Remove several obsolete packages Most more than 5 years old

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: Remove several obsolete packages Most more than 5 years old
From: Jason W. Bacon <bacon4000%gmail.com@localhost>
Date: Wed, 28 Dec 2022 16:13:21 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed Dec 28 10:13:21 2022 -0600
Changeset:	c79f2c1eb98e9345956745daef429e2db652b5ae

Modified Files:
	Makefile
Removed Files:
	antlr/Makefile
	armadillo/Makefile
	blasr/Makefile
	blasr_libcpp/Makefile
	bowtie/Makefile
	cdbfasta/Makefile
	cluster-admin/Makefile
	daligner/Makefile
	dazz_db/Makefile
	denyhosts/Makefile
	diffanal/Makefile
	dlpoly-classic/Makefile
	gromacs/Makefile
	gromacs2018/Makefile
	hmmer/Makefile
	lmod/Makefile
	man2html/Makefile
	meep-mpi/Makefile
	meep-openmpi/Makefile
	meep/Makefile
	mpb-openmpi/Makefile
	mpb/Makefile
	multichoose/Makefile
	numactl/Makefile
	openmx-openmpi/Makefile
	py-ffc/Makefile
	py-fiat/Makefile
	py-pbfalcon/Makefile
	py-pypeflow/Makefile
	py-snakemake/Makefile
	py-ufl/Makefile
	py-viper/Makefile
	python3/Makefile
	singularity/Makefile
	tophat/Makefile

Log Message:
Remove several obsolete packages
Most more than 5 years old

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=c79f2c1eb98e9345956745daef429e2db652b5ae

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                |  35 ----------------
 antlr/Makefile          | 106 ------------------------------------------------
 armadillo/Makefile      |  38 -----------------
 blasr/Makefile          |  68 -------------------------------
 blasr_libcpp/Makefile   |  96 -------------------------------------------
 bowtie/Makefile         |  52 ------------------------
 cdbfasta/Makefile       |  32 ---------------
 cluster-admin/Makefile  |  31 --------------
 daligner/Makefile       |  73 ---------------------------------
 dazz_db/Makefile        |  59 ---------------------------
 denyhosts/Makefile      |  74 ---------------------------------
 diffanal/Makefile       |  22 ----------
 dlpoly-classic/Makefile |  46 ---------------------
 gromacs/Makefile        |  35 ----------------
 gromacs2018/Makefile    |  35 ----------------
 hmmer/Makefile          |  54 ------------------------
 lmod/Makefile           |  33 ---------------
 man2html/Makefile       |  27 ------------
 meep-mpi/Makefile       |  33 ---------------
 meep-openmpi/Makefile   |  37 -----------------
 meep/Makefile           |  53 ------------------------
 mpb-openmpi/Makefile    |  35 ----------------
 mpb/Makefile            |  29 -------------
 multichoose/Makefile    |  25 ------------
 numactl/Makefile        |  20 ---------
 openmx-openmpi/Makefile |  60 ---------------------------
 py-ffc/Makefile         |  26 ------------
 py-fiat/Makefile        |  21 ----------
 py-pbfalcon/Makefile    |  55 -------------------------
 py-pypeflow/Makefile    |  29 -------------
 py-snakemake/Makefile   |  26 ------------
 py-ufl/Makefile         |  28 -------------
 py-viper/Makefile       |  27 ------------
 python3/Makefile        |  21 ----------
 singularity/Makefile    |  64 -----------------------------
 tophat/Makefile         |  40 ------------------
 36 files changed, 1545 deletions(-)

diffs:
diff --git a/Makefile b/Makefile
index ca6910a7ff..4a52db087d 100644
--- a/Makefile
+++ b/Makefile
@@ -152,7 +152,6 @@ SUBDIR+=	android-tools-adb
 SUBDIR+=	angelscript
 SUBDIR+=	ansible-junos-stdlib
 SUBDIR+=	anthy-dic-jis34
-SUBDIR+=	antlr
 SUBDIR+=	antlr3-c
 SUBDIR+=	aoi
 SUBDIR+=	aokell
@@ -210,7 +209,6 @@ SUBDIR+=	arm-eabi-gdb
 SUBDIR+=	arm-elf-binutils
 SUBDIR+=	arm-elf-gcc47
 SUBDIR+=	arm-trusted-firmware-sun50i_a64-crust
-SUBDIR+=	armadillo
 SUBDIR+=	arpdig
 SUBDIR+=	arphic-ukai-ttf
 SUBDIR+=	arphic-uming-ttf
@@ -292,8 +290,6 @@ SUBDIR+=	biz-ud-gothic-ttf
 SUBDIR+=	biz-ud-mincho-ttf
 SUBDIR+=	bkcrack
 SUBDIR+=	blad
-SUBDIR+=	blasr
-SUBDIR+=	blasr_libcpp
 SUBDIR+=	blast2go
 SUBDIR+=	bleachbit
 SUBDIR+=	blink
@@ -323,7 +319,6 @@ SUBDIR+=	boost-yap
 SUBDIR+=	bore
 SUBDIR+=	boringssl
 SUBDIR+=	botan3
-SUBDIR+=	bowtie
 SUBDIR+=	bowtie2
 SUBDIR+=	bpcscripts
 SUBDIR+=	bpytop
@@ -406,7 +401,6 @@ SUBDIR+=	catpoint-git
 SUBDIR+=	cb2bib
 SUBDIR+=	ccnet-server
 SUBDIR+=	ccrypt
-SUBDIR+=	cdbfasta
 SUBDIR+=	cddlib
 SUBDIR+=	cde
 SUBDIR+=	cdhit
@@ -489,7 +483,6 @@ SUBDIR+=	clisp-hg
 SUBDIR+=	clock-signal
 SUBDIR+=	clockspeed
 SUBDIR+=	cloud-nuke
-SUBDIR+=	cluster-admin
 SUBDIR+=	clustershell
 SUBDIR+=	clutter-gst
 SUBDIR+=	cm-unicode-ttf
@@ -601,7 +594,6 @@ SUBDIR+=	d-feet
 SUBDIR+=	d1x-rebirth
 SUBDIR+=	d2
 SUBDIR+=	d2x-rebirth
-SUBDIR+=	daligner
 SUBDIR+=	dangerzone
 SUBDIR+=	daphne
 SUBDIR+=	darcs
@@ -612,7 +604,6 @@ SUBDIR+=	dasht
 SUBDIR+=	datamash
 SUBDIR+=	dates
 SUBDIR+=	davical-git
-SUBDIR+=	dazz_db
 SUBDIR+=	dbf
 SUBDIR+=	dbus-dfbsd
 SUBDIR+=	dbus-explorer
@@ -637,7 +628,6 @@ SUBDIR+=	deluge
 SUBDIR+=	delve
 SUBDIR+=	dendrite
 SUBDIR+=	denise
-SUBDIR+=	denyhosts
 SUBDIR+=	depsolver
 SUBDIR+=	deskcribe
 SUBDIR+=	desktop-data-model
@@ -656,7 +646,6 @@ SUBDIR+=	diablo
 SUBDIR+=	dict-est-rus
 SUBDIR+=	dict-freedict-eng-ara
 SUBDIR+=	dict-freedict-eng-fra
-SUBDIR+=	diffanal
 SUBDIR+=	digitemp
 SUBDIR+=	dillo-devel
 SUBDIR+=	ding
@@ -671,7 +660,6 @@ SUBDIR+=	divecmd
 SUBDIR+=	diveintopython
 SUBDIR+=	dlib
 SUBDIR+=	dlib-cpp
-SUBDIR+=	dlpoly-classic
 SUBDIR+=	dlt-daemon
 SUBDIR+=	dlt-viewer
 SUBDIR+=	dma
@@ -1432,8 +1420,6 @@ SUBDIR+=	greenbone-security-assistant
 SUBDIR+=	gretl
 SUBDIR+=	greybird-theme
 SUBDIR+=	grisbi
-SUBDIR+=	gromacs
-SUBDIR+=	gromacs2018
 SUBDIR+=	groovy
 SUBDIR+=	grpc-java
 SUBDIR+=	grsync
@@ -1541,7 +1527,6 @@ SUBDIR+=	hijra
 SUBDIR+=	hisat2
 SUBDIR+=	hisat2-simde
 SUBDIR+=	hlint
-SUBDIR+=	hmmer
 SUBDIR+=	honggfuzz-git
 SUBDIR+=	honk
 SUBDIR+=	hoogle
@@ -2297,7 +2282,6 @@ SUBDIR+=	lives
 SUBDIR+=	lizardfs
 SUBDIR+=	llilc-git
 SUBDIR+=	lmdbg-current
-SUBDIR+=	lmod
 SUBDIR+=	lnd
 SUBDIR+=	lodepng-git
 SUBDIR+=	logcli
@@ -2359,7 +2343,6 @@ SUBDIR+=	malaga
 SUBDIR+=	maloc
 SUBDIR+=	man
 SUBDIR+=	man-db
-SUBDIR+=	man2html
 SUBDIR+=	manatee
 SUBDIR+=	mapnik
 SUBDIR+=	marathon-scenarios
@@ -2399,9 +2382,6 @@ SUBDIR+=	mdadm
 SUBDIR+=	mdbtools
 SUBDIR+=	mdpress
 SUBDIR+=	mediawiki-mode
-SUBDIR+=	meep
-SUBDIR+=	meep-mpi
-SUBDIR+=	meep-openmpi
 SUBDIR+=	meka-git
 SUBDIR+=	melonds
 SUBDIR+=	memdump
@@ -2493,8 +2473,6 @@ SUBDIR+=	mozjpeg
 SUBDIR+=	mozldap
 SUBDIR+=	mozplugger
 SUBDIR+=	mp3chop
-SUBDIR+=	mpb
-SUBDIR+=	mpb-openmpi
 SUBDIR+=	mpc-el
 SUBDIR+=	mpdecimal
 SUBDIR+=	mpg123-jack
@@ -2535,7 +2513,6 @@ SUBDIR+=	mudlet-301
 SUBDIR+=	muffin
 SUBDIR+=	mule11
