Mock Version: 3.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target x86_64 --nodeps /builddir/build/SPECS/R-CRAN-GenomeAdmixR.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1682241178.397352/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 0x7f4b39940050>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.2apy1o74:/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.2apy1o74:/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', 'd4bddfd516294ac1b32b5ae855ea4141', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1682241178.397352/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.2apy1o74:/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/R-CRAN-GenomeAdmixR.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
warning: source_date_epoch_from_changelog set but %changelog is missing
Building target platforms: x86_64
Building for target x86_64
Wrote: /builddir/build/SRPMS/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.src.rpm
RPM build warnings:
    source_date_epoch_from_changelog set but %changelog is missing
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target x86_64 --nodeps /builddir/build/SPECS/R-CRAN-GenomeAdmixR.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1682241178.397352/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 0x7f4b39940050>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.2apy1o74:/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.2apy1o74:/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', '0bd6b4064f9f41f8bbd7b42b18b62272', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1682241178.397352/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.2apy1o74:/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/R-CRAN-GenomeAdmixR.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
warning: source_date_epoch_from_changelog set but %changelog is missing
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.HmMEBo
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf GenomeAdmixR
+ /usr/bin/mkdir -p GenomeAdmixR
+ cd GenomeAdmixR
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/GenomeAdmixR_2.1.7.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ find -type f -executable -exec grep -Iq . '{}' ';' -exec sed -i -e '$a\' '{}' ';'
+ '[' -d GenomeAdmixR/src ']'
+ find GenomeAdmixR/src -type f -exec sed -i s@/usr/bin/strip@/usr/bin/true@g '{}' ';'
+ '[' -d GenomeAdmixR/src ']'
+ find GenomeAdmixR/src/Makevars GenomeAdmixR/src/Makevars.win -type f -exec sed -i s@-g0@@g '{}' ';'
+ find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' '{}' ';'
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.ZYu5Ih
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ 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 GenomeAdmixR
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.pFPkjv
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64
++ dirname /builddir/build/BUILDROOT/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ 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 GenomeAdmixR
+ mkdir -p /builddir/build/BUILDROOT/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64/usr/local/lib/R/library
+ /usr/bin/R CMD INSTALL -l /builddir/build/BUILDROOT/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64/usr/local/lib/R/library GenomeAdmixR
* installing *source* package 'GenomeAdmixR' ...
** package 'GenomeAdmixR' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (GCC) 13.0.1 20230419 (Red Hat 13.0.1-0)'
using C++14
g++ -std=gnu++14 -I"/usr/include/R" -DNDEBUG  -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I/usr/local/include    -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -flto -c Fish.cpp -o Fish.o
g++ -std=gnu++14 -I"/usr/include/R" -DNDEBUG  -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I/usr/local/include    -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -flto -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/usr/include/R" -DNDEBUG  -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I/usr/local/include    -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -flto -c helper_functions.cpp -o helper_functions.o
helper_functions.cpp: In function 'arma::mat update_frequency_tibble(const std::vector<Fish>&, double, const std::vector<int>&, int, double)':
helper_functions.cpp:128:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Fish>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  128 |  for (int i = 0; i < v.size(); ++i) {
      |                  ~~^~~~~~~~~~
In file included from /usr/include/c++/13/vector:62,
                 from helper_functions.h:11,
                 from helper_functions.cpp:8:
In function 'std::__copy_move<false, true, std::random_access_iterator_tag>::__copy_m<double const, double>(double const*, double const*, double*)double*',
    inlined from 'std::__copy_move_a2<false, double const*, double*>(double const*, double const*, double*)double*' at /usr/include/c++/13/bits/stl_algobase.h:506:30,
    inlined from 'std::__copy_move_a1<false, double const*, double*>(double const*, double const*, double*)double*' at /usr/include/c++/13/bits/stl_algobase.h:533:42,
    inlined from 'std::__copy_move_a<false, __gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, double*>(__gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, __gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, double*)double*' at /usr/include/c++/13/bits/stl_algobase.h:540:31,
    inlined from 'std::copy<__gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, double*>(__gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, __gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, double*)double*' at /usr/include/c++/13/bits/stl_algobase.h:633:7,
    inlined from 'std::__uninitialized_copy<true>::__uninit_copy<__gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, double*>(__gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, __gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, double*)double*' at /usr/include/c++/13/bits/stl_uninitialized.h:147:27,
    inlined from 'std::uninitialized_copy<__gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, double*>(__gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, __gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, double*)double*' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from 'std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, double*, double>(__gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, __gnu_cxx::__normal_iterator<double const*, std::vector<double, std::allocator<double> > >, double*, std::allocator<double>&)double*' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from 'std::vector<double, std::allocator<double> >::vector(std::vector<double, std::allocator<double> > const&)' at /usr/include/c++/13/bits/stl_vector.h:601:31,
    inlined from 'scale_markers(std::vector<double, std::allocator<double> > const&, double)' at helper_functions.cpp:625:12:
/usr/include/c++/13/bits/stl_algobase.h:437:30: warning: 'memmove' forming offset 8 is out of the bounds [0, 8] [-Warray-bounds=]
  437 |             __builtin_memmove(__result, __first, sizeof(_Tp) * _Num);
      |             ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/include/R" -DNDEBUG  -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I/usr/local/include    -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -flto -c simulate.cpp -o simulate.o
In file included from /usr/local/lib/R/library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /usr/local/lib/R/library/RcppParallel/include/RcppParallel.h:21,
                 from simulate.cpp:20:
/usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.'
