files/patch-openscad.pro
+++ b/cad/openscad-devel/files/patch-openscad.pro
@ -1,6 +1,12 @@
--- openscad.pro.orig	2018-04-22 17:21:31.278695000 +0000
-+++ openscad.pro	2018-04-22 17:21:39.335408000 +0000
-@@ -106,4 +106,8 @@
+--- openscad.pro.orig	2018-04-19 22:08:08 UTC
+++ openscad.pro
+@@ -1,3 +1,4 @@
+CONFIG+=experimental
+ # Environment variables which can be set to specify library locations:
+ # MPIRDIR
+ # MPFRDIR
+@@ -105,6 +106,10 @@ mingw* {
+ CONFIG += qt
 QT += widgets concurrent
 
 +freebsd* {
@ -9,3 +15,4 @@
 +
 netbsd* {
    QMAKE_LFLAGS += -L/usr/X11R7/lib
+    QMAKE_LFLAGS += -Wl,-R/usr/X11R7/lib
--- a/cad/openscad-devel/files/patch-src-ModuleCache.h
+++ b/cad/openscad-devel/files/patch-src-ModuleCache.h
@ -1,8 +1,10 @@
--- src/ModuleCache.h.orig	2018-04-22 17:10:59.553926000 +0000
-+++ src/ModuleCache.h	2018-04-22 17:11:26.751065000 +0000
-@@ -2,4 +2,5 @@
+--- src/ModuleCache.h.orig	2018-04-19 22:08:08 UTC
+++ src/ModuleCache.h
+@@ -1,6 +1,7 @@
+ #pragma once
 
 #include <string>
 +#include <time.h>
 #include <unordered_map>
 
+ /*!
--- a/chinese/wordpress-zh_CN/Makefile
+++ b/chinese/wordpress-zh_CN/Makefile
@ -33,7 +33,9 @@ SUB_FILES=	pkg-message
 pre-everything::
 	@${ECHO_CMD} "If you want to upgrade, you must read upgrade document."
 	@${ECHO_CMD} ""
+.  if !(defined(PACKAGE_BUILDING) || defined(BATCH))
 	@sleep 1
+.  endif

 pre-install:
 	${ECHO_CMD} '@owner www' > ${PLIST}
--- a/chinese/wordpress-zh_TW/Makefile
+++ b/chinese/wordpress-zh_TW/Makefile
@ -33,7 +33,9 @@ SUB_FILES=	pkg-message
 pre-everything::
 	@${ECHO_CMD} "If you want to upgrade, you must read upgrade document."
 	@${ECHO_CMD} ""
+.  if !(defined(PACKAGE_BUILDING) || defined(BATCH))
 	@sleep 1
+.  endif

 pre-install:
 	${ECHO_CMD} '@owner www' > ${PLIST}
--- a/comms/py-hidapi/pkg-descr
+++ b/comms/py-hidapi/pkg-descr
@ -1,3 +1,3 @@
 Cython interface to comms/hidapi.

-WWW: https://pypi.python.org/pypi/hidapi
+WWW: https://pypi.org/project/hidapi/
--- a/comms/qpage/Makefile
+++ b/comms/qpage/Makefile
@ -50,7 +50,9 @@ pre-patch:
 	@${ECHO_MSG} ""
 	@${ECHO_MSG} "Press ^C now to stop the build and set make options."
 	@${ECHO_MSG} "You may find it necessary to 'make clean' before restarting the build."
+.  if !(defined(PACKAGE_BUILDING) || defined(BATCH))
 	@sleep 2
+.  endif
 .endif

 post-patch:
--- a/converters/py-better-bencode/pkg-descr
+++ b/converters/py-better-bencode/pkg-descr
@ -1,3 +1,3 @@
 Fast, standard compliant Bencode serialization.

-WWW: https://pypi.python.org/pypi/better-bencode
+WWW: https://pypi.org/project/better-bencode/
--- a/converters/py-pint/pkg-descr
+++ b/converters/py-pint/pkg-descr
@ -7,5 +7,5 @@ constants. Due to its modular design, you can extend (or even rewrite!) the
 complete list without changing the source code. It supports a lot of numpy
 mathematical operations without monkey patching or wrapping numpy.

-WWW: https://pypi.python.org/pypi/Pint
+WWW: https://pypi.org/project/Pint/
 WWW: https://github.com/hgrecco/pint
--- a/converters/py-unidecode/pkg-descr
+++ b/converters/py-unidecode/pkg-descr
@ -5,4 +5,4 @@ The representation is almost always an attempt at *transliteration*
 -- i.e., conveying, in Roman letters, the pronunciation expressed by
 the text in some other writing system. (See the example above)

-WWW: https://pypi.python.org/pypi/Unidecode
+WWW: https://pypi.org/project/Unidecode/
--- a/converters/py-zfec/pkg-descr
+++ b/converters/py-zfec/pkg-descr
@ -7,4 +7,4 @@ that if some blocks are lost then the original data can be recovered
 from the remaining blocks. The zfec package includes command-line
 tools, C API, Python API, and Haskell API.

