Mock Version: 3.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-CRAN-CASMAP.spec'], chrootPath='/var/lib/mock/fedora-38-x86_64-1682112925.668424/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.dh2mj0pf:/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.dh2mj0pf:/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', '14c77a26b6ce4b94a7d11133fa9a73e2', '-D', '/var/lib/mock/fedora-38-x86_64-1682112925.668424/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.dh2mj0pf:/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-CASMAP.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-CASMAP-0.6.1-3.fc38.copr5815886.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-CASMAP.spec'], chrootPath='/var/lib/mock/fedora-38-x86_64-1682112925.668424/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.dh2mj0pf:/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.dh2mj0pf:/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', 'a9499ebe7a5b492fbd370112aaf568ff', '-D', '/var/lib/mock/fedora-38-x86_64-1682112925.668424/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.dh2mj0pf:/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-CASMAP.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.8DkfTk + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf CASMAP + /usr/bin/mkdir -p CASMAP + cd CASMAP + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/CASMAP_0.6.1.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\' '{}' ';' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.3fjGVC + 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 CASMAP + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.DdSTGW + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64 ++ dirname /builddir/build/BUILDROOT/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.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 CASMAP + mkdir -p /builddir/build/BUILDROOT/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/usr/local/lib/R/library + /usr/bin/R CMD INSTALL -l /builddir/build/BUILDROOT/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/usr/local/lib/R/library CASMAP * installing *source* package 'CASMAP' ... ** package 'CASMAP' successfully unpacked and MD5 sums checked ** using staged installation ** libs 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../inst/include -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 ArrayFile.cpp -o ArrayFile.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 CumulativeTimeMeasurement.cpp -o CumulativeTimeMeasurement.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 Exception.cpp -o Exception.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 FeatureSet.cpp -o FeatureSet.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 FilterIntervals.cpp -o FilterIntervals.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 Genotype.cpp -o Genotype.o In file included from ../inst/include/Genotype.h:14, from Genotype.cpp:8: ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ In file included from ../inst/include/Genotype.h:15: ../inst/include/Phenotype.h:222:28: note: by 'virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)' 222 | virtual Phenotype& operator=(const Phenotype& other); | ^~~~~~~~ ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ ../inst/include/Genotype.h:69:27: note: by 'virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)' 69 | virtual Genotype& operator=(const Genotype& other); | ^~~~~~~~ g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 PValues.cpp -o PValues.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 Phenotype.cpp -o Phenotype.o In file included from ../inst/include/Phenotype.h:16, from Phenotype.cpp:8: ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ ../inst/include/Phenotype.h:222:28: note: by 'virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)' 222 | virtual Phenotype& operator=(const Phenotype& other); | ^~~~~~~~ g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 Profiler.cpp -o Profiler.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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../inst/include -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 SignificantFeaturesSearch.cpp -o SignificantFeaturesSearch.o In file included from ../inst/include/Genotype.h:14, from ../inst/include/SignificantFeaturesSearch.h:15, from SignificantFeaturesSearch.cpp:9: ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ In file included from ../inst/include/Genotype.h:15: ../inst/include/Phenotype.h:222:28: note: by 'virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)' 222 | virtual Phenotype& operator=(const Phenotype& other); | ^~~~~~~~ ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ ../inst/include/Genotype.h:69:27: note: by 'virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)' 69 | virtual Genotype& operator=(const Genotype& other); | ^~~~~~~~ g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 SignificantFeaturesSearchTaroneCmh.cpp -o SignificantFeaturesSearchTaroneCmh.o In file included from ../inst/include/Genotype.h:14, from ../inst/include/SignificantFeaturesSearch.h:15, from ../inst/include/SignificantFeaturesSearchWithCovariates.h:11, from ../inst/include/SignificantFeaturesSearchTaroneCmh.h:16, from SignificantFeaturesSearchTaroneCmh.cpp:8: ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ In file included from ../inst/include/Genotype.h:15: ../inst/include/Phenotype.h:222:28: note: by 'virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)' 