 SUBDIR+=	multi-gitter
-SUBDIR+=	multichoose
 SUBDIR+=	multisync
 SUBDIR+=	multisync-backup
 SUBDIR+=	multisync-ldap
@@ -2703,7 +2680,6 @@ SUBDIR+=	nuclei
 SUBDIR+=	nuget-git
 SUBDIR+=	nullpop
 SUBDIR+=	num-utils
-SUBDIR+=	numactl
 SUBDIR+=	nuppelvideo
 SUBDIR+=	nushell
 SUBDIR+=	nuspell
@@ -2777,7 +2753,6 @@ SUBDIR+=	opengrok
 SUBDIR+=	openjazz
 SUBDIR+=	openjdk8-openjfx-hg
 SUBDIR+=	openlogos
-SUBDIR+=	openmx-openmpi
 SUBDIR+=	opennurbs
 SUBDIR+=	openra
 SUBDIR+=	openrw-git
@@ -3846,9 +3821,7 @@ SUBDIR+=	py-fealty
 SUBDIR+=	py-fedmsg
 SUBDIR+=	py-fermilab
 SUBDIR+=	py-feyn
-SUBDIR+=	py-ffc
 SUBDIR+=	py-ffmpeg-normalize
-SUBDIR+=	py-fiat
 SUBDIR+=	py-figleaf
 SUBDIR+=	py-fileinspector
 SUBDIR+=	py-fiona
@@ -4378,7 +4351,6 @@ SUBDIR+=	py-path-and-address
 SUBDIR+=	py-pathos
 SUBDIR+=	py-patool
 SUBDIR+=	py-pattyrn
-SUBDIR+=	py-pbfalcon
 SUBDIR+=	py-pcapy
 SUBDIR+=	py-pdf2image
 SUBDIR+=	py-pdfminer-six
@@ -4500,7 +4472,6 @@ SUBDIR+=	py-pynest2d
 SUBDIR+=	py-pynfo
 SUBDIR+=	py-pynn
 SUBDIR+=	py-pyon
-SUBDIR+=	py-pypeflow
 SUBDIR+=	py-pyphant
 SUBDIR+=	py-pypi-browser
 SUBDIR+=	py-pypi-cli
@@ -4706,7 +4677,6 @@ SUBDIR+=	py-smcp
 SUBDIR+=	py-smell
 SUBDIR+=	py-smi
 SUBDIR+=	py-smop
-SUBDIR+=	py-snakemake
 SUBDIR+=	py-snmp
 SUBDIR+=	py-sode
 SUBDIR+=	py-sofa
@@ -4904,7 +4874,6 @@ SUBDIR+=	py-u-msgpack
 SUBDIR+=	py-u2flib-server
 SUBDIR+=	py-ua-parser
 SUBDIR+=	py-ubjson
-SUBDIR+=	py-ufl
 SUBDIR+=	py-umalqurra
 SUBDIR+=	py-unidecode
 SUBDIR+=	py-unidiff
@@ -4937,7 +4906,6 @@ SUBDIR+=	py-verilog
 SUBDIR+=	py-version-control-tools-hg
 SUBDIR+=	py-versioneer
 SUBDIR+=	py-vespa
-SUBDIR+=	py-viper
 SUBDIR+=	py-virtualenv-clone
 SUBDIR+=	py-vis
 SUBDIR+=	py-visa
@@ -5025,7 +4993,6 @@ SUBDIR+=	pypod
 SUBDIR+=	pysite
 SUBDIR+=	pystring
 SUBDIR+=	pythia6
-SUBDIR+=	python3
 SUBDIR+=	pythoncad
 SUBDIR+=	pythontoolkit
 SUBDIR+=	pywm
@@ -5343,7 +5310,6 @@ SUBDIR+=	simple-scan
 SUBDIR+=	simplec
 SUBDIR+=	simulavr-git
 SUBDIR+=	singular
-SUBDIR+=	singularity
 SUBDIR+=	sipp
 SUBDIR+=	siptoolbox
 SUBDIR+=	sipwitch
@@ -5764,7 +5730,6 @@ SUBDIR+=	todotxt-git
 SUBDIR+=	tolua++
 SUBDIR+=	tome
 SUBDIR+=	tome2
-SUBDIR+=	tophat
 SUBDIR+=	tops-bin
 SUBDIR+=	tor-browser
 SUBDIR+=	tor-dev
diff --git a/antlr/Makefile b/antlr/Makefile
deleted file mode 100644
index cb8d4645bb..0000000000
--- a/antlr/Makefile
+++ /dev/null
@@ -1,106 +0,0 @@
-# $NetBSD$
-
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
-
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-#CONFLICTS=		pccts-[0-9]*
-#USE_JAVA=		yes
-#JAVA_VERSION=		1.6+
-#PORT_CLASSPATH=	${WRKSRC}/antlrall.jar:.
-#SUB_FILES=		antlr.sh
-#OPTIONS_DEFINE=	PYTHON DOCS
-#OPTIONS_SUB=		yes
-#.if ${PORT_OPTIONS:MPYTHON}
-# Unknown tool: USE_TOOLS=	python
-#PORTDOCS+=		python-runtime.html
-#ANTLR_PYTHON=		${WRKSRC}/lib/python
-#.endif
-#post-configure:
-#.if ${PORT_OPTIONS:MPYTHON}
-#	(cd ${ANTLR_PYTHON} && ${PYTHON_CMD} setup.py config)
-#.endif
-#.if defined(WITH_BUILT_JAVA_LIB)
-#pre-build:
-#	(cd ${WRKSRC} && ${JAVA} -classpath "${PORT_CLASSPATH}" antlr.build.Tool build)
-#	(cd ${WRKSRC} && ${JAVA} -classpath "${PORT_CLASSPATH}" antlr.build.Tool jar)
-#.endif
-#.if ${PORT_OPTIONS:MPYTHON}
-#post-build:
-#	(cd ${ANTLR_PYTHON} && ${PYTHON_CMD} setup.py build && \
-#	${PYTHON_CMD} ${PYTHON_LIBDIR}/compileall.py ${ANTLR_PYTHON})
-#.endif
-#.if ${PORT_OPTIONS:MPYTHON}
-#	@(cd ${ANTLR_PYTHON} && ${PYTHON_CMD} setup.py install --root=${DESTDIR})
-#.endif
-
-DISTNAME=	antlr-${PORTVERSION}
-CATEGORIES=	devel
-MASTER_SITES=	http://www.antlr2.org/download/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://www.antlr2.org/
-
-COMMENT=	ANother Tool for Language Recognition
-LICENSE=	public-domain
-
-HAS_CONFIGURE=	yes
-# Needs java and javac or gcj?
-# On CentOS, yum install java-1.7.0-openjdk-devel.x86_64 or similar
-# pkgsrc openjdk package does not build on Linux
-# FIXME: Add a check here to notify users trying to install
-USE_JAVA=	yes
-
-CHECK_PORTABILITY_SKIP=	configure.in
-
-# Just assuming C and C++: Adjust this!
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	gmake
-
-CONFIGURE_ENV=	JAVAC="${JAVAC}" JAR="${JAR}" JAVA="${JAVA}" CLASSPATH="${PORT_CLASSPATH}"
-
-CONFIGURE_ARGS=	--disable-csharp --prefix=${PREFIX}
-
-PORTVERSION=	2.7.7
-DOCSDIR=	${PREFIX}/share/doc/antlr
-PORTDOCS=	ANTLRException.gif closure.gif cpp-runtime.html \
-		csharp-runtime.html err.html glossary.html hidden.stream.gif \
-		index.html inheritance.html j-guru-blue.jpg jguru-logo.gif \
-		lexer.html lexer.to.parser.tokens.gif logo.gif metalang.html \
-		optional.gif options.html posclosure.gif runtime.html sor.html \
-		stream.perspectives.gif stream.selector.gif \
-		stream.splitter.gif streams.html subrule.gif trees.html \
-		vocab.html
-
-# /usr/ports/Mk/bsd/java.mk
-JAVAJARDIR=	${PREFIX}/share/java/classes
-JAVA_VERSION=	1.6
-
-# Hack to simulate FreeBSD's SUB feature.  Is there a canonical way to handle
-# this in pkgsrc?
-SUBST_CLASSES+=	sh
-SUBST_FILES.sh=	${WRKDIR}/antlr.sh
-SUBST_STAGE.sh=	post-patch
-SUBST_SED.sh=	-e 's|%%JAVA_VERSION%%|${JAVA_VERSION}|'
-SUBST_SED.sh+=	-e 's|%%LOCALBASE%%/bin/java|java|'
-SUBST_SED.sh+=	-e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|'
-
-INSTALLATION_DIRS=	${JAVAJARDIR} bin include/antlr lib ${DOCSDIR}
-
-post-extract:
-	(cd ${WRKSRC} && ${CP} antlr.jar antlrall.jar)
-	cp ${FILESDIR}/antlr.sh.in ${WRKDIR}/antlr.sh
-
-do-install:
-	${INSTALL_DATA} ${WRKSRC}/antlr.jar ${DESTDIR}${JAVAJARDIR}
-	${INSTALL_SCRIPT} ${WRKDIR}/antlr.sh ${DESTDIR}${PREFIX}/bin/antlr
-	${INSTALL_DATA} ${WRKSRC}/lib/cpp/antlr/*.hpp \
-		${DESTDIR}${PREFIX}/include/antlr
-	${INSTALL_DATA} ${WRKSRC}/lib/cpp/src/libantlr.a ${DESTDIR}${PREFIX}/lib
-	(cd ${WRKSRC}/doc && ${INSTALL_DATA} ${PORTDOCS} ${DESTDIR}${DOCSDIR})
-
-.include "../../lang/python/application.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/armadillo/Makefile b/armadillo/Makefile
deleted file mode 100644
index d98022f90d..0000000000
--- a/armadillo/Makefile
+++ /dev/null
@@ -1,38 +0,0 @@
-# $NetBSD: Makefile,v 1.13 2014/10/02 15:31:38 uccwen Exp $
-
-DISTNAME=	armadillo-9.${DIST_MINOR}.3
-PKGNAME=	armadillo-9.${PKG_MINOR}.3
-PKGREVISION=	1
-CATEGORIES=	math
-MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=arma/}
-EXTRACT_SUFX=	.tar.xz
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://sourceforge.net/projects/arma/
-COMMENT=	C++ linear algebra library
-LICENSE=	mpl-2.0
-
-USE_TOOLS+=	cmake
-USE_LANGUAGES+=	c c++
-USE_CMAKE=	yes
-
-# OS X cannot handle components > 255 in a library version, so strip
-# the last digit from Aramdillo's 3-digit minor version.