-WWW: https://pypi.python.org/pypi/zfec
+WWW: https://pypi.org/project/zfec/
--- a/converters/zbase32/pkg-descr
+++ b/converters/zbase32/pkg-descr
@ -1,4 +1,4 @@
 zbase32 is a base32 encoder/decoder. It is an alternate
 base32 encoder but not RFC 3548 compliant.

-WWW: https://pypi.python.org/pypi/zbase32
+WWW: https://pypi.org/project/zbase32/
--- a/databases/Makefile
+++ b/databases/Makefile
@ -561,6 +561,7 @@
    SUBDIR += pecl-mongodb
    SUBDIR += pecl-pdo_user
    SUBDIR += pecl-redis
+    SUBDIR += pecl-redis3
    SUBDIR += pecl-rrd
    SUBDIR += pecl-rrd1
    SUBDIR += pecl-tokyo_tyrant
--- a/databases/firebird25-client/Makefile
+++ b/databases/firebird25-client/Makefile
@ -1,8 +1,6 @@
-# Created by: Alonso Cárdenas Márquez <acm@FreeBSD.org>
 # $FreeBSD$

 PORTNAME=	firebird
-PORTREVISION=	3
 PKGNAMESUFFIX=	${PORTVERSION:R:S/.//}-client

 COMMENT=	Firebird-2 database client
--- a/databases/firebird25-server/Makefile
+++ b/databases/firebird25-server/Makefile
@ -1,16 +1,14 @@
-# Created by: Alonso Cárdenas Márquez <acm@FreeBSD.org>
 # $FreeBSD$

 PORTNAME=	firebird
-PORTVERSION=	2.5.6
-PORTREVISION=	5
+PORTVERSION=	2.5.8
 CATEGORIES?=	databases
-MASTER_SITES=	SF/${PORTNAME}/${PORTNAME}/${PORTVERSION:S/.0//}-Release/
+MASTER_SITES=	https://github.com/FirebirdSQL/${PORTNAME}/releases/download/R2_5_8/
 PKGNAMESUFFIX?=	${PORTVERSION:R:S/.//}-server
-DISTNAME=	${PORTNAME:S/f/F/}-${PORTVERSION}.27020-0
+DISTNAME=	${PORTNAME:S/f/F/}-${PORTVERSION}.27089-0
 DIST_SUBDIR=	${PORTNAME}

-MAINTAINER=	ports@FreeBSD.org
+MAINTAINER=	acm@FreeBSD.org
 COMMENT?=	Firebird-2 relational database (server)

 LICENSE=	IDPL IPL
--- a/databases/firebird25-server/distinfo
+++ b/databases/firebird25-server/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1468845026
-SHA256 (firebird/Firebird-2.5.6.27020-0.tar.bz2) = 8e416f2f9a8f1fce2aa872925ca2016010878265ec56fe0a32a73e0080378826
-SIZE (firebird/Firebird-2.5.6.27020-0.tar.bz2) = 13610463
+TIMESTAMP = 1524662189
+SHA256 (firebird/Firebird-2.5.8.27089-0.tar.bz2) = d87d774736edb1eacc242c68831edb3575c28cc61378491f42f8932bf9975678
+SIZE (firebird/Firebird-2.5.8.27089-0.tar.bz2) = 13401870
--- a/databases/flamerobin/Makefile
+++ b/databases/flamerobin/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	flamerobin
 PORTVERSION=	0.9.2
-PORTREVISION=	5
+PORTREVISION=	6
 CATEGORIES=	databases
 MASTER_SITES=	SF
 DISTNAME=	${PORTNAME}-${PORTVERSION}-src
--- a/databases/fpc-ibase/Makefile
+++ b/databases/fpc-ibase/Makefile
@ -1,6 +1,7 @@
 # Created by: John Merryweather Cooper
 # $FreeBSD$

+PORTREVISION=	1
 CATEGORIES=	databases lang
 PKGNAMESUFFIX=	-ibase

--- a/databases/luasql-firebird/Makefile
+++ b/databases/luasql-firebird/Makefile
@ -1,6 +1,8 @@
 # Created by: Martin Matuska <martin@matuska.org>
 # $FreeBSD$

+PORTREVISION=	1
+
 LUASQL_DRIVER=	firebird

 MASTERDIR=	${.CURDIR}/../luasql-mysql
--- a/databases/nagios-check_postgres_replication/pkg-descr
+++ b/databases/nagios-check_postgres_replication/pkg-descr
@ -13,4 +13,4 @@ including:
 * Default options
 * Persistent "cookies" to retain state information between check runs

-WWW: https://pypi.python.org/pypi/nagiosplugin
+WWW: https://pypi.org/project/nagiosplugin/
--- a/databases/p5-DBD-InterBase/Makefile
+++ b/databases/p5-DBD-InterBase/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	DBD-InterBase
 PORTVERSION=	0.48
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	databases perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
--- a/databases/pecl-redis/Makefile
+++ b/databases/pecl-redis/Makefile
@ -1,7 +1,7 @@
 # $FreeBSD$