222 | virtual Phenotype& operator=(const Phenotype& other); | ^~~~~~~~ ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ ../inst/include/Genotype.h:69:27: note: by 'virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)' 69 | virtual Genotype& operator=(const Genotype& other); | ^~~~~~~~ SignificantFeaturesSearchTaroneCmh.cpp: In member function 'virtual void SignificantPattern::SignificantFeaturesSearchTaroneCmh::freq_destructor()': SignificantFeaturesSearchTaroneCmh.cpp:104:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 104 | if (freq_par_cov[0]) delete [] freq_par_cov[0]; freq_par_cov[0] = 0; | ^~ SignificantFeaturesSearchTaroneCmh.cpp:104:57: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 104 | if (freq_par_cov[0]) delete [] freq_par_cov[0]; freq_par_cov[0] = 0; | ^~~~~~~~~~~~ g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 SignificantFeaturesSearchWithCovariates.cpp -o SignificantFeaturesSearchWithCovariates.o In file included from ../inst/include/Genotype.h:14, from ../inst/include/SignificantFeaturesSearch.h:15, from ../inst/include/SignificantFeaturesSearchWithCovariates.h:11, from SignificantFeaturesSearchWithCovariates.cpp:8: ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ In file included from ../inst/include/Genotype.h:15: ../inst/include/Phenotype.h:222:28: note: by 'virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)' 222 | virtual Phenotype& operator=(const Phenotype& other); | ^~~~~~~~ ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ ../inst/include/Genotype.h:69:27: note: by 'virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)' 69 | virtual Genotype& operator=(const Genotype& other); | ^~~~~~~~ g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 SignificantIntervalSearch.cpp -o SignificantIntervalSearch.o In file included from ../inst/include/Genotype.h:14, from ../inst/include/SignificantFeaturesSearch.h:15, from ../inst/include/SignificantIntervalSearch.h:13, from SignificantIntervalSearch.cpp:9: ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ In file included from ../inst/include/Genotype.h:15: ../inst/include/Phenotype.h:222:28: note: by 'virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)' 222 | virtual Phenotype& operator=(const Phenotype& other); | ^~~~~~~~ ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ ../inst/include/Genotype.h:69:27: note: by 'virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)' 69 | virtual Genotype& operator=(const Genotype& other); | ^~~~~~~~ g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 SignificantIntervalSearchChi.cpp -o SignificantIntervalSearchChi.o In file included from ../inst/include/Genotype.h:14, from ../inst/include/SignificantFeaturesSearch.h:15, from ../inst/include/SignificantIntervalSearch.h:13, from ../inst/include/SignificantIntervalSearchFais.h:11, from ../inst/include/SignificantIntervalSearchChi.h:21, from SignificantIntervalSearchChi.cpp:5: ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ In file included from ../inst/include/Genotype.h:15: ../inst/include/Phenotype.h:222:28: note: by 'virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)' 222 | virtual Phenotype& operator=(const Phenotype& other); | ^~~~~~~~ ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ ../inst/include/Genotype.h:69:27: note: by 'virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)' 69 | virtual Genotype& operator=(const Genotype& other); | ^~~~~~~~ g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 SignificantIntervalSearchExact.cpp -o SignificantIntervalSearchExact.o In file included from ../inst/include/Genotype.h:14, from ../inst/include/SignificantFeaturesSearch.h:15, from ../inst/include/SignificantIntervalSearch.h:13, from ../inst/include/SignificantIntervalSearchFais.h:11, from ../inst/include/SignificantIntervalSearchExact.h:21, from SignificantIntervalSearchExact.cpp:8: ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ In file included from ../inst/include/Genotype.h:15: ../inst/include/Phenotype.h:222:28: note: by 'virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)' 222 | virtual Phenotype& operator=(const Phenotype& other); | ^~~~~~~~ ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ ../inst/include/Genotype.h:69:27: note: by 'virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)' 69 | virtual Genotype& operator=(const Genotype& other); | ^~~~~~~~ g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 SignificantIntervalSearchFais.cpp -o SignificantIntervalSearchFais.o In file included from ../inst/include/Genotype.h:14, from ../inst/include/SignificantFeaturesSearch.h:15, from ../inst/include/SignificantIntervalSearch.h:13, from ../inst/include/SignificantIntervalSearchFais.h:11, from SignificantIntervalSearchFais.cpp:8: ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ In file included from ../inst/include/Genotype.h:15: ../inst/include/Phenotype.h:222:28: note: by 'virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)' 222 | virtual Phenotype& operator=(const Phenotype& other); | ^~~~~~~~ ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ ../inst/include/Genotype.h:69:27: note: by 'virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)' 69 | virtual Genotype& operator=(const Genotype& other); | ^~~~~~~~ g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 SignificantIntervalSearchFastCmh.cpp -o SignificantIntervalSearchFastCmh.o In file included from ../inst/include/Genotype.h:14, from ../inst/include/SignificantFeaturesSearch.h:15, from ../inst/include/SignificantIntervalSearch.h:13, from ../inst/include/SignificantIntervalSearchFastCmh.h:11, from SignificantIntervalSearchFastCmh.cpp:8: ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ In file included from ../inst/include/Genotype.h:15: ../inst/include/Phenotype.h:222:28: note: by 'virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)' 222 | virtual Phenotype& operator=(const Phenotype& other); | ^~~~~~~~ ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ ../inst/include/Genotype.h:69:27: note: by 'virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)' 69 | virtual Genotype& operator=(const Genotype& other); | ^~~~~~~~ g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 SignificantItemsetSearch.cpp -o SignificantItemsetSearch.o In file included from ../inst/include/Genotype.h:14, from ../inst/include/SignificantFeaturesSearch.h:15, from ../inst/include/SignificantItemsetSearch.h:11, from SignificantItemsetSearch.cpp:8: ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ In file included from ../inst/include/Genotype.h:15: ../inst/include/Phenotype.h:222:28: note: by 'virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)' 222 | virtual Phenotype& operator=(const Phenotype& other); | ^~~~~~~~ ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ ../inst/include/Genotype.h:69:27: note: by 'virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)' 69 | virtual Genotype& operator=(const Genotype& other); | ^~~~~~~~ g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 SignificantItemsetSearchFacs.cpp -o SignificantItemsetSearchFacs.o In file included from ../inst/include/Genotype.h:14, from ../inst/include/SignificantFeaturesSearch.h:15, from ../inst/include/SignificantItemsetSearch.h:11, from ../inst/include/SignificantItemsetSearchFacs.h:11, from SignificantItemsetSearchFacs.cpp:8: ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ In file included from ../inst/include/Genotype.h:15: ../inst/include/Phenotype.h:222:28: note: by 'virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)' 222 | virtual Phenotype& operator=(const Phenotype& other); | ^~~~~~~~ ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ ../inst/include/Genotype.h:69:27: note: by 'virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)' 69 | virtual Genotype& operator=(const Genotype& other); | ^~~~~~~~ g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 Summary.cpp -o Summary.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 TransactionsData.cpp -o TransactionsData.o In file included from ../inst/include/Genotype.h:14, from ../inst/include/TransactionsData.h:13, from TransactionsData.cpp:14: ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ In file included from ../inst/include/Genotype.h:15: ../inst/include/Phenotype.h:222:28: note: by 'virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)' 222 | virtual Phenotype& operator=(const Phenotype& other); | ^~~~~~~~ ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ ../inst/include/Genotype.h:69:27: note: by 'virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)' 69 | virtual Genotype& operator=(const Genotype& other); | ^~~~~~~~ g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 double_comp.cpp -o double_comp.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 gamma.cpp -o gamma.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 pval.cpp -o pval.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I../inst/include -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 sigpatsearch.cpp -o sigpatsearch.o In file included from ../inst/include/Genotype.h:14, from ../inst/include/SignificantFeaturesSearch.h:15, from sigpatsearch.cpp:6: ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ In file included from ../inst/include/Genotype.h:15: ../inst/include/Phenotype.h:222:28: note: by 'virtual SignificantPattern::Phenotype& SignificantPattern::Phenotype::operator=(const SignificantPattern::Phenotype&)' 222 | virtual Phenotype& operator=(const Phenotype& other); | ^~~~~~~~ ../inst/include/ArrayFile.h:80:28: warning: 'virtual SignificantPattern::ArrayFile& SignificantPattern::ArrayFile::operator=(const SignificantPattern::ArrayFile&)' was hidden [-Woverloaded-virtual=] 80 | virtual ArrayFile& operator=(const ArrayFile& other); | ^~~~~~~~ ../inst/include/Genotype.h:69:27: note: by 'virtual SignificantPattern::Genotype& SignificantPattern::Genotype::operator=(const SignificantPattern::Genotype&)' 69 | virtual Genotype& operator=(const Genotype& other); | ^~~~~~~~ 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 CASMAP.so ArrayFile.o CumulativeTimeMeasurement.o Exception.o FeatureSet.o FilterIntervals.o Genotype.o PValues.o Phenotype.o Profiler.o RcppExports.o SignificantFeaturesSearch.o SignificantFeaturesSearchTaroneCmh.o SignificantFeaturesSearchWithCovariates.o SignificantIntervalSearch.o SignificantIntervalSearchChi.o SignificantIntervalSearchExact.o SignificantIntervalSearchFais.o SignificantIntervalSearchFastCmh.o SignificantItemsetSearch.o SignificantItemsetSearchFacs.o Summary.o TransactionsData.o double_comp.o gamma.o pval.o sigpatsearch.o -L/usr/lib64/R/lib -lR installing to /builddir/build/BUILDROOT/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/usr/local/lib/R/library/00LOCK-CASMAP/00new/CASMAP/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'CASMAP' finding HTML links ... done CASMAP-class html CASMAPenv