-PKG_MINOR=	40
-DIST_MINOR=	${PKG_MINOR}0
-
-CMAKE_ARGS+=	-DINSTALL_LIB_DIR=${PREFIX}/lib
-CONFIGURE_ENV+=	LAPACK_LIBS=${LAPACK_LIBS:Q} BLAS_LIBS=${BLAS_LIBS:Q}
-
-SUBST_CLASSES=		minor
-SUBST_STAGE.minor=	post-patch
-SUBST_FILES.minor=	CMakeLists.txt
-SUBST_SED.minor=	-e "s|ARMA_MINOR ${DIST_MINOR}|ARMA_MINOR ${PKG_MINOR}|g"
-
-.include "../../mk/blas.buildlink3.mk"
-.include "../../wip/superlu/buildlink3.mk"
-.include "../../math/arpack-ng/buildlink3.mk"
-.include "../../devel/boost-libs/buildlink3.mk"
-.include "../../devel/boost-headers/buildlink3.mk"
-.include "../../devel/hdf5/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/blasr/Makefile b/blasr/Makefile
deleted file mode 100644
index 0985636cbd..0000000000
--- a/blasr/Makefile
+++ /dev/null
@@ -1,68 +0,0 @@
-# $NetBSD$
-
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
-
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-DISTNAME=	blasr-${PORTVERSION}
-CATEGORIES=	biology
-MASTER_SITES=	http://acadix.biz/Ports/distfiles/
-EXTRACT_SUFX=	.tar.xz
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-COMMENT=	PacBio(R) long read aligner
-# Double-check this
-LICENSE=	modified-bsd
-
-# Just assuming C and C++: Adjust this!
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	gmake
-
-SUBST_CLASSES+=		bash
-SUBST_STAGE.bash=	post-patch
-SUBST_FILES.bash=	${WRKSRC}/makefile
-SUBST_SED.bash=		-e 's|/bin/bash|${PREFIX}/bin/bash|g'
-SUBST_SED.bash+=	-e 's|-ldl||g'
-
-SUBST_CLASSES+=		libs
-SUBST_STAGE.libs=	post-configure
-SUBST_FILES.libs=	${WRKSRC}/defines.mk
-SUBST_SED.libs=		-e 's|-ldl||g'
-SUBST_SED.libs+=	-e 's|-static||g'
-
-CXXFLAGS+=	-I${PREFIX}/include/blasr_libcpp \
-		-I${PREFIX}/include/blasr_libcpp/hdf \
-		-I${PREFIX}/include/blasr_libcpp/pbdata \
-		-I${PREFIX}/include/blasr_libcpp/alignment \
-		-I${PREFIX}/include
-MAKE_FILE=	makefile
-
-PORTVERSION=	2015.08.17
-
-AUTO_MKDIRS=	yes
-
-do-configure:
-	cd ${WRKSRC} && ./configure.py --no-pbbam \
-		NOPBBAM=1 HDF5_INCLUDE=${PREFIX}/include \
-		HDF5_LIB=${PREFIX}/lib
-
-do-install:
-	${INSTALL_PROGRAM} \
-		${WRKSRC}/blasr \
-		${WRKSRC}/utils/loadPulses \
-		${WRKSRC}/utils/pls2fasta \
-		${WRKSRC}/utils/samFilter \
-		${WRKSRC}/utils/samtoh5 \
-		${WRKSRC}/utils/samtom4 \
-		${WRKSRC}/utils/sawriter \
-		${WRKSRC}/utils/sdpMatcher \
-		${WRKSRC}/utils/toAfg \
-		${DESTDIR}${PREFIX}/bin
-
-.include "../../devel/boost-libs/buildlink3.mk"
-.include "../../devel/hdf5-c++/buildlink3.mk"
-.include "../../wip/blasr_libcpp/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/blasr_libcpp/Makefile b/blasr_libcpp/Makefile
deleted file mode 100644
index 4e9ba02ea2..0000000000
--- a/blasr_libcpp/Makefile
+++ /dev/null
@@ -1,96 +0,0 @@
-# $NetBSD: Makefile,v 1.5 2015/09/16 15:50:07 outpaddling Exp $
-
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
-
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-## Requires 64-bit long
-#NOT_FOR_ARCHS=	i386
-
-DISTNAME=	blasr_libcpp-${PORTVERSION}
-CATEGORIES=	biology
-# FreeBSD MASTER_SITE_SUBDIR:
-MASTER_SITES=	http://acadix.biz/Ports/distfiles/
-EXTRACT_SUFX=	.tar.xz
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-
-COMMENT=	Library for analyzing PacBio sequences
-# Double-check this
-LICENSE=	modified-bsd
-
-# Not needed yet, but developers don't want to support CentOS 6
-# with it's GCC 4.4.
-# GCC_REQD=	4.9 4.8
-
-# Pessimistic assumption.  Test and change if possible.
-# MAKE_JOBS_SAFE=	no
-
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	gmake bash:run
-
-# Broken: hdf5-c++>=1.8:../../devel/hdf5-c++
-
-SUBST_CLASSES+=		bash
-SUBST_STAGE.bash=	post-patch
-SUBST_FILES.bash=	${WRKSRC}/makefile
-SUBST_SED.bash=		-e 's|/bin/bash|${TOOLS_BASH}|g'
-
-SUBST_CLASSES+=		pbbam
-SUBST_STAGE.pbbam=	post-configure
-SUBST_FILES.pbbam=	${WRKSRC}/libconfig.h
-SUBST_SED.pbbam=	-e 's|define|undef|'
-
-SUBST_CLASSES+=gcc44
-SUBST_STAGE.gcc44=	post-patch
-SUBST_FILES.gcc44=	${WRKSRC}/*/*
-SUBST_SED.gcc44=	-e 's|c++11|c++0x|g' \
-
-.include "../../mk/bsd.prefs.mk"
-
-.if ${OPSYS} == Darwin
-SUBST_CLASSES+=		headers
-SUBST_STAGE.headers=	post-patch
-SUBST_FILES.headers=	hdf/*.hpp pbdata/saf/*.hpp
-SUBST_SED.headers=	-e 's|\<cstdint\>|\<stdint.h\>|g' \
-			-e 's|\<cinttypes\>|\<inttypes.h\>|g'
-SUBST_CLASSES+=		uintmax
-SUBST_STAGE.uintmax=	post-patch
-SUBST_FILES.uintmax=	${WRKSRC}/alignment/suffixarray/SuffixArray.hpp
-SUBST_SED.uintmax=	-e 's|UINT_MAX|INT_MAX|g'
-.endif
-
-# XXX buildlink should take care of this for you
-CXXFLAGS+=	-I${PREFIX}/include -O
-MAKE_FILE=	makefile
-
-PORTNAME=	blasr_libcpp
-PORTVERSION=	2015.08.17
-
-# You may need this, especially if using do-install.
-# Note: Depends on PLIST.
-#AUTO_MKDIRS=	yes
-
-do-configure:
-	cd ${WRKSRC} && ./configure.py --no-pbbam \
-		HDF5_INCLUDE=${PREFIX}/include HDF5_LIB=${PREFIX}/lib
-
-do-install:
-# XXX I suggest using pax(1) instead of this
-	${MKDIR} ${DESTDIR}${PREFIX}/include ${DESTDIR}${PREFIX}/lib
-	cd ${WRKSRC} && for fn in `find . -name '*.h' -o -name '*.hpp'`; do \
-		dir=`dirname $$fn | cut -d / -f 2-`; \
-		${MKDIR} ${DESTDIR}${PREFIX}/include/${PORTNAME}/$$dir; \
-		${INSTALL_DATA} $$fn ${DESTDIR}${PREFIX}/include/${PORTNAME}/$$dir; \
-	done
-	for fn in `find ${WRKSRC} -name '*.a'`; do \
-		${INSTALL_DATA} $$fn ${DESTDIR}${PREFIX}/lib; \
-	done
-
-.include "../../devel/boost-libs/buildlink3.mk"
-.include "../../lang/python/application.mk"
-.include "../../devel/hdf5-c++/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/bowtie/Makefile b/bowtie/Makefile
deleted file mode 100644
index 5c1523e7e0..0000000000
--- a/bowtie/Makefile
+++ /dev/null
@@ -1,52 +0,0 @@
-# $NetBSD: Makefile,v 1.9 2015/01/28 16:21:48 outpaddling Exp $
-
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
-
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-# .if ${ARCH} == i386
-# MAKE_ENV+=	POPCNT_CAPABILITY=0
-# .endif
-
-DISTNAME=	bowtie-1.1.2
-CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_GITHUB:=BenLangmead/}
-GITHUB_TAG=	v${PKGVERSION_NOREV}
-
-OWNER=		bacon%NetBSD.org@localhost
-COMMENT=	Ultrafast, memory-efficient short read aligner
-LICENSE=	artistic
-
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	gmake perl:run pax
-REPLACE_PYTHON=	bowtie bowtie-build bowtie-inspect
-REPLACE_PERL=	scripts/*.pl
-
-SUBST_CLASSES+=		lock_guard
-SUBST_STAGE.lock_guard=	post-patch
-SUBST_FILES.lock_guard=	hit.h log.h
-SUBST_SED.lock_guard=	-e 's|lock_guard<MUTEX_T>|tthread::lock_guard<MUTEX_T>|g'
-
-DATADIR=	${PREFIX}/share/bowtie
-DOCSDIR=	${PREFIX}/share/doc/bowtie
-
-INSTALLATION_DIRS=	bin share/bowtie share/docs/bowtie
-
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/bowtie-*-[ls] ${DESTDIR}${PREFIX}/bin
-	${INSTALL_SCRIPT} \
-		${WRKSRC}/bowtie \
-		${WRKSRC}/bowtie-build \
-		${WRKSRC}/bowtie-inspect \
-		${WRKSRC}/scripts/*.sh \
-		${WRKSRC}/scripts/*.pl \
-		${DESTDIR}${PREFIX}/bin
-	${MKDIR} ${DESTDIR}${DATADIR}
-	(cd ${WRKSRC} && ${PAX} -wr genomes indexes reads ${DESTDIR}${DATADIR})
-	(cd ${WRKSRC}/doc && ${PAX} -wr * ${DESTDIR}${DOCSDIR})
-
-.include "../../lang/python/application.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/cdbfasta/Makefile b/cdbfasta/Makefile
deleted file mode 100644
index ef949e4814..0000000000
--- a/cdbfasta/Makefile
+++ /dev/null
@@ -1,32 +0,0 @@
-# $NetBSD$
-
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
-
-DISTNAME=	cdbfasta-${PORTVERSION}
-CATEGORIES=	biology
-MASTER_SITES=	http://acadix.biz/Ports/distfiles/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-COMMENT=	Fast indexing and retrieval of fasta records from flat file databases
-# LICENSE=	Unspecified
-
-# Pessimistic assumption.  Test and change if possible.
