aboshkin
commented
7 years ago Please apply the following patch to ngs-tools/tools/sra-search.Makefile:
--- a/tools/sra-search/Makefile +++ b/tools/sra-search/Makefile @@ -58,6 +58,9 @@ SRA_SEARCH_SRC = \ searchblock \ vdb-search \ main \
- fragmentmatchiterator \
- blobmatchiterator \
- referencematchiterator \
Apologies for the inconvenience. This will be fixed in the upcoming release.
From: Valerii Lashmanov [mailto:notifications@github.com] Sent: Wednesday, August 30, 2017 2:40 PM To: ncbi/ngs-tools ngs-tools@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [ncbi/ngs-tools] Linking error during sra-search build (#7)
Hi,
I'm getting linking error trying to build ngs-tools.
make
make[1]: Entering directory `/home/zilek2/ngs/ngs-tools/ngs-vdb/src'
make /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/ilib/ngs-vdb
make[2]: Entering directory `/home/zilek2/ngs/ngs-tools/ngs-vdb/src'
ar rc /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/ilib/libngs-vdb.a /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/ngs-vdb/src/FragmentBlob.o /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/ngs-vdb/src/FragmentBlobIterator.o /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/ngs-vdb/src/NGS-VDB.o /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/ngs-vdb/src/VdbReadCollection.o
make[2]: Leaving directory `/home/zilek2/ngs/ngs-tools/ngs-vdb/src'
make[1]: Leaving directory `/home/zilek2/ngs/ngs-tools/ngs-vdb/src'
make[1]: Entering directory `/home/zilek2/ngs/ngs-tools/tools/sra-search'
make /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/bin/sra-search
make[2]: Entering directory `/home/zilek2/ngs/ngs-tools/tools/sra-search'
g++ -o /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/bin/sra-search.2.8.2 /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/tools/sra-search/searchblock.o /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/tools/sra-search/vdb-search.o /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/tools/sra-search/main.o -L/home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/ilib -lngs-vdb -L/home/zilek2/ncbi-outdir/ngs-sdk/linux/gcc/x86_64/rel/lib -L/home/zilek2/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -lncbi-ngs-c++ -lncbi-vdb-static -lngs-c++ -lpthread -ldl
/home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/tools/sra-search/vdb-search.o: In function `VdbSearch::VdbSearch(VdbSearch::Settings const&)':
vdb-search.cpp:(.text+0x16b7): undefined reference to `BlobMatchIterator::BlobMatchIterator(SearchBlock::Factory&, std::string const&)'
vdb-search.cpp:(.text+0x172a): undefined reference to `FragmentMatchIterator::FragmentMatchIterator(SearchBlock::Factory&, std::string const&, ngs::Read::ReadCategory)'
vdb-search.cpp:(.text+0x1807): undefined reference to `ReferenceMatchIterator::ReferenceMatchIterator(SearchBlock::Factory&, std::string const&, std::vector<ReferenceSpec, std::allocator
collect2: error: ld returned 1 exit status
make[2]: *** [/home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/bin/sra-search] Error 1
make[2]: Leaving directory `/home/zilek2/ngs/ngs-tools/tools/sra-search'
make[1]: *** [std] Error 2
make[1]: Leaving directory `/home/zilek2/ngs/ngs-tools/tools/sra-search'
It seems that sra-search needs to link to ./tools/sra-search/blobmatchiterator.cpp, which is not presented.
grep BlobMatchIterator -R .
./tools/sra-search/blobmatchiterator.cpp:////////////////////////////////// BlobMatchIterator
./tools/sra-search/blobmatchiterator.cpp:BlobMatchIterator :: BlobMatchIterator ( SearchBlock :: Factory& p_factory, const std::string& p_accession )
./tools/sra-search/blobmatchiterator.cpp:BlobMatchIterator :: ~BlobMatchIterator ()
./tools/sra-search/blobmatchiterator.cpp:BlobMatchIterator :: NextBuffer ()
./tools/sra-search/blobmatchiterator.hpp:class BlobMatchIterator : public MatchIterator
./tools/sra-search/blobmatchiterator.hpp: BlobMatchIterator ( SearchBlock :: Factory& p_factory, const std::string& p_accession );
./tools/sra-search/blobmatchiterator.hpp: virtual ~BlobMatchIterator ();
./tools/sra-search/vdb-search.cpp: m_searches . push ( new BlobMatchIterator ( m_sbFactory, *i ) );
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Hi,
I'm getting linking error trying to build ngs-tools.
It seems that sra-search needs to link to
./tools/sra-search/blobmatchiterator.cpp, which is not presented.