Index: head/biology/pbbam/Makefile =================================================================== --- head/biology/pbbam/Makefile (revision 518333) +++ head/biology/pbbam/Makefile (revision 518334) @@ -1,34 +1,36 @@ # $FreeBSD$ PORTNAME= pbbam DISTVERSION= 0.18.0 # Test with biology/unanimity before upgrading! PORTREVISION= 3 CATEGORIES= biology -MAINTAINER= jwb@FreeBSD.org +# As of March 2018, unanimity is no longer open source. +# See https://github.com/PacificBiosciences/ccs. +MAINTAINER= ports@FreeBSD.org COMMENT= PacBio BAM C++ library, with SWIG bindings LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt LIB_DEPENDS= libhts.so:biology/htslib \ libboost_regex.so:devel/boost-libs # Meson needs BOOST_ROOT=${LOCALBASE} # https://github.com/mesonbuild/meson/issues/2239 USES= compiler:c++14-lang localbase meson pkgconfig python USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= PacificBiosciences pre-configure: @${REINPLACE_CMD} -e "s|'python'|'${PYTHON_VERSION}'|g" \ ${WRKSRC}/meson.build post-install: ${RLN} ${STAGEDIR}${PREFIX}/lib/libpbbam.so.${PORTVERSION} \ ${STAGEDIR}${PREFIX}/lib/libpbbam.so.0.18 ${RLN} ${STAGEDIR}${PREFIX}/lib/libpbbam.so.${PORTVERSION} \ ${STAGEDIR}${PREFIX}/lib/libpbbam.so.0 .include Index: head/biology/pbcopper/Makefile =================================================================== --- head/biology/pbcopper/Makefile (revision 518333) +++ head/biology/pbcopper/Makefile (revision 518334) @@ -1,29 +1,31 @@ # $FreeBSD$ PORTNAME= pbcopper DISTVERSION= 0.4.1 # Test with biology/unanimity before upgrading! PORTREVISION= 3 CATEGORIES= biology -MAINTAINER= jwb@FreeBSD.org +# As of March 2018, unanimity is no longer open source. +# See https://github.com/PacificBiosciences/ccs. +MAINTAINER= ports@FreeBSD.org COMMENT= Core C++ library for Pacific Biosciences tools LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt LIB_DEPENDS= libboost_regex.so:devel/boost-libs # Meson needs BOOST_ROOT=${LOCALBASE} # https://github.com/mesonbuild/meson/issues/2239 USES= compiler:c++14-lang localbase meson USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= PacificBiosciences post-install: ${RLN} ${STAGEDIR}${PREFIX}/lib/libpbcopper.so.${PORTVERSION} \ ${STAGEDIR}${PREFIX}/lib/libpbcopper.so.0.4 ${RLN} ${STAGEDIR}${PREFIX}/lib/libpbcopper.so.${PORTVERSION} \ ${STAGEDIR}${PREFIX}/lib/libpbcopper.so.0 .include Index: head/biology/pbseqan/Makefile =================================================================== --- head/biology/pbseqan/Makefile (revision 518333) +++ head/biology/pbseqan/Makefile (revision 518334) @@ -1,28 +1,30 @@ # $FreeBSD$ PORTNAME= pbseqan DISTVERSION= g20171011 CATEGORIES= biology -MAINTAINER= jwb@FreeBSD.org +# As of March 2018, unanimity is no longer open source. +# See https://github.com/PacificBiosciences/ccs. +MAINTAINER= ports@FreeBSD.org COMMENT= Pacific Biosciences patched and stripped down SeqAn LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE DEPRECATED= Upstream merged into SeqAn project: Use biology/seqan USE_GITHUB= yes GH_ACCOUNT= PacificBiosciences GH_PROJECT= seqan GH_TAGNAME= 21d95d737d8decb5cc3693b9065d81e831e7f57d NO_BUILD= yes NO_ARCH= yes do-install: @${MKDIR} ${STAGEDIR}${PREFIX}/include/PacBio cd ${WRKSRC}/include/seqan && \ ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/include/PacBio/seqan .include Index: head/biology/unanimity/Makefile =================================================================== --- head/biology/unanimity/Makefile (revision 518333) +++ head/biology/unanimity/Makefile (revision 518334) @@ -1,46 +1,48 @@ # $FreeBSD$ PORTNAME= unanimity DISTVERSIONPREFIX= v DISTVERSION= 3.4.1 PORTREVISION= 3 CATEGORIES= biology -MAINTAINER= jwb@FreeBSD.org +# As of March 2018, unanimity is no longer open source. +# See https://github.com/PacificBiosciences/ccs. +MAINTAINER= ports@FreeBSD.org COMMENT= Pacific Biosciences consensus library and applications BROKEN= unfetchable LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_aarch64= fails to compile: mmintrin.h:47:5: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'? # Very sensitive to pbbam and pbcopper versions! # Fully test new combinations and upgrade them together. BUILD_DEPENDS= seqan>=2.4.0:biology/seqan \ swig30>=3.0:devel/swig30 \ ${PYNUMPY} LIB_DEPENDS= libhts.so:biology/htslib \ libboost_regex.so:devel/boost-libs \ libpbbam.so.0.18.0:biology/pbbam \ libpbcopper.so.0.4.1:biology/pbcopper RUN_DEPENDS= ${PYNUMPY} # Meson needs BOOST_ROOT=${LOCALBASE} # https://github.com/mesonbuild/meson/issues/2239 USES= compiler:c++14-lang localbase meson pkgconfig python:2.7 USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= PacificBiosciences CFLAGS_i386= -msse2 -Wno-c++11-narrowing LDFLAGS+= -lexecinfo post-install: ${RLN} ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0.0 \ ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0 ${RLN} ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3.0.0 \ ${STAGEDIR}${PREFIX}/lib/libunanimity.so.3 .include