Mock Version: 1.2.12 ENTER do(['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/autodock_vina.spec'], chrootPath='/var/lib/mock/epel-7-x86_64-mockbuilder-7770/root'shell=FalseprintOutput=Falseenv={'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=0logger=uid=1001) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/autodock_vina.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOSTNAME': 'mock'} and shell False error: Macro %py2_install has unterminated body error: Macro %py2_install has unterminated body warning: Could not canonicalize hostname: copr-builder-808055515 Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/autodock_vina-1.1.2-4.el7.centos.src.rpm error: Macro %py2_install has unterminated body error: Macro %py2_install has unterminated body Child return code was: 0 LEAVE do --> ENTER do(['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/autodock_vina.spec '], chrootPath='/var/lib/mock/epel-7-x86_64-mockbuilder-7770/root'shell=FalseprintOutput=Falseenv={'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=0logger=uid=1001) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/autodock_vina.spec '] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOSTNAME': 'mock'} and shell False error: Macro %py2_install has unterminated body error: Macro %py2_install has unterminated body Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.XiLdtx + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf autodock_vina_1_1_2 + /usr/bin/gzip -dc /builddir/build/SOURCES/autodock_vina_1_1_2.tgz + /usr/bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + cd autodock_vina_1_1_2 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #1 (autodock-vina-fix_boost.patch):' Patch #1 (autodock-vina-fix_boost.patch): + /usr/bin/cat /builddir/build/SOURCES/autodock-vina-fix_boost.patch + /usr/bin/patch -p1 --fuzz=0 patching file src/main/main.cpp patching file src/split/split.cpp + find src -type f -exec dos2unix '{}' ';' dos2unix: converting file src/split/split.cpp to Unix format ... dos2unix: converting file src/main/main.cpp to Unix format ... dos2unix: converting file src/lib/weighted_terms.h to Unix format ... dos2unix: converting file src/lib/weighted_terms.cpp to Unix format ... dos2unix: converting file src/lib/triangular_matrix_index.h to Unix format ... dos2unix: converting file src/lib/tree.h to Unix format ... dos2unix: converting file src/lib/terms.h to Unix format ... dos2unix: converting file src/lib/terms.cpp to Unix format ... dos2unix: converting file src/lib/tee.h to Unix format ... dos2unix: converting file src/lib/szv_grid.h to Unix format ... dos2unix: converting file src/lib/szv_grid.cpp to Unix format ... dos2unix: converting file src/lib/statistics.h to Unix format ... dos2unix: converting file src/lib/ssd.h to Unix format ... dos2unix: converting file src/lib/ssd.cpp to Unix format ... dos2unix: converting file src/lib/scoring_function.h to Unix format ... dos2unix: converting file src/lib/recent_history.h to Unix format ... dos2unix: converting file src/lib/random.h to Unix format ... dos2unix: converting file src/lib/random.cpp to Unix format ... dos2unix: converting file src/lib/quaternion.h to Unix format ... dos2unix: converting file src/lib/quaternion.cpp to Unix format ... dos2unix: converting file src/lib/quasi_newton.h to Unix format ... dos2unix: converting file src/lib/quasi_newton.cpp to Unix format ... dos2unix: converting file src/lib/precalculate.h to Unix format ... dos2unix: converting file src/lib/pdb.h to Unix format ... dos2unix: converting file src/lib/pdb.cpp to Unix format ... dos2unix: converting file src/lib/parse_pdbqt.h to Unix format ... dos2unix: converting file src/lib/parse_pdbqt.cpp to Unix format ... dos2unix: converting file src/lib/parse_error.h to Unix format ... dos2unix: converting file src/lib/parallel_progress.h to Unix format ... dos2unix: converting file src/lib/parallel_progress.cpp to Unix format ... dos2unix: converting file src/lib/parallel_mc.h to Unix format ... dos2unix: converting file src/lib/parallel_mc.cpp to Unix format ... dos2unix: converting file src/lib/parallel.h to Unix format ... dos2unix: converting file src/lib/non_cache.h to Unix format ... dos2unix: converting file src/lib/non_cache.cpp to Unix format ... dos2unix: converting file src/lib/naive_non_cache.h to Unix format ... dos2unix: converting file src/lib/naive_non_cache.cpp to Unix format ... dos2unix: converting file src/lib/my_pid.h to Unix format ... dos2unix: converting file src/lib/my_pid.cpp to Unix format ... dos2unix: converting file src/lib/mutate.h to Unix format ... dos2unix: converting file