andante compilation error

gistfile1.sh

dhcp-172-17-187-12:Andante david$ make
gcc   -I.  -I../../lm  -I../liborc   -c -o alloc_structures.o alloc_structures.c
gcc   -I.  -I../../lm  -I../liborc   -c -o andante.o andante.c
gcc   -I.  -I../../lm  -I../liborc   -c -o assign_radii.o assign_radii.c
gcc   -I.  -I../../lm  -I../liborc   -c -o borrow_chi.o borrow_chi.c
gcc   -I.  -I../../lm  -I../liborc   -c -o build_stuff.o build_stuff.c
gcc   -I.  -I../../lm  -I../liborc   -c -o check_rotamers.o check_rotamers.c
gcc   -I.  -I../../lm  -I../liborc   -c -o combo_utility.o combo_utility.c
gcc   -I.  -I../../lm  -I../liborc   -c -o create_rotamer_library.o create_rotamer_library.c
gcc   -I.  -I../../lm  -I../liborc   -c -o d5_util1.o d5_util1.c
gcc   -I.  -I../../lm  -I../liborc   -c -o dee_functions.o dee_functions.c
gcc   -I.  -I../../lm  -I../liborc   -c -o dee_functions2.o dee_functions2.c
gcc   -I.  -I../../lm  -I../liborc   -c -o dee_sa_combo.o dee_sa_combo.c
gcc   -I.  -I../../lm  -I../liborc   -c -o disul5.o disul5.c
gcc   -I.  -I../../lm  -I../liborc   -c -o dyn_clash_array.o dyn_clash_array.c
gcc   -I.  -I../../lm  -I../liborc   -c -o init_options.o init_options.c
gcc   -I.  -I../../lm  -I../liborc   -c -o input.o input.c
gcc   -I.  -I../../lm  -I../liborc   -c -o morph.o morph.c
gcc   -I.  -I../../lm  -I../liborc   -c -o penult_lib_choose.o penult_lib_choose.c
gcc   -I.  -I../../lm  -I../liborc   -c -o preprocess_H3.o preprocess_H3.c
gcc   -I.  -I../../lm  -I../liborc   -c -o ran2.o ran2.c
gcc   -I.  -I../../lm  -I../liborc   -c -o read_tem_file.o read_tem_file.c
gcc   -I.  -I../../lm  -I../liborc   -c -o restrict12.o restrict12.c
gcc   -I.  -I../../lm  -I../liborc   -c -o restrict_rotamers.o restrict_rotamers.c
gcc   -I.  -I../../lm  -I../liborc -o Andante  alloc_structures.o  andante.o  assign_radii.o  borrow_chi.o  borrowed_clashes.o  build_stuff.o  check_rotamers.o  clash_check.o  combo_utility.o  create_rotamer_library.o  d5_util1.o  d5_util2.o  dee_functions.o  dee_functions2.o  dee_sa_combo.o  dee_utilty.o  disul4.o  disul5.o  disul5_data.o  dyn_clash_array.o  hbond_acceptor.o  init_options.o  input.o  keep_connect.o  load_bb_lib.o  morph.o  morph_utility.o  no_borrow.o  penult_lib_choose.o  pid_choose.o  preprocess_H3.o  ran2.o  read_ali.o  read_tem_file.o  reset_clear.o  restrict12.o  restrict_rotamers.o  sa_combos.o  user_opts_help.o  utility.o  utility2.o  utility3.o  utility4.o -lm  ../liborc/liborc.a
ld: warning: ld: warning: ld: warning: ld: warning: ignoring file borrowed_clashes.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): borrowed_clashes.oignoring file dee_utilty.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): dee_utilty.oignoring file clash_check.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): clash_check.oignoring file d5_util2.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): d5_util2.o



ld: warning: ignoring file disul4.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): disul4.o
ld: warning: ignoring file load_bb_lib.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): load_bb_lib.o
ld: warning: ignoring file disul5_data.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): disul5_data.o
ld: warning: ignoring file morph_utility.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): morph_utility.o
ld: warning: ignoring file no_borrow.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): no_borrow.o
ld: warning: ignoring file read_ali.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): read_ali.o
ld: warning: ignoring file pid_choose.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): pid_choose.o
ld: warning: ignoring file keep_connect.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): keep_connect.o
ld: warning: ignoring file hbond_acceptor.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): hbond_acceptor.o
ld: warning: ignoring file utility.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): utility.o
ld: warning: ignoring file user_opts_help.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): user_opts_help.o
ld: warning: ignoring file utility4.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): utility4.o
ld: warning: ignoring file utility2.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): utility2.o
ld: warning: ignoring file reset_clear.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): reset_clear.o
ld: warning: ignoring file sa_combos.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): sa_combos.o
