[Seqan-dev] find() build woes

[Jared Wilkening <jared@mcs.anl.gov>]

Hi all,

I have been trying to get a bit of code running using the SeqAn lib
but keep hitting an issue when I have find in my
code.

To check if it was an issue with my code or something else I attempted
to build test_index.cpp from svn_repo .../projects/tests/index/.

My setup:
gcc version 4.1.2
Seqan_Release_1.2 from the website

g++ -c -I. test_index.cpp                //No issues
g++ test_index.o -o test_index      //This blows up with the same
issues that I get in my code: see errors below

errors:
test_index.o: In function `main':
test_index.cpp:(.text+0xe0e2): undefined reference to `testQGramIndex()'
test_index.cpp:(.text+0xe11f): undefined reference to `testShapes()'
test_index.cpp:(.text+0xe18c): undefined reference to `testBWTWalk(char const*)'
test_index.cpp:(.text+0xe1f4): undefined reference to `testIndexCreation()'
test_index.o: In function `bool seqan::awriteAt<void,
seqan::Pair<seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned char, 7u,
void>, seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&,
seqan::Pair<seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned char, 7u,
void>, seqan::Tag<seqan::_Compressed> > const*, unsigned long, long,
aiocb&)':
test_index.cpp:(.text._ZN5seqan8awriteAtIvNS_4PairINS1_ImmNS_3TagINS_11_CompressedEEEEENS_5TupleIhLj7EvEES4_EEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_T1_T2_R5aiocb[bool
seqan::awriteAt<void, seqan::Pair<seqan::Pair<unsigned long, unsigned
long, seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned char,
7u, void>, seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&,
seqan::Pair<seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned char, 7u,
void>, seqan::Tag<seqan::_Compressed> > const*, unsigned long, long,
aiocb&)]+0xb8): undefined reference to `aio_write64'
test_index.o: In function `bool seqan::awriteAt<void,
seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&, seqan::Pair<unsigned long,
unsigned long, seqan::Tag<seqan::_Compressed> > const*, unsigned long,
long, aiocb&)':
test_index.cpp:(.text._ZN5seqan8awriteAtIvNS_4PairImmNS_3TagINS_11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_T1_T2_R5aiocb[bool
seqan::awriteAt<void, seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&, seqan::Pair<unsigned long,
unsigned long, seqan::Tag<seqan::_Compressed> > const*, unsigned long,
long, aiocb&)]+0x9a): undefined reference to `aio_write64'
test_index.o: In function `bool seqan::awriteAt<void,
seqan::Pair<unsigned long, seqan::Tuple<unsigned long, 7u, void>,
seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&, seqan::Pair<unsigned long,
seqan::Tuple<unsigned long, 7u, void>, seqan::Tag<seqan::_Compressed>
> const*, unsigned long, long, aiocb&)':
test_index.cpp:(.text._ZN5seqan8awriteAtIvNS_4PairImNS_5TupleImLj7EvEENS_3TagINS_11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_T1_T2_R5aiocb[bool
seqan::awriteAt<void, seqan::Pair<unsigned long, seqan::Tuple<unsigned
long, 7u, void>, seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&, seqan::Pair<unsigned long,
seqan::Tuple<unsigned long, 7u, void>, seqan::Tag<seqan::_Compressed>
> const*, unsigned long, long, aiocb&)]+0x9a): undefined reference to
`aio_write64'
test_index.o: In function `bool seqan::awriteAt<void,
seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>,
seqan::Tuple<unsigned long, 6u, void>, seqan::Tag<seqan::_Compressed>
>, unsigned long, long>(seqan::File<seqan::Async<void> >&,
seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>,
seqan::Tuple<unsigned long, 6u, void>, seqan::Tag<seqan::_Compressed>
> const*, unsigned long, long, aiocb&)':
test_index.cpp:(.text._ZN5seqan8awriteAtIvNS_6TripleImNS_5TupleImLj3EvEENS2_ImLj6EvEENS_3TagINS_11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_T1_T2_R5aiocb[bool
seqan::awriteAt<void, seqan::Triple<unsigned long,
seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 6u,
void>, seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&, seqan::Triple<unsigned long,
seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 6u,
void>, seqan::Tag<seqan::_Compressed> > const*, unsigned long, long,
