Re: [Seqan-dev] find() build woes

["Weese, David" <weese@campus.fu-berlin.de>]

Hi Jared,

you have to compile all .cpp files within a test folder (like test/
index/). Then you need to link all of them and also link against the
rt-library with the "-lrt" option. You find general information about
building on our website and in the Trac Wiki (Development Link), see
"Getting Started".

Regards,
David


--
David Weese                             weese@inf.fu-berlin.de
Freie Universität Berlin                http://www.inf.fu-berlin.de/
Institut für Informatik                 Phone: +49 30 838 75246
Takustraße 9                                    Algorithmic Bioinformatics
14195 Berlin                                    Room 021

Am 09.11.2009 um 23:05 schrieb Jared Wilkening:

> 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
>
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