Bioinformatics.org
[Regeneron]
Not logged in
  • Log in
  • Bioinformatics.org
    Membership (41443+) Group hosting [?] Wiki
    Franklin Award
    Sponsorships

    Careers
    About bioinformatics
    Bioinformatics training
    Bioinformatics jobs

    Research
    All information groups
    Online databases Online analysis tools Online education tools More tools

    Development
    All software groups
    FTP repository
    SVN & CVS repositories [?]
    Mailing lists

    Forums
    News & Commentary
  • Submit
  • Archives
  • Subscribe

  • Jobs Forum
    (Career Center)
  • Submit
  • Archives
  • Subscribe
  • CD-HIT: Sequence clustering software - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #324 ] compiling CD-Hit under x86_64-suse-linux: not possible !
    Date:
    11/22/06 10:13
    Submitted by:
    unset
    Assigned to:
    unset
    Category:
    Compiling
    Priority:
    5
    Ticket group:
    Critical
    Resolution:
    Resolved
    Summary:
    compiling CD-Hit under x86_64-suse-linux: not possible !
    Original submission:
    When I try to compile cd-hit-2006-0411 under x86_64-suse-linux, I got the following warnins and fatal errors:

    g++ -O2 mcd-hit.o cd-hi-class.o -o mcd-hit
    /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: warning: i386 architecture of input file `mcd-hit.o' is incompatible with i386:x86-64 output
    /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: warning: i386 architecture of input file `cd-hi-class.o' is incompatible with i386:x86-64 output
    mcd-hit.o(.text+0xa25): In function `read_swap_iseq(int, char*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::read(char*, int)'
    mcd-hit.o(.text+0xa47): In function `read_swap_iseq(int, char*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::read(char*, int)'
    mcd-hit.o(.text+0xa7a): In function `read_swap_iseq(int, char*)':
    : undefined reference to `operator new[](unsigned)'
    mcd-hit.o(.text+0xa9f): In function `read_swap_iseq(int, char*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::read(char*, int)'
    mcd-hit.o(.text+0xc17): In function `read_swap_iseq(int, char*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::read(char*, int)'
    mcd-hit.o(.text+0x18ae): In function `main':
    : undefined reference to `operator new[](unsigned)'
    mcd-hit.o(.text+0x18cb): In function `main':
    : undefined reference to `operator new[](unsigned)'
    mcd-hit.o(.text+0x18e8): In function `main':
    : undefined reference to `operator new[](unsigned)'
    mcd-hit.o(.text+0x1905): In function `main':
    : undefined reference to `operator new[](unsigned)'
    mcd-hit.o(.text+0x191f): In function `main':
    : undefined reference to `operator new[](unsigned)'
    mcd-hit.o(.text+0x1939): more undefined references to `operator new[](unsigned)' follow
    cd-hi-class.o(.text+0x2d83): In function `db_seq_no_test(std::basic_ifstream<char, std::char_traits<char> >&)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::read(char*, int)'
    cd-hi-class.o(.text+0x2e1a): In function `old_clstr_read_in(std::basic_ifstream<char, std::char_traits<char> >&, int&, int&, int*, int*, int*, char*, int*, int*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::getline(char*, int, char)'
    cd-hi-class.o(.text+0x317a): In function `db_read_des(std::basic_ifstream<char, std::char_traits<char> >&, int, int, char**)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::getline(char*, int, char)'
    cd-hi-class.o(.text+0x327d): In function `db_read_des(std::basic_ifstream<char, std::char_traits<char> >&, int, int, char**)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x32e4): In function `db_read_des(std::basic_ifstream<char, std::char_traits<char> >&, int, int, char**)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x33b2): In function `db_read_and_write(std::basic_ifstream<char, std::char_traits<char> >&, std::basic_ofstream<char, std::char_traits<char> >&, int, int, char**, int*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::getline(char*, int, char)'
    cd-hi-class.o(.text+0x34a4): In function `db_read_and_write(std::basic_ifstream<char, std::char_traits<char> >&, std::basic_ofstream<char, std::char_traits<char> >&, int, int, char**, int*)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x35a4): In function `db_read_and_write(std::basic_ifstream<char, std::char_traits<char> >&, std::basic_ofstream<char, std::char_traits<char> >&, int, int, char**, int*)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x367d): In function `db_read_in2_old(std::basic_ifstream<char, std::char_traits<char> >&, int, int&, char**, int*, int, int*, int*, int*, int*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::getline(char*, int, char)'
    cd-hi-class.o(.text+0x3788): In function `db_read_in2_old(std::basic_ifstream<char, std::char_traits<char> >&, int, int&, char**, int*, int, int*, int*, int*, int*)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x3841): In function `db_read_in2_old(std::basic_ifstream<char, std::char_traits<char> >&, int, int&, char**, int*, int, int*, int*, int*, int*)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x3c41): In function `db2_seqs_divide_segs(int, int, int*, char**, long long, int, int&, int*, int*)':
    : undefined reference to `__divdi3'
    cd-hi-class.o(.text+0x3e0c): In function `sort_seqs_divide_segs(int, int, int*, int*, char**, long long, int, int&, int*, int*, char (*) [1280], char*)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x3e1e): In function `sort_seqs_divide_segs(int, int, int*, int*, char**, long long, int, int&, int*, int*, char (*) [1280], char*)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x413f): In function `sort_seqs_divide_segs(int, int, int*, int*, char**, long long, int, int&, int*, int*, char (*) [1280], char*)':
    : undefined reference to `__divdi3'
    cd-hi-class.o(.text+0x48f3): In function `old_clstr_seq_no_test(std::basic_ifstream<char, std::char_traits<char> >&)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::read(char*, int)'
    cd-hi-class.o(.text+0x49c1): In function `db_read_in_lenf(std::basic_ifstream<char, std::char_traits<char> >&, int&, int*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::getline(char*, int, char)'