ld: warning: ignoring file utility3.o, file was built for unsupported file format ( 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 0x00 ) which is not the architecture being linked (x86_64): utility3.o
ld: warning: ignoring file ../liborc/liborc.a, file was built for archive which is not the architecture being linked (x86_64): ../liborc/liborc.a
Undefined symbols for architecture x86_64:
  "_Alloc_Heavy_Atoms", referenced from:
      _check_atom_allocation in input.o
  "_AssignAtom", referenced from:
      _mutant_lib_rotamers in build_stuff.o
      _check_atom_allocation in input.o
      _load_parent_coordinates in input.o
  "_Build_missing_CB", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
      _morph in morph.o
  "_CB_defined", referenced from:
      _build_rot in build_stuff.o
      _CB_d_OK in d5_util1.o
      _quick_check in d5_util1.o
  "_CC_DATA", referenced from:
      _chi2_penalty in d5_util1.o
      _CA_d_OK in d5_util1.o
      _CB_d_OK in d5_util1.o
      _SG_d_OK in d5_util1.o
      _quick_check in d5_util1.o
      _score_vdw_clashes in disul5.o
      _score_cc_orient in disul5.o
      ...
  "_CYS_clash_HETATMS", referenced from:
      _new_disulphide in disul5.o
  "_Calc_Distance", referenced from:
      _CA_d_OK in d5_util1.o
      _CB_d_OK in d5_util1.o
      _quick_check in d5_util1.o
      _score_vdw_clashes in disul5.o
  "_CreateFRAGMENT", referenced from:
      _morph in morph.o
  "_DSP", referenced from:
      _new_disulphide in disul5.o
  "_FreeFRAGMENT", referenced from:
      _borrow_chi1 in borrow_chi.o
      _morph in morph.o
      _preprocess_H3_data in preprocess_H3.o
  "_ORC_MODAA_HANDLING", referenced from:
      _main in andante.o
  "_OutputPDB", referenced from:
      _borrow_chi1 in borrow_chi.o
      _build_mutant_residue_rotamers in build_stuff.o
      _check_rotamers in check_rotamers.o
      _create_rotamer_library in create_rotamer_library.o
      _morph in morph.o
  "_RES_CheckAtomOrder", referenced from:
      _check_atom_allocation in input.o
  "_ReadPDB", referenced from:
      _borrow_chi1 in borrow_chi.o
      _check_rotamers in check_rotamers.o
      _create_rotamer_library in create_rotamer_library.o
      _load_parent_coordinates in input.o
      _preprocess_H3_data in preprocess_H3.o
  "_ResIndex", referenced from:
      _assign_rotamer_atom_radii in assign_radii.o
      _check_atom_allocation in input.o
      _load_parent_coordinates in input.o
  "_SA_combos", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
     (maybe you meant: _dee_SA_combos)
  "_SeqIndex", referenced from:
      _mutant_lib_rotamers in build_stuff.o
      _check_atom_allocation in input.o
      _load_parent_coordinates in input.o
      _update_parent_data in input.o
  "_SeqRes", referenced from:
      _mutant_lib_rotamers in build_stuff.o
  "_UpdateDerivedPDB", referenced from:
      _borrow_chi1 in borrow_chi.o
      _check_rotamers in check_rotamers.o
      _create_rotamer_library in create_rotamer_library.o
      _update_parent_data in input.o
  "_acc_donor_library_rotamers", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_add_Esingle", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_alloc_morph_coord_memory", referenced from:
      _morph in morph.o
  "_anything_undefined_check", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_approx_CC_bonds4", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_assign_PDB_hbond_designation", referenced from:
      _borrow_chi1 in borrow_chi.o
      _check_rotamers in check_rotamers.o
      _create_rotamer_library in create_rotamer_library.o
  "_assign_SYBYL_Radii", referenced from:
      _borrow_chi1 in borrow_chi.o
      _check_rotamers in check_rotamers.o
      _create_rotamer_library in create_rotamer_library.o
  "_assign_sec_str", referenced from:
      _borrow_chi1 in borrow_chi.o
      _check_rotamers in check_rotamers.o
      _create_rotamer_library in create_rotamer_library.o
  "_assign_target_pdb_ali_index", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
      _morph in morph.o
  "_auto_check_gaps", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
      _preprocess_H3_data in preprocess_H3.o
  "_back_bone_atom_clashes", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_calc_disulphide_variables", referenced from:
      _new_disulphide in disul5.o
  "_check_parent_str_ali_match", referenced from:
      _load_parent_coordinates in input.o
      _update_parent_data in input.o