-MAKE_JOBS_SAFE=	no
-
-# Just assuming C and C++: Adjust this!
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	gmake
-
-WRKSRC=		${WRKDIR}/cdbfasta
-
-PORTVERSION=	2010.07.22
-
-AUTO_MKDIRS=	yes
-
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/cdbfasta ${DESTDIR}${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/cdbyank ${DESTDIR}${PREFIX}/bin
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/cluster-admin/Makefile b/cluster-admin/Makefile
deleted file mode 100644
index 4b09e95260..0000000000
--- a/cluster-admin/Makefile
+++ /dev/null
@@ -1,31 +0,0 @@
-# $NetBSD$
-
-DISTNAME=	cluster-admin-0.4
-CATEGORIES=	sysutils
-MASTER_SITES=	http://acadix.biz/Ports/distfiles/ \
-		http://outpaddling.mooo.com/~bacon/Acadix/Ports/distfiles/
-EXTRACT_SUFX=	.tar.xz
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://acadix.biz/Ports/distfiles/
-COMMENT=	HPC cluster admin tools
-LICENSE=	2-clause-bsd
-
-# Add py-hostlist dep
-
-DATADIR=	${PREFIX}/share/cluster-admin
-
-SUBST_CLASSES+=		sbin
-SUBST_STAGE.sbin=	pre-configure
-SUBST_FILES.sbin+=	Common/Src/cluster-passwd.c
-SUBST_SED.sbin=		-e 's|/usr/local/sbin|${PREFIX}/sbin|g'
-
-DEPENDS+=	auto-admin>=0.4.9:../../uwm-pkgsrc-wip/auto-admin
-
-USE_TOOLS+=	bash
-
-.include "../../mk/bsd.prefs.mk"
-
-MAKE_ENV+=	PREFIX=${PREFIX} DATADIR=${DATADIR}
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/daligner/Makefile b/daligner/Makefile
deleted file mode 100644
index f59dbff757..0000000000
--- a/daligner/Makefile
+++ /dev/null
@@ -1,73 +0,0 @@
-# $NetBSD$
-
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
-
-## Must use the same version of dazz_db, daligner, pypeflow, and falcon!
-
-DISTNAME=	daligner-${PORTVERSION}
-CATEGORIES=	biology
-MASTER_SITES=	http://acadix.biz/Ports/distfiles/
-EXTRACT_SUFX=	.tar.xz
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-COMMENT=	Find all significant local alignments between reads
-# Double-check this
-LICENSE=	modified-bsd
-
-# Pessimistic assumption.  Test and change if possible.
-# MAKE_JOBS_SAFE=	no
-
-# Just assuming C and C++: Adjust this!
-USE_LANGUAGES=	c
-USE_TOOLS+=	gmake
-
-# OS X Snow Leopard doesn't suppot no-unused-result and dies of an
-# internal compiler error if we use -O2 or higher
-SUBST_CLASSES+=		makefile
-SUBST_STAGE.makefile=	post-patch
-SUBST_FILES.makefile=	${WRKSRC}/GNUmakefile
-SUBST_SED.makefile=	-e 's|-Wno-unused-result||g'
-SUBST_SED.makefile+=	-e 's|-O3|-O|g'
-
-CFLAGS+=	-I${PREFIX}/include
-MAKE_FILE=	GNUmakefile
-
-PORTVERSION=	2015.10.28
-
-AUTO_MKDIRS=	yes
-
-post-patch:
-	for f in ${WRKSRC}/py_utils/*.py; do \
-		${PRINTF} "#!${PYTHONBIN}\\n" > $$f.temp; \
-		${CAT} $$f >> $$f.temp; \
-		${MV} -f $$f.temp $$f; \
-	done
-
-do-install:
-	${INSTALL_PROGRAM} \
-		${WRKSRC}/DB2Falcon \
-		${WRKSRC}/HPCdaligner \
-		${WRKSRC}/HPCmapper \
-		${WRKSRC}/LA4Falcon \
-		${WRKSRC}/LAcat \
-		${WRKSRC}/LAcheck \
-		${WRKSRC}/LAmerge \
-		${WRKSRC}/LAshow \
-		${WRKSRC}/LAsort \
-		${WRKSRC}/LAsplit \
-		${WRKSRC}/daligner \
-		${WRKSRC}/daligner_p \
-		${DESTDIR}${PREFIX}/bin
-	${INSTALL_SCRIPT} \
-		${WRKSRC}/py_utils/*.py \
-		${DESTDIR}${PREFIX}/bin
-	${INSTALL_DATA} \
-		${WRKSRC}/*.h \
-		${DESTDIR}${PREFIX}/include
-	${AR} rs ${DESTDIR}${PREFIX}/lib/libdaligner.a \
-		${WRKSRC}/align.o
-
-.include "../../wip/dazz_db/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/dazz_db/Makefile b/dazz_db/Makefile
deleted file mode 100644
index 67f6da8578..0000000000
--- a/dazz_db/Makefile
+++ /dev/null
@@ -1,59 +0,0 @@
-# $NetBSD$
-
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
-
-# Must use the same version of dazz_db, daligner, pypeflow, and falcon!
-
-DISTNAME=	dazz_db-${PORTVERSION}
-CATEGORIES=	biology
-MASTER_SITES=	http://acadix.biz/Ports/distfiles/
-EXTRACT_SUFX=	.tar.xz
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-COMMENT=	Dresden assembler for long read DNA projects
-# Double-check this
-LICENSE=	modified-bsd
-
-# Pessimistic assumption.  Test and change if possible.
-# MAKE_JOBS_SAFE=	no
-
-USE_LANGUAGES=	c
-USE_TOOLS+=	gmake
-MAKE_FILE=	GNUmakefile
-
-# OS X Snow Leopard doesn't suppot no-unused-result and dies of an
-# internal compiler error if we use -O2 or higher
-SUBST_CLASSES+=		makefile
-SUBST_STAGE.makefile=	post-patch
-SUBST_FILES.makefile=	${WRKSRC}/GNUmakefile
-SUBST_SED.makefile=	-e 's|-Wno-unused-result||g' \
-			-e 's|-O3|-O|g'
-
-PORTVERSION=	2015.10.28
-
-AUTO_MKDIRS=	yes
-
-do-install:
-	${INSTALL_PROGRAM} \
-		${WRKSRC}/Catrack \
-		${WRKSRC}/DAM2fasta \
-		${WRKSRC}/DB2fasta \
-		${WRKSRC}/DB2quiva \
-		${WRKSRC}/DBdust \
-		${WRKSRC}/DBrm \
-		${WRKSRC}/DBshow \
-		${WRKSRC}/DBsplit \
-		${WRKSRC}/DBstats \
-		${WRKSRC}/fasta2DAM \
-		${WRKSRC}/fasta2DB \
-		${WRKSRC}/quiva2DB \
-		${WRKSRC}/simulator \
-		${DESTDIR}${PREFIX}/bin
-	${INSTALL_DATA} \
-		${WRKSRC}/*.h ${DESTDIR}${PREFIX}/include
-	${INSTALL_DATA} \
-		${WRKSRC}/libdazzdb.a ${DESTDIR}${PREFIX}/lib
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/denyhosts/Makefile b/denyhosts/Makefile
deleted file mode 100644
index cc02d91af3..0000000000
--- a/denyhosts/Makefile
+++ /dev/null
@@ -1,74 +0,0 @@
-# $NetBSD$
-
-DISTNAME=	DenyHosts-2.6
-CATEGORIES=	security
-MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=denyhosts/}
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://downloads.sourceforge.net/project/denyhosts/denyhosts/2.6/
-COMMENT=	Block hosts with too many failed login attempts
-LICENSE=	gnu-gpl-v2
-
-PYDISTUTILSPKG=	yes
-
-SUBST_CLASSES+=		setup
-SUBST_STAGE.setup=	post-patch
-SUBST_FILES.setup=	setup.py \
-			README.txt \
-			daemon-control-dist \
-			denyhosts.cfg-dist
-SUBST_SED.setup=	-e "s|/usr/share|${PREFIX}/share|g"
-
-SUBST_CLASSES+=		lock
-SUBST_STAGE.lock=	post-patch
-SUBST_FILES.lock=	README.txt \
-			daemon-control-dist \
-			denyhosts.cfg-dist
-SUBST_SED.lock=		-e "s|/var/lock/subsys|/var/run|g"
-
-SUBST_CLASSES+=		bin
-SUBST_STAGE.bin=	post-patch
-SUBST_FILES.bin=	README.txt \
-			daemon-control-dist
-SUBST_SED.bin=		-e "s|/usr/bin/denyhosts.py|${PREFIX}/bin/denyhosts.py|g"
-
-SUBST_CLASSES+=		python
-SUBST_STAGE.python=	post-patch
-SUBST_FILES.python=	daemon-control-dist \
-			setup.py \
-			denyhosts.py \
-			plugins/test_deny.py
-SUBST_SED.python=	-e "s|/usr/bin/env python|${PYTHONBIN}|g"
-SUBST_SED.python+=	-e "s|/usr/bin/python|${PYTHONBIN}|g"
-
-SUBST_CLASSES+=		config
-SUBST_STAGE.config=	post-patch
-SUBST_FILES.config=	denyhosts.cfg-dist
-SUBST_SED.config=	-e "s|/etc/hosts.deny|${DENIED_HOSTS_FILE}|g"
-SUBST_SED.config+=	-e "s|DAEMON_SLEEP = 30s|DAEMON_SLEEP = 10s|g"
-SUBST_SED.config+=	-e "s|\#BLOCK_SERVICE = ALL|BLOCK_SERVICE = ALL|g"
-SUBST_SED.config+=	-e "s|BLOCK_SERVICE  = sshd|\#BLOCK_SERVICE  = sshd|g"
-
-SUBST_CLASSES+=		env
-SUBST_STAGE.env=	post-patch
-SUBST_FILES.env=	scripts/*.py
-SUBST_SED.env=		-e 's|/bin/env python|${PYTHONBIN}|g'
-
-DENIED_HOSTS_FILE=	/etc/hosts.deniedssh
-
-.include "../../mk/bsd.prefs.mk"
-
-post-install:
-	touch ${DENIED_HOSTS_FILE}
-	chmod 600 ${DENIED_HOSTS_FILE}
-.if !exists(${DESTDIR}${PREFIX}/share/denyhosts/denyhosts.cfg)
-	${INSTALL_DATA} ${DESTDIR}${PREFIX}/share/denyhosts/denyhosts.cfg-dist \
-		${DESTDIR}${PREFIX}/share/denyhosts/denyhosts.cfg
-.endif
-.if ${OPSYS} == Linux && !exists(/etc/init.d/denyhosts)
-	${ECHO} "Linux init scripts are in"
-	${ECHO} ${DESTDIR}${PREFIX}/share/denyhosts/daemon-control-dist
-.endif
-
-.include "../../lang/python/extension.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/diffanal/Makefile b/diffanal/Makefile
deleted file mode 100644
index 4046d37185..0000000000
--- a/diffanal/Makefile
+++ /dev/null
@@ -1,22 +0,0 @@
-# $NetBSD$
-#
-###########################################################
-#                  Generated by fbsd2pkg                  #
-#              Tue May 17 17:34:20 CDT 2022               #
-###########################################################
-
-DISTNAME=	diffanal-0.1.0.21
-CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_GITHUB:=auerlab/}