aiocb&)]+0xb1): undefined reference to `aio_write64'
test_index.o: In function `bool seqan::awriteAt<void,
seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>,
seqan::Tuple<unsigned long, 4u, void>, seqan::Tag<seqan::_Compressed>
>, unsigned long, long>(seqan::File<seqan::Async<void> >&,
seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>,
seqan::Tuple<unsigned long, 4u, void>, seqan::Tag<seqan::_Compressed>
> const*, unsigned long, long, aiocb&)':
test_index.cpp:(.text._ZN5seqan8awriteAtIvNS_6TripleImNS_5TupleImLj3EvEENS2_ImLj4EvEENS_3TagINS_11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_T1_T2_R5aiocb[bool
seqan::awriteAt<void, seqan::Triple<unsigned long,
seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 4u,
void>, seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&, seqan::Triple<unsigned long,
seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 4u,
void>, seqan::Tag<seqan::_Compressed> > const*, unsigned long, long,
aiocb&)]+0x9a): undefined reference to `aio_write64'
test_index.o:test_index.cpp:(.text._ZN5seqan8awriteAtIvNS_6TripleImNS_5TupleImLj3EvEENS2_ImLj5EvEENS_3TagINS_11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPKT0_T1_T2_R5aiocb[bool
seqan::awriteAt<void, seqan::Triple<unsigned long,
seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u,
void>, seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&, seqan::Triple<unsigned long,
seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 5u,
void>, seqan::Tag<seqan::_Compressed> > const*, unsigned long, long,
aiocb&)]+0xb1): more undefined references to `aio_write64' follow
test_index.o: In function `seqan::waitFor(aiocb&)':
test_index.cpp:(.text._ZN5seqan7waitForER5aiocb[seqan::waitFor(aiocb&)]+0x23):
undefined reference to `aio_suspend64'
test_index.o: In function `seqan::waitFor(aiocb&, long)':
test_index.cpp:(.text._ZN5seqan7waitForER5aiocbl[seqan::waitFor(aiocb&,
long)]+0x1d): undefined reference to `aio_error64'
test_index.cpp:(.text._ZN5seqan7waitForER5aiocbl[seqan::waitFor(aiocb&,
long)]+0xbc): undefined reference to `aio_suspend64'
test_index.o: In function `bool
seqan::cancel<void>(seqan::File<seqan::Async<void> >&, aiocb&)':
test_index.cpp:(.text._ZN5seqan6cancelIvEEbRNS_4FileINS_5AsyncIT_EEEER5aiocb[bool
seqan::cancel<void>(seqan::File<seqan::Async<void> >&, aiocb&)]+0x1c):
undefined reference to `aio_cancel64'
test_index.o: In function `bool seqan::areadAt<void,
seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&, seqan::Pair<unsigned long,
unsigned long, seqan::Tag<seqan::_Compressed> >*, unsigned long, long,
aiocb&)':
test_index.cpp:(.text._ZN5seqan7areadAtIvNS_4PairImmNS_3TagINS_11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPT0_T1_T2_R5aiocb[bool
seqan::areadAt<void, seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&, seqan::Pair<unsigned long,
unsigned long, seqan::Tag<seqan::_Compressed> >*, unsigned long, long,
aiocb&)]+0x9a): undefined reference to `aio_read64'
test_index.o: In function `bool seqan::areadAt<void,
seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>,
seqan::Tuple<unsigned long, 6u, void>, seqan::Tag<seqan::_Compressed>
>, unsigned long, long>(seqan::File<seqan::Async<void> >&,
seqan::Triple<unsigned long, seqan::Tuple<unsigned long, 3u, void>,
seqan::Tuple<unsigned long, 6u, void>, seqan::Tag<seqan::_Compressed>
>*, unsigned long, long, aiocb&)':
test_index.cpp:(.text._ZN5seqan7areadAtIvNS_6TripleImNS_5TupleImLj3EvEENS2_ImLj6EvEENS_3TagINS_11_CompressedEEEEEmlEEbRNS_4FileINS_5AsyncIT_EEEEPT0_T1_T2_R5aiocb[bool
seqan::areadAt<void, seqan::Triple<unsigned long,
seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 6u,
void>, seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&, seqan::Triple<unsigned long,
seqan::Tuple<unsigned long, 3u, void>, seqan::Tuple<unsigned long, 6u,
void>, seqan::Tag<seqan::_Compressed> >*, unsigned long, long,
aiocb&)]+0xb1): undefined reference to `aio_read64'
test_index.o: In function `bool seqan::areadAt<void,
seqan::Triple<seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned long, 3u,
void>, seqan::Tuple<unsigned char, 6u, void>,
seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&,
seqan::Triple<seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned long, 3u,
void>, seqan::Tuple<unsigned char, 6u, void>,
seqan::Tag<seqan::_Compressed> >*, unsigned long, long, aiocb&)':
test_index.cpp:(.text._ZN5seqan7areadAtIvNS_6TripleINS_4PairImmNS_3TagINS_11_CompressedEEEEENS_5TupleImLj3EvEENS7_IhLj6EvEES5_EEmlEEbRNS_4FileINS_5AsyncIT_EEEEPT0_T1_T2_R5aiocb[bool
seqan::areadAt<void, seqan::Triple<seqan::Pair<unsigned long, unsigned
long, seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned long,
3u, void>, seqan::Tuple<unsigned char, 6u, void>,
seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&,
seqan::Triple<seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned long, 3u,
void>, seqan::Tuple<unsigned char, 6u, void>,
seqan::Tag<seqan::_Compressed> >*, unsigned long, long,
aiocb&)]+0x97): undefined reference to `aio_read64'
test_index.o: In function `bool seqan::areadAt<void,
seqan::Triple<seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned long, 3u,
void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::_Dna>, 6u,
seqan::Tag<seqan::_Compressed> >, seqan::Tag<seqan::_Compressed> >,
unsigned long, long>(seqan::File<seqan::Async<void> >&,
seqan::Triple<seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned long, 3u,
void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::_Dna>, 6u,
seqan::Tag<seqan::_Compressed> >, seqan::Tag<seqan::_Compressed> >*,
unsigned long, long, aiocb&)':
test_index.cpp:(.text._ZN5seqan7areadAtIvNS_6TripleINS_4PairImmNS_3TagINS_11_CompressedEEEEENS_5TupleImLj3EvEENS7_INS_10SimpleTypeIhNS_4_DnaEEELj6ES5_EES5_EEmlEEbRNS_4FileINS_5AsyncIT_EEEEPT0_T1_T2_R5aiocb[bool
seqan::areadAt<void, seqan::Triple<seqan::Pair<unsigned long, unsigned
long, seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned long,
3u, void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::_Dna>,
6u, seqan::Tag<seqan::_Compressed> >, seqan::Tag<seqan::_Compressed>
>, unsigned long, long>(seqan::File<seqan::Async<void> >&,
seqan::Triple<seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned long, 3u,
void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::_Dna>, 6u,
seqan::Tag<seqan::_Compressed> >, seqan::Tag<seqan::_Compressed> >*,
unsigned long, long, aiocb&)]+0xbd): undefined reference to
`aio_read64'
test_index.o: In function `bool seqan::areadAt<void,
seqan::Triple<seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned long, 3u,
void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::_Dna5>,
6u, seqan::Tag<seqan::_Compressed> >, seqan::Tag<seqan::_Compressed>
>, unsigned long, long>(seqan::File<seqan::Async<void> >&,
seqan::Triple<seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned long, 3u,
void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::_Dna5>,
6u, seqan::Tag<seqan::_Compressed> >, seqan::Tag<seqan::_Compressed>
>*, unsigned long, long, aiocb&)':
test_index.cpp:(.text._ZN5seqan7areadAtIvNS_6TripleINS_4PairImmNS_3TagINS_11_CompressedEEEEENS_5TupleImLj3EvEENS7_INS_10SimpleTypeIhNS_5_Dna5EEELj6ES5_EES5_EEmlEEbRNS_4FileINS_5AsyncIT_EEEEPT0_T1_T2_R5aiocb[bool
seqan::areadAt<void, seqan::Triple<seqan::Pair<unsigned long, unsigned
long, seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned long,
3u, void>, seqan::Tuple<seqan::SimpleType<unsigned char,
seqan::_Dna5>, 6u, seqan::Tag<seqan::_Compressed> >,
seqan::Tag<seqan::_Compressed> >, unsigned long,
long>(seqan::File<seqan::Async<void> >&,
seqan::Triple<seqan::Pair<unsigned long, unsigned long,
seqan::Tag<seqan::_Compressed> >, seqan::Tuple<unsigned long, 3u,
void>, seqan::Tuple<seqan::SimpleType<unsigned char, seqan::_Dna5>,
6u, seqan::Tag<seqan::_Compressed> >, seqan::Tag<seqan::_Compressed>
>*, unsigned long, long, aiocb&)]+0xbd): undefined reference to
`aio_read64'
test_index.o:test_index.cpp:(.text._ZN5seqan7areadAtIvcmlEEbRNS_4FileINS_5AsyncIT_EEEEPT0_T1_T2_R5aiocb[bool
seqan::areadAt<void, char, unsigned long,
long>(seqan::File<seqan::Async<void> >&, char*, unsigned long, long,
aiocb&)]+0x8c): more undefined references to `aio_read64' follow
collect2: ld returned 1 exit status

Any ideas?

Cheers,
Jared Wilkening