 PORTNAME=	redis
-PORTVERSION=	3.1.6
+PORTVERSION=	4.0.2
 CATEGORIES=	databases

 MAINTAINER=	daniel@blodan.se
@ -10,6 +10,8 @@ COMMENT=	Extension to access Redis
 LICENSE=	PHP301
 LICENSE_FILE=	${WRKSRC}/COPYING

+CONFLICTS_INSTALL=	pecl-redis3
+
 USES=		php:pecl
 USE_PHP=	session:build

--- a/databases/pecl-redis/distinfo
+++ b/databases/pecl-redis/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1515603372
-SHA256 (PECL/redis-3.1.6.tgz) = b229274cdc14c22efc41fefa00db4dc5bb32a997d6811278662a043a76aa2600
-SIZE (PECL/redis-3.1.6.tgz) = 199920
+TIMESTAMP = 1524662694
+SHA256 (PECL/redis-4.0.2.tgz) = 36fa980831091efca6586fa347283f79587293aa93c7d42e948e6137bfd90ac8
+SIZE (PECL/redis-4.0.2.tgz) = 212617
--- a/databases/pecl-redis3/Makefile
+++ b/databases/pecl-redis3/Makefile
@ -0,0 +1,25 @@
+# $FreeBSD$
+
+PORTNAME=	redis
+PORTVERSION=	3.1.6
+CATEGORIES=	databases
+PKGNAMESUFFIX=	3
+
+MAINTAINER=	daniel@blodan.se
+COMMENT=	Extension to access Redis
+
+LICENSE=	PHP301
+LICENSE_FILE=	${WRKSRC}/COPYING
+
+CONFLICTS_INSTALL=	pecl-redis
+
+USES=		php:pecl
+USE_PHP=	session:build
+
+OPTIONS_DEFINE=	IGBINARY
+IGBINARY_DESC=	Build with Igbinary serializer
+
+IGBINARY_CONFIGURE_ENABLE=	redis-igbinary
+IGBINARY_USE=			php=igbinary:build
+
+.include <bsd.port.mk>
--- a/databases/pecl-redis3/distinfo
+++ b/databases/pecl-redis3/distinfo
@ -0,0 +1,3 @@
+TIMESTAMP = 1515603372
+SHA256 (PECL/redis-3.1.6.tgz) = b229274cdc14c22efc41fefa00db4dc5bb32a997d6811278662a043a76aa2600
+SIZE (PECL/redis-3.1.6.tgz) = 199920
--- a/databases/pecl-redis3/pkg-descr
+++ b/databases/pecl-redis3/pkg-descr
@ -0,0 +1,5 @@
+This extension provides an API for communicating with Redis database,
+a persistent key-value database with built-in net interface written
+in ANSI-C for Posix systems.
+
+WWW: https://pecl.php.net/package/redis
--- a/databases/php56-interbase/Makefile
+++ b/databases/php56-interbase/Makefile
@ -1,6 +1,7 @@
 # Created by: Alex Dupre <ale@FreeBSD.org>
 # $FreeBSD$

+PORTREVISION=	1
 CATEGORIES=	databases

 MASTERDIR=	${.CURDIR}/../../lang/php56
--- a/databases/php56-pdo_firebird/Makefile
+++ b/databases/php56-pdo_firebird/Makefile
@ -1,6 +1,7 @@
 # Created by: Alex Dupre <ale@FreeBSD.org>
 # $FreeBSD$

+PORTREVISION=	1
 CATEGORIES=	databases

 MASTERDIR=	${.CURDIR}/../../lang/php56
--- a/databases/php70-interbase/Makefile
+++ b/databases/php70-interbase/Makefile
@ -1,6 +1,7 @@
 # Created by: Alex Dupre <ale@FreeBSD.org>
 # $FreeBSD$

+PORTREVISION=	1
 CATEGORIES=	databases

 MASTERDIR=	${.CURDIR}/../../lang/php70
--- a/databases/php70-pdo_firebird/Makefile
+++ b/databases/php70-pdo_firebird/Makefile
@ -1,6 +1,7 @@
 # Created by: Alex Dupre <ale@FreeBSD.org>
 # $FreeBSD$

+PORTREVISION=	1
 CATEGORIES=	databases

 MASTERDIR=	${.CURDIR}/../../lang/php70
--- a/databases/php71-interbase/Makefile
+++ b/databases/php71-interbase/Makefile
@ -1,5 +1,6 @@
 # $FreeBSD$

+PORTREVISION=	1
 CATEGORIES=	databases

 MASTERDIR=	${.CURDIR}/../../lang/php71
--- a/databases/php71-pdo_firebird/Makefile
+++ b/databases/php71-pdo_firebird/Makefile
@ -1,5 +1,6 @@
 # $FreeBSD$

+PORTREVISION=	1
 CATEGORIES=	databases

 MASTERDIR=	${.CURDIR}/../../lang/php71
--- a/databases/php72-interbase/Makefile
+++ b/databases/php72-interbase/Makefile
@ -1,5 +1,6 @@
 # $FreeBSD$

+PORTREVISION=	1
 CATEGORIES=	databases

 MASTERDIR=	${.CURDIR}/../../lang/php72
--- a/databases/php72-pdo_firebird/Makefile
+++ b/databases/php72-pdo_firebird/Makefile
@ -1,5 +1,6 @@
 # $FreeBSD$

+PORTREVISION=	1
 CATEGORIES=	databases

 MASTERDIR=	${.CURDIR}/../../lang/php72
--- a/databases/py-dbf/pkg-descr
+++ b/databases/py-dbf/pkg-descr
@ -6,4 +6,4 @@ Text is returned as unicode, and codepage settings in tables are
 honored. Documentation needs work, but author is very responsive
 to e-mails.

