Mock Version: 3.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-CRAN-bio3d.spec'], chrootPath='/var/lib/mock/fedora-38-x86_64-1682111675.738233/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.b97h_z0f:/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.b97h_z0f:/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', '9871166f05584044b94e3128ccd0c149', '-D', '/var/lib/mock/fedora-38-x86_64-1682111675.738233/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.b97h_z0f:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-CRAN-bio3d.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-bio3d-2.4.4-1.fc38.copr5815739.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-bio3d.spec'], chrootPath='/var/lib/mock/fedora-38-x86_64-1682111675.738233/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.b97h_z0f:/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.b97h_z0f:/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', '1c32359fa9bf40f88db3e6738db8bd20', '-D', '/var/lib/mock/fedora-38-x86_64-1682111675.738233/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.b97h_z0f:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/R-CRAN-bio3d.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.PNK5lv + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf bio3d + /usr/bin/mkdir -p bio3d + cd bio3d + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/bio3d_2.4-4.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 bio3d/src ']' + find bio3d/src -type f -exec sed -i s@/usr/bin/strip@/usr/bin/true@g '{}' ';' + '[' -d bio3d/src ']' + find bio3d/src/Makevars -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.IpVvnR + 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 + 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 bio3d + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.s5oHLF + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.x86_64 ++ dirname /builddir/build/BUILDROOT/R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.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 + 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 bio3d + mkdir -p /builddir/build/BUILDROOT/R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.x86_64/usr/local/lib/R/library + /usr/bin/R CMD INSTALL -l /builddir/build/BUILDROOT/R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.x86_64/usr/local/lib/R/library bio3d * installing *source* package 'bio3d' ... ** package 'bio3d' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (GCC) 13.0.1 20230401 (Red Hat 13.0.1-0)' using C++ compiler: 'g++ (GCC) 13.0.1 20230401 (Red Hat 13.0.1-0)' using C++11 g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I'/usr/local/lib/R/library/Rcpp/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++11 -I"/usr/include/R" -DNDEBUG -I. -I'/usr/local/lib/R/library/Rcpp/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 gzstream.cpp -o gzstream.o gcc -I"/usr/include/R" -DNDEBUG -I. -I'/usr/local/lib/R/library/Rcpp/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 init.c -o init.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I'/usr/local/lib/R/library/Rcpp/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 read_cif.cpp -o read_cif.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I'/usr/local/lib/R/library/Rcpp/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 read_crd.cpp -o read_crd.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I'/usr/local/lib/R/library/Rcpp/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 read_pdb.cpp -o read_pdb.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I'/usr/local/lib/R/library/Rcpp/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 read_prmtop.cpp -o read_prmtop.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I. -I'/usr/local/lib/R/library/Rcpp/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 utils.cpp -o utils.o g++ -std=gnu++11 -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 bio3d.so RcppExports.o gzstream.o init.o read_cif.o read_crd.o read_pdb.o read_prmtop.o utils.o -lz -L/usr/lib64/R/lib -lR installing to /builddir/build/BUILDROOT/R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.x86_64/usr/local/lib/R/library/00LOCK-bio3d/00new/bio3d/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'bio3d' finding HTML links ... done aa.index html aa.table html aa123 html aa2index html aa2mass html aanma.pdb html aanma.pdbs html aln2html html angle.xyz html as.fasta html as.pdb html as.select html atom.index html atom.select html atom2ele html atom2mass html atom2xyz html basename.pdb html bhattacharyya html binding.site html bio3d.package html biounit html blast.pdb html bounds html bounds.sse html bwr.colors html cat.pdb html chain.pdb html check.utility html clean.pdb html cmap html cna html cnapath html com html combine.select html community.aln html community.tree