src/lib/mutate.cpp to Unix format ... dos2unix: converting file src/lib/monte_carlo.h to Unix format ... dos2unix: converting file src/lib/monte_carlo.cpp to Unix format ... dos2unix: converting file src/lib/model.h to Unix format ... dos2unix: converting file src/lib/model.cpp to Unix format ... dos2unix: converting file src/lib/matrix.h to Unix format ... dos2unix: converting file src/lib/manifold.h to Unix format ... dos2unix: converting file src/lib/manifold.cpp to Unix format ... dos2unix: converting file src/lib/macros.h to Unix format ... dos2unix: converting file src/lib/int_pow.h to Unix format ... dos2unix: converting file src/lib/incrementable.h to Unix format ... dos2unix: converting file src/lib/igrid.h to Unix format ... dos2unix: converting file src/lib/grid_dim.h to Unix format ... dos2unix: converting file src/lib/grid.h to Unix format ... dos2unix: converting file src/lib/grid.cpp to Unix format ... dos2unix: converting file src/lib/file.h to Unix format ... dos2unix: converting file src/lib/everything.h to Unix format ... dos2unix: converting file src/lib/everything.cpp to Unix format ... dos2unix: converting file src/lib/current_weights.h to Unix format ... dos2unix: converting file src/lib/current_weights.cpp to Unix format ... dos2unix: converting file src/lib/curl.h to Unix format ... dos2unix: converting file src/lib/coords.h to Unix format ... dos2unix: converting file src/lib/coords.cpp to Unix format ... dos2unix: converting file src/lib/convert_substring.h to Unix format ... dos2unix: converting file src/lib/conf.h to Unix format ... dos2unix: converting file src/lib/common.h to Unix format ... dos2unix: converting file src/lib/cache.h to Unix format ... dos2unix: converting file src/lib/cache.cpp to Unix format ... dos2unix: converting file src/lib/brick.h to Unix format ... dos2unix: converting file src/lib/bfgs.h to Unix format ... dos2unix: converting file src/lib/atom_type.h to Unix format ... dos2unix: converting file src/lib/atom_constants.h to Unix format ... dos2unix: converting file src/lib/atom_base.h to Unix format ... dos2unix: converting file src/lib/atom.h to Unix format ... dos2unix: converting file src/lib/array3d.h to Unix format ... + find src -type f -exec chmod -x '{}' ';' + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.MvB6HP + umask 022 + cd /builddir/build/BUILD + cd autodock_vina_1_1_2 + make -C build/linux/release GPP=g++ BOOST_VERSION=1_47 C_PLATFORM=-pthread BASE=/usr BOOST_LIB_VERSION=-mt -j2 'C_OPTIONS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG' make: Entering directory `/builddir/build/BUILD/autodock_vina_1_1_2/build/linux/release' g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -I ../../../src/lib -o main.o -c ../../../src/main/main.cpp g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o cache.o -c ../../../src/lib/cache.cpp In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/cache.h:29, from ../../../src/lib/cache.cpp:41: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/cache.h:29, from ../../../src/lib/cache.cpp:41: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/cache.h:29, from ../../../src/lib/cache.cpp:41: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/cache.h:29, from ../../../src/lib/cache.cpp:41: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/parse_pdbqt.h:26, from ../../../src/main/main.cpp:33: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/parse_pdbqt.h:26, from ../../../src/main/main.cpp:33: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/parse_pdbqt.h:26, from ../../../src/main/main.cpp:33: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/parse_pdbqt.h:26, from ../../../src/main/main.cpp:33: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o coords.o -c ../../../src/lib/coords.cpp In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/coords.h:27, from ../../../src/lib/coords.cpp:23: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o current_weights.o -c ../../../src/lib/current_weights.cpp In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/terms.h:27, from ../../../src/lib/current_weights.h:26, from ../../../src/lib/current_weights.cpp:23: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/terms.h:27, from ../../../src/lib/current_weights.h:26, from ../../../src/lib/current_weights.cpp:23: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/terms.h:27, from ../../../src/lib/current_weights.h:26, from ../../../src/lib/current_weights.cpp:23: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/terms.h:27, from ../../../src/lib/current_weights.h:26, from ../../../src/lib/current_weights.cpp:23: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ ../../../src/lib/current_weights.cpp: In function 'flv current_weights(const terms&)': ../../../src/lib/current_weights.cpp:45:5: warning: unused variable 'tmp_size' [-Wunused-variable] sz tmp_size = tmp.size(); ^ ../../../src/lib/current_weights.cpp:46:5: warning: unused variable 'conf_indep_size' [-Wunused-variable] sz conf_indep_size = t.size_conf_independent(true); ^ ../../../src/lib/current_weights.cpp:47:5: warning: unused variable 't_size' [-Wunused-variable] sz t_size = t.size(); ^ ../../../src/lib/current_weights.cpp:48:5: warning: unused variable 't_names_size' [-Wunused-variable] sz t_names_size = t.get_names(true).size(); ^ g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o everything.o -c ../../../src/lib/everything.cpp g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o grid.o -c ../../../src/lib/grid.cpp g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o szv_grid.o -c ../../../src/lib/szv_grid.cpp In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/terms.h:27, from ../../../src/lib/everything.h:26, from ../../../src/lib/everything.cpp:23: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/terms.h:27, from ../../../src/lib/everything.h:26, from ../../../src/lib/everything.cpp:23: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/terms.h:27, from ../../../src/lib/everything.h:26, from ../../../src/lib/everything.cpp:23: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/terms.h:27, from ../../../src/lib/everything.h:26, from ../../../src/lib/everything.cpp:23: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ ../../../src/lib/everything.cpp: In constructor 'ad4_solvation::ad4_solvation(fl, fl, bool, fl)': ../../../src/lib/everything.cpp:64:7: warning: 'ad4_solvation::charge_dependent' will be initialized after [-Wreorder] bool charge_dependent; ^ ../../../src/lib/everything.cpp:62:5: warning: 'fl ad4_solvation::desolvation_sigma' [-Wreorder] fl desolvation_sigma; ^ ../../../src/lib/everything.cpp:65:2: warning: when initialized here [-Wreorder] ad4_solvation(fl desolvation_sigma_, fl solvation_q_, bool charge_dependent_, fl cutoff_) : distance_additive(cutoff_), solvation_q(solvation_q_), charge_dependent(charge_dependent_), desolvation_sigma(desolvation_sigma_) { ^ ../../../src/lib/everything.cpp: In member function 'virtual fl ad4_solvation::eval(const atom_base&, const atom_base&, fl) const': ../../../src/lib/everything.cpp:75:6: warning: unused variable 't1' [-Wunused-variable] sz t1 = a.ad; ^ ../../../src/lib/everything.cpp:76:6: warning: unused variable 't2' [-Wunused-variable] sz t2 = b.ad; ^ ../../../src/lib/everything.cpp: In constructor 'everything::everything()': ../../../src/lib/everything.cpp:303:17: warning: unused variable 'd' [-Wunused-variable] const unsigned d = 0; // default ^ In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/szv_grid.h:26, from ../../../src/lib/szv_grid.cpp:23: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/szv_grid.h:26, from ../../../src/lib/szv_grid.cpp:23: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/szv_grid.h:26, from ../../../src/lib/szv_grid.cpp:23: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/szv_grid.h:26, from ../../../src/lib/szv_grid.cpp:23: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o manifold.o -c ../../../src/lib/manifold.cpp g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o model.o -c ../../../src/lib/model.cpp In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/ssd.h:26, from ../../../src/lib/manifold.h:28, from ../../../src/lib/manifold.cpp:23: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/ssd.h:26, from ../../../src/lib/manifold.h:28, from ../../../src/lib/manifold.cpp:23: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/ssd.h:26, from ../../../src/lib/manifold.h:28, from ../../../src/lib/manifold.cpp:23: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/ssd.h:26, from ../../../src/lib/manifold.h:28, from ../../../src/lib/manifold.cpp:23: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/model.cpp:23: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/model.cpp:23: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/model.cpp:23: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/model.cpp:23: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ ../../../src/lib/model.cpp: In member function 'void model::assign_bonds(const distance_type_matrix&)': ../../../src/lib/model.cpp:344:14: warning: unused variable 'bond_length' [-Wunused-variable] const fl bond_length = i_atom.optimal_covalent_bond_length(j_atom); ^ ../../../src/lib/model.cpp: In member