   21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                                                                                                          ^
g++ -std=gnu++14 -I"/usr/include/R" -DNDEBUG  -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I/usr/local/include    -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -flto -c simulate_emp.cpp -o simulate_emp.o
In file included from /usr/local/lib/R/library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /usr/local/lib/R/library/RcppParallel/include/RcppParallel.h:21,
                 from simulate_emp.cpp:24:
/usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.'
   21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                                                                                                          ^
g++ -std=gnu++14 -I"/usr/include/R" -DNDEBUG  -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I/usr/local/include    -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -flto -c simulate_migration.cpp -o simulate_migration.o
In file included from /usr/local/lib/R/library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /usr/local/lib/R/library/RcppParallel/include/RcppParallel.h:21,
                 from simulate_migration.cpp:22:
/usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.'
   21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                                                                                                          ^
g++ -std=gnu++14 -I"/usr/include/R" -DNDEBUG  -I'/usr/local/lib/R/library/Rcpp/include' -I'/usr/local/lib/R/library/RcppArmadillo/include' -I'/usr/local/lib/R/library/RcppParallel/include' -I/usr/local/include    -fpic  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -flto -c simulate_migration_emp.cpp -o simulate_migration_emp.o
In file included from /usr/local/lib/R/library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /usr/local/lib/R/library/RcppParallel/include/RcppParallel.h:21,
                 from simulate_migration_emp.cpp:20:
/usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.'
   21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                                                                                                          ^
simulate_migration_emp.cpp: In function 'Rcpp::List simulate_migration_emp_cpp(const Rcpp::NumericMatrix&, const Rcpp::NumericMatrix&, const Rcpp::NumericVector&, Rcpp::NumericMatrix, const Rcpp::NumericVector&, int, double, bool, bool, const Rcpp::NumericVector&, bool, double, double, const Rcpp::NumericMatrix&, int, const Rcpp::NumericVector&)':
simulate_migration_emp.cpp:425:25: warning: comparison of integer expressions of different signedness: 'int' and '__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type' {aka 'long unsigned int'} [-Wsign-compare]
  425 |       for (int j = 0; j < pop_size[1]; ++j) {
g++ -std=gnu++14 -shared -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -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 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -flto -fpic -L/usr/lib64/R/lib -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 -o GenomeAdmixR.so Fish.o RcppExports.o helper_functions.o simulate.o simulate_emp.o simulate_migration.o simulate_migration_emp.o -L/usr/lib64 -Wl,-rpath,/usr/lib64 -ltbb -ltbbmalloc -L/usr/lib64/R/lib -lR
installing to /builddir/build/BUILDROOT/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64/usr/local/lib/R/library/00LOCK-GenomeAdmixR/00new/GenomeAdmixR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomeAdmixR'
    finding HTML links ... done
    GenomeAdmixR-package                    html  
    ancestry_module                         html  
    calculate_allele_frequencies            html  
    calculate_average_ld                    html  
    calculate_dist_junctions                html  
    calculate_fst                           html  
    calculate_heterozygosity                html  
    calculate_ld                            html  
    calculate_marker_frequency              html  
    combine_input_data                      html  
    create_artificial_genomeadmixr_data     html  
    create_iso_female                       html  
    dgrp2.3R.5k.data                        html  
    iso_female_ancestry                     html  
    iso_female_sequence                     html  
    load_population                         html  
    migration_settings                      html  
    plink_to_genomeadmixr_data              html  
    plot.individual                         html  
    plot_chromosome                         html  
    plot_difference_frequencies             html  
    plot_dist_junctions                     html  
    plot_frequencies                        html  
    plot_joyplot_frequencies                html  
    plot_over_time                          html  
    plot_start_end                          html  
    print.genomeadmixr_data                 html  
    print.individual                        html  
    print.population                        html  
