Scanning dependencies of target bioshell [ 1%] Building CXX object src/CMakeFiles/bioshell.dir/core/BioShellEnvironment.cc.o [ 2%] Building CXX object src/CMakeFiles/bioshell.dir/core/alignment/TMAlign.cc.o [ 3%] Building CXX object src/CMakeFiles/bioshell.dir/core/alignment/Target.cc.o [ 4%] Building CXX object src/CMakeFiles/bioshell.dir/core/alignment/Template.cc.o [ 4%] Building CXX object src/CMakeFiles/bioshell.dir/core/alignment/scoring/LocalStructure5.cc.o [ 5%] Building CXX object src/CMakeFiles/bioshell.dir/core/alignment/scoring/LocalStructure7.cc.o [ 6%] Building CXX object src/CMakeFiles/bioshell.dir/core/alignment/PairwiseAlignment.cc.o [ 7%] Building CXX object src/CMakeFiles/bioshell.dir/core/alignment/on_alignment_computations.cc.o [ 8%] Building CXX object src/CMakeFiles/bioshell.dir/core/alignment/tasks/alignment_utility_tasks.cc.o [ 9%] Building CXX object src/CMakeFiles/bioshell.dir/core/alignment/scoring/Picasso3.cc.o [ 9%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/basic/Vec3.cc.o [ 10%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/basic/Vec3Cubic.cc.o [ 11%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/io/XML.cc.o [ 12%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/io/XMLElement.cc.o [ 13%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/io/ss2_io.cc.o [ 14%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/io/pir_io.cc.o [ 14%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/io/Pdb.cc.o [ 15%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/io/alignment_io.cc.o [ 16%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/io/Cif.cc.o [ 17%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/io/fasta_io.cc.o [ 18%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/io/clustalw_io.cc.o [ 19%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/io/DataTable.cc.o [ 20%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/io/load_decoys.cc.o [ 20%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/structural/PdbAtom.cc.o [ 21%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/structural/Residue.cc.o [ 22%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/structural/Chain.cc.o [ 23%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/structural/Structure.cc.o [ 24%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/structural/structure_selectors.cc.o [ 25%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/sequence/Sequence.cc.o [ 25%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/sequence/SequenceProfile.cc.o [ 26%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/sequence/SequenceFilter.cc.o [ 27%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/sequence/sequence_utils.cc.o [ 28%] Building CXX object src/CMakeFiles/bioshell.dir/core/data/sequence/ReduceSequenceAlphabet.cc.o [ 29%] Building CXX object src/CMakeFiles/bioshell.dir/core/calc/structural/classify_hec.cc.o [ 30%] Building CXX object src/CMakeFiles/bioshell.dir/core/calc/structural/TorsionBinType.cc.o [ 30%] Building CXX object src/CMakeFiles/bioshell.dir/core/calc/structural/protein_angles.cc.o [ 31%] Building CXX object src/CMakeFiles/bioshell.dir/core/calc/structural/transformations/Rototranslation.cc.o [ 32%] Building CXX object src/CMakeFiles/bioshell.dir/core/calc/structural/transformations/PairwiseCrmsd.cc.o [ 33%] Building CXX object src/CMakeFiles/bioshell.dir/core/calc/structural/transformations/PairwiseStructureComparison.cc.o [ 34%] Building CXX object src/CMakeFiles/bioshell.dir/core/calc/structural/transformations/PairwiseTMScore.cc.o [ 35%] Building CXX object src/CMakeFiles/bioshell.dir/core/calc/structural/transformations/TMScore.cc.o [ 35%] Building CXX object src/CMakeFiles/bioshell.dir/core/calc/structural/transformations/transformation_utils.cc.o [ 36%] Building CXX object src/CMakeFiles/bioshell.dir/core/calc/structural/HydrogenBondGeometry.cc.o [ 37%] Building CXX object src/CMakeFiles/bioshell.dir/core/chemical/Monomer.cc.o [ 38%] Building CXX object src/CMakeFiles/bioshell.dir/core/chemical/monomer_io.cc.o [ 39%] Building CXX object src/CMakeFiles/bioshell.dir/core/chemical/AtomicElement.cc.o [ 40%] Building CXX object src/CMakeFiles/bioshell.dir/core/chemical/BondType.cc.o [ 41%] Building CXX object src/CMakeFiles/bioshell.dir/core/chemical/ChiAnglesDefinition.cc.o [ 41%] Building CXX object src/CMakeFiles/bioshell.dir/core/chemical/molecule_utils.cc.o [ 42%] Building CXX object src/CMakeFiles/bioshell.dir/utils/io_utils.cc.o [ 43%] Building CXX object src/CMakeFiles/bioshell.dir/utils/Logger.cc.o [ 44%] Building CXX object src/CMakeFiles/bioshell.dir/utils/LogManager.cc.o [ 45%] Building CXX object src/CMakeFiles/bioshell.dir/utils/ProfilingManager.cc.o [ 46%] Building CXX object src/CMakeFiles/bioshell.dir/utils/options/OptionParser.cc.o [ 46%] Building CXX object src/CMakeFiles/bioshell.dir/utils/options/Option.cc.o [ 47%] Building CXX object src/CMakeFiles/bioshell.dir/utils/options/options.cc.o [ 48%] Building CXX object src/CMakeFiles/bioshell.dir/utils/options/input_utils.cc.o [ 49%] Building CXX object src/CMakeFiles/bioshell.dir/utils/options/select_utils.cc.o [ 50%] Building CXX object src/CMakeFiles/bioshell.dir/utils/exit.cc.o [ 51%] Building CXX object src/CMakeFiles/bioshell.dir/utils/string_utils.cc.o [ 51%] Building CXX object src/CMakeFiles/bioshell.dir/ui/tasks/Task.cc.o [ 52%] Building CXX object src/CMakeFiles/bioshell.dir/ui/tasks/Variables.cc.o [ 53%] Building CXX object src/CMakeFiles/bioshell.dir/ui/tasks/Protocol.cc.o [ 54%] Building CXX object src/CMakeFiles/bioshell.dir/ui/tasks/ProtocolTask.cc.o [ 55%] Building CXX object src/CMakeFiles/bioshell.dir/ui/tasks/FileFromTemplate.cc.o [ 56%] Building CXX object src/CMakeFiles/bioshell.dir/ui/tasks/ExternalTask.cc.o [ 56%] Building CXX object src/CMakeFiles/bioshell.dir/ui/tasks/Declare.cc.o [ 57%] Building CXX object src/CMakeFiles/bioshell.dir/ui/tasks/ForEach.cc.o [ 58%] Building CXX object src/CMakeFiles/bioshell.dir/ui/tasks/MakeDir.cc.o [ 59%] Building CXX object src/CMakeFiles/bioshell.dir/ui/tasks/ChangeDir.cc.o [ 60%] Building CXX object src/CMakeFiles/bioshell.dir/utils/web_utils.cc.o [ 61%] Building CXX object src/CMakeFiles/bioshell.dir/external/web++.cc.o [ 62%] Building CXX object src/CMakeFiles/bioshell.dir/tests/UnitTests.cc.o Linking CXX static library /home/bioshell/public_html/builds/bin/libbioshell.a [ 62%] Built target bioshell Scanning dependencies of target alignc [ 62%] Building CXX object src/CMakeFiles/alignc.dir/apps/bioshell/alignc.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/alignc [ 62%] Built target alignc Scanning dependencies of target ar_mc [ 63%] Building CXX object src/CMakeFiles/ar_mc.dir/tests/simulations/ar_mc.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/ar_mc [ 63%] Built target ar_mc Scanning dependencies of target biosimulations [ 63%] Building CXX object src/CMakeFiles/biosimulations.dir/simulations/cartesian/ff/mf/MeanFieldDistribution1D.cc.o [ 64%] Building CXX object src/CMakeFiles/biosimulations.dir/simulations/cartesian/ff/mf/MeanFieldDistribution2D.cc.o Linking CXX static library /home/bioshell/public_html/builds/bin/libbiosimulations.a [ 64%] Built target biosimulations Scanning dependencies of target cabs++ [ 65%] Building CXX object src/CMakeFiles/cabs++.dir/apps/biosimulations/cabs++.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/cabs++ [ 65%] Built target cabs++ Scanning dependencies of target classify_hec [ 66%] Building CXX object src/CMakeFiles/classify_hec.dir/tests/core/classify_hec.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/classify_hec [ 66%] Built target classify_hec Scanning dependencies of target clust [ 67%] Building CXX object src/CMakeFiles/clust.dir/apps/bioshell/clust.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/clust [ 67%] Built target clust Scanning dependencies of target explain_energy [ 68%] Building CXX object src/CMakeFiles/explain_energy.dir/apps/user-apps/dgront/explain_energy.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/explain_energy [ 68%] Built target explain_energy Scanning dependencies of target list_atoms [ 68%] Building CXX object src/CMakeFiles/list_atoms.dir/tests/core/list_atoms.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/list_atoms [ 68%] Built target list_atoms Scanning dependencies of target make_cabsbb [ 69%] Building CXX object src/CMakeFiles/make_cabsbb.dir/apps/user-apps/adawid/make_cabsbb.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/make_cabsbb [ 69%] Built target make_cabsbb Scanning dependencies of target make_rotamers [ 70%] Building CXX object src/CMakeFiles/make_rotamers.dir/apps/user-apps/adawid/make_rotamers.