-WWW: https://pypi.python.org/pypi/dbf
+WWW: https://pypi.org/project/dbf/
--- a/databases/py-fdb/Makefile
+++ b/databases/py-fdb/Makefile
@ -3,6 +3,7 @@

 PORTNAME=	fdb
 PORTVERSION=	1.8
+PORTREVISION=	1
 CATEGORIES=	databases python
 MASTER_SITES=	CHEESESHOP
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
--- a/databases/py-flask-sqlalchemy/pkg-descr
+++ b/databases/py-flask-sqlalchemy/pkg-descr
@ -1,3 +1,3 @@
 Flask-SQLAlchemy adds support for SQLAlchemy to your Flask application.

-WWW: https://pypi.python.org/pypi/Flask-SQLAlchemy
+WWW: https://pypi.org/project/Flask-SQLAlchemy/
--- a/databases/py-geoalchemy/pkg-descr
+++ b/databases/py-geoalchemy/pkg-descr
@ -2,4 +2,4 @@ GeoAlchemy is an extension of SQLAlchemy. It provides support for Geospatial
 data types at the ORM layer using SQLAlchemy. It aims to support spatial
 operations and relations specified by the Open Geospatial Consortium (OGC).

-WWW: https://pypi.python.org/pypi/GeoAlchemy
+WWW: https://pypi.org/project/GeoAlchemy/
--- a/databases/py-geoalchemy2/pkg-descr
+++ b/databases/py-geoalchemy2/pkg-descr
@ -5,4 +5,4 @@ Simpler to use, and simpler to maintain.

 Git repository: https://github.com/geoalchemy/geoalchemy2

-WWW: https://pypi.python.org/pypi/GeoAlchemy2
+WWW: https://pypi.org/project/GeoAlchemy2/
--- a/databases/py-influxdb/pkg-descr
+++ b/databases/py-influxdb/pkg-descr
@ -1,3 +1,3 @@
 InfluxDB-Python is a client for interacting with InfluxDB.

-WWW: https://pypi.python.org/pypi/influxdb
+WWW: https://pypi.org/project/influxdb/
--- a/databases/py-leveldb/pkg-descr
+++ b/databases/py-leveldb/pkg-descr
@ -4,5 +4,5 @@ from the LevelDB API, except for:
 - Snapshots
 - All iteration except for single-step forward

-WWW: https://pypi.python.org/pypi/leveldb
+WWW: https://pypi.org/project/leveldb/
 WWW: https://github.com/rjpower/py-leveldb
--- a/databases/py-motor/pkg-descr
+++ b/databases/py-motor/pkg-descr
@ -1,4 +1,4 @@
 Motor presents a callback- or Future-based API for non-blocking access to
 MongoDB from Tornado or asyncio.

-WWW: https://pypi.python.org/pypi/motor
+WWW: https://pypi.org/project/motor/
--- a/databases/py-mycli/pkg-descr
+++ b/databases/py-mycli/pkg-descr
@ -1,5 +1,5 @@
 mycli is a command line interface for MySQL, MariaDB, and Percona with
 auto-completion and syntax highlighting.

-WWW: https://pypi.python.org/pypi/mycli
+WWW: https://pypi.org/project/mycli/
 WWW: https://www.mycli.net/
--- a/databases/py-pgcli/pkg-descr
+++ b/databases/py-pgcli/pkg-descr
@ -1,5 +1,5 @@
 pgcli is a command line interface for Postgres with auto-completion and syntax
 highlighting.

-WWW: https://pypi.python.org/pypi/pgcli
+WWW: https://pypi.org/project/pgcli/
 WWW: https://www.pgcli.com/
--- a/databases/py-pgspecial/pkg-descr
+++ b/databases/py-pgspecial/pkg-descr
@ -1,5 +1,5 @@
 This package provides an API to execute meta-commands (AKA "special", or
 "backslash commands") on PostgreSQL.

-WWW: https://pypi.python.org/pypi/pgspecial
+WWW: https://pypi.org/project/pgspecial/
 WWW: https://github.com/dbcli/pgspecial
--- a/databases/py-pickledb/pkg-descr
+++ b/databases/py-pickledb/pkg-descr
@ -1,5 +1,5 @@
 pickleDB is a lightweight, fast, and simple database based on Python's own
 json module.