html SignificantIntervalSearchChi-class html SignificantIntervalSearchExact-class html SignificantIntervalSearchFastCmh-class html SignificantItemsetSearchFacs-class html checkIsBoolean html getExampleCovariatesFilename html getExampleDataFilename html getExampleLabelsFilename html getExampleSignificantRegionsFilename html getHigherOrderEpistasisString html getMinModeLength html getParentFunctionName html getRegionGWASString html isHigherOrderEpistasisString html isInOpenInterval html isRegionGWASString html lib_delete_search_chi html lib_delete_search_e html lib_delete_search_facs html lib_delete_search_fastcmh html lib_execute_int html lib_execute_iset html lib_filter_intervals_write_to_file html lib_get_filtered_intervals html lib_get_result_facs html lib_get_result_fais html lib_get_result_int html lib_get_result_iset html lib_get_significant_intervals html lib_get_significant_itemsets html lib_new_search_chi html lib_new_search_e html lib_new_search_facs html lib_new_search_fastcmh html lib_profiler_write_to_file html lib_pvals_significant_ints_write_to_file html lib_pvals_significant_isets_write_to_file html lib_pvals_testable_ints_write_to_file html lib_pvals_testable_isets_write_to_file html lib_read_covariates_file_facs html lib_read_covariates_file_fastcmh html lib_read_eth_files html lib_read_eth_files_with_cov_facs html lib_read_eth_files_with_cov_fastcmh html lib_read_plink_files html lib_read_plink_files_with_cov_facs html lib_read_plink_files_with_cov_fastcmh html lib_summary_write_to_file_facs html lib_summary_write_to_file_fais html lib_summary_write_to_file_fastcmh html lib_write_eth_files_int html lib_write_eth_files_iset html lib_write_eth_files_with_cov_facs html lib_write_eth_files_with_cov_fastcmh html m_SignificantFeaturesSearch-class html m_SignificantFeaturesSearchWithCovariates-class html m_SignificantIntervalSearch-class html m_SignificantIntervalSearchFais-class html m_SignificantItemsetSearch-class html modeErrorMessage html modeLengthErrorMessage html modeNeedsMoreChars 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 (CASMAP) + test -d CASMAP/src + cd CASMAP/src + rm -f ArrayFile.o CumulativeTimeMeasurement.o Exception.o FeatureSet.o FilterIntervals.o Genotype.o PValues.o Phenotype.o Profiler.o RcppExports.o SignificantFeaturesSearch.o SignificantFeaturesSearchTaroneCmh.o SignificantFeaturesSearchWithCovariates.o SignificantIntervalSearch.o SignificantIntervalSearchChi.o SignificantIntervalSearchExact.o SignificantIntervalSearchFais.o SignificantIntervalSearchFastCmh.o SignificantItemsetSearch.o SignificantItemsetSearchFacs.o Summary.o TransactionsData.o double_comp.o gamma.o pval.o sigpatsearch.o CASMAP.so + rm -f /builddir/build/BUILDROOT/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/usr/local/lib/R/library/R.css + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 0.6.1-3.fc38.copr5815886 --unique-debug-suffix -0.6.1-3.fc38.copr5815886.x86_64 --unique-debug-src-base R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/CASMAP extracting debug info from /builddir/build/BUILDROOT/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/usr/local/lib/R/library/CASMAP/libs/CASMAP.so original debug info size: 5220kB, size after compression: 4492kB /usr/bin/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 637 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-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/pval.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/gamma.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/double_comp.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/TransactionsData.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/Summary.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/SignificantItemsetSearchFacs.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/SignificantItemsetSearch.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/SignificantIntervalSearchFastCmh.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/SignificantIntervalSearchFais.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/SignificantIntervalSearchExact.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/SignificantIntervalSearchChi.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/SignificantIntervalSearch.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/SignificantFeaturesSearchWithCovariates.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/SignificantFeaturesSearchTaroneCmh.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/SignificantFeaturesSearch.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/Profiler.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/Phenotype.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/PValues.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/Genotype.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/FilterIntervals.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/FeatureSet.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/Exception.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/CumulativeTimeMeasurement.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/src/ArrayFile.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/types.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/pval.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/gamma.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/double_comp.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/chi2.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/TransactionsData.