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/make_rotamers [ 70%] Built target make_rotamers Scanning dependencies of target monomers [ 71%] Building CXX object src/CMakeFiles/monomers.dir/tests/core/monomers.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/monomers [ 71%] Built target monomers Scanning dependencies of target polymer [ 72%] Building CXX object src/CMakeFiles/polymer.dir/apps/biosimulations/polymer.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/polymer [ 72%] Built target polymer Scanning dependencies of target seqc [ 73%] Building CXX object src/CMakeFiles/seqc.dir/apps/bioshell/seqc.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/seqc [ 73%] Built target seqc Scanning dependencies of target str_align [ 73%] Building CXX object src/CMakeFiles/str_align.dir/apps/bioshell/str_align.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/str_align [ 73%] Built target str_align Scanning dependencies of target str_calc [ 74%] Building CXX object src/CMakeFiles/str_calc.dir/apps/bioshell/str_calc.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/str_calc [ 74%] Built target str_calc Scanning dependencies of target strc [ 75%] Building CXX object src/CMakeFiles/strc.dir/apps/bioshell/strc.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/strc [ 75%] Built target strc Scanning dependencies of target superimposer [ 76%] Building CXX object src/CMakeFiles/superimposer.dir/apps/web-apps/superimposer.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/superimposer [ 76%] Built target superimposer Scanning dependencies of target tasks [ 77%] Building CXX object src/CMakeFiles/tasks.dir/apps/biosimulations/tasks.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/tasks [ 77%] Built target tasks Scanning dependencies of target test_algorithms [ 78%] Building CXX object src/CMakeFiles/test_algorithms.dir/tests/core/test_algorithms.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_algorithms [ 78%] Built target test_algorithms Scanning dependencies of target test_algorithms_trees [ 78%] Building CXX object src/CMakeFiles/test_algorithms_trees.dir/tests/core/test_algorithms_trees.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_algorithms_trees [ 78%] Built target test_algorithms_trees Scanning dependencies of target test_alignment_scoring [ 79%] Building CXX object src/CMakeFiles/test_alignment_scoring.dir/tests/core/test_alignment_scoring.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_alignment_scoring [ 79%] Built target test_alignment_scoring Scanning dependencies of target test_alignments [ 80%] Building CXX object src/CMakeFiles/test_alignments.dir/tests/core/test_alignments.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_alignments [ 80%] Built target test_alignments Scanning dependencies of target test_calc_clustering [ 81%] Building CXX object src/CMakeFiles/test_calc_clustering.dir/tests/core/test_calc_clustering.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_calc_clustering [ 81%] Built target test_calc_clustering Scanning dependencies of target test_calc_numeric [ 82%] Building CXX object src/CMakeFiles/test_calc_numeric.dir/tests/core/test_calc_numeric.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_calc_numeric [ 82%] Built target test_calc_numeric Scanning dependencies of target test_calc_statistics [ 83%] Building CXX object src/CMakeFiles/test_calc_statistics.dir/tests/core/test_calc_statistics.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_calc_statistics [ 83%] Built target test_calc_statistics Scanning dependencies of target test_calc_structural [ 84%] Building CXX object src/CMakeFiles/test_calc_structural.dir/tests/core/test_calc_structural.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_calc_structural [ 84%] Built target test_calc_structural Scanning dependencies of target test_calc_structural_transformations [ 84%] Building CXX object src/CMakeFiles/test_calc_structural_transformations.dir/tests/core/test_calc_structural_transformations.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_calc_structural_transformations [ 84%] Built target test_calc_structural_transformations Scanning dependencies of target test_cartesian_ff_mf [ 85%] Building CXX object src/CMakeFiles/test_cartesian_ff_mf.dir/tests/simulations/test_cartesian_ff_mf.