-WWW: https://pypi.python.org/pypi/pickleDB
+WWW: https://pypi.org/project/pickleDB/
 WWW: https://github.com/patx/pickledb
--- a/databases/py-pyhs/pkg-descr
+++ b/databases/py-pyhs/pkg-descr
@ -2,4 +2,4 @@ pyhs (python-handler-socket) is a Python client library for the
 HandlerSocket <https://github.com/ahiguti/HandlerSocket-Plugin-for-MySQL/>
 MySQL plugin.

-WWW: https://pypi.python.org/pypi/python-handler-socket
+WWW: https://pypi.org/project/python-handler-socket/
--- a/databases/py-python-memcached/pkg-descr
+++ b/databases/py-python-memcached/pkg-descr
@ -5,6 +5,6 @@ value automatically going in and out of the memcached.

 The Python API, while tested, has not experienced real-world production use.

-WWW: https://pypi.python.org/pypi/python-memcached
+WWW: https://pypi.org/project/python-memcached/
 WWW: http://www.tummy.com/software/python-memcached/
 WWW: https://github.com/linsomniac/python-memcached
--- a/databases/py-sqlparse/pkg-descr
+++ b/databases/py-sqlparse/pkg-descr
@ -1,5 +1,5 @@
 sqlparse is a non-validating SQL parser module.
 It provides support for parsing, splitting and formatting SQL statements.

-WWW: https://pypi.python.org/pypi/sqlparse
+WWW: https://pypi.org/project/sqlparse/
 WWW: https://github.com/andialbrecht/sqlparse
--- a/databases/py-sqlparse020/pkg-descr
+++ b/databases/py-sqlparse020/pkg-descr
@ -3,5 +3,5 @@ It provides support for parsing, splitting and formatting SQL statements.

 This is version 0.2.0 which is needed by calendarserver.

-WWW: https://pypi.python.org/pypi/sqlparse
+WWW: https://pypi.org/project/sqlparse/
 WWW: https://github.com/andialbrecht/sqlparse
--- a/databases/py-tarantool/pkg-descr
+++ b/databases/py-tarantool/pkg-descr
@ -1,4 +1,4 @@
 This package is a pure-python client library for Tarantool Database.

-WWW: https://pypi.python.org/pypi/tarantool
+WWW: https://pypi.org/project/tarantool/
 WWW: https://github.com/tarantool/tarantool-python
--- a/databases/py-zodbpickle/pkg-descr
+++ b/databases/py-zodbpickle/pkg-descr
@ -8,4 +8,4 @@ Under Py3k, this package forks the pickle module (and the supporting
 C extension) from both Python 3.2 and Python 3.3. The fork add support
 for the noload operations used by ZODB.

-WWW: https://pypi.python.org/pypi/zodbpickle
+WWW: https://pypi.org/project/zodbpickle/
--- a/databases/qt4-ibase-plugin/Makefile
+++ b/databases/qt4-ibase-plugin/Makefile
@ -1,7 +1,7 @@
 # Created by: Michael Nottebrock <lofi@FreeBSD.org>
 # $FreeBSD$

-PORTREVISION=	2
+PORTREVISION=	3

 COMMENT=	Qt InterBase/Firebird database plugin
 DB=		ibase
--- a/databases/qt5-sqldrivers-ibase/Makefile
+++ b/databases/qt5-sqldrivers-ibase/Makefile
@ -1,5 +1,7 @@
 # $FreeBSD$

+PORTREVISION=	1
+
 DB=		IBase
 DB_DESC=	InterBase/Firebird

--- a/databases/soci/Makefile
+++ b/databases/soci/Makefile
@ -3,7 +3,7 @@

 PORTNAME=	soci
 PORTVERSION=	3.2.2
-PORTREVISION=	10
+PORTREVISION=	11
 CATEGORIES=	databases
 MASTER_SITES=	SF/${PORTNAME}/${PORTNAME}/${PORTNAME}-${PORTVERSION}

--- a/deskutils/py-pystash/pkg-descr
+++ b/deskutils/py-pystash/pkg-descr
@ -1,4 +1,4 @@
 Save your code snippets in the cloud (http://trystash.com/) from
 the command line.

-WWW: https://pypi.python.org/pypi/pystash
+WWW: https://pypi.org/project/pystash/
--- a/devel/Makefile
+++ b/devel/Makefile
@ -314,6 +314,7 @@
    SUBDIR += cligen
    SUBDIR += clinfo
    SUBDIR += clisp-hyperspec
+    SUBDIR += clixon
    SUBDIR += clojure-cider
    SUBDIR += cloudabi
    SUBDIR += cloudabi-toolchain
--- a/devel/amd64-gcc/Makefile
+++ b/devel/amd64-gcc/Makefile
@ -1,12 +1,11 @@
 # $FreeBSD$

-PORTREVISION=	1
 PKGNAMEPREFIX=	amd64-
 PLIST=	${.CURDIR}/pkg-plist

 MASTERDIR=	${.CURDIR}/../powerpc64-gcc
 GCC_TARGET=	x86_64-unknown-${OPSYS:tl}${OSREL}
-BU_PREFIX=	x86_64-${OPSYS:tl}
+BU_PREFIX=	x86_64-unknown-${OPSYS:tl}${OSREL}
 FREEBSD_EXTENSION=	yes