-GITHUB_TAG=	f5f29e07e345829c82cab97b8e4245cc41deab3c
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://github.com/auerlab/diffanal
-COMMENT=	Fast, simple differential analysis
-LICENSE=	2-clause-bsd
-
-pre-build:
-	cd ${WRKSRC} && make depend PREFIX=${PREFIX}
-
-.include "../../wip/biolibc/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/dlpoly-classic/Makefile b/dlpoly-classic/Makefile
deleted file mode 100644
index 4a22d5d4b9..0000000000
--- a/dlpoly-classic/Makefile
+++ /dev/null
@@ -1,46 +0,0 @@
-# $NetBSD: Makefile,v 1.3 2013/03/22 00:38:01 outpaddling Exp $
-
-DISTNAME=	dl_class_1.8
-PKGNAME=	dlpoly-classic-1.8
-CATEGORIES=	science
-MASTER_SITES=	http://ccpforge.cse.rl.ac.uk/gf/download/frsrelease/238/2028/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://ccpforge.cse.rl.ac.uk/gf/download/frsrelease/238/2028/
-COMMENT=	General purpose classical molecular dynamics
-LICENSE=	original-bsd
-
-USE_LANGUAGES=	c fortran
-USE_TOOLS+=	gmake
-
-# Use gfortran if it's installed as a base compiler outside pkgsrc
-# rather than install f2c or g95 unnecessarily
-FC=		gfortran
-
-BUILD_WRKSRC=	${WRKSRC}/source
-
-AUTO_MKDIRS=	yes
-
-do-build:
-	(cd ${BUILD_WRKSRC} && \
-	        ${CP} -f ${WRKSRC}/build/MakeSEQ Makefile && \
-		${MAKE} ${FC})
-	(cd ${BUILD_WRKSRC} && \
-		${MAKE} clean && \
-		${CP} -f ${WRKSRC}/build/MakePAR Makefile && \
-		${MAKE} gfortran)
-
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/execute/dlpoly-classic \
-		${DESTDIR}${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/execute/dlpoly-classic-mpi \
-		${DESTDIR}${PREFIX}/bin
-
-# Temporary hack to use openmpi from outside pkgsrc
-# Link fails with non-pkgsrc openmpi on RHEL
-# mpif77 cannot find -lmpi_f77
-#.include "../../mk/bsd.prefs.mk"
-#.if ${OPSYS} != "Linux"
-.include "../../parallel/openmpi/buildlink3.mk"
-#.endif
-.include "../../mk/bsd.pkg.mk"
diff --git a/gromacs/Makefile b/gromacs/Makefile
deleted file mode 100644
index eefcd3c5aa..0000000000
--- a/gromacs/Makefile
+++ /dev/null
@@ -1,35 +0,0 @@
-# $NetBSD: Makefile,v 1.17 2018/08/22 09:42:59 wiz Exp $
-#
-
-DISTNAME=		gromacs-2019
-PKGREVISION=		1
-CATEGORIES=		science
-MASTER_SITES=		ftp://ftp.gromacs.org/pub/gromacs/
-
-MAINTAINER=		bacon%NetBSD.org@localhost
-HOMEPAGE=		http://www.gromacs.org/
-COMMENT=		Molecular dynamics package
-LICENSE=		gnu-gpl-v2
-
-USE_LANGUAGES=		c c++
-USE_TOOLS+=		cmake pkg-config
-USE_CMAKE=		yes
-
-.include "options.mk"
-
-USE_TOOLS+=		perl:run
-REPLACE_PERL=		scripts/demux.pl scripts/xplor2gmx.pl
-
-CHECK_INTERPRETER_SKIP+=	share/gromacs/tutor/gmxdemo/demo
-
-.include "../../mk/bsd.prefs.mk"
-
-.if ${MACHINE_ARCH} == "i386"
-CFLAGS+=	-msse -msse2
-.endif
-
-.include "../../math/fftw/buildlink3.mk"
-.include "../../math/gsl/buildlink3.mk"	# optional
-.include "../../parallel/hwloc/buildlink3.mk"
-.include "../../textproc/libxml2/buildlink3.mk"	# optional
-.include "../../mk/bsd.pkg.mk"
diff --git a/gromacs2018/Makefile b/gromacs2018/Makefile
deleted file mode 100644
index 895179dd3a..0000000000
--- a/gromacs2018/Makefile
+++ /dev/null
@@ -1,35 +0,0 @@
-# $NetBSD: Makefile,v 1.17 2018/08/22 09:42:59 wiz Exp $
-#
-
-DISTNAME=		gromacs-2018.4
-PKGREVISION=		1
-CATEGORIES=		science
-MASTER_SITES=		ftp://ftp.gromacs.org/pub/gromacs/
-
-MAINTAINER=		bacon%NetBSD.org@localhost
-HOMEPAGE=		http://www.gromacs.org/
-COMMENT=		Molecular dynamics package
-LICENSE=		gnu-gpl-v2
-
-USE_LANGUAGES=		c c++
-USE_TOOLS+=		cmake pkg-config
-USE_CMAKE=		yes
-
-.include "options.mk"
-
-USE_TOOLS+=		perl:run
-REPLACE_PERL=		scripts/demux.pl scripts/xplor2gmx.pl
-
-CHECK_INTERPRETER_SKIP+=	share/gromacs/tutor/gmxdemo/demo
-
-.include "../../mk/bsd.prefs.mk"
-
-.if ${MACHINE_ARCH} == "i386"
-CFLAGS+=	-msse -msse2
-.endif
-
-.include "../../math/fftw/buildlink3.mk"
-.include "../../math/gsl/buildlink3.mk"	# optional
-.include "../../parallel/hwloc/buildlink3.mk"
-.include "../../textproc/libxml2/buildlink3.mk"	# optional
-.include "../../mk/bsd.pkg.mk"
diff --git a/hmmer/Makefile b/hmmer/Makefile
deleted file mode 100644
index a47d34d892..0000000000
--- a/hmmer/Makefile
+++ /dev/null
@@ -1,54 +0,0 @@
-# $NetBSD$
-#
-###########################################################
-#                  Generated by fbsd2pkg                  #
-#              Tue Nov  6 08:54:26 CST 2018               #
-###########################################################
-
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-#TEST_TARGET=		check
-#SHEBANG_GLOB=		*.pl
-#OPTIONS_DEFINE=	DOCS EXAMPLES TEST
-#DOCFILES=		Userguide.pdf
-#EXAMPLES=		7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.sto \
-#			Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.sto \
-#			globins4.hmm globins4.sto globins45.fa
-#TEST_VARS=		use_perl5=build
-#post-build-TEST-on:	do-test
-#post-install:
-#	@${STRIP} ${DESTDIR}${PREFIX}/bin/*
-#post-install-DOCS-on:
-#	@${MKDIR} ${DESTDIR}${DOCSDIR}
-#	${INSTALL_DATA} ${DOCFILES:S,^,${WRKSRC}/,} ${DESTDIR}${DOCSDIR}
-#post-install-EXAMPLES-on:
-#	@${MKDIR} ${DESTDIR}${EXAMPLESDIR}
-#	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/tutorial/,} ${DESTDIR}${EXAMPLESDIR}
-
-DISTNAME=	hmmer-${PV}
-CATEGORIES=	biology
-MASTER_SITES=	http://eddylab.org/software/hmmer/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://hmmer.org/
-COMMENT=	Profile hidden Markov models for biological sequence analysis
-LICENSE=	modified-bsd
-
-# Requires SSE2 or AltiVec instructions
-ONLY_FOR_PLATFORM=	*-*-x86_64 *-*-i386 *-*-ia64 *-*-powerpc *-*-powerpc64
-
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	gmake perl:test
-GNU_CONFIGURE=	yes
-REPLACE_PERL=	easel/devkit/*
-
-MAKE_FLAGS+=	V=1
-
-PV=		3.2.1
-#SITE_PERL=	${PREFIX}/share
-#DATADIR=	${PREFIX}/share/hmmer
-#DOCSDIR=	${PREFIX}/share/doc/hmmer
-#EXAMPLESDIR=	${PREFIX}/share/examples/hmmer
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/lmod/Makefile b/lmod/Makefile
deleted file mode 100644
index 25746353de..0000000000
--- a/lmod/Makefile
+++ /dev/null
@@ -1,33 +0,0 @@
-# $NetBSD: Makefile,v 1.1 2013/12/11 19:13:31 outpaddling Exp $
-
-DISTNAME=	Lmod-5.2
-CATEGORIES=	sysutils
-MASTER_SITES=	http://downloads.sourceforge.net/project/lmod/
-EXTRACT_SUFX=	.tar.bz2
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://downloads.sourceforge.net/project/lmod/
-COMMENT=	Dynamic modification of a user's environment
-LICENSE=	mit
-
-.include "../../mk/bsd.prefs.mk"
-
-DEPENDS+=	${LUA_PKGPREFIX}-filesystem-[0-9]*:../../devel/lua-filesystem
-DEPENDS+=	${LUA_PKGPREFIX}-posix-[0-9]*:../../devel/lua-posix
-.if ${OPSYS} != "Linux"	# Part of base on CentOS and zsh pkg does not build
-DEPENDS+=	zsh-[0-9]*:../../shells/zsh
-.endif
-
-WRKSRC=		${WRKDIR}/Lmod-5.2
-GNU_CONFIGURE=	yes
-MAKE_FILE=	makefile
-USE_TOOLS+=	gmake
-
-post-install:
-	${MKDIR} -p ${DESTDIR}${PREFIX}/bin
-	${LN} -s ${DESTDIR}${PREFIX}/lmod/5.2/libexec/lmod \
-		${DESTDIR}${PREFIX}/bin
-
-.include "../../lang/lua/application.mk"
-.include "../../lang/lua/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/man2html/Makefile b/man2html/Makefile
deleted file mode 100644
index 1963eb4b93..0000000000
--- a/man2html/Makefile
+++ /dev/null
@@ -1,27 +0,0 @@
-# $NetBSD$
-
-DISTNAME=	man2html3.0.1
-PKGNAME=	${DISTNAME:S/html/html-/}
-CATEGORIES=	textproc
-MASTER_SITES+=	https://acadix.biz/Ports/distfiles/
-MASTER_SITES+=	http://hydra.nac.uci.edu/indiv/ehood/tar/
-MASTER_SITES+=	${MASTER_SITE_PERL_CPAN:=../../authors/Earl_Hood/}
-MASTER_SITES+=	http://people.freebsd.org/~demon/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://www.nongnu.org/man2html/
-COMMENT=	Convert nroff(1) man pages to HTML
-LICENSE=	gnu-gpl-v2
-
-USE_TOOLS+=	perl:run
-NO_BUILD=	yes
-
-REPLACE_PERL=	man2html
-
-INSTALLATION_DIRS=	bin ${PREFIX}/${PKGMANDIR}/man1
-
-do-install:
-	${INSTALL_SCRIPT} ${WRKSRC}/man2html ${DESTDIR}/${PREFIX}/bin
-	${INSTALL_MAN} ${WRKSRC}/doc/man2html.1 ${DESTDIR}/${PREFIX}/${PKGMANDIR}/man1