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_cartesian_ff_mf [ 85%] Built target test_cartesian_ff_mf Scanning dependencies of target test_cartesian_movers [ 86%] Building CXX object src/CMakeFiles/test_cartesian_movers.dir/tests/simulations/test_cartesian_movers.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_cartesian_movers [ 86%] Built target test_cartesian_movers Scanning dependencies of target test_chemical [ 87%] Building CXX object src/CMakeFiles/test_chemical.dir/tests/core/test_chemical.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_chemical [ 87%] Built target test_chemical Scanning dependencies of target test_data_basic [ 88%] Building CXX object src/CMakeFiles/test_data_basic.dir/tests/core/test_data_basic.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_data_basic [ 88%] Built target test_data_basic Scanning dependencies of target test_data_io [ 89%] Building CXX object src/CMakeFiles/test_data_io.dir/tests/core/test_data_io.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_data_io [ 89%] Built target test_data_io Scanning dependencies of target test_data_io_xml [ 89%] Building CXX object src/CMakeFiles/test_data_io_xml.dir/tests/core/test_data_io_xml.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_data_io_xml [ 89%] Built target test_data_io_xml Scanning dependencies of target test_data_sequence [ 90%] Building CXX object src/CMakeFiles/test_data_sequence.dir/tests/core/test_data_sequence.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_data_sequence [ 90%] Built target test_data_sequence Scanning dependencies of target test_data_stream [ 91%] Building CXX object src/CMakeFiles/test_data_stream.dir/tests/ui/test_data_stream.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_data_stream [ 91%] Built target test_data_stream Scanning dependencies of target test_data_structural [ 92%] Building CXX object src/CMakeFiles/test_data_structural.dir/tests/core/test_data_structural.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_data_structural [ 92%] Built target test_data_structural Scanning dependencies of target test_io_utils [ 93%] Building CXX object src/CMakeFiles/test_io_utils.dir/tests/utils/test_io_utils.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_io_utils [ 93%] Built target test_io_utils Scanning dependencies of target test_options [ 94%] Building CXX object src/CMakeFiles/test_options.dir/tests/utils/test_options.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_options [ 94%] Built target test_options Scanning dependencies of target test_rama_ff [ 94%] Building CXX object src/CMakeFiles/test_rama_ff.dir/tests/simulations/test_rama_ff.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_rama_ff [ 94%] Built target test_rama_ff Scanning dependencies of target test_sse [ 95%] Building CXX object src/CMakeFiles/test_sse.dir/tests/core/test_sse.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_sse [ 95%] Built target test_sse Scanning dependencies of target test_string_utils [ 96%] Building CXX object src/CMakeFiles/test_string_utils.dir/tests/utils/test_string_utils.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_string_utils [ 96%] Built target test_string_utils Scanning dependencies of target test_tasks [ 97%] Building CXX object src/CMakeFiles/test_tasks.dir/tests/ui/test_tasks.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_tasks [ 97%] Built target test_tasks Scanning dependencies of target test_thread_pool [ 98%] Building CXX object src/CMakeFiles/test_thread_pool.dir/tests/utils/test_thread_pool.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_thread_pool [ 98%] Built target test_thread_pool Scanning dependencies of target test_web_utils [ 99%] Building CXX object src/CMakeFiles/test_web_utils.dir/tests/utils/test_web_utils.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/test_web_utils [ 99%] Built target test_web_utils Scanning dependencies of target threading1D [100%] Building CXX object src/CMakeFiles/threading1D.dir/apps/web-apps/threading1D/threading1D.cc.o Linking CXX executable /home/bioshell/public_html/builds/bin/threading1D [100%] Built target threading1D