 BROKEN_aarch64=		invalid output constraint '=a' in assembler
--- a/devel/awscli/Makefile
+++ b/devel/awscli/Makefile
@ -2,7 +2,7 @@
 # $FreeBSD$

 PORTNAME=	awscli
-PORTVERSION=	1.15.7
+PORTVERSION=	1.15.8
 CATEGORIES=	devel
 MASTER_SITES=	CHEESESHOP

@ -12,7 +12,7 @@ COMMENT=	Universal Command Line Interface for Amazon Web Services
 LICENSE=	APACHE20
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt

-RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}botocore>=1.10.7:devel/py-botocore@${PY_FLAVOR} \
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}botocore>=1.10.8:devel/py-botocore@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}colorama>=0.2.5:devel/py-colorama@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}s3transfer>=0.1.12:net/py-s3transfer@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}docutils>=0.10:textproc/py-docutils@${PY_FLAVOR} \
--- a/devel/awscli/distinfo
+++ b/devel/awscli/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1524555881
-SHA256 (awscli-1.15.7.tar.gz) = 8c85c355ed9a1cb5219c7cd7f67ce0dbf16c0bf67828cae434325e1245f580d3
-SIZE (awscli-1.15.7.tar.gz) = 591004
+TIMESTAMP = 1524645490
+SHA256 (awscli-1.15.8.tar.gz) = 5d57f93c686b6a97e845264130a530b26932553f45ad6197c81f60dca9a7fe23
+SIZE (awscli-1.15.8.tar.gz) = 591068
--- a/devel/bbfreeze-loader/pkg-descr
+++ b/devel/bbfreeze-loader/pkg-descr
@ -1,4 +1,4 @@
 bbfreeze-loader provides binary dependencies for bbfreeze, utility to create
 standalone executables from Python scripts.

-WWW: https://pypi.python.org/pypi/bbfreeze-loader
+WWW: https://pypi.org/project/bbfreeze-loader/
--- a/devel/bbfreeze/pkg-descr
+++ b/devel/bbfreeze/pkg-descr
@ -12,4 +12,4 @@ It has the following features:
  - Automatic pathname rewriting (pathnames in tracebacks are relative)
  - New distutils command: bdist_bbfreeze

-WWW: https://pypi.python.org/pypi/bbfreeze
+WWW: https://pypi.org/project/bbfreeze/
--- a/devel/bugzilla44/pkg-descr
+++ b/devel/bugzilla44/pkg-descr
@ -19,4 +19,4 @@ These include:
    Bugzilla email interface and checkin/checkout scripts)
  * too many more features to list