    read_input_data                         html  
    save_population                         html  
    sequence_module                         html  
    simulate_admixture                      html  
    simulate_ancestry                       html  
    simulate_ancestry_migration             html  
    simulate_sequence                       html  
    simulate_sequence_migration             html  
    simulation_data_to_genomeadmixr_data    html  
    vcfR_to_genomeadmixr_data               html  
    write_as_plink                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeAdmixR)
+ test -d GenomeAdmixR/src
+ cd GenomeAdmixR/src
+ rm -f Fish.o RcppExports.o helper_functions.o simulate.o simulate_emp.o simulate_migration.o simulate_migration_emp.o GenomeAdmixR.so
+ rm -f /builddir/build/BUILDROOT/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64/usr/local/lib/R/library/R.css
+ find /builddir/build/BUILDROOT/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64/usr/local/lib/R/library -type f -exec sed -i s@/builddir/build/BUILDROOT/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64@@g '{}' ';'
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 2.1.7-1.fc39.copr5832313 --unique-debug-suffix -2.1.7-1.fc39.copr5832313.x86_64 --unique-debug-src-base R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/GenomeAdmixR
extracting debug info from /builddir/build/BUILDROOT/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64/usr/local/lib/R/library/GenomeAdmixR/libs/GenomeAdmixR.so
original debug info size: 5344kB, size after compression: 4432kB
/usr/bin/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
251 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/redhat/brp-mangle-shebangs
*** WARNING: ./usr/src/debug/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64/GenomeAdmixR/src/simulate_migration_emp.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64/GenomeAdmixR/src/simulate_migration.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64/GenomeAdmixR/src/simulate.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64/GenomeAdmixR/src/random_functions.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64/GenomeAdmixR/src/helper_functions.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64/GenomeAdmixR/src/helper_functions.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64/GenomeAdmixR/src/Fish.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64/GenomeAdmixR/src/Fish.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/local/lib/R/library/GenomeAdmixR/doc/Demonstrate_isofemales.Rmd is executable but has no shebang, removing executable bit
*** WARNING: ./usr/local/lib/R/library/GenomeAdmixR/doc/Joyplots.Rmd is executable but has no shebang, removing executable bit
*** WARNING: ./usr/local/lib/R/library/GenomeAdmixR/doc/Visualization.Rmd is executable but has no shebang, removing executable bit
*** WARNING: ./usr/local/lib/R/library/GenomeAdmixR/doc/Walkthrough.Rmd is executable but has no shebang, removing executable bit
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2
+ /usr/lib/rpm/redhat/brp-python-hardlink
Processing files: R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64
Provides: R-CRAN-GenomeAdmixR = 2.1.7-1.fc39.copr5832313 R-CRAN-GenomeAdmixR(x86-64) = 2.1.7-1.fc39.copr5832313
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(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) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.5)(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_3.4.19)(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) libtbb.so.2()(64bit) rtld(GNU_HASH)
Processing files: R-CRAN-GenomeAdmixR-debugsource-2.1.7-1.fc39.copr5832313.x86_64
Provides: R-CRAN-GenomeAdmixR-debugsource = 2.1.7-1.fc39.copr5832313 R-CRAN-GenomeAdmixR-debugsource(x86-64) = 2.1.7-1.fc39.copr5832313
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-CRAN-GenomeAdmixR-debuginfo-2.1.7-1.fc39.copr5832313.x86_64
Provides: R-CRAN-GenomeAdmixR-debuginfo = 2.1.7-1.fc39.copr5832313 R-CRAN-GenomeAdmixR-debuginfo(x86-64) = 2.1.7-1.fc39.copr5832313 debuginfo(build-id) = 376ec3c2602ee4985d6e2bb90e45e530f1fc05a6
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: R-CRAN-GenomeAdmixR-debugsource(x86-64) = 2.1.7-1.fc39.copr5832313
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64
Wrote: /builddir/build/RPMS/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64.rpm
Wrote: /builddir/build/RPMS/R-CRAN-GenomeAdmixR-debugsource-2.1.7-1.fc39.copr5832313.x86_64.rpm
Wrote: /builddir/build/RPMS/R-CRAN-GenomeAdmixR-debuginfo-2.1.7-1.fc39.copr5832313.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.DpY29g
+ umask 022
+ cd /builddir/build/BUILD
+ cd GenomeAdmixR
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-CRAN-GenomeAdmixR-2.1.7-1.fc39.copr5832313.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.6N6sWT
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf GenomeAdmixR GenomeAdmixR.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
RPM build warnings:
    source_date_epoch_from_changelog set but %changelog is missing
Child return code was: 0