    cd-hi-class.o(.text+0x4b4a): In function `db_read_in_len(std::basic_ifstream<char, std::char_traits<char> >&, int, int&, int*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::getline(char*, int, char)'
    cd-hi-class.o(.text+0x4d01): In function `db_read_in_old(std::basic_ifstream<char, std::char_traits<char> >&, int, int&, char**, int*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::getline(char*, int, char)'
    cd-hi-class.o(.text+0x4e1a): In function `db_read_in_old(std::basic_ifstream<char, std::char_traits<char> >&, int, int&, char**, int*)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x4e7b): In function `db_read_in_old(std::basic_ifstream<char, std::char_traits<char> >&, int, int&, char**, int*)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x509f): In function `db_read_in(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::getline(char*, int, char)'
    cd-hi-class.o(.text+0x514c): In function `db_read_in(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*)':
    : undefined reference to `std::basic_ostream<char, std::char_traits<char> >::write(char const*, int)'
    cd-hi-class.o(.text+0x521e): In function `db_read_in(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*)':
    : undefined reference to `std::basic_ostream<char, std::char_traits<char> >::write(char const*, int)'
    cd-hi-class.o(.text+0x523f): In function `db_read_in(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*)':
    : undefined reference to `std::basic_ostream<char, std::char_traits<char> >::write(char const*, int)'
    cd-hi-class.o(.text+0x52d1): In function `db_read_in(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x53bf): In function `db_read_in(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x54a0): In function `db_read_in(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*)':
    : undefined reference to `std::basic_ostream<char, std::char_traits<char> >::write(char const*, int)'
    cd-hi-class.o(.text+0x54bb): In function `db_read_in(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*)':
    : undefined reference to `std::basic_ostream<char, std::char_traits<char> >::write(char const*, int)'
    cd-hi-class.o(.text+0x5842): In function `IDX_TBL::read_tbl(char*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::read(char*, int)'
    cd-hi-class.o(.text+0x5865): In function `IDX_TBL::read_tbl(char*)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x5880): In function `IDX_TBL::read_tbl(char*)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x58ab): In function `IDX_TBL::read_tbl(char*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::read(char*, int)'
    cd-hi-class.o(.text+0x58cf): In function `IDX_TBL::read_tbl(char*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::read(char*, int)'
    cd-hi-class.o(.text+0x5c4a): In function `read_swap_iseq1(int, char**, char*, int, char*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::read(char*, int)'
    cd-hi-class.o(.text+0x5c66): In function `read_swap_iseq1(int, char**, char*, int, char*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::read(char*, int)'
    cd-hi-class.o(.text+0x5c80): In function `read_swap_iseq1(int, char**, char*, int, char*)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x5ca7): In function `read_swap_iseq1(int, char**, char*, int, char*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::read(char*, int)'
    cd-hi-class.o(.text+0x5ffd): In function `IDX_TBL::write_tbl(char*)':
    : undefined reference to `std::basic_ostream<char, std::char_traits<char> >::write(char const*, int)'
    cd-hi-class.o(.text+0x6026): In function `IDX_TBL::write_tbl(char*)':
    : undefined reference to `std::basic_ostream<char, std::char_traits<char> >::write(char const*, int)'
    cd-hi-class.o(.text+0x604a): In function `IDX_TBL::write_tbl(char*)':
    : undefined reference to `std::basic_ostream<char, std::char_traits<char> >::write(char const*, int)'
    cd-hi-class.o(.text+0x63fb): In function `db_read_in2(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*, int, int*, int*, int*, int*)':
    : undefined reference to `std::basic_istream<char, std::char_traits<char> >::getline(char*, int, char)'
    cd-hi-class.o(.text+0x64eb): In function `db_read_in2(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*, int, int*, int*, int*, int*)':
    : undefined reference to `std::basic_ostream<char, std::char_traits<char> >::write(char const*, int)'
    cd-hi-class.o(.text+0x6506): In function `db_read_in2(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*, int, int*, int*, int*, int*)':
    : undefined reference to `std::basic_ostream<char, std::char_traits<char> >::write(char const*, int)'
    cd-hi-class.o(.text+0x6656): In function `db_read_in2(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*, int, int*, int*, int*, int*)':
    : undefined reference to `std::basic_ostream<char, std::char_traits<char> >::write(char const*, int)'
    cd-hi-class.o(.text+0x6749): In function `db_read_in2(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*, int, int*, int*, int*, int*)':
    : undefined reference to `std::basic_ostream<char, std::char_traits<char> >::write(char const*, int)'
    cd-hi-class.o(.text+0x676a): In function `db_read_in2(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*, int, int*, int*, int*, int*)':
    : undefined reference to `std::basic_ostream<char, std::char_traits<char> >::write(char const*, int)'
    cd-hi-class.o(.text+0x6812): In function `db_read_in2(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*, int, int*, int*, int*, int*)':
    : undefined reference to `operator new[](unsigned)'
    cd-hi-class.o(.text+0x68ce): In function `db_read_in2(std::basic_ifstream<char, std::char_traits<char> >&, char*, int, int, int&, char**, int*, int, int*, int*, int*, int*)':
    : undefined reference to `operator new[](unsigned)'
    /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: BFD 2.15.90.0.1.1 20040303 (SuSE Linux) internal error, aborting at ../../bfd/reloc.c line 4274 in bfd_generic_get_relocated_section_contents