function 'fl model::rmsd_upper_bound(const model&) const': ../../../src/lib/model.cpp:757:15: warning: unused variable 'b' [-Wunused-variable] const atom& b = m.atoms[i]; ^ ../../../src/lib/model.cpp: In member function 'fl model::rmsd_ligands_upper_bound(const model&) const': ../../../src/lib/model.cpp:779:16: warning: unused variable 'b' [-Wunused-variable] const atom& b = m.atoms[i]; ^ g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o monte_carlo.o -c ../../../src/lib/monte_carlo.cpp g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o mutate.o -c ../../../src/lib/mutate.cpp In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/ssd.h:26, from ../../../src/lib/monte_carlo.h:26, from ../../../src/lib/monte_carlo.cpp:23: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/ssd.h:26, from ../../../src/lib/monte_carlo.h:26, from ../../../src/lib/monte_carlo.cpp:23: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/ssd.h:26, from ../../../src/lib/monte_carlo.h:26, from ../../../src/lib/monte_carlo.cpp:23: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/ssd.h:26, from ../../../src/lib/monte_carlo.h:26, from ../../../src/lib/monte_carlo.cpp:23: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/mutate.h:26, from ../../../src/lib/mutate.cpp:23: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/mutate.h:26, from ../../../src/lib/mutate.cpp:23: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/mutate.h:26, from ../../../src/lib/mutate.cpp:23: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/mutate.h:26, from ../../../src/lib/mutate.cpp:23: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o my_pid.o -c ../../../src/lib/my_pid.cpp g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o naive_non_cache.o -c ../../../src/lib/naive_non_cache.cpp g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o non_cache.o -c ../../../src/lib/non_cache.cpp In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/naive_non_cache.h:27, from ../../../src/lib/naive_non_cache.cpp:23: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/naive_non_cache.h:27, from ../../../src/lib/naive_non_cache.cpp:23: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/naive_non_cache.h:27, from ../../../src/lib/naive_non_cache.cpp:23: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/naive_non_cache.h:27, from ../../../src/lib/naive_non_cache.cpp:23: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/szv_grid.h:26, from ../../../src/lib/non_cache.h:27, from ../../../src/lib/non_cache.cpp:23: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/szv_grid.h:26, from ../../../src/lib/non_cache.h:27, from ../../../src/lib/non_cache.cpp:23: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/szv_grid.h:26, from ../../../src/lib/non_cache.h:27, from ../../../src/lib/non_cache.cpp:23: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/szv_grid.h:26, from ../../../src/lib/non_cache.h:27, from ../../../src/lib/non_cache.cpp:23: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ In file included from ../../../src/lib/non_cache.cpp:23:0: ../../../src/lib/non_cache.h: In constructor 'non_cache::non_cache(const model&, const grid_dims&, const precalculate*, fl)': ../../../src/lib/non_cache.h:38:22: warning: 'non_cache::p' will be initialized after [-Wreorder] const precalculate* p; ^ ../../../src/lib/non_cache.h:34:5: warning: 'fl non_cache::slope' [-Wreorder] fl slope; ^ ../../../src/lib/non_cache.cpp:26:1: warning: when initialized here [-Wreorder] non_cache::non_cache(const model& m, const grid_dims& gd_, const precalculate* p_, fl slope_) : sgrid(m, szv_grid_dims(gd_), p_->cutoff_sqr()), gd(gd_), p(p_), slope(slope_) {} ^ g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o parallel_mc.o -c ../../../src/lib/parallel_mc.cpp g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o parse_pdbqt.o -c ../../../src/lib/parse_pdbqt.cpp In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/ssd.h:26, from ../../../src/lib/monte_carlo.h:26, from ../../../src/lib/parallel_mc.h:26, from ../../../src/lib/parallel_mc.cpp:24: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/ssd.h:26, from ../../../src/lib/monte_carlo.h:26, from ../../../src/lib/parallel_mc.h:26, from ../../../src/lib/parallel_mc.cpp:24: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/ssd.h:26, from ../../../src/lib/monte_carlo.h:26, from ../../../src/lib/parallel_mc.h:26, from ../../../src/lib/parallel_mc.cpp:24: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/ssd.h:26, from ../../../src/lib/monte_carlo.h:26, from ../../../src/lib/parallel_mc.h:26, from ../../../src/lib/parallel_mc.cpp:24: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/parse_pdbqt.h:26, from ../../../src/lib/parse_pdbqt.cpp:30: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/parse_pdbqt.h:26, from ../../../src/lib/parse_pdbqt.cpp:30: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/parse_pdbqt.h:26, from ../../../src/lib/parse_pdbqt.cpp:30: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/parse_pdbqt.h:26, from ../../../src/lib/parse_pdbqt.cpp:30: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o pdb.o -c ../../../src/lib/pdb.cpp g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o quasi_newton.o -c ../../../src/lib/quasi_newton.cpp g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o quaternion.o -c ../../../src/lib/quaternion.cpp In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/quasi_newton.h:26, from ../../../src/lib/quasi_newton.cpp:23: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/quasi_newton.h:26, from ../../../src/lib/quasi_newton.cpp:23: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/quasi_newton.h:26, from ../../../src/lib/quasi_newton.cpp:23: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/quasi_newton.h:26, from ../../../src/lib/quasi_newton.cpp:23: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ In file included from ../../../src/lib/quasi_newton.cpp:24:0: ../../../src/lib/bfgs.h: In instantiation of 'fl bfgs(F&, Conf&, Change&, unsigned int, fl, sz) [with F = quasi_newton_aux; Conf = conf; Change = change; fl = double; sz = long unsigned int]': ../../../src/lib/quasi_newton.cpp:40:74: required from here ../../../src/lib/bfgs.h:132:8: warning: unused variable 'h_updated' [-Wunused-variable] bool h_updated = bfgs_update(h, p, y, alpha); ^ g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o random.o -c ../../../src/lib/random.cpp g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o ssd.o -c ../../../src/lib/ssd.cpp g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o terms.o -c ../../../src/lib/terms.cpp In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/ssd.h:26, from ../../../src/lib/ssd.cpp:23: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/ssd.h:26, from ../../../src/lib/ssd.cpp:23: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/ssd.h:26, from ../../../src/lib/ssd.cpp:23: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/ssd.h:26, from ../../../src/lib/ssd.cpp:23: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -o weighted_terms.o -c ../../../src/lib/weighted_terms.cpp In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/terms.h:27, from ../../../src/lib/terms.cpp:23: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/terms.h:27, from ../../../src/lib/terms.cpp:23: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/terms.h:27, from ../../../src/lib/terms.cpp:23: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/terms.h:27, from ../../../src/lib/terms.cpp:23: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ In file included from ../../../src/lib/atom_type.h:26:0, from ../../../src/lib/atom_base.h:26, from ../../../src/lib/atom.h:26, from ../../../src/lib/tree.h:27, from ../../../src/lib/model.h:29, from ../../../src/lib/terms.h:27, from ../../../src/lib/weighted_terms.h:26, from ../../../src/lib/weighted_terms.cpp:23: ../../../src/lib/atom_constants.h: In function 'fl xs_radius(sz)': ../../../src/lib/atom_constants.h:230:11: warning: unused variable 'n' [-Wunused-variable] const sz n = sizeof(xs_vdw_radii) / sizeof(const fl); ^ In file included from ../../../src/lib/model.h:29:0, from ../../../src/lib/terms.h:27, from ../../../src/lib/weighted_terms.h:26, from ../../../src/lib/weighted_terms.cpp:23: ../../../src/lib/tree.h: In constructor 'frame::frame(const vec&)': ../../../src/lib/tree.h:50:6: warning: 'frame::orientation_q' will be initialized after [-Wreorder] qt orientation_q; ^ ../../../src/lib/tree.h:49:6: warning: 'mat frame::orientation_m' [-Wreorder] mat orientation_m; ^ ../../../src/lib/tree.h:30:2: warning: when initialized here [-Wreorder] frame(const vec& origin_) : origin(origin_), orientation_q(qt_identity), orientation_m(quaternion_to_r3(qt_identity)) {} ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/terms.h:27, from ../../../src/lib/weighted_terms.h:26, from ../../../src/lib/weighted_terms.cpp:23: ../../../src/lib/precalculate.h: In constructor 'precalculate::precalculate(const scoring_function&, fl, fl)': ../../../src/lib/precalculate.h:166:42: warning: 'precalculate::data' will be initialized after [-Wreorder] triangular_matrix data; ^ ../../../src/lib/precalculate.h:164:15: warning: 'atom_type::t precalculate::m_atom_typing_used' [-Wreorder] atom_type::t