Mock Version: 3.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/dssp.spec'], chrootPath='/var/lib/mock/fedora-rawhide-i686-1671864207.906282/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.xozvl9ag:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.xozvl9ag:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'efb635d9754041a281948e0feb532db2', '-D', '/var/lib/mock/fedora-rawhide-i686-1671864207.906282/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.xozvl9ag:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/dssp.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1658361600 Wrote: /builddir/build/SRPMS/dssp-3.0.0-16.fc38.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps /builddir/build/SPECS/dssp.spec'], chrootPath='/var/lib/mock/fedora-rawhide-i686-1671864207.906282/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.xozvl9ag:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.xozvl9ag:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '39151e25f82042cca4f44db1ad7e7902', '-D', '/var/lib/mock/fedora-rawhide-i686-1671864207.906282/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.xozvl9ag:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps /builddir/build/SPECS/dssp.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1658361600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.6FwPLw + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf dssp-3.0.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/dssp-3.0.0.tgz + STATUS=0 + '[' 0 -ne 0 ']' + cd dssp-3.0.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #1 (dssp-make.patch):' Patch #1 (dssp-make.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .make --fuzz=0 patching file makefile Patch #2 (dssp-tuple.patch): + echo 'Patch #2 (dssp-tuple.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .tuple --fuzz=0 patching file src/primitives-3d.h patching file src/structure.h patching file src/primitives-3d.cpp patching file src/dssp.cpp patching file src/structure.cpp + chmod -x src/buffer.h + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.nNyLtU + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd dssp-3.0.0 + '[' -f /usr/lib/libboost_thread-mt.so ']' + echo 'BOOST_LIB_SUFFIX = ' + echo 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/include LDOPTS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L/usr/lib' + make -j2 mkdir -p obj g++ -MD -c -o obj/mkdssp.o src/mkdssp.cpp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/include -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG g++ -MD -c -o obj/dssp.o src/dssp.cpp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/include -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG In file included from src/mkdssp.cpp:14: src/iocif.h:70:39: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 70 | struct const_iterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 73 | typedef std::iterator base_type; | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from src/dssp.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ g++ -MD -c -o obj/primitives-3d.o src/primitives-3d.cpp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/include -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG g++ -MD -c -o obj/structure.o src/structure.cpp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/include -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG g++ -MD -c -o obj/utils.o src/utils.cpp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/include -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG In file included from src/structure.cpp:13: src/iocif.h:70:39: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 70 | struct const_iterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 73 | typedef std::iterator base_type; | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/date_time/time_clock.hpp:17, from /usr/include/boost/thread/thread_time.hpp:9, from /usr/include/boost/thread/lock_types.hpp:18, from /usr/include/boost/thread/pthread/mutex.hpp:16, from /usr/include/boost/thread/mutex.hpp:16, from src/buffer.h:16, from src/structure.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ src/structure.h: In constructor 'MResidue::MResidue(int32, char, MResidue*)': src/structure.h:283:17: warning: 'MResidue::mRadius' will be initialized after [-Wreorder] 283 | double mRadius; | ^~~~~~~ src/structure.h:274:33: warning: 'MAtom MResidue::mH' [-Wreorder] 274 | MAtom mC, mN, mCA, mO, mH; | ^~ src/structure.cpp:440:1: warning: when initialized here [-Wreorder] 440 | MResidue::MResidue(int32 inNumber, char inTypeCode, MResidue* inPrevious) | ^~~~~~~~ src/structure.h: In constructor 'MProtein::MProtein(const std::string&, MChain*)': src/structure.h:430:40: warning: 'MProtein::mNrOfHBondsInAntiparallelBridges' will be initialized after [-Wreorder] 430 | uint32 mNrOfHBondsInParallelBridges, mNrOfHBondsInAntiparallelBridges; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/structure.h:424:17: warning: 'uint32 MProtein::mResidueCount' [-Wreorder] 424 | uint32 mResidueCount, mChainBreaks; | ^~~~~~~~~~~~~ src/structure.cpp:1031:1: warning: when initialized here [-Wreorder] 1031 | MProtein::MProtein(const std::string& inID, MChain* inChain) | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/format/alt_sstream.hpp:22, from /usr/include/boost/format/internals.hpp:24, from /usr/include/boost/format.hpp:38, from src/utils.h:15, from src/utils.cpp:7: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ g++ -MD -c -o obj/mas.o src/mas.cpp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/include -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG g++ -MD -c -o obj/iocif.o src/iocif.cpp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/include -iquote src -g -Wall -Wno-multichar -pthread -O3 -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG In file included from src/iocif.cpp:1: src/iocif.h:70:39: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 70 | struct const_iterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 73 | typedef std::iterator base_type; | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ g++ -o mkdssp obj/mkdssp.o obj/dssp.o obj/primitives-3d.o obj/structure.o obj/utils.o obj/mas.o obj/iocif.o -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -L/usr/lib -lboost_thread -lboost_filesystem -lboost_program_options -lboost_iostreams -lboost_system -lz -lbz2 -g -pthread + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Fyljvn + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386 ++ dirname /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd dssp-3.0.0 + make install DEST_DIR=/usr DESTDIR=/builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386 install -d /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386/usr/bin /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386/usr/share/man/man1 install -m 755 mkdssp /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386/usr/bin/mkdssp install doc/mkdssp.1 /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386/usr/share/man/man1/mkdssp.1 + chmod -x /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386/usr/share/man/man1/mkdssp.1 + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 3.0.0-16.fc38 --unique-debug-suffix -3.0.0-16.fc38.i386 --unique-debug-src-base dssp-3.0.0-16.fc38.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/dssp-3.0.0 extracting debug info from /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386/usr/bin/mkdssp original debug info size: 7688kB, size after compression: 7204kB /usr/bin/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 356 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/utils.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/utils.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/structure.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/structure.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/primitives-3d.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/primitives-3d.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/mkdssp.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/matrix.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/mas.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/mas.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/iocif.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/iocif.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/dssp.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/dssp.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.i386/src/align-2d.h is executable but has no shebang, removing executable bit + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: dssp-3.0.0-16.fc38.i686 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.SunsbX + umask 022 + cd /builddir/build/BUILD + cd dssp-3.0.0 + DOCDIR=/builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386/usr/share/doc/dssp + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386/usr/share/doc/dssp + cp -pr changelog /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386/usr/share/doc/dssp + cp -pr README.txt /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386/usr/share/doc/dssp + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.R0LPJY + umask 022 + cd /builddir/build/BUILD + cd dssp-3.0.0 + LICENSEDIR=/builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386/usr/share/licenses/dssp + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386/usr/share/licenses/dssp + cp -pr LICENSE_1_0.txt /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386/usr/share/licenses/dssp + RPM_EC=0 ++ jobs -p + exit 0 Provides: dssp = 3.0.0-16.fc38 dssp(x86-32) = 3.0.0-16.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libboost_program_options.so.1.78.0 libboost_thread.so.1.78.0 libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.3.2) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.34) libc.so.6(GLIBC_2.4) libgcc_s.so.1 libgcc_s.so.1(GCC_3.0) libgcc_s.so.1(GCC_3.3.1) libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libstdc++.so.6 libstdc++.so.6(CXXABI_1.3) libstdc++.so.6(CXXABI_1.3.9) libstdc++.so.6(GLIBCXX_3.4) libstdc++.so.6(GLIBCXX_3.4.11) libstdc++.so.6(GLIBCXX_3.4.15) libstdc++.so.6(GLIBCXX_3.4.20) libstdc++.so.6(GLIBCXX_3.4.21) libstdc++.so.6(GLIBCXX_3.4.26) libstdc++.so.6(GLIBCXX_3.4.29) libstdc++.so.6(GLIBCXX_3.4.30) libstdc++.so.6(GLIBCXX_3.4.9) rtld(GNU_HASH) Processing files: dssp-debugsource-3.0.0-16.fc38.i686 Provides: dssp-debugsource = 3.0.0-16.fc38 dssp-debugsource(x86-32) = 3.0.0-16.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: dssp-debuginfo-3.0.0-16.fc38.i686 Provides: debuginfo(build-id) = c1718a6a895bcdb6524879174990bec20ef8aa61 dssp-debuginfo = 3.0.0-16.fc38 dssp-debuginfo(x86-32) = 3.0.0-16.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: dssp-debugsource(x86-32) = 3.0.0-16.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386 Wrote: /builddir/build/RPMS/dssp-3.0.0-16.fc38.i686.rpm Wrote: /builddir/build/RPMS/dssp-debugsource-3.0.0-16.fc38.i686.rpm Wrote: /builddir/build/RPMS/dssp-debuginfo-3.0.0-16.fc38.i686.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.tcWmOc + umask 022 + cd /builddir/build/BUILD + cd dssp-3.0.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.i386 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.fm7aF8 + umask 022 + cd /builddir/build/BUILD + rm -rf dssp-3.0.0 dssp-3.0.0.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0