  "_check_str_ali_match", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_chi_ang_diff", referenced from:
      _check_rotamers in check_rotamers.o
      _diff_flip_chi_check in check_rotamers.o
      _set_restrict_chi12_rotamers in restrict12.o
      _set_restrict_chi1_rotamers in restrict_rotamers.o
  "_choose_chi1", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_choose_chi12", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_choose_chi123", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_choose_chi1234", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_clean_sidechain_coords", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_clear_initial_coords", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_cmd_options", referenced from:
      _main in andante.o
  "_color_conserved", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_color_single", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_conserved_check", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_energy", referenced from:
      _score_vdw_clashes in disul5.o
  "_estimate_rot_clashes", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_first_check_for_user_conserved_keep", referenced from:
      _borrow_chi1 in borrow_chi.o
      _check_rotamers in check_rotamers.o
      _create_rotamer_library in create_rotamer_library.o
  "_fragment_integrity_check", referenced from:
      _borrow_chi1 in borrow_chi.o
      _check_rotamers in check_rotamers.o
      _create_rotamer_library in create_rotamer_library.o
  "_het_E_rotamer", referenced from:
      _build_mutant_residue_rotamers in build_stuff.o
  "_initialise_cc_data", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_initialise_residues", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_is_defined_atom", referenced from:
      _score_vdw_clashes in disul5.o
  "_keep_CC_connect_records", referenced from:
      _borrow_chi1 in borrow_chi.o
      _check_rotamers in check_rotamers.o
      _create_rotamer_library in create_rotamer_library.o
      _morph in morph.o
  "_load_bb_lib", referenced from:
      _borrow_chi1 in borrow_chi.o
      _check_rotamers in check_rotamers.o
      _create_rotamer_library in create_rotamer_library.o
  "_load_crescendo_data", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_load_force_ranges", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_load_pdb", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_lock_best_pair", referenced from:
      _new_disulphide in disul5.o
  "_log_best_pair", referenced from:
      _new_disulphide in disul5.o
  "_missing_bb_atom_check", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_no_borrow", referenced from:
      _main in andante.o
  "_output_user_keep_file", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_positive_chi_value", referenced from:
      _new_chi2_penalty in d5_util1.o
  "_read_SYBYL_atom_info", referenced from:
      _main in andante.o
  "_read_ali", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
      _morph in morph.o
      _preprocess_H3_data in preprocess_H3.o
  "_rebuild_keep", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_reset_conserved_status", referenced from:
      _mutant_lib_rotamers in build_stuff.o
  "_reset_sidechain_coords", referenced from:
      _mutant_lib_rotamers in build_stuff.o
      _new_disulphide in disul5.o
  "_reset_template_skip", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_residual_clash_check", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_restricted_chi12_check", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_restricted_chi1_check", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_rot_bb_E", referenced from:
      _build_mutant_residue_rotamers in build_stuff.o
  "_rot_cons_E", referenced from:
      _build_mutant_residue_rotamers in build_stuff.o
  "_rot_energies", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_sc_sc_clash", referenced from:
      _expand_clusters in combo_utility.o
      _label_interacting_groups in combo_utility.o
      _starting_clashes in combo_utility.o
      _one_useable_rot_check in combo_utility.o
      _SA_pre_calc_clashes in dee_functions2.o
  "_split_clusters", referenced from:
      _borrow_chi1 in borrow_chi.o
      _create_rotamer_library in create_rotamer_library.o
  "_what_pid_range", referenced from:
      _restrict_chi12_rotamers in restrict12.o
      _restrict_chi1_rotamers in restrict_rotamers.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make: *** [Andante] Error 1