Mock Version: 5.0 Mock Version: 5.0 Mock Version: 5.0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-Rsamtools.spec'], chrootPath='/var/lib/mock/f40-build-789414-135700/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=604800uid=982gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.1x_qzwzx:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.1x_qzwzx:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '743bf7e8228043ef8c88617e3d20b1f8', '-D', '/var/lib/mock/f40-build-789414-135700/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.1x_qzwzx:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-Rsamtools.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 Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1705881600 Wrote: /builddir/build/SRPMS/R-Rsamtools-2.12.0-6.fc40.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-Rsamtools.spec'], chrootPath='/var/lