Mock Version: 5.0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-CRAN-BDgraph.spec'], chrootPath='/var/lib/mock/fedora-39-x86_64-1692161677.700836/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=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.8azs1hmk:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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.8azs1hmk:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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', '7f344172f85a40a4b91818305f8266d0', '-D', '/var/lib/mock/fedora-39-x86_64-1692161677.700836/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.8azs1hmk:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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 x86_64 --nodeps /builddir/build/SPECS/R-CRAN-BDgraph.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 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-BDgraph-2.72-1.fc39.copr6291085.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-BDgraph.spec'], chrootPath='/var/lib/mock/fedora-39-x86_64-1692161677.700836/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=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.8azs1hmk:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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.8azs1hmk:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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', '29a1e164f34142cd83e44f6da4ea703c', '-D', '/var/lib/mock/fedora-39-x86_64-1692161677.700836/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.8azs1hmk:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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 x86_64 --nodeps /builddir/build/SPECS/R-CRAN-BDgraph.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 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.9k4fJ3 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf BDgraph + /usr/bin/mkdir -p BDgraph + cd BDgraph + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/BDgraph_2.72.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + rm -rf /builddir/build/BUILD/BDgraph-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/BDgraph-SPECPARTS + /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 BDgraph/src ']' + find BDgraph/src -type f -exec sed -i s@/usr/bin/strip@/usr/bin/true@g '{}' ';' + '[' -d BDgraph/src ']' + find BDgraph/src/Makevars BDgraph/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.9me0Wp + 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 -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 -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 BDgraph + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.wFYeXy + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64 ++ dirname /builddir/build/BUILDROOT/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.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 -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 -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 BDgraph + mkdir -p /builddir/build/BUILDROOT/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/usr/local/lib/R/library + /usr/bin/R CMD INSTALL -l /builddir/build/BUILDROOT/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/usr/local/lib/R/library BDgraph * installing *source* package 'BDgraph' ... file 'THANKS' has the wrong MD5 checksum ** using staged installation ** libs using C compiler: 'gcc (GCC) 13.2.1 20230728 (Red Hat 13.2.1-1)' using C++ compiler: 'g++ (GCC) 13.2.1 20230728 (Red Hat 13.2.1-1)' using C++11 gcc -I"/usr/include/R" -DNDEBUG -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 -c BDgraph_init.c -o BDgraph_init.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -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 -c copula.cpp -o copula.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -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 -c gcgm_DMH.cpp -o gcgm_DMH.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -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 -c gcgm_bd.cpp -o gcgm_bd.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -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 -c gcgm_dw_bd.cpp -o gcgm_dw_bd.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -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 -c ggm_DMH.cpp -o ggm_DMH.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -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 -c ggm_bd.cpp -o ggm_bd.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -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 -c ggm_mpl_bd.cpp -o ggm_mpl_bd.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -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 -c gm_mpl_Hill_Climb.cpp -o gm_mpl_Hill_Climb.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -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 -c gm_mpl_bd_dis.cpp -o gm_mpl_bd_dis.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -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 -c gm_rj.cpp -o gm_rj.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -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 -c matrix.cpp -o matrix.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -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 -c omp_set_num_cores.cpp -o omp_set_num_cores.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -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 -c rgwish.cpp -o rgwish.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -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 -c tgm_bd.cpp -o tgm_bd.o g++ -std=gnu++11 -shared -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 BDgraph.so BDgraph_init.o copula.o gcgm_DMH.o gcgm_bd.o gcgm_dw_bd.o ggm_DMH.o ggm_bd.o ggm_mpl_bd.o gm_mpl_Hill_Climb.o gm_mpl_bd_dis.o gm_rj.o matrix.o omp_set_num_cores.o rgwish.o tgm_bd.o -fopenmp -lflexiblas -lflexiblas -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR matrix.cpp: In function 'transfer_data': matrix.cpp:1117:50: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1117 | string *unique_patterns = new string[ *n ]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ installing to /builddir/build/BUILDROOT/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/usr/local/lib/R/library/00LOCK-BDgraph/00new/BDgraph/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'BDgraph' finding HTML links ... done BDgraph-package html adj2link html auc html bdgraph html bdgraph.dw html bdgraph.mpl html bdgraph.npn html bdgraph.sim html bdw.reg html bf html compare html conf.mat html conf.mat.plot html covariance html ddweibull html geneExpression html gnorm html graph.sim html link2adj html pgraph html plinks html plot.bdgraph html plot.graph html finding level-2 HTML links ... done plot.sim html plotcoda html plotroc html posterior.predict html precision html predict.bdgraph html print.bdgraph html print.sim html reinis html rgwish html rmvnorm html roc html rwish html select html sparsity html summary.bdgraph html surveyData html traceplot html trensfer html *** copying figures ** 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 (BDgraph) + test -d BDgraph/src + cd BDgraph/src + rm -f BDgraph_init.o copula.o gcgm_DMH.o gcgm_bd.o gcgm_dw_bd.o ggm_DMH.o ggm_bd.o ggm_mpl_bd.o gm_mpl_Hill_Climb.o gm_mpl_bd_dis.o gm_rj.o matrix.o omp_set_num_cores.o rgwish.o tgm_bd.o BDgraph.so + rm -f /builddir/build/BUILDROOT/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/usr/local/lib/R/library/R.css + find /builddir/build/BUILDROOT/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/usr/local/lib/R/library -type f -exec sed -i s@/builddir/build/BUILDROOT/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64@@g '{}' ';' + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 2.72-1.fc39.copr6291085 --unique-debug-suffix -2.72-1.fc39.copr6291085.x86_64 --unique-debug-src-base R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/BDgraph find-debuginfo: starting Extracting debug info from 1 files DWARF-compressing 1 files sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64 908 blocks find-debuginfo: done + /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-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/util.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/tgm_bd.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/rgwish.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/rgwish.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/omp_set_num_cores.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/matrix.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/matrix.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/gm_rj.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/gm_mpl_bd_dis.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/gm_mpl_Hill_Climb.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/ggm_mpl_bd.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/ggm_bd.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/ggm_DMH.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/gcgm_dw_bd.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/gcgm_bd.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/gcgm_DMH.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/copula.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/copula.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64/BDgraph/src/BDgraph_init.c is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/BDgraph/CITATION is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/BDgraph/TODO is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/BDgraph/doc/BDgraph-Examples.Rmd is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/BDgraph/doc/Introduction-BDgraph.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-BDgraph-2.72-1.fc39.copr6291085.x86_64 Provides: R-CRAN-BDgraph = 2.72-1.fc39.copr6291085 R-CRAN-BDgraph(x86-64) = 2.72-1.fc39.copr6291085 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_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.4)(64bit) libflexiblas.so.3()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) rtld(GNU_HASH) Processing files: R-CRAN-BDgraph-debugsource-2.72-1.fc39.copr6291085.x86_64 Provides: R-CRAN-BDgraph-debugsource = 2.72-1.fc39.copr6291085 R-CRAN-BDgraph-debugsource(x86-64) = 2.72-1.fc39.copr6291085 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-CRAN-BDgraph-debuginfo-2.72-1.fc39.copr6291085.x86_64 Provides: R-CRAN-BDgraph-debuginfo = 2.72-1.fc39.copr6291085 R-CRAN-BDgraph-debuginfo(x86-64) = 2.72-1.fc39.copr6291085 debuginfo(build-id) = 9c11ab51f988c85a7b889c193c6d7cfdce2f8f42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-CRAN-BDgraph-debugsource(x86-64) = 2.72-1.fc39.copr6291085 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64 Wrote: /builddir/build/RPMS/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64.rpm Wrote: /builddir/build/RPMS/R-CRAN-BDgraph-debugsource-2.72-1.fc39.copr6291085.x86_64.rpm Wrote: /builddir/build/RPMS/R-CRAN-BDgraph-debuginfo-2.72-1.fc39.copr6291085.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.pv2jUD + umask 022 + cd /builddir/build/BUILD + cd BDgraph + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-CRAN-BDgraph-2.72-1.fc39.copr6291085.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.Q6QmZS + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/BDgraph-SPECPARTS + rm -rf BDgraph BDgraph.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