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/meep-mpi/Makefile b/meep-mpi/Makefile
deleted file mode 100644
index ed59a98be1..0000000000
--- a/meep-mpi/Makefile
+++ /dev/null
@@ -1,33 +0,0 @@
-# $NetBSD: Makefile,v 1.4 2012/10/15 19:21:45 asau Exp $
-#
-
-DISTNAME=	meep-1.1.1
-PKGNAME=	meep-mpi-1.1.1
-CATEGORIES=	science
-MASTER_SITES=	http://ab-initio.mit.edu/meep/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://ab-initio.mit.edu/meep/
-COMMENT=	FDTD simulation software to model electromagnetic systems
-LICENSE=	gnu-gpl-v3
-
-DEPENDS+=	bash-[0-9]*:../../shells/bash
-
-GNU_CONFIGURE=	yes
-USE_LIBTOOL=	yes
-USE_LANGUAGES=	c c++
-
-# Redirect headers and data to avoid conflict with meep.
-# Better to install whole thing to another prefix like mpi/openmpi?
-CONFIGURE_ARGS+=	--with-libctl=${PREFIX}/share/libctl \
-			--with-mpi \
-			--includedir=${PREFIX}/include/meep-mpi \
-			--datadir=${PREFIX}/share/meep-mpi
-
-.include "../../wip/mpb/buildlink3.mk"
-.include "../../math/gsl/buildlink3.mk"
-.include "../../devel/gettext-lib/buildlink3.mk"
-.include "../../converters/libiconv/buildlink3.mk"
-.include "../../math/harminv/buildlink3.mk"
-.include "../../parallel/openmpi/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/meep-openmpi/Makefile b/meep-openmpi/Makefile
deleted file mode 100644
index fabfd74752..0000000000
--- a/meep-openmpi/Makefile
+++ /dev/null
@@ -1,37 +0,0 @@
-# $NetBSD: Makefile,v 1.4 2013/06/25 12:49:00 outpaddling Exp $
-#
-
-DISTNAME=	meep-1.2
-PKGNAME=	meep-openmpi-1.2
-CATEGORIES=	science
-MASTER_SITES=	http://ab-initio.mit.edu/meep/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://ab-initio.mit.edu/meep/
-COMMENT=	FDTD simulation software to model electromagnetic systems
-LICENSE=	gnu-gpl-v3
-
-DEPENDS+=	bash-[0-9]*:../../shells/bash
-
-# GNU_CONFIGURE overrides --prefix
-HAS_CONFIGURE=	yes
-USE_LIBTOOL=	yes
-USE_LANGUAGES=	c c++ fortran77
-
-CONFIGURE_ARGS+=	--with-libctl=${PREFIX}/share/libctl \
-			--with-mpi \
-			--prefix=${MPI_PREFIX:Q} \
-			--mandir=${MPI_PREFIX:Q}/man
-
-MESSAGE_SUBST+=		PREFIX=${PREFIX}
-
-.include "../../wip/mpb-openmpi/buildlink3.mk"
-.include "../../math/gsl/buildlink3.mk"
-# Should this be satisfied by fftw2-openmpi from mpb-openmpi?
-.include "../../math/fftw2/buildlink3.mk"
-.include "../../devel/gettext-lib/buildlink3.mk"
-.include "../../converters/libiconv/buildlink3.mk"
-.include "../../math/harminv/buildlink3.mk"
-.include "../../graphics/png/buildlink3.mk"
-.include "../../wip/openmpi163/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/meep/Makefile b/meep/Makefile
deleted file mode 100644
index 69efe0f5c4..0000000000
--- a/meep/Makefile
+++ /dev/null
@@ -1,53 +0,0 @@
-# $NetBSD: Makefile,v 1.19 2013/06/25 12:48:32 outpaddling Exp $
-
-DISTNAME=	meep-1.2
-CATEGORIES=	science
-MASTER_SITES=	http://ab-initio.mit.edu/meep/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://ab-initio.mit.edu/meep/
-COMMENT=	FDTD simulation software to model electromagnetic systems
-LICENSE=	gnu-gpl-v3
-
-GNU_CONFIGURE=	yes
-USE_LIBTOOL=	yes
-USE_LANGUAGES=	c c++ fortran77
-
-CONFIGURE_ARGS+=	--with-libctl=${BUILDLINK_PREFIX.libctl}/share/libctl
-
-MESSAGE_SUBST+=		PREFIX=${PREFIX}
-
-TEST_TARGET=	check
-
-# ERROR: file: "libguile-srfi-srfi-1-v-3", message: "file not found"
-# Why does this have no effect?  No sign of it in config.log.
-# LDFLAGS+=	${LINKER_RPATH_FLAG}${PREFIX}/lib
-
-# Temporary hack until I figure out how to properly tweak LDFLAGS
-# Why doesn't COMPILER_RPATH_FLAG work here?  ( expands to -L )
-# Doesn't fix the libguile issue anyway
-# SUBST_CLASSES+=		ldflags
-# SUBST_STAGE.ldflags=	post-configure
-# SUBST_FILES.ldflags=	Makefile
-# SUBST_SED.ldflags=	-e "s|-L${PREFIX}/lib|-L${PREFIX}/lib -Wl,-rpath,${PREFIX}/lib|g"
-
-.include "../../mk/bsd.prefs.mk"
-
-# Hack to work around problem finding libguile*.dylib
-# Darwin needs libguile with a .so suffix and LD_LIBRARY_PATH to include
-# Latest seems to only need LD_LIBRARY_PATH
-# ${LOCALBASE}/lib
-.if ${OPSYS} == "Darwin"
-#.for l in ${PREFIX}/lib/libguile-srfi-srfi-*.dylib
-#post-install:
-#	${CP} ${l} ${l%.dylib}.so
-#.endfor
-.endif
-
-.include "../../wip/mpb/buildlink3.mk"
-.include "../../math/gsl/buildlink3.mk"
-.include "../../devel/gettext-lib/buildlink3.mk"
-.include "../../converters/libiconv/buildlink3.mk"
-.include "../../math/harminv/buildlink3.mk"
-.include "../../graphics/png/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/mpb-openmpi/Makefile b/mpb-openmpi/Makefile
deleted file mode 100644
index 4ff0774b23..0000000000
--- a/mpb-openmpi/Makefile
+++ /dev/null
@@ -1,35 +0,0 @@
-# $NetBSD: Makefile,v 1.2 2013/09/01 17:10:37 asau Exp $
-#
-
-DISTNAME=	mpb-1.4.2
-PKGNAME=	mpb-openmpi-1.4.2
-PKGREVISION=	1
-CATEGORIES=	science
-MASTER_SITES=	http://ab-initio.mit.edu/mpb/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://ab-initio.mit.edu/mpb/
-COMMENT=	MIT Photonic Bands
-LICENSE=	gnu-gpl-v3
-
-# Use HAS_CONFIGURE, not GNU_CONFIGURE, otherwise --prefix= will be overridden
-HAS_CONFIGURE=	yes
-USE_LIBTOOL=	yes
-USE_LANGUAGES=	c fortran77
-
-# --prefix=${DESTDIR}... can replace patches as long as HAS_CONFIGURE is used
-CONFIGURE_ARGS+=	--with-libctl=${PREFIX}/share/libctl \
-			--with-mpi \
-			--prefix=${MPI_PREFIX:Q} \
-			--mandir=${MPI_PREFIX:Q}/man
-# Prevent picking up wrong sh:
-CONFIGURE_ENV+=		SH_JOB=${TOOLS_PATH.sh}
-
-CFLAGS+=	-DH5_USE_16_API=1
-
-.include "../../mk/blas.buildlink3.mk"
-.include "../../devel/hdf5/buildlink3.mk"
-.include "../../wip/fftw2-openmpi/buildlink3.mk"
-.include "../../devel/readline/buildlink3.mk"
-.include "../../devel/libctl/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/mpb/Makefile b/mpb/Makefile
deleted file mode 100644
index 7c8cc54f07..0000000000
--- a/mpb/Makefile
+++ /dev/null
@@ -1,29 +0,0 @@
-# $NetBSD: Makefile,v 1.10 2013/09/01 17:10:37 asau Exp $
-#
-
-DISTNAME=	mpb-1.4.2
-PKGREVISION=	1
-CATEGORIES=	science
-MASTER_SITES=	http://ab-initio.mit.edu/mpb/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://ab-initio.mit.edu/mpb/
-COMMENT=	MIT Photonic Bands
-LICENSE=	gnu-gpl-v3
-
-GNU_CONFIGURE=	yes
-USE_LIBTOOL=	yes
-USE_LANGUAGES=	c fortran77
-USE_TOOLS+=	gsed
-
-CONFIGURE_ARGS+=	--with-libctl=${BUILDLINK_PREFIX.libctl}/share/libctl
-# Prevent picking up wrong sh:
-CONFIGURE_ENV+=		SH_JOB=${TOOLS_PATH.sh}
-CFLAGS+=		-DH5_USE_16_API=1
-
-.include "../../mk/blas.buildlink3.mk"
-.include "../../devel/hdf5/buildlink3.mk"
-.include "../../math/fftw2/buildlink3.mk"
-.include "../../devel/readline/buildlink3.mk"
-.include "../../devel/libctl/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/multichoose/Makefile b/multichoose/Makefile
deleted file mode 100644
index bf9334abc3..0000000000
--- a/multichoose/Makefile
+++ /dev/null
@@ -1,25 +0,0 @@
-# $NetBSD$
-#
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
-
-DISTNAME=	multichoose-0.0.0.20151117
-CATEGORIES=	math
-MASTER_SITES=	${MASTER_SITE_GITHUB:=ekg/}
-GITHUB_TAG=	3b8d14e616c719de88261614f0e78195d8ed49e9
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://github.com/ekg/multichoose
-COMMENT=	Generate multiset combinations (n multichoose k)
-LICENSE=	mit
-
-USE_LANGUAGES=	c c++
-REPLACE_PYTHON=	*.py
-
-INSTALL_TARGET=	install-strip
-
-pre-configure:
-	${CP} ${FILESDIR}/Makefile ${WRKSRC}
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/numactl/Makefile b/numactl/Makefile
deleted file mode 100644
index ae5b5e52b1..0000000000
--- a/numactl/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# $NetBSD$
-
-DISTNAME=	numactl-2.0.11
-CATEGORIES=	sysutils
-#MASTER_SITES=	ftp://oss.sgi.com/www/projects/libnuma/download/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-#HOMEPAGE=	ftp://oss.sgi.com/www/projects/libnuma/download/
-COMMENT=	Non Uniform Memory Access tools
-#LICENSE=	# TODO: (see mk/license.mk)
-
-# numactl and the demo programs are under the GNU General Public License, v.2
-# libnuma is under the GNU Lesser General Public License, v2.1.