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/Summary.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/SignificantItemsetSearchFacs.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/SignificantItemsetSearch.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/SignificantIntervalSearchFastCmh.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/SignificantIntervalSearchFais.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/SignificantIntervalSearchExact.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/SignificantIntervalSearchChi.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/SignificantIntervalSearch.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/SignificantFeaturesSearchWithCovariates.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/SignificantFeaturesSearchTaroneCmh.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/SignificantFeaturesSearch.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/Profiler.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/Phenotype.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/PValues.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/Genotype.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/FilterIntervals.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/FeatureSet.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/Exception.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/CumulativeTimeMeasurement.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64/CASMAP/inst/include/ArrayFile.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/types.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/pval.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/mem_rss.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/gamma.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/double_comp.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/chi2.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/TransactionsData.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/Summary.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/SignificantItemsetSearchFacs.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/SignificantItemsetSearch.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/SignificantIntervalSearchFastCmh.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/SignificantIntervalSearchFais.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/SignificantIntervalSearchExact.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/SignificantIntervalSearchChi.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/SignificantIntervalSearch.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/SignificantFeaturesSearchWithCovariates.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/SignificantFeaturesSearchTaroneCmh.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/SignificantFeaturesSearch.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/Profiler.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/Phenotype.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/PValues.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/Genotype.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/FilterIntervals.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/FeatureSet.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/Exception.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/CumulativeTimeMeasurement.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/CASMAP.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/include/ArrayFile.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/extdata/CASMAP_example_labels_1.txt is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/extdata/CASMAP_example_data_1.txt is executable but has no shebang, removing executable bit *** WARNING: ./usr/local/lib/R/library/CASMAP/extdata/CASMAP_example_covariates_1.txt 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-CASMAP-0.6.1-3.fc38.copr5815886.x86_64 Provides: R-CRAN-CASMAP = 0.6.1-3.fc38.copr5815886 R-CRAN-CASMAP(x86-64) = 0.6.1-3.fc38.copr5815886 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_1.3.8)(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) rtld(GNU_HASH) Processing files: R-CRAN-CASMAP-debugsource-0.6.1-3.fc38.copr5815886.x86_64 Provides: R-CRAN-CASMAP-debugsource = 0.6.1-3.fc38.copr5815886 R-CRAN-CASMAP-debugsource(x86-64) = 0.6.1-3.fc38.copr5815886 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-CRAN-CASMAP-debuginfo-0.6.1-3.fc38.copr5815886.x86_64 Provides: R-CRAN-CASMAP-debuginfo = 0.6.1-3.fc38.copr5815886 R-CRAN-CASMAP-debuginfo(x86-64) = 0.6.1-3.fc38.copr5815886 debuginfo(build-id) = ae04ae1e0f49125fde7bf5cc22fb21efdf4c396e Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-CRAN-CASMAP-debugsource(x86-64) = 0.6.1-3.fc38.copr5815886 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64 Wrote: /builddir/build/RPMS/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64.rpm Wrote: /builddir/build/RPMS/R-CRAN-CASMAP-debugsource-0.6.1-3.fc38.copr5815886.x86_64.rpm Wrote: /builddir/build/RPMS/R-CRAN-CASMAP-debuginfo-0.6.1-3.fc38.copr5815886.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.kFNwtZ + umask 022 + cd /builddir/build/BUILD + cd CASMAP + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-CRAN-CASMAP-0.6.1-3.fc38.copr5815886.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.YBSDfc + umask 022 + cd /builddir/build/BUILD + rm -rf CASMAP CASMAP.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