    /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld: Please report this bug.

    Does anybody else tried to compile on this architecture before ?
    Please log in to add comments and receive followups via email.
    Followups
    Comment Date By
    9b65dc3b07a361a375d263e945c6dd04
    <a href="http://njdokj.info/85148bbfee5cba218ad75f83009b07a6/9b65dc3b07a361a375d263e945c6dd04"> http://njdokj.info/85148bbfee5cba218ad75f83009b07a6/9b65dc3b07a361a375d263e945c6dd04 </a>
    http://njdokj.info/85148bbfee5cba218ad75f83009b07a6/9b65dc3b07a361a375d263e945c6dd04
    [url]http://njdokj.info/85148bbfee5cba218ad75f83009b07a6/9b65dc3b07a361a375d263e945c6dd04[url]
    07/31/08 03:47 unset
    I was searching for info on whether our compiled code is okay even though we get the same warnings. We had a similar problem compiling Sybase access software (thought it did compile). The issue was that the sbyase libraries we had were not 64-bit compatible. So the fix is get the 64-bit libraries OR, with C, compile with the -m32 switch. 01/04/07 11:45 unset
    No results for "Dependent on ticket"
    No results for "Dependent on Task"
    No other tickets are dependent on this ticket
    Ticket change history
    Field Old value Date By
    status_id Pending 05/16/11 00:56 liwz
    resolution_id Unset 05/16/11 00:56 liwz
    close_date 12/31/69 19:00 05/16/11 00:56 liwz

     

    Copyright © 2019 · Scilico, LLC