-WWW: http://www.bugzilla.org/
+WWW: https://www.bugzilla.org/
--- a/devel/clixon/Makefile
+++ b/devel/clixon/Makefile
@ -0,0 +1,28 @@
+# $FreeBSD$
+
+PORTNAME=	clixon
+DISTVERSION=	3.6.0.b.20180424
+CATEGORIES=	devel
+
+MAINTAINER=	dcornejo@netgate.com
+COMMENT=	CLIgen is a Command-Line Interface generator
+
+LICENSE=	APACHE20
+LICENSE_FILE=	${WRKSRC}/LICENSE.md
+
+LIB_DEPENDS=	libcligen.so:devel/cligen \
+		libfcgi.so:www/fcgi
+
+USES=		gmake
+
+USE_LDCONFIG=	yes
+USE_GITHUB=	yes
+GH_ACCOUNT=	clicon
+GH_TAGNAME=	d57a6cf53cdda4a3e5da122eb34de5ce069676f0
+
+GNU_CONFIGURE=	yes
+CONFIGURE_ARGS=	--with-cligen=${LOCALBASE} --sysconfdir=${ETCDIR}
+
+MAKE_JOBS_UNSAFE=yes
+
+.include <bsd.port.mk>
--- a/devel/clixon/distinfo
+++ b/devel/clixon/distinfo
@ -0,0 +1,3 @@
+TIMESTAMP = 1524681931
+SHA256 (clicon-clixon-3.6.0.b.20180424-d57a6cf53cdda4a3e5da122eb34de5ce069676f0_GH0.tar.gz) = 3985436b89f0e1547ac8d49b277877a1cd5b4001bc2fbca14ffc217d81dcdca9
+SIZE (clicon-clixon-3.6.0.b.20180424-d57a6cf53cdda4a3e5da122eb34de5ce069676f0_GH0.tar.gz) = 697630
--- a/devel/clixon/files/patch-apps_netconf_Makefile.in
+++ b/devel/clixon/files/patch-apps_netconf_Makefile.in
@ -0,0 +1,11 @@
+--- apps/netconf/Makefile.in.orig	2018-04-15 09:53:12 UTC
+++ apps/netconf/Makefile.in
+@@ -44,7 +44,7 @@ bindir 		= @bindir@
+ libdir		= @libdir@
+ mandir		= @mandir@
+ libexecdir	= @libexecdir@
+-wwwdir  	= /www-data
+wwwdir  	= @prefix@/sbin
+ localstatedir	= @localstatedir@
+ sysconfdir	= @sysconfdir@
+ includedir	= @includedir@
--- a/devel/clixon/files/patch-apps_restconf_Makefile.in
+++ b/devel/clixon/files/patch-apps_restconf_Makefile.in
@ -0,0 +1,30 @@
+--- apps/restconf/Makefile.in.orig	2018-04-24 15:43:19 UTC
+++ apps/restconf/Makefile.in
+@@ -44,7 +44,7 @@ bindir 		= @bindir@
+ libdir		= @libdir@
+ mandir		= @mandir@
+ libexecdir	= @libexecdir@
+-wwwdir  	= /www-data
+wwwdir  	= @sbindir@
+ localstatedir	= @localstatedir@
+ sysconfdir	= @sysconfdir@
+ includedir	= @includedir@
+@@ -101,14 +101,14 @@ install:	install-lib $(APPL)
+ 	install -m 0755 -s $(APPL) $(DESTDIR)$(wwwdir)
+ 
+ install-lib: $(MYLIB)
+-	install -d $(DESTDIR)$(libdir) 
+-	install $(MYLIB) $(DESTDIR)$(libdir) 
+	install -d -m 0755 $(DESTDIR)$(libdir) 
+	install -m 0644 -s $(MYLIB) $(DESTDIR)$(libdir) 
+ 	ln -sf $(MYLIB) $(DESTDIR)$(libdir)/$(MYLIBSO)     # -l:libclixon_restconf.so.2
+ 	ln -sf $(MYLIBSO) $(DESTDIR)$(libdir)/$(MYLIBLINK) # -l:libclixon_restconf.so
+ 
+ install-include:	clixon_restconf.h
+-	install -d $(DESTDIR)$(includedir)/clixon
+-	install -m 644 $^ $(DESTDIR)$(includedir)/clixon
+	install -d -m 0755 $(DESTDIR)$(includedir)/clixon
+	install -m 0644 $^ $(DESTDIR)$(includedir)/clixon
+ 
+ uninstall:
+ 	rm -f $(DESTDIR)$(wwwdir)/$(APPL)
--- a/devel/clixon/pkg-descr
+++ b/devel/clixon/pkg-descr
@ -0,0 +1,7 @@
+Clixon is a CLI/network interfaced configuration database tool
+
+Using Clixon you can create CLI, RESTCONF, and NETCONF interfaces to manage a
+configuration database. It also provides the mechanism to validate and configure
+system components.
+
+WWW: http://www.clicon.org/
--- a/devel/clixon/pkg-plist
+++ b/devel/clixon/pkg-plist
@ -0,0 +1,30 @@
+bin/clixon_cli
+bin/clixon_netconf
+bin/datastore_client
+%%ETCDIR%%/clixonrc
+lib/libclixon.so
+lib/libclixon.so.3
+lib/libclixon.so.3.6
+lib/libclixon_backend.so
+lib/libclixon_backend.so.3
+lib/libclixon_backend.so.3.6
+lib/libclixon_cli.so
+lib/libclixon_cli.so.3
+lib/libclixon_cli.so.3.6
+lib/libclixon_netconf.so
+lib/libclixon_netconf.so.3
+lib/libclixon_netconf.so.3.6
+lib/libclixon_restconf.so
+lib/libclixon_restconf.so.3
+lib/libclixon_restconf.so.3.6
+lib/xmldb/text.so
+sbin/clixon_backend
+sbin/clixon_restconf
+%%DATADIR%%/clixon-config@2018-02-12.yang
+%%DATADIR%%/clixon.mk
+%%DATADIR%%/ietf-inet-types@2013-07-15.yang
+%%DATADIR%%/ietf-netconf-acm@2018-02-14.yang
+%%DATADIR%%/ietf-netconf@2011-06-01.yang
+%%DATADIR%%/ietf-yang-types@2013-07-15.yang
+@dir lib/clixon/plugins/backend
+@dir lib/clixon/plugins/cli
--- a/devel/cram/pkg-descr
+++ b/devel/cram/pkg-descr
@ -2,4 +2,4 @@ Cram is a functional testing framework for command line applications. Cram
 tests look like snippets of interactive shell sessions. Cram runs each command
 and compares the command output in the test with the command's actual output.

-WWW: https://pypi.python.org/pypi/cram
+WWW: https://pypi.org/project/cram/
--- a/devel/erlang-recon/Makefile
+++ b/devel/erlang-recon/Makefile
@ -1,7 +1,7 @@
 # $FreeBSD$

 PORTNAME=	recon
-PORTVERSION=	2.3.4
+PORTVERSION=	2.3.5
 CATEGORIES=	devel
 PKGNAMEPREFIX=	erlang-

