Failing to build diamond with blast database support

[jnarag]

Hoping someone can help interpret this error message below when I try to compile diamond with blast database support. It seems that the several instances of "undefined reference" is problematic but not sure how to resolve this? I am able to install blast from source code (version 2.15). Any insight would be much appreciated!

In file included from /home/zoo/zool1166/BLAST2.15/include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_dataextract.hpp:37:0,
                 from /home/zoo/zool1166/diamond-2.1.8/src/data/blastdb/blastdb.cpp:24:
/home/zoo/zool1166/BLAST2.15/include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_seqid.hpp: In copy constructor ‘ncbi::CBlastDBSeqId::CBlastDBSeqId(const ncbi::CBlastDBSeqId&)’:
/home/zoo/zool1166/BLAST2.15/include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_seqid.hpp:74:5: warning: base class ‘class ncbi::CObject’ should be explicitly initialized in the copy constructor [-Wextra]
     CBlastDBSeqId(const CBlastDBSeqId& rhs) {
     ^~~~~~~~~~~~~
At global scope:
cc1plus: warning: unrecognized command line option ‘-Wno-unknown-warning-option’
cc1plus: warning: unrecognized command line option ‘-Wno-deprecated-copy’
[100%] Linking CXX executable diamond
CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: In function `BlastDB::taxon_scientific_name[abi:cxx11](int) const':
blastdb.cpp:(.text+0x11b2): undefined reference to `ncbi::CSeqDBTaxInfo::GetTaxNames(int, ncbi::SSeqDBTaxInfo&)'
CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: In function `BlastDB::filter_by_accession(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
blastdb.cpp:(.text+0x162c): undefined reference to `ncbi::CSeqDB::AccessionsToOids(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<int, std::allocator<int> >&) const'
CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: In function `BlastDB::seqid[abi:cxx11](long) const':
blastdb.cpp:(.text+0x24c7): undefined reference to `ncbi::CSeqDB::GetBioseq(int, long, ncbi::objects::CSeq_id const*) const'
CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: In function `BlastDB::dict_title[abi:cxx11](long, unsigned long) const':
blastdb.cpp:(.text+0x2700): undefined reference to `ncbi::CSeqDB::GetBioseq(int, long, ncbi::objects::CSeq_id const*) const'
CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: In function `BlastDB::id_len(SequenceFile::SeqInfo const&, SequenceFile::SeqInfo const&)':
blastdb.cpp:(.text+0x3315): undefined reference to `ncbi::CSeqDB::GetBioseq(int, long, ncbi::objects::CSeq_id const*) const'
CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: In function `BlastDB::read_id_data(long, char*, unsigned long)':
blastdb.cpp:(.text+0x350f): undefined reference to `ncbi::CSeqDB::GetBioseq(int, long, ncbi::objects::CSeq_id const*) const'
CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: In function `BlastDB::read_seq(std::vector<signed char, std::allocator<signed char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::vector<char, std::allocator<char> >*)':
blastdb.cpp:(.text+0x4d48): undefined reference to `ncbi::CSeqDB::GetBioseq(int, long, ncbi::objects::CSeq_id const*) const'
CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: In function `BlastDB::prep_blast_db(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
blastdb.cpp:(.text+0x5ceb): undefined reference to `ncbi::CSeqDB::CSeqDB(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, ncbi::CSeqDB::ESeqType, ncbi::CSeqDBGiList*, bool)'
CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: In function `BlastDB::db_version() const':
blastdb.cpp:(.text+0x6e8): undefined reference to `ncbi::CSeqDB::GetBlastDbVersion() const'
/home/zoo/zool1166/BLAST2.15/lib/libblastdb_format.a(blastdb_dataextract.o): In function `ncbi::CBlastDBExtractor::SetSeqId(ncbi::CBlastDBSeqId const&, bool)':
blastdb_dataextract.cpp:(.text+0x198a): undefined reference to `ncbi::CSeqDB::GetBioseq(int, long, ncbi::objects::CSeq_id const*) const'
blastdb_dataextract.cpp:(.text+0x1b12): undefined reference to `ncbi::CSeqDB::GetBioseqNoData(int, long, ncbi::objects::CSeq_id const*) const'
blastdb_dataextract.cpp:(.text+0x1c18): undefined reference to `ncbi::CSeqDB::GiToOid(long, int&) const'
/home/zoo/zool1166/BLAST2.15/lib/libblastdb_format.a(blastdb_dataextract.o): In function `ncbi::CBlastDBExtractor::x_ExtractTaxId()':
blastdb_dataextract.cpp:(.text+0x7ee2): undefined reference to `ncbi::CSeqDB::GetTaxIDs(int, std::map<long, int, std::less<long>, std::allocator<std::pair<long const, int> > >&, bool) const'
/home/zoo/zool1166/BLAST2.15/lib/libblastdb_format.a(blastdb_dataextract.o): In function `ncbi::CBlastDBExtractor::x_ExtractLeafTaxIds(std::set<int, std::less<int>, std::allocator<int> >&)':
blastdb_dataextract.cpp:(.text+0x8725): undefined reference to `ncbi::CSeqDB::GetLeafTaxIDs(int, std::map<long, std::set<int, std::less<int>, std::allocator<int> >, std::less<long>, std::allocator<std::pair<long const, std::set<int, std::less<int>, std::allocator<int> > > > >&, bool) const'
/home/zoo/zool1166/BLAST2.15/lib/libblastdb_format.a(seq_writer.o): In function `ncbi::CSeqFormatter::DumpAll(ncbi::CSeqDB&, ncbi::CSeqFormatterConfig)':
seq_writer.cpp:(.text+0x1bda): undefined reference to `ncbi::CSeqDB::GetBioseq(int, long, ncbi::objects::CSeq_id const*) const'
collect2: error: ld returned 1 exit status
CMakeFiles/diamond.dir/build.make:4439: recipe for target 'diamond' failed
make[2]: *** [diamond] Error 1
CMakeFiles/Makefile2:180: recipe for target 'CMakeFiles/diamond.dir/all' failed
make[1]: *** [CMakeFiles/diamond.dir/all] Error 2
Makefile:140: recipe for target 'all' failed
make: *** [all] Error 2

[bbuchfink]

This could be a problem with the latest BLAST version, you can try using an older one.