Mock Version: 3.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/dssp.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1671864156.697203/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fbcc459fa90>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.d28s959a:/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.d28s959a:/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', 'abc6a84013e644f9b08f2391c8f4fff4', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1671864156.697203/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.d28s959a:/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;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --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;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: x86_64
Building for target x86_64
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 x86_64 --nodeps /builddir/build/SPECS/dssp.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1671864156.697203/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fbcc459fa90>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.d28s959a:/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.d28s959a:/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', 'c147eb27f909428ba6398c511f5b7130', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1671864156.697203/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.d28s959a:/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;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --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;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1658361600
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.YLHZv6
+ 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.E0ECQV
+ 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 -m64 -mtune=generic -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 -m64 -mtune=generic -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/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/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd dssp-3.0.0
+ '[' -f /usr/lib64/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 -m64 -mtune=generic -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/lib64'
+ 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 -m64 -mtune=generic -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 -m64 -mtune=generic -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<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
70 | struct const_iterator : public std::iterator<std::forward_iterator_tag,
| ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66,
from /usr/include/c++/13/string:47,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/ostream:40,
from /usr/include/c++/13/iostream:41,
from src/dssp.h:12,
from src/mkdssp.cpp:13:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
src/iocif.h:73:18: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
73 | typedef std::iterator<std::forward_iterator_tag, const row> 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 <boost/bind/bind.hpp> + 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 -m64 -mtune=generic -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 -m64 -mtune=generic -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 -m64 -mtune=generic -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<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
70 | struct const_iterator : public std::iterator<std::forward_iterator_tag,
| ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66,
from /usr/include/c++/13/string:47,
from src/mas.h:12,
from src/align-2d.h:12,
from src/structure.h:9,
from src/structure.cpp:9:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
src/iocif.h:73:18: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
73 | typedef std::iterator<std::forward_iterator_tag, const row> 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 <boost/bind/bind.hpp> + 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 <boost/bind/bind.hpp> + 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 -m64 -mtune=generic -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 -m64 -mtune=generic -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<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
70 | struct const_iterator : public std::iterator<std::forward_iterator_tag,
| ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66,
from /usr/include/c++/13/string:47,
from src/mas.h:12,
from src/iocif.h:6:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
src/iocif.h:73:18: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
73 | typedef std::iterator<std::forward_iterator_tag, const row> 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/lib64 -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.yHkyeg
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64
++ dirname /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64
+ 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 -m64 -mtune=generic -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 -m64 -mtune=generic -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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/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 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/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/lib64:
+ 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.x86_64
install -d /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64/usr/bin /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64/usr/share/man/man1
install -m 755 mkdssp /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64/usr/bin/mkdssp
install doc/mkdssp.1 /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64/usr/share/man/man1/mkdssp.1
+ chmod -x /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64/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.x86_64 --unique-debug-src-base dssp-3.0.0-16.fc38.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/dssp-3.0.0
extracting debug info from /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64/usr/bin/mkdssp
original debug info size: 8044kB, size after compression: 7504kB
/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.x86_64/src/utils.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.x86_64/src/utils.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.x86_64/src/structure.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.x86_64/src/structure.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.x86_64/src/primitives-3d.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.x86_64/src/primitives-3d.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.x86_64/src/mkdssp.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.x86_64/src/matrix.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.x86_64/src/mas.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.x86_64/src/mas.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.x86_64/src/iocif.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.x86_64/src/iocif.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.x86_64/src/dssp.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.x86_64/src/dssp.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/dssp-3.0.0-16.fc38.x86_64/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.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.bpn7Va
+ umask 022
+ cd /builddir/build/BUILD
+ cd dssp-3.0.0
+ DOCDIR=/builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64/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.x86_64/usr/share/doc/dssp
+ cp -pr changelog /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64/usr/share/doc/dssp
+ cp -pr README.txt /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64/usr/share/doc/dssp
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.VUsgm0
+ umask 022
+ cd /builddir/build/BUILD
+ cd dssp-3.0.0
+ LICENSEDIR=/builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64/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.x86_64/usr/share/licenses/dssp
+ cp -pr LICENSE_1_0.txt /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64/usr/share/licenses/dssp
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: dssp = 3.0.0-16.fc38 dssp(x86-64) = 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()(64bit) libboost_thread.so.1.78.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.34)(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_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.9)(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_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH)
Processing files: dssp-debugsource-3.0.0-16.fc38.x86_64
Provides: dssp-debugsource = 3.0.0-16.fc38 dssp-debugsource(x86-64) = 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.x86_64
Provides: debuginfo(build-id) = 4d831b06fc39ab0d1a5e76523536fc001d3c3de1 dssp-debuginfo = 3.0.0-16.fc38 dssp-debuginfo(x86-64) = 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(x86-64) = 3.0.0-16.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64
Wrote: /builddir/build/RPMS/dssp-3.0.0-16.fc38.x86_64.rpm
Wrote: /builddir/build/RPMS/dssp-debugsource-3.0.0-16.fc38.x86_64.rpm
Wrote: /builddir/build/RPMS/dssp-debuginfo-3.0.0-16.fc38.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.iJtXTZ
+ umask 022
+ cd /builddir/build/BUILD
+ cd dssp-3.0.0
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/dssp-3.0.0-16.fc38.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.doAkbt
+ 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