-
-ONLY_FOR_PLATFORM=	Linux-*-*
-
-WRKSRC=		${WRKDIR}/numactl-2.0.11
-GNU_CONFIGURE=	yes
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/openmx-openmpi/Makefile b/openmx-openmpi/Makefile
deleted file mode 100644
index 9444bc2c4c..0000000000
--- a/openmx-openmpi/Makefile
+++ /dev/null
@@ -1,60 +0,0 @@
-# $NetBSD: Makefile,v 1.5 2013/06/22 15:54:28 outpaddling Exp $
-
-DISTNAME=	openmx3.7
-PKGNAME=	openmx-openmpi-3.7
-PKGREVISION=	1
-CATEGORIES=	science
-MASTER_SITES=	http://www.openmx-square.org/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://www.openmx-square.org/
-COMMENT=	Nano-scale material simulations based on DFT
-LICENSE=	gnu-gpl-v1
-
-WRKSRC=		${WRKDIR}/${DISTNAME}/source
-MAKE_FILE=	makefile
-# check_lead and MAIN_TRAN_Display targets fail to build
-BUILD_TARGET=	All \
-		DosMain \
-		jx \
-		analysis_example \
-		esp \
-		OpticalConductivityMain \
-		polB \
-		test_mpi \
-		TranMain \
-		TranMain_NC
-USE_TOOLS+=	gmake
-
-# FIXME: CentOS installation didn't notice that fortran was missing from
-# USE_LANGUAGES, but RHEL 5 did.
-USE_LANGUAGES=	c fortran
-
-SUBST_CLASSES+=		compile
-SUBST_FILES.compile=	${WRKSRC}/makefile
-SUBST_STAGE.compile=	post-patch
-SUBST_SED.compile=	-e "s|-openmp -O3 -I/usr/local/include|-fopenmp ${CFLAGS}|g"
-SUBST_SED.compile+=	-e "s|-lg2c -static||g"
-# SUBST_SED.compile+=	-e "s|-L/usr/local/lib|-L${MPI_PREFIX}/lib -Wl,-rpath,${MPI_PREFIX}/lib -L${PREFIX}/lib -Wl,-rpath,${PREFIX}/lib|g"
-SUBST_SED.compile+=	-e "s|-L/usr/local/lib|-L${MPI_PREFIX}/lib ${COMPILER_RPATH_FLAG}${MPI_PREFIX}/lib -L${PREFIX}/lib ${COMPILER_RPATH_FLAG}${PREFIX}/lib|g"
-SUBST_SED.compile+=	-e 's|$$(CC) $$(OBJS)|$$(FC) $$(OBJS)|g'
-
-# Some build targets "install" binaries into ${WRKDIR}/${DISTNAME}/work, so we
-# remove them before installing the work dir to share/openmx
-do-install:
-	${MKDIR} ${DESTDIR}${MPI_PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/openmx ${DESTDIR}${MPI_PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/TranMain ${DESTDIR}${MPI_PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/TranMain_NC ${DESTDIR}${MPI_PREFIX}/bin
-	${MKDIR} ${DESTDIR}${MPI_PREFIX}/share/openmx
-	${CP} -R ${WRKDIR}/${DISTNAME}/work ${DESTDIR}${MPI_PREFIX}/share/openmx
-.for f in DosMain jx analysis_example esp OpticalConductivityMain polB test_mpi
-	${CP} ${WRKDIR}/${DISTNAME}/work/${f} ${DESTDIR}${MPI_PREFIX}/bin
-	${RM} ${DESTDIR}${MPI_PREFIX}/share/openmx/work/${f}
-.endfor
-
-.include "../../wip/openmpi163/buildlink3.mk"
-.include "../../mk/blas.buildlink3.mk"
-# Investigate: Any advantage to using fftw-openmpi?
-.include "../../math/fftw/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/py-ffc/Makefile b/py-ffc/Makefile
deleted file mode 100644
index f888f8dd4a..0000000000
--- a/py-ffc/Makefile
+++ /dev/null
@@ -1,26 +0,0 @@
-# $NetBSD: Makefile,v 1.9 2014/06/01 12:49:41 thomasklausner Exp $
-#
-
-DISTNAME=	ffc-${MMVERSION}.0
-PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
-CATEGORIES=	math python
-MASTER_SITES=	http://launchpad.net/ffc/${MMVERSION}.x/${MMVERSION}.0/+download/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://launchpad.net/ffc
-COMMENT=	C++ code generator for multilinear forms
-
-LICENSE=	gnu-lgpl-v3
-
-
-PYDISTUTILSPKG=	yes
-
-MMVERSION=	1.2
-
-SUBST_CLASSES+=		man
-SUBST_FILES.man=	setup.py
-SUBST_STAGE.man=	post-patch
-SUBST_SED.man=		-e 's|"share", ||g'
-
-.include "../../lang/python/extension.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/py-fiat/Makefile b/py-fiat/Makefile
deleted file mode 100644
index adf041e703..0000000000
--- a/py-fiat/Makefile
+++ /dev/null
@@ -1,21 +0,0 @@
-# $NetBSD: Makefile,v 1.6 2014/06/01 12:49:41 thomasklausner Exp $
-#
-
-DISTNAME=	fiat-${MMVERSION}
-CATEGORIES=	math python
-MASTER_SITES=	http://launchpad.net/fiat/${MMVERSION}.x/release-${MMVERSION}/+download/
-PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://launchpad.net/fiat
-COMMENT=	Finite element Automatic Tabulator
-
-
-LICENSE=	gnu-lgpl-v3
-
-PYDISTUTILSPKG=	yes
-
-MMVERSION=	1.1
-
-.include "../../lang/python/extension.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/py-pbfalcon/Makefile b/py-pbfalcon/Makefile
deleted file mode 100644
index c2ac5989b0..0000000000
--- a/py-pbfalcon/Makefile
+++ /dev/null
@@ -1,55 +0,0 @@
-# $NetBSD$
-
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
-
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-# Must use the exact same version of dazz_db, daligner, pypeflow, and falcon!
-# Distfiles are rolled from a FALCON-integrate snapshot to ensure that
-# this is possible.
-# FIXME: Get to a newer version of rdflib and eliminate rdfextras
-# Unknown tool: USE_TOOLS=	python
-#post-stage:
-#	${STRIP_CMD} ${DESTDIR}${PREFIX}/lib/python2.7/site-packages/falcon_kit/*.so
-
-DISTNAME=	pbfalcon-${PORTVERSION}
-PKGNAME=	${PYPKGPREFIX}-pbfalcon-${PORTVERSION}
-CATEGORIES=	biology
-MASTER_SITES=	http://acadix.biz/Ports/distfiles/
-EXTRACT_SUFX=	.tar.xz
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-
-COMMENT=	Experimental PacBio diploid assembler
-# Double-check this
-LICENSE=	modified-bsd
-
-# Pessimistic assumption.  Test and change if possible.
-# MAKE_JOBS_SAFE=	no
-
-# Just assuming C and C++: Adjust this!
