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Linking CXX executable diamond fails during make #808

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Monkjj opened this issue May 22, 2024 · 1 comment
Open

Linking CXX executable diamond fails during make #808

Monkjj opened this issue May 22, 2024 · 1 comment

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@Monkjj
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Monkjj commented May 22, 2024 •
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I am trying to build diamond v2.1.9 from source with BLAST support. I have followed the instructions. I am using BLAST2.15 on a virtual machine running Ubuntu 20.04.6. I had to manually install the missing libraries liblmdb and libzstd. liblmdb was installed using apt and I also installed libzstd first using apt, which resolved the error for zstd NOT FOUND. However, after that I'm encountering the following issue:

[ 99%] Building CXX object CMakeFiles/diamond.dir/src/util/io/zstd_stream.cpp.o
In file included from /home/johjan/BLAST2.15/include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_dataextract.hpp:37,
                 from /home/johjan/diamond-2.1.9/src/data/blastdb/blastdb.cpp:24:
/home/johjan/BLAST2.15/include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_seqid.hpp: In copy constructor ‘ncbi::CBlastDBSeqId::CBlastDBSeqId(const ncbi::CBlastDBSeqId&)’:
/home/johjan/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]
   74 |     CBlastDBSeqId(const CBlastDBSeqId& rhs) {
      |     ^~~~~~~~~~~~~
At global scope:
cc1plus: warning: unrecognized command line option ‘-Wno-unknown-warning-option’
[100%] Linking CXX executable diamond
/usr/bin/ld: CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: in function `BlastDB::seqid[abi:cxx11](long) const':
blastdb.cpp:(.text+0xe40): undefined reference to `ncbi::CSeqDB::GetBioseq(int, long, ncbi::objects::CSeq_id const*) const'
/usr/bin/ld: CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: in function `best_id(std::__cxx11::list<ncbi::CRef<ncbi::objects::CSeq_id, ncbi::CObjectCounterLocker>, std::allocator<ncbi::CRef<ncbi::objects::CSeq_id, ncbi::CObjectCounterLocker> > > const&)':
blastdb.cpp:(.text+0xf04): undefined reference to `ncbi::objects::CSeq_id::AdjustScore(int, unsigned int) const'
/usr/bin/ld: blastdb.cpp:(.text+0xf31): undefined reference to `ncbi::objects::CSeq_id::AdjustScore(int, unsigned int) const'
/usr/bin/ld: CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: in function `BlastDB::id_len(SequenceFile::SeqInfo const&, SequenceFile::SeqInfo const&)':
blastdb.cpp:(.text+0x1a68): undefined reference to `ncbi::CSeqDB::GetBioseq(int, long, ncbi::objects::CSeq_id const*) const'
/usr/bin/ld: CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: in function `BlastDB::read_id_data(long, char*, unsigned long)':
blastdb.cpp:(.text+0x1c42): undefined reference to `ncbi::CSeqDB::GetBioseq(int, long, ncbi::objects::CSeq_id const*) const'
/usr/bin/ld: 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+0x38cf): undefined reference to `ncbi::CSeqDB::GetBioseq(int, long, ncbi::objects::CSeq_id const*) const'
/usr/bin/ld: blastdb.cpp:(.text+0x3f94): undefined reference to `ncbi::objects::CScopeInfo_Base::x_ResetTSE_Lock()'
/usr/bin/ld: blastdb.cpp:(.text+0x3fd4): undefined reference to `ncbi::objects::CScopeInfo_Base::x_ResetTSE_Lock()'
/usr/bin/ld: CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: in function `ncbi::objects::CSeq_id::FastaAARank(ncbi::CRef<ncbi::objects::CSeq_id, ncbi::CObjectCounterLocker> const&)':
blastdb.cpp:(.text._ZN4ncbi7objects7CSeq_id11FastaAARankERKNS_4CRefIS1_NS_20CObjectCounterLockerEEE[_ZN4ncbi7objects7CSeq_id11FastaAARankERKNS_4CRefIS1_NS_20CObjectCounterLockerEEE]+0x1e): undefined reference to `ncbi::objects::CSeq_id::AdjustScore(int, unsigned int) const'
/usr/bin/ld: CMakeFiles/diamond.dir/src/data/blastdb/blastdb.cpp.o: in function `ncbi::CRef<ncbi::objects::CScopeInfo_Base, ncbi::objects::CScopeInfoLocker>::Reset()':
blastdb.cpp:(.text._ZN4ncbi4CRefINS_7objects15CScopeInfo_BaseENS1_16CScopeInfoLockerEE5ResetEv[_ZN4ncbi4CRefINS_7objects15CScopeInfo_BaseENS1_16CScopeInfoLockerEE5ResetEv]+0x54): undefined reference to `ncbi::objects::CScopeInfo_Base::x_ResetTSE_Lock()'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/diamond.dir/build.make:2595: diamond] Error 1
make[1]: *** [CMakeFiles/Makefile2:84: CMakeFiles/diamond.dir/all] Error 2
make: *** [Makefile:141: all] Error 2

Since there is already a warning with something that seems to involve zstd, I tried building zstd from source (make and make install), which completed successfully, but didn't affect the error when trying to install diamond again.

This is the CMakeCache.txt:

# This is the CMakeCache file.
# For build in directory: /home/johjan/diamond-2.1.9/bin
# It was generated by CMake: /usr/bin/cmake
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//Path to a library.
BLASTDB_LIBRARY:FILEPATH=/usr/lib/ncbi-blast+/libblastdb.so

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CMAKE_PROJECT_NAME:STATIC=DIAMOND

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CMAKE_RANLIB:FILEPATH=/usr/bin/ranlib

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CMAKE_READELF:FILEPATH=/usr/bin/readelf

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//Path to a library.
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