--- a/devel/erlang-recon/distinfo
+++ b/devel/erlang-recon/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1510583044
-SHA256 (ferd-recon-2.3.4_GH0.tar.gz) = c441e4cf9785cd58982e26ba6b98286a0bc138a5e55d2e8e710c0e811cc12810
-SIZE (ferd-recon-2.3.4_GH0.tar.gz) = 205885
+TIMESTAMP = 1524642949
+SHA256 (ferd-recon-2.3.5_GH0.tar.gz) = c87cb433f51bd2eb9020b38cac126461c0654a2b19a664505535d9d773cc47c6
+SIZE (ferd-recon-2.3.5_GH0.tar.gz) = 205881
--- a/devel/etcd32/Makefile
+++ b/devel/etcd32/Makefile
@ -1,7 +1,7 @@
 # $FreeBSD$

 PORTNAME=	etcd
-PORTVERSION=	3.2.18
+PORTVERSION=	3.2.19
 DISTVERSIONPREFIX=	v
 CATEGORIES=	devel
 PKGNAMEPREFIX=	coreos-
--- a/devel/etcd32/distinfo
+++ b/devel/etcd32/distinfo
@ -1,3 +1,3 @@
-TIMESTAMP = 1522768139
-SHA256 (coreos-etcd-v3.2.18_GH0.tar.gz) = 4dd9bbc406e55e9ba39aaf411a5488b6bc24bbd6cb0cbd66be698e50f4d0c24d
-SIZE (coreos-etcd-v3.2.18_GH0.tar.gz) = 3070500
+TIMESTAMP = 1524640674
+SHA256 (coreos-etcd-v3.2.19_GH0.tar.gz) = c127d54388f13db51ef552228a0521bb6319886df9f98fb4ad650ed482b31a22
+SIZE (coreos-etcd-v3.2.19_GH0.tar.gz) = 3239457
--- a/devel/hgsvn/pkg-descr
+++ b/devel/hgsvn/pkg-descr
@ -15,4 +15,4 @@ Three scripts are provided:
   be run multiple times.
 * hgpushsvn pushes your local Mercurial commits back to the SVN repository.

-WWW: https://pypi.python.org/pypi/hgsvn
+WWW: https://pypi.org/project/hgsvn/
--- a/devel/meson/Makefile
+++ b/devel/meson/Makefile
@ -14,7 +14,7 @@ LICENSE_FILE=	${WRKSRC}/COPYING

 RUN_DEPENDS=	ninja:devel/ninja

-USES=		python:3.4+
+USES=		python:3.5+
 USE_PYTHON=	autoplist distutils noflavors
 NO_ARCH=	yes

--- a/devel/pep8/pkg-descr
+++ b/devel/pep8/pkg-descr
@ -1,4 +1,4 @@
 pep8 is a tool to check your Python code against some of the style conventions
 in PEP 8.

-WWW: https://pypi.python.org/pypi/pep8
+WWW: https://pypi.org/project/pep8/
--- a/devel/py-Acquisition/pkg-descr
+++ b/devel/py-Acquisition/pkg-descr
@ -1,4 +1,4 @@
 Acquisition is a mechanism that allows objects to obtain attributes from the
 containment hierarchy they're in.

-WWW: https://pypi.python.org/pypi/Acquisition
+WWW: https://pypi.org/project/Acquisition/
--- a/devel/py-BytecodeAssembler/pkg-descr
+++ b/devel/py-BytecodeAssembler/pkg-descr
@ -4,4 +4,4 @@ tracking, line number table generation, constant and variable name index
 tracking, etc. That way, you can focus your attention on the desired
 semantics of your bytecode instead of on these mechanical issues.

-WWW: https://pypi.python.org/pypi/BytecodeAssembler
+WWW: https://pypi.org/project/BytecodeAssembler/
--- a/devel/py-DateTime/pkg-descr
+++ b/devel/py-DateTime/pkg-descr
@ -2,4 +2,4 @@ This package provides a DateTime data type, as known from Zope 2.
 Unless you need to communicate with Zope 2 APIs, you're probably
 better off using Python's built-in datetime module.

-WWW: https://pypi.python.org/pypi/DateTime
+WWW: https://pypi.org/project/DateTime/
--- a/devel/py-DocumentTemplate/pkg-descr
+++ b/devel/py-DocumentTemplate/pkg-descr
@ -6,4 +6,4 @@ logic and loops.
 Inside Zope environments page templates and TAL have superseded
 DTML for most use cases.

-WWW: https://pypi.python.org/pypi/DocumentTemplate
+WWW: https://pypi.org/project/DocumentTemplate/
--- a/devel/py-ExtensionClass/pkg-descr
+++ b/devel/py-ExtensionClass/pkg-descr
@ -1,4 +1,4 @@
 This package provides a metaclass that allows classes implemented
 in extension modules to be subclassed in Python.

-WWW: https://pypi.python.org/pypi/ExtensionClass
+WWW: https://pypi.org/project/ExtensionClass/
--- a/devel/py-Faker/pkg-descr
+++ b/devel/py-Faker/pkg-descr
@ -6,4 +6,4 @@ data taken from a production service, Faker is for you.
 Faker is heavily inspired by PHP's [Faker][php-faker], Perl's
 [Data::Faker][perl-faker], and by ruby's [Faker][ruby-faker].

-WWW: https://pypi.python.org/pypi/Faker
+WWW: https://pypi.org/project/Faker/
--- a/Show More
+++ b/Show More