diff --git a/biology/ngs-sdk/Makefile b/biology/ngs-sdk/Makefile index ca7321dc39fc..6382f767caa6 100644 --- a/biology/ngs-sdk/Makefile +++ b/biology/ngs-sdk/Makefile @@ -1,44 +1,44 @@ PORTNAME= ngs DISTVERSION= 2.11.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology PKGNAMESUFFIX= -sdk MAINTAINER= yuri@FreeBSD.org COMMENT= Tools and libraries for using data in the INSDC Sequence Read Archives LICENSE= PD LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_aarch64= fails to configure: unsupported architecture 'FreeBSD' BROKEN_riscv64= fails to configure: unsupported architecture 'FreeBSD' NOT_FOR_ARCHS= powerpc64 NOT_FOR_ARCHS_REASON= os-arch.prl needs to be taught about powerpc64 USES= compiler:c++11-lang gmake perl5 USE_PERL5= build USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= ncbi HAS_CONFIGURE= yes CONFIGURE_ARGS= --prefix="${STAGEDIR}${PREFIX}" --build-prefix="${WRKSRC}/build" ALL_TARGET= ngs-sdk post-extract: @cd ${WRKSRC}/ngs-sdk/ngs/unix && ${LN} -s x86_64 amd64 do-install: # install target from the project breaks: https://github.com/ncbi/ngs/issues/34 # install headers cd ${WRKSRC}/ngs-sdk && ${COPYTREE_SHARE} ngs ${STAGEDIR}${PREFIX}/include ${RM} -r ${STAGEDIR}${PREFIX}/include/ngs/win # install libraries cd ${WRKSRC}/build/ngs-sdk/FreeBSD/clang/amd64/rel/lib && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/lib - # remove static libs built instead of shared libs, see https://github.com/ncbi/ngs/issues/33 - cd ${STAGEDIR}${PREFIX}/lib && ${RM} libngs-c++.a* libngs-adapt-c++.a* + # The above command 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. # strip ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libngs-sdk.so.2.11.0 .include diff --git a/biology/ngs-sdk/pkg-plist b/biology/ngs-sdk/pkg-plist index 5b9c929a1a46..93a82bd6b5e9 100644 --- a/biology/ngs-sdk/pkg-plist +++ b/biology/ngs-sdk/pkg-plist @@ -1,94 +1,100 @@ include/ngs/Alignment.hpp include/ngs/AlignmentIterator.hpp include/ngs/ErrorMsg.hpp include/ngs/Fragment.hpp include/ngs/FragmentIterator.hpp include/ngs/Package.hpp include/ngs/Pileup.hpp include/ngs/PileupEvent.hpp include/ngs/PileupEventIterator.hpp include/ngs/PileupIterator.hpp include/ngs/Read.hpp include/ngs/ReadCollection.hpp include/ngs/ReadGroup.hpp include/ngs/ReadGroupIterator.hpp include/ngs/ReadIterator.hpp include/ngs/Reference.hpp include/ngs/ReferenceIterator.hpp include/ngs/ReferenceSequence.hpp include/ngs/Statistics.hpp include/ngs/StringRef.hpp include/ngs/adapter/AlignmentItf.hpp include/ngs/adapter/ErrorMsg.hpp include/ngs/adapter/FragmentItf.hpp include/ngs/adapter/PileupEventItf.hpp include/ngs/adapter/PileupItf.hpp include/ngs/adapter/ReadCollectionItf.hpp include/ngs/adapter/ReadGroupItf.hpp include/ngs/adapter/ReadItf.hpp include/ngs/adapter/Refcount.hpp include/ngs/adapter/ReferenceItf.hpp include/ngs/adapter/ReferenceSequenceItf.hpp include/ngs/adapter/StatisticsItf.hpp include/ngs/adapter/StringItf.hpp include/ngs/adapter/defs.h include/ngs/inl/Alignment.hpp include/ngs/inl/AlignmentIterator.hpp include/ngs/inl/Fragment.hpp include/ngs/inl/FragmentIterator.hpp include/ngs/inl/Package.hpp include/ngs/inl/Pileup.hpp include/ngs/inl/PileupEvent.hpp include/ngs/inl/PileupEventIterator.hpp include/ngs/inl/PileupIterator.hpp include/ngs/inl/Read.hpp include/ngs/inl/ReadCollection.hpp include/ngs/inl/ReadGroup.hpp include/ngs/inl/ReadGroupIterator.hpp include/ngs/inl/ReadIterator.hpp include/ngs/inl/Reference.hpp include/ngs/inl/ReferenceIterator.hpp include/ngs/inl/ReferenceSequence.hpp include/ngs/inl/Statistics.hpp include/ngs/inl/StringRef.hpp include/ngs/itf/AlignmentItf.h include/ngs/itf/AlignmentItf.hpp include/ngs/itf/ErrBlock.h include/ngs/itf/ErrBlock.hpp include/ngs/itf/ErrorMsg.hpp include/ngs/itf/FragmentItf.h include/ngs/itf/FragmentItf.hpp include/ngs/itf/PackageItf.hpp include/ngs/itf/PileupEventItf.h include/ngs/itf/PileupEventItf.hpp include/ngs/itf/PileupItf.h include/ngs/itf/PileupItf.hpp include/ngs/itf/ReadCollectionItf.h include/ngs/itf/ReadCollectionItf.hpp include/ngs/itf/ReadGroupItf.h include/ngs/itf/ReadGroupItf.hpp include/ngs/itf/ReadItf.h include/ngs/itf/ReadItf.hpp include/ngs/itf/Refcount.h include/ngs/itf/Refcount.hpp include/ngs/itf/ReferenceItf.h include/ngs/itf/ReferenceItf.hpp include/ngs/itf/ReferenceSequenceItf.h include/ngs/itf/ReferenceSequenceItf.hpp include/ngs/itf/StatisticsItf.h include/ngs/itf/StatisticsItf.hpp include/ngs/itf/StringItf.h include/ngs/itf/StringItf.hpp include/ngs/itf/VTable.h include/ngs/itf/VTable.hpp include/ngs/itf/defs.h include/ngs/unix/amd64 include/ngs/unix/arm64/atomic32.h include/ngs/unix/fat86/atomic32.h include/ngs/unix/i386/atomic32.h include/ngs/unix/x86_64/atomic32.h lib/libngs-adapt-c++-static.a +lib/libngs-adapt-c++.a +lib/libngs-adapt-c++.a.2 +lib/libngs-adapt-c++.a.2.11.0 lib/libngs-c++-static.a +lib/libngs-c++.a +lib/libngs-c++.a.2 +lib/libngs-c++.a.2.11.0 lib/libngs-sdk.so lib/libngs-sdk.so.2 lib/libngs-sdk.so.2.11.0