m_atom_typing_used; ^ In file included from ../../../src/lib/model.h:31:0, from ../../../src/lib/terms.h:27, from ../../../src/lib/weighted_terms.h:26, from ../../../src/lib/weighted_terms.cpp:23: ../../../src/lib/precalculate.h:112:2: warning: when initialized here [-Wreorder] precalculate(const scoring_function& sf, fl v = max_fl, fl factor_ = 32) : // sf should not be discontinuous, even near cutoff, for the sake of the derivatives ^ g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -I ../../../src/lib -o split.o -c ../../../src/split/split.cpp g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -L/usr/lib -L. -o vina main.o cache.o coords.o current_weights.o everything.o grid.o szv_grid.o manifold.o model.o monte_carlo.o mutate.o my_pid.o naive_non_cache.o non_cache.o parallel_mc.o parse_pdbqt.o pdb.o quasi_newton.o quaternion.o random.o ssd.o terms.o weighted_terms.o -l boost_system-mt -l boost_thread-mt -l boost_serialization-mt -l boost_filesystem-mt -l boost_program_options-mt ../../../src/split/split.cpp: In function 'int main(int, char**)': ../../../src/split/split.cpp:135:13: warning: unused variable 'advanced' [-Wunused-variable] const bool advanced = false; ^ g++ -pthread -ansi -Wno-long-long -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -DNDEBUG -I /usr/include -L/usr/lib -L. -o vina_split split.o -l boost_system-mt -l boost_thread-mt -l boost_serialization-mt -l boost_filesystem-mt -l boost_program_options-mt make: Leaving directory `/builddir/build/BUILD/autodock_vina_1_1_2/build/linux/release' + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.TqPRfQ + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64 ++ dirname /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64 + cd autodock_vina_1_1_2 + rm -rf /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64 + mkdir -p /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64//usr/bin + install build/linux/release/vina build/linux/release/vina_split /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64//usr/bin + mkdir -p /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64//usr/share/man/man1 + install -m 644 /builddir/build/SOURCES/vina.1 /builddir/build/SOURCES/vina_split.1 /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64//usr/share/man/man1 + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 /builddir/build/BUILD/autodock_vina_1_1_2 extracting debug info from /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64/usr/bin/vina_split extracting debug info from /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64/usr/bin/vina /usr/lib/rpm/sepdebugcrcfix: Updated 2 CRC32s, 0 CRC32s did match. 566 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-compress + /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/lib/rpm/redhat/brp-java-repack-jars Processing files: autodock_vina-1.1.2-4.el7.centos.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.3Xqz7V + umask 022 + cd /builddir/build/BUILD + cd autodock_vina_1_1_2 + DOCDIR=/builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64/usr/share/doc/autodock_vina-1.1.2 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64/usr/share/doc/autodock_vina-1.1.2 + cp -pr LICENSE /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64/usr/share/doc/autodock_vina-1.1.2 + exit 0 Provides: autodock_vina = 1.1.2-4.el7.centos autodock_vina(x86-64) = 1.1.2-4.el7.centos Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libboost_filesystem-mt.so.1.53.0()(64bit) libboost_program_options-mt.so.1.53.0()(64bit) libboost_serialization-mt.so.1.53.0()(64bit) libboost_system-mt.so.1.53.0()(64bit) libboost_thread-mt.so.1.53.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_4.0.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libpthread.so.0(GLIBC_2.3.2)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH) Processing files: autodock_vina-debuginfo-1.1.2-4.el7.centos.x86_64 Provides: autodock_vina-debuginfo = 1.1.2-4.el7.centos autodock_vina-debuginfo(x86-64) = 1.1.2-4.el7.centos Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64 warning: Could not canonicalize hostname: copr-builder-808055515 Wrote: /builddir/build/RPMS/autodock_vina-1.1.2-4.el7.centos.x86_64.rpm Wrote: /builddir/build/RPMS/autodock_vina-debuginfo-1.1.2-4.el7.centos.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.lTmCDh + umask 022 + cd /builddir/build/BUILD + cd autodock_vina_1_1_2 + rm -rf /builddir/build/BUILDROOT/autodock_vina-1.1.2-4.el7.centos.x86_64 + exit 0 error: Macro %py2_install has unterminated body error: Macro %py2_install has unterminated body Child return code was: 0 LEAVE do -->