html consensus html conserv html convert.pdb html core.cmap html core.find html cov.nma html covsoverlap html dccm html dccm.enma html dccm.gnm html dccm.nma html dccm.pca html dccm.xyz html deformation.nma html diag.ind html difference.vector html dist.xyz html dm html dssp html elements html entropy html example.data html filter.cmap html filter.dccm html filter.identity html filter.rmsd html fit.xyz html fluct.nma html formula2mass html gap.inspect html geostas html get.pdb html get.seq html gnm html hclustplot html hmmer html identify.cna html inner.prod html inspect.connectivity html is.gap html is.mol2 html is.pdb html is.select html is.xyz html layout.cna html lbio3d html load.enmff html mask.dccm html mktrj html motif.find html mustang html network.amendment html nma html nma.pdb html nma.pdbs html normalize.vector html orient.pdb html overlap html pairwise html pca html pca.array html pca.pdbs html pca.tor html pca.xyz html pdb.annotate html pdb2aln html pdb2aln.ind html pdb2sse html pdbaln html pdbfit html pdbs2pdb html pdbs2sse html pdbseq html pdbsplit html pfam html plot.bio3d html plot.cmap html plot.cna html plot.core html plot.dccm html plot.dmat html plot.enma html plot.fasta html plot.fluct html plot.geostas html plot.hmmer html plot.matrix.loadings html plot.nma html plot.pca html plot.pca.loadings html plot.rmsip html print.cna html print.core html print.fasta html print.xyz html project.pca html prune.cna html pymol html read.all html read.cif html read.crd html read.crd.amber html read.crd.charmm html read.dcd html read.fasta html read.fasta.pdb html read.mol2 html read.ncdf html read.pdb html read.pdcBD html read.pqr html read.prmtop html rgyr html rle2 html rmsd html rmsf html rmsip html sdENM html seq2aln html seqaln html seqaln.pair html seqbind html seqidentity html setup.ncore html sip html sse.bridges html store.atom html struct.aln html torsion.pdb html torsion.xyz html trim.mol2 html trim.pdb html trim.pdbs html trim.xyz html unbound html uniprot html var.xyz html vec2resno html vmd.cna html vmd_colors html wrap.tor html write.crd html write.fasta html write.mol2 html write.ncdf html write.pdb html write.pir html write.pqr 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 (bio3d) + test -d bio3d/src + cd bio3d/src + rm -f RcppExports.o gzstream.o init.o read_cif.o read_crd.o read_pdb.o read_prmtop.o utils.o bio3d.so + rm -f /builddir/build/BUILDROOT/R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.x86_64/usr/local/lib/R/library/R.css + find /builddir/build/BUILDROOT/R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.x86_64/usr/local/lib/R/library -type f -exec sed -i s@/builddir/build/BUILDROOT/R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.x86_64@@g '{}' ';' + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 2.4.4-1.fc38.copr5815739 --unique-debug-suffix -2.4.4-1.fc38.copr5815739.x86_64 --unique-debug-src-base R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/bio3d extracting debug info from /builddir/build/BUILDROOT/R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.x86_64/usr/local/lib/R/library/bio3d/libs/bio3d.so original debug info size: 2620kB, size after compression: 2284kB /usr/bin/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 76 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 + /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-bio3d-2.4.4-1.fc38.copr5815739.x86_64 Provides: R-CRAN-bio3d = 2.4.4-1.fc38.copr5815739 R-CRAN-bio3d(x86-64) = 2.4.4-1.fc38.copr5815739 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) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: R-CRAN-bio3d-debugsource-2.4.4-1.fc38.copr5815739.x86_64 Provides: R-CRAN-bio3d-debugsource = 2.4.4-1.fc38.copr5815739 R-CRAN-bio3d-debugsource(x86-64) = 2.4.4-1.fc38.copr5815739 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-CRAN-bio3d-debuginfo-2.4.4-1.fc38.copr5815739.x86_64 Provides: R-CRAN-bio3d-debuginfo = 2.4.4-1.fc38.copr5815739 R-CRAN-bio3d-debuginfo(x86-64) = 2.4.4-1.fc38.copr5815739 debuginfo(build-id) = f5c0031c06456ab8c0bd8c345303c2b29152636d Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-CRAN-bio3d-debugsource(x86-64) = 2.4.4-1.fc38.copr5815739 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.x86_64 Wrote: /builddir/build/RPMS/R-CRAN-bio3d-debuginfo-2.4.4-1.fc38.copr5815739.x86_64.rpm Wrote: /builddir/build/RPMS/R-CRAN-bio3d-debugsource-2.4.4-1.fc38.copr5815739.x86_64.rpm Wrote: /builddir/build/RPMS/R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.PUAA2S + umask 022 + cd /builddir/build/BUILD + cd bio3d + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-CRAN-bio3d-2.4.4-1.fc38.copr5815739.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.y8wXDg + umask 022 + cd /builddir/build/BUILD + rm -rf bio3d bio3d.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