Compilation Error 1 after ‘make gcc’ command

[Anonymous]

Hi,

I am new to Rosetta.

While compiling Rosetta with the ‘make gcc’ command, I got an error

undefined reference to `_deflate’
collect2: ld returned 1 exit status
make: *** [rosetta.gcc] Error 1

I am pasting the whole page below.

Could someone please let me know how could I correct this error?

I am running it in cygwin (linux like environment) in Windows.

Thank you.

---

$ make gcc

ranlib ‘lib/i686-pc-linux-gnu/libz.a’
g++ -static -Llib .gcc.version_rosetta.o .gcc.gl_graphics.o .gcc.pose.o .gcc.pose_dna.o .gcc.aa_name_conversion.o .gcc.aaproperties_pack.o .gcc.abrelax.o .gcc.add_pser.o .gcc.after_opts.o .gcc.analyze_interface_ddg.o .gcc.analyze_interface_ddg_ns.o .gcc.angles.o .gcc.angles_ns.o .gcc.antibody_modeling.o .gcc.are_they_neighbors.o .gcc.assemble_domains.o .gcc.atom_chem.o .gcc.atom_descriptor.o .gcc.atom_tree_minimize.o .gcc.atom_tree_routines.o .gcc.barcode_classes.o .gcc.barcode_stats.o .gcc.barcode_stats_classes.o .gcc.bond_angle.o .gcc.bonds_class.o .gcc.ccd_functions.o .gcc.cenlist.o .gcc.chuck.o .gcc.cluster_fragments.o .gcc.cluster_mutE.o .gcc.ConformerLibHandler.o .gcc.constraints.o .gcc.CorrelatedSimAnnealer.o .gcc.count_pair.o .gcc.counters.o .gcc.crankshaft.o .gcc.csa_main.o .gcc.cst_allow_move.o .gcc.cst_countpair.o .gcc.cst_descriptor.o .gcc.cst_functions.o .gcc.cst_packer.o .gcc.cst_set.o .gcc.current_pose.o .gcc.current_packer_cst.o .gcc.DebuggingAnnealer.o .gcc.decoy_features.o .gcc.decoystats.o .gcc.decoystats_classes.o .gcc.decoystats_interface.o .gcc.decoystats_interface_classes.o .gcc.decoystats_ns.o .gcc.design.o .gcc.design_structure.o .gcc.DesignMap.o .gcc.diagnostics_rosetta.o .gcc.dipolar.o .gcc.dipolar_ns.o .gcc.DirectedSimAnnealer.o .gcc.disulfides.o .gcc.DnaPose.o .gcc.dna.o .gcc.dna_classes.o .gcc.dna_am_min.o .gcc.dna_motifs.o .gcc.dna_motifs_ns.o .gcc.dna_ns.o .gcc.dock_ensemble.o .gcc.dock_fab.o .gcc.dock_loops.o .gcc.dock_loops_ns.o .gcc.dock_pivot.o .gcc.dock_pivot_ns.o .gcc.dock_structure.o .gcc.docking.o .gcc.docking_constraints.o .gcc.docking_db.o .gcc.dock_loop_ensemble.o .gcc.dock_loop_ensemble_ns.o .gcc.docking_minimize.o .gcc.docking_minimize_ns.o .gcc.docking_movement.o .gcc.docking_ns.o .gcc.docking_score.o .gcc.docking_scoring.o .gcc.docking_unbound.o .gcc.DomainInsertionMode.o .gcc.domins_fullatom.o .gcc.domins_ns.o .gcc.domins_score.o .gcc.dssp.o .gcc.dummy_model.o .gcc.dunbrack_pack.o .gcc.Dunbrack4D.o .gcc.Dunbrack5D.o .gcc.electron_density.o .gcc.elliptic_msd.o .gcc.enzyme.o .gcc.enzyme_ns.o .gcc.EquivResfileReader.o .gcc.etable.o .gcc.etable_class.o .gcc.etable_manager.o .gcc.evolve.o .gcc.evolve_ns.o .gcc.favor_residue_ns.o .gcc.featurizer.o .gcc.featurizer_classes.o .gcc.fibril.o .gcc.files_paths.o .gcc.filters.o .gcc.FixbbSimAnnealer.o .gcc.Flag.o .gcc.flexibility.o .gcc.fold_abinitio.o .gcc.fold_abinitio_csa.o .gcc.fold_constraints.o .gcc.fold_loops.o .gcc.fold_membrane.o .gcc.fold_tree.o .gcc.force_barcode.o .gcc.fragment_class.o .gcc.fragments.o .gcc.fragments_ns.o .gcc.fragments_pose.o .gcc.free_energy_estimate.o .gcc.fullatom.o .gcc.fullatom_energies.o .gcc.fullatom_energy.o .gcc.fullatom_extra_props.o .gcc.fullatom_id.o .gcc.fullatom_sasa.o .gcc.fullatom_sasa_ns.o .gcc.fullatom_setup.o .gcc.ga_seq_opt.o .gcc.gb_elec.o .gcc.gb_elec_ns.o .gcc.geometric_solvation.o .gcc.geometric_solvation_ns.o .gcc.gunn.o .gcc.grid_docking.o .gcc.hbonds.o .gcc.hbonds_geom.o .gcc.hbonds_ns.o .gcc.homolog_distances.o .gcc.HBondSet.o .gcc.idealize.o .gcc.initialize.o .gcc.input_pdb.o .gcc.int_fullatom_energies.o .gcc.InteractionGraphBase.o .gcc.InteractionGraphSupport.o .gcc.interface.o .gcc.ise.o .gcc.ise_movies.o .gcc.jmp_directions.o .gcc.jmp_maps.o .gcc.job_distributor.o .gcc.jump_classes.o .gcc.jumping_diagnostics.o .gcc.jumping_loops.o .gcc.jumping_minimize.o .gcc.jumping_ns.o .gcc.jumping_pairings.o .gcc.jumping_pairings_ns.o .gcc.jumping_refold.o .gcc.jumping_util.o .gcc.kin_atom.o .gcc.kin_atom_bad_return_vals.o .gcc.kin_atom_tree.o .gcc.kin_bonded_atom.o .gcc.kin_bonded_atom_FS.o .gcc.kin_coords.o .gcc.kin_fixed_atom.o .gcc.kin_id.o .gcc.kin_jump_atom.o .gcc.kin_jump_atom_FS.o .gcc.kin_min.o .gcc.kin_moving_atom.o .gcc.kin_stub.o .gcc.kin_test.o .gcc.kin_util.o .gcc.knots.o .gcc.LazyInteractionGraph.o .gcc.lig_looprlx.o .gcc.ligand.o .gcc.ligand_ns.o .gcc.LinearMemoryInteractionGraph.o .gcc.loop_class.o .gcc.loop_relax.o .gcc.loops.o .gcc.loops_ns.o .gcc.main.o .gcc.make_pdb.o .gcc.maps.o .gcc.maps_ns.o .gcc.map_sequence.o .gcc.maxsub.o .gcc.maxsub_threshold.o .gcc.MinimalistInteractionGraph.o .gcc.minimize.o .gcc.minimize_chi.o .gcc.minimize_ns.o .gcc.min_debug_ns.o .gcc.misc.o .gcc.misc_removal.o .gcc.monte_carlo.o .gcc.MultiCoolAnnealer.o .gcc.multistate_design.o .gcc.namespace_assemble_options.o .gcc.namespace_best_position_init_common.o .gcc.namespace_cold.o .gcc.namespace_fa_lj_rep_slope_setting.o .gcc.namespace_findUU_public.o .gcc.namespace_fullatom_flag.o .gcc.namespace_fullatom_init.o .gcc.namespace_lj_etable_settings.o .gcc.namespace_low_pose.o .gcc.namespace_options.o .gcc.namespace_rotamers_setting.o .gcc.namespace_trajectory.o .gcc.native.o .gcc.nblist.o .gcc.nblist_ns.o .gcc.NegativeDesign.o .gcc.OneGeneTwoProteins.o .gcc.OnTheFlyInteractionGraph.o .gcc.options.o .gcc.orient_rms.o .gcc.output_decoy.o .gcc.pack.o .gcc.pack_bump_selector.o .gcc.pack_bump_selector_ns.o .gcc.packer_weights.o .gcc.PackerTask.o .gcc.PackerTaskResidueWeights.o .gcc.packing_measures.o .gcc.ParallelSimAnneal.o .gcc.ParallelSimAnnealBase.o .gcc.param.o .gcc.param_aa.o .gcc.param_pack.o .gcc.param_rotamer_trie.o .gcc.param_torsion.o .gcc.PDInteractionGraph.o .gcc.pdb.o .gcc.pdbstatistics_pack.o .gcc.pdbstats.o .gcc.pdbstats_ns.o .gcc.pH_main.o .gcc.pH_ns.o .gcc.pKa_mode.o .gcc.planes.o .gcc.planes_ns.o .gcc.pose_abinitio.o .gcc.pose_backrub_controller.o .gcc.pose_backrub.o .gcc.pose_benchmark.o .gcc.pose_constraints.o .gcc.pose_correlated_angles.o .gcc.pose_design.o .gcc.pose_disulfides.o .gcc.pose_docking.o .gcc.pose_docking_flexible.o .gcc.pose_fold_and_dock.o .gcc.pose_idealize.o .gcc.pose_io.o .gcc.pose_jjh_loops.o .gcc.pose_ligand.o .gcc.pose_looping.o .gcc.pose_loops.o .gcc.pose_main.o .gcc.pose_movie.o .gcc.pose_param.o .gcc.pose_peptide_docking.o .gcc.pose_private.o .gcc.pose_relax.o .gcc.pose_rms.o .gcc.pose_rna.o .gcc.pose_rna_csa.o .gcc.pose_rna_featurizer.o .gcc.pose_rna_fullatom.o .gcc.pose_rna_fragments.o .gcc.pose_rna_fragments_classes.o .gcc.pose_rna_jumping.o .gcc.pose_rna_ns.o .gcc.pose_rna_pdbstats.o .gcc.pose_rotamer_controller.o .gcc.pose_rotamer_trials.o .gcc.pose_sse.o .gcc.pose_symmetric_docking.o .gcc.pose_util.o .gcc.pose_vdw.o .gcc.PrecomputedInteractionGraph.o .gcc.prof.o .gcc.protein_graphics.o .gcc.ramachandran.o .gcc.random_numbers.o .gcc.rb_class.o .gcc.rb_relax.o .gcc.read_aa_ss.o .gcc.read_aaproperties.o .gcc.read_paths.o .gcc.recover.o .gcc.refine_structure.o .gcc.refold.o .gcc.refold_ns.o .gcc.relax.o .gcc.relax_structure.o .gcc.remodel.o .gcc.repeat.o .gcc.ResidueData.o .gcc.rms.o .gcc.rotamer_descriptor.o .gcc.Rotamer.o .gcc.RotamerAssigningAnnealer.o .gcc.RotamerDots.o .gcc.RotamerOptions.o .gcc.RotamerSet.o .gcc.rotamer_explosion.o .gcc.rotamer_functions.o .gcc.rotamer_trial_energies.o .gcc.rotamer_trials.o .gcc.rotamer_trie_calc_energies.o .gcc.saxs_model.o .gcc.runlevel.o .gcc.score.o .gcc.score_data.o .gcc.score_ns.o .gcc.sheet_filter.o .gcc.sidechain_bond_angles.o .gcc.silent_input.o .gcc.smallmove.o .gcc.shotgun.o .gcc.SimAnnealerBase.o .gcc.socketcom.o .gcc.SplicedProtein.o .gcc.spline.o .gcc.ssblocks.o .gcc.start.o .gcc.status.o .gcc.structure.o .gcc.surface.o .gcc.SurfaceMode.o .gcc.symmetric_design.o .gcc.symmetry_info.o .gcc.T32S3.o .gcc.taboo_search.o .gcc.template_pack.o .gcc.termini.o .gcc.tether.o .gcc.tether_ns.o .gcc.timer.o .gcc.torsion_bbmove_trials.o .gcc.trajectory.o .gcc.util_basic.o .gcc.util_interpolate.o .gcc.util_vector.o .gcc.vdw.o .gcc.void.o .gcc.void_ns.o .gcc.watchdog.o .gcc.water.o .gcc.water_ns.o .gcc.weights_manager.o .gcc.wobble.o .gcc.XUtilities.o .gcc.triangleIterator.o .gcc.marchingCubes.o .gcc.dim.o .gcc.char.functions.o .gcc.Cstring.o .gcc.Dimension.o .gcc.DimensionExpression.o .gcc.DimensionExpressionRef.o .gcc.DynamicIndexRange.o .gcc.formatted.i.o .gcc.formatted.o.o .gcc.Fstring.o .gcc.IndexRange.o .gcc.Observer.o .gcc.ObserverMulti.o .gcc.Star.o .gcc.string.functions.o .gcc.Time_Date.o .gcc.ObserverGraph.o .gcc.ObserverMediator.o .gcc.constants.o .gcc.basic_sys_util.o .gcc.exit.o .gcc.file_sys_util.o .gcc.FileName.o .gcc.gzip_util.o .gcc.PathName.o .gcc.izstream.o .gcc.ocstream.o .gcc.ozstream.o .gcc.OptionCollection.o .gcc.OptionKeys.o .gcc.ReferenceCount.o .gcc.ReferenceCountMI_.o .gcc.boinc_util.o lib/i686-pc-linux-gnu/libz.a -o rosetta.gcc
.gcc.pose.o:pose.cc:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE11reset_stateEv[zlib_stream::basic_zip_streambuf, std::allocator, unsigned char, std::allocator >::reset_state()]+0x34): undefined reference to `_deflateReset’
.gcc.pose.o:pose.cc:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcESaIcEhSaIhEED1Ev[zlib_stream::basic_unzip_streambuf, std::allocator, unsigned char, std::allocator >::~basic_unzip_streambuf()]+0x17): undefined reference to `_inflateEnd’
