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BIO-DIKU / klust

Efficient DNA/RNA sequence clustering using *k*-mers as an approximation for sequence similarity.
GNU General Public License v2.0
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Linking with BioIO SeqEntry not working #63

Closed ahovgaard closed 9 years ago

ahovgaard commented 9 years ago

I can't seem to get klust working with BioIO's SeqEntry. I include it with:

#include <BioIO/seq_entry.h>

and it almost compiles, but fails with link errors like the following:

CMakeFiles/klust.dir/src/fasta_writer.cc.o: In function `FastaWriter::write(SeqEntry const&)':
/home/akh/uni/BIO-DIKU/klust/src/fasta_writer.cc:72: undefined reference to `SeqEntry::seq() const'
maasha commented 9 years ago

Hm, are the BioIO tests are passing and do they include testing of FastaWriter::write?

ahovgaard commented 9 years ago

I am trying to make klust use the SeqEntry class from BioIO instead of the older version currently in klust. BioIO does not have a FastaWriter class yet. I think it's just a problem with linking or something and not about BioIO.

ahovgaard commented 9 years ago

I got it working now. I moved this part of CMakeLists.txt:

# Link BioIO
include_directories(${bioio_INSTALL_DIR}/include)
link_libraries(${bioio_INSTALL_DIR}/lib/libBioIO.a)

above the add_executable part. I also removed the ${BIOIO_LIBRARY} variable references since I cannot see it defined anywhere and it works without.

maasha commented 9 years ago

Super, close the issue then.