-USE_LANGUAGES=	c c++
-# PYDISTUTILSPKG=	yes
-
-DEPENDS+=	${PYPKGPREFIX}-networkx>=0:../../math/py-networkx
-DEPENDS+=	${PYPKGPREFIX}-pypeflow>=0:../../wip/py-pypeflow
-DEPENDS+=	${PYPKGPREFIX}-rdflib-3.4.0:../../wip/py-rdflib340
-DEPENDS+=	${PYPKGPREFIX}-rdfextras>=0:../../wip/py-rdfextras
-
-PORTVERSION=	2015.10.28
-EGG_NAME=	falcon_kit-0.4.0
-
-post-patch:
-	for f in ${WRKSRC}/src/py_scripts/*.py; do \
-		${PRINTF} "#!${PYTHONBIN}\\n\\n" > $$f.temp; \
-		${CAT} $$f >> $$f.temp; \
-		${MV} -f $$f.temp $$f; \
-	done
-
-.include "../../lang/python/egg.mk"
-.include "../../wip/dazz_db/buildlink3.mk"
-.include "../../wip/daligner/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/py-pypeflow/Makefile b/py-pypeflow/Makefile
deleted file mode 100644
index 870b4b979e..0000000000
--- a/py-pypeflow/Makefile
+++ /dev/null
@@ -1,29 +0,0 @@
-# $NetBSD$
-
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
-#
-# Must use the same version of dazz_db, daligner, pypeflow, and falcon!
-
-DISTNAME=	pypeflow-${PORTVERSION}
-PKGNAME=	${PYPKGPREFIX}-pypeflow-${PORTVERSION}
-CATEGORIES=	biology
-MASTER_SITES=	http://acadix.biz/Ports/distfiles/
-EXTRACT_SUFX=	.tar.xz
-
-HOMEPAGE=	https://github.com/PacificBiosciences/pypeFLOW
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-
-COMMENT=	Lightweight and reusable make/flow data process library
-LICENSE=	mit
-
-EGG_NAME=	pypeflow-0.1.1
-
-WRKSRC=		${WRKDIR}/${DISTNAME}
-
-PORTVERSION=	2015.10.28
-
-.include "../../lang/python/egg.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/py-snakemake/Makefile b/py-snakemake/Makefile
deleted file mode 100644
index 122c1fe4a6..0000000000
--- a/py-snakemake/Makefile
+++ /dev/null
@@ -1,26 +0,0 @@
-# $NetBSD$
-#
-###########################################################
-#                  Generated by fbsd2pkg                  #
-#              Mon Nov  5 14:50:56 CST 2018               #
-###########################################################
-
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-DISTNAME=	snakemake-${PV}
-PKGNAME=	${PYPKGPREFIX}-snakemake-${PV}
-CATEGORIES=	python
-MASTER_SITES=	${MASTER_SITE_PYPI:=s/snakemake/}
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://pypi.python.org/pypi/snakemake
-COMMENT=	Reduce the complexity of creating workflows
-LICENSE=	mit
-
-PYTHON_VERSIONS_INCOMPATIBLE=	27
-
-PV=		5.2.0
-
-.include "../../lang/python/egg.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/py-ufl/Makefile b/py-ufl/Makefile
deleted file mode 100644
index 7a4e68aacf..0000000000
--- a/py-ufl/Makefile
+++ /dev/null
@@ -1,28 +0,0 @@
-# $NetBSD: Makefile,v 1.7 2014/06/01 12:49:47 thomasklausner Exp $
-#
-
-DISTNAME=	ufl-${MMVERSION}.0
-CATEGORIES=	devel python
-MASTER_SITES=	http://launchpad.net/ufl/${MMVERSION}.x/${MMVERSION}.0/+download/
-PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://launchpad.net/ufl
-COMMENT=	Unified Form Language for finite element discretizations
-
-
-LICENSE=	gnu-lgpl-v3
-
-PYDISTUTILSPKG=	yes
-
-MMVERSION=	1.2
-
-SUBST_CLASSES+=		man
-SUBST_FILES.man=	setup.py
-SUBST_STAGE.man=	post-patch
-SUBST_SED.man=		-e 's|"share", ||g'
-
-# todo: depends distutils
-.include "../../lang/python/extension.mk"
-.include "../../devel/swig2/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/py-viper/Makefile b/py-viper/Makefile
deleted file mode 100644
index 7ced267b9b..0000000000
--- a/py-viper/Makefile
+++ /dev/null
@@ -1,27 +0,0 @@
-# $NetBSD: Makefile,v 1.7 2014/06/01 12:49:47 thomasklausner Exp $
-#
-
-DISTNAME=	viper-${MMVERSION}.1
-PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=	1
-CATEGORIES=	graphics python
-MASTER_SITES=	http://launchpad.net/fenics-viper/${MMVERSION}.x/${MMVERSION}.1/+download/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://launchpad.net/fenics-viper
-COMMENT=	Scientific plotter and run-time visualization module
-
-
-LICENSE=	gnu-lgpl-v3
-
-PYDISTUTILSPKG=	yes
-
-MMVERSION=	1.0
-
-SUBST_CLASSES+=		man
-SUBST_FILES.man=	setup.py
-SUBST_STAGE.man=	post-patch
-SUBST_SED.man=		-e 's|"share", ||g'
-
-.include "../../lang/python/extension.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/python3/Makefile b/python3/Makefile
deleted file mode 100644
index a4d4fc05a1..0000000000
--- a/python3/Makefile
+++ /dev/null
@@ -1,21 +0,0 @@
-# $NetBSD$
-#
-
-PKGNAME=	python3-3
-CATEGORIES=	python meta-pkgs
-MASTER_SITES=	# empty
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-COMMENT=	Wrapper linking current python3.x to python3 and python
-LICENSE=	python-software-foundation
-
-NO_BUILD=	YES
-
-INSTALLATION_DIRS=	bin
-
-do-install:
-	${LN} -s ${PYTHONBIN} ${DESTDIR}${PREFIX}/bin/python3
-	${LN} -s ${PYTHONBIN} ${DESTDIR}${PREFIX}/bin/python
-
-.include "../../lang/python/application.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/singularity/Makefile b/singularity/Makefile
deleted file mode 100644
index 8721778071..0000000000
--- a/singularity/Makefile
+++ /dev/null
@@ -1,64 +0,0 @@
-# $NetBSD$
-#
-###########################################################
-#                  Generated by fbsd2pkg                  #
-#              Fri Jun  1 21:50:38 CDT 2018               #
-###########################################################
-
-DISTNAME=	singularity-${PV}
-CATEGORIES=	emulators
-MASTER_SITES=	${MASTER_SITE_GITHUB:=singularityware/}
-GITHUB_PROJECT=	singularity
-GITHUB_TAG=	${PV}
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://github.com/singularityware/singularity
-COMMENT=	Application container for Linux
-LICENSE=	modified-bsd
-
-DEPENDS+=	squashfs>=0:../../filesystems/squashfs
-
-REPLACE_PYTHON=		libexec/helpers/*/*.py
-REPLACE_PYTHON+=	libexec/python/*.py
-REPLACE_PYTHON+=	libexec/python/*/*.py
-REPLACE_PYTHON+=	libexec/python/*/*/*.py
-REPLACE_BASH+=		bin/singularity.in
-
-SUBST_CLASSES+=		path
-SUBST_STAGE.path=	pre-configure
-SUBST_FILES.path=	bin/singularity.in
-SUBST_SED.path=		-e 's|/usr/local|${PREFIX}|g'
-
-USE_TOOLS+=	autoconf automake autoreconf bash
-USE_LIBTOOL=	yes
-GNU_CONFIGURE=	yes
-
-PV=			2.5.1
-CONFIG_SHELL=		${BASH}
-# CHECK_PORTABILITY_SKIP=	configure
-
-# Requires clone()
-ONLY_FOR_PLATFORM=	Linux-*-*
-
-EGDIR=			${PREFIX}/share/examples/${PKGBASE}
-PKG_SYSCONFSUBDIR=	${PKGBASE}
-CONF_FILES+=		${EGDIR}/default-nsswitch.conf ${PKG_SYSCONFDIR}/default-nsswitch.conf
-CONF_FILES+=		${EGDIR}/init ${PKG_SYSCONFDIR}/init
-CONF_FILES+=		${EGDIR}/nvliblist.conf ${PKG_SYSCONFDIR}/nvliblist.conf
-CONF_FILES+=		${EGDIR}/singularity.conf ${PKG_SYSCONFDIR}/singularity.conf
-
-INSTALLATION_DIRS=	${EGDIR}
-
-pre-configure:
-	cd ${WRKSRC} && autoreconf -if
-
-# FIXME: Should this be necessary?
-post-install:
-	${MV} ${DESTDIR}${PKG_SYSCONFDIR}/*.conf ${DESTDIR}${EGDIR}
-	${MV} ${DESTDIR}${PKG_SYSCONFDIR}/init ${DESTDIR}${EGDIR}
-	${CHMOD} a-w ${DESTDIR}${PREFIX}/libexec/singularity/bin/*-suid
-
-.include "../../archivers/libarchive/buildlink3.mk"
-.include "../../security/openssl/buildlink3.mk"
-.include "../../lang/python/application.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/tophat/Makefile b/tophat/Makefile
deleted file mode 100644
index fdc7e96c59..0000000000
--- a/tophat/Makefile
+++ /dev/null
@@ -1,40 +0,0 @@
-# $NetBSD$
-#
-###########################################################
-#                  Generated by fbsd2pkg                  #
-#              Thu Mar  3 09:54:03 CST 2016               #
-###########################################################
-
-DISTNAME=	tophat-${PORTVERSION}
-CATEGORIES=	biology
-# Note: Distfiles on Github are not the same as those here
-MASTER_SITES=	http://ccb.jhu.edu/software/tophat/downloads/
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://ccb.jhu.edu/software/tophat/index.shtml
-COMMENT=	Fast splice junction mapper for RNA-Seq reads
-LICENSE=	boost-license
-
-MAKE_JOBS_SAFE=	no
-
-DEPENDS+=	bowtie2>=0:../../wip/bowtie2
-
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	gmake
-GNU_CONFIGURE=	yes
-
-REPLACE_PYTHON=	src/bed_to_juncs
-REPLACE_PYTHON=	src/contig_to_chr_coords
-REPLACE_PYTHON=	src/sra_to_solid
-REPLACE_PYTHON=	src/tophat-fusion-post
-REPLACE_PYTHON=	src/tophat.py
-REPLACE_BASH=	src/tophat2.sh
-
-CFLAGS+=	-Wno-unused
-
-PORTVERSION=	2.1.1
-
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../lang/python/application.mk"
-.include "../../devel/boost-libs/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
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