.gcc.pose.o:pose.cc:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcESaIcEhSaIhEED0Ev[zlib_stream::basic_unzip_streambuf, std::allocator, unsigned char, std::allocator >::~basic_unzip_streambuf()]+0x17): undefined reference to `_inflateEnd’
.gcc.pose.o:pose.cc:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE5flushEi[zlib_stream::basic_zip_streambuf, std::allocator, unsigned char, std::allocator >::flush(int)]+0x47): undefined reference to `_crc32′
.gcc.pose.o:pose.cc:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE5flushEi[zlib_stream::basic_zip_streambuf, std::allocator, unsigned char, std::allocator >::flush(int)]+0x69): undefined reference to `_deflate’
.gcc.pose.o:pose.cc:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcESaIcEhSaIhEEC1ERSijjj[zlib_stream::basic_unzip_streambuf, std::allocator, unsigned char, std::allocator >::basic_unzip_streambuf(std::basic_istream >&, unsigned int, unsigned int, unsigned int)]+0x13a): undefined reference to `_inflateInit2_’
.gcc.pose.o:pose.cc:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcESaIcEhSaIhEE17unzip_from_streamEPci[zlib_stream::basic_unzip_streambuf, std::allocator, unsigned char, std::allocator >::unzip_from_stream(char*, int)]+0x30): undefined reference to `_inflate’
.gcc.pose.o:pose.cc:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcESaIcEhSaIhEE17unzip_from_streamEPci[zlib_stream::basic_unzip_streambuf, std::allocator, unsigned char, std::allocator >::unzip_from_stream(char*, int)]+0x86): undefined reference to `_crc32′
.gcc.ozstream.o:ozstream.cc:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEED1Ev[zlib_stream::basic_zip_streambuf, std::allocator, unsigned char, std::allocator >::~basic_zip_streambuf()]+0x2a): undefined reference to `_deflateEnd’
.gcc.ozstream.o:ozstream.cc:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEED0Ev[zlib_stream::basic_zip_streambuf, std::allocator, unsigned char, std::allocator >::~basic_zip_streambuf()]+0x2a): undefined reference to `_deflateEnd’
.gcc.ozstream.o:ozstream.cc:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEEC1ERSojNS_9EStrategyEjjj[zlib_stream::basic_zip_streambuf, std::allocator, unsigned char, std::allocator >::basic_zip_streambuf(std::basic_ostream >&, unsigned int, zlib_stream::EStrategy, unsigned int, unsigned int, unsigned int)]+0x18c): undefined reference to `_deflateInit2_’
.gcc.ozstream.o:ozstream.cc:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE13zip_to_streamEPci[zlib_stream::basic_zip_streambuf, std::allocator, unsigned char, std::allocator >::zip_to_stream(char*, int)]+0x3e): undefined reference to `_crc32′
.gcc.ozstream.o:ozstream.cc:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE13zip_to_streamEPci[zlib_stream::basic_zip_streambuf, std::allocator, unsigned char, std::allocator >::zip_to_stream(char*, int)]+0x5c): undefined reference to `_deflate’
collect2: ld returned 1 exit status
make: *** [rosetta.gcc] Error 1

[Anonymous]

Hi,

Which version of gcc compiler are You using?
I had some problems with compiling too, but then I switched to an older version of gcc and it compiled successfully.

Do you have zlib library on your disk?

Bob3k

[Author]

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