diff --git a/biology/ncbi-vdb/Makefile b/biology/ncbi-vdb/Makefile index e3ec6af6a55b..99f88f4f7131 100644 --- a/biology/ncbi-vdb/Makefile +++ b/biology/ncbi-vdb/Makefile @@ -1,64 +1,64 @@ PORTNAME= ncbi-vdb DISTVERSION= 2.11.0 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= mzaki@niid.go.jp COMMENT= NCBI's virtualized back-end for accessing Sequence Read Archive LICENSE= PD LICENSE_FILE= ${WRKSRC}/LICENSE ONLY_FOR_ARCHS= amd64 i386 ONLY_FOR_ARCHS_REASON= libs/search/nucstrstr.c requires SSE2 instructions BUILD_DEPENDS= bash:shells/bash \ libepoll-shim>0:devel/libepoll-shim LIB_DEPENDS= libxml2.so:textproc/libxml2 \ libhdf5.so:science/hdf5 \ libmbedtls.so:security/mbedtls USES= compiler:c11 gmake localbase:ldflags perl5 shebangfix USE_PERL5= build USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= ncbi GH_TUPLE+= ncbi:ngs:${DISTVERSION}:ngs # ported as biology/ngs-sdk SHEBANG_GLOB= *.sh *.pl GNU_CONFIGURE= yes CONFIGURE_ARGS= --with-xml2-prefix=${LOCALBASE} \ --with-hdf5-prefix=${LOCALBASE} \ --with-mbedtls-prefix=${LOCALBASE} \ CC="${CC}" CXX="${CXX}" TOOLS="${CHOSEN_COMPILER_TYPE}" MAKE_ARGS+= CCNAME=${CC} CXXNAME=${CXX} PKGCFLAGS="${CFLAGS}" CFLAGS+= -I${WRKSRC}/lib MAKE_JOBS_UNSAFE= yes post-extract: @${LN} -sf ${WRKSRC_ngs} ${WRKDIR}/ngs @${LN} -sf ${WRKSRC} ${WRKDIR}/${PORTNAME} pre-patch: @${CP} ${FILESDIR}/Makefile.bsd ${WRKSRC}/build/ @for f in ${WRKSRC}/build/ld.linux.*.sh; do ${CP} -p $${f} $${f%linux*}bsd$${f#*linux}; done @${CP} -p ${WRKSRC}/build/ld.linux.gcc.sh ${WRKSRC}/build/ld.bsd.clang.sh @${MKDIR} ${WRKSRC}/interfaces/os/bsd @${CP} -p ${WRKSRC}/interfaces/os/mac/endian.h ${WRKSRC}/interfaces/os/bsd/ post-patch: @${GREP} -q '@@PREFIX@@' ${WRKSRC}/libs/kfg/config.c || (echo "@@PREFIX@@ in file/patch-libs_kfg_config.c is overwritten probably due to using 'make makepatch'"; exit 1) @${REINPLACE_CMD} -e 's#@@PREFIX@@#"${PREFIX}"#' ${WRKSRC}/libs/kfg/config.c post-configure: @${ECHO} ${CHOSEN_COMPILER_TYPE} > ${WRKSRC}/build/COMP -post-install: - # remove static libs built instead of shared libs, see https://github.com/ncbi/ncbi-vdb/issues/36 - cd ${STAGEDIR}${PREFIX}/lib && ${RM} libkdf5.a* libncbi-ngs-c++.a* libncbi-ngs.a* libncbi-vdb.a* libncbi-wvdb.a* +# The 'install' target installs broken-looking static libs with symlinks. +# This is intentional, see comments https://github.com/ncbi/ncbi-vdb/issues/36#issuecomment-817990790 This may change in future versions. .include diff --git a/biology/ncbi-vdb/pkg-plist b/biology/ncbi-vdb/pkg-plist index bd0a6d8f1054..8473b7790ed2 100644 --- a/biology/ncbi-vdb/pkg-plist +++ b/biology/ncbi-vdb/pkg-plist @@ -1,17 +1,32 @@ include/ncbi-vdb/NGS.hpp lib/libkdf5-static.a +lib/libkdf5.a +lib/libkdf5.a.2 +lib/libkdf5.a.2.11.0 lib/libkdf5.so lib/libkdf5.so.2 lib/libkdf5.so.2.11.0 lib/libncbi-ngs-c++-static.a +lib/libncbi-ngs-c++.a +lib/libncbi-ngs-c++.a.2 +lib/libncbi-ngs-c++.a.2.11.0 lib/libncbi-ngs-static.a +lib/libncbi-ngs.a +lib/libncbi-ngs.a.2 +lib/libncbi-ngs.a.2.11.0 lib/libncbi-vdb-static.a +lib/libncbi-vdb.a +lib/libncbi-vdb.a.2 +lib/libncbi-vdb.a.2.11.0 lib/libncbi-vdb.so lib/libncbi-vdb.so.2 lib/libncbi-vdb.so.2.11.0 lib/libncbi-wvdb-static.a +lib/libncbi-wvdb.a +lib/libncbi-wvdb.a.2 +lib/libncbi-wvdb.a.2.11.0 lib/libncbi-wvdb.so lib/libncbi-wvdb.so.2 lib/libncbi-wvdb.so.2.11.0 lib/ncbi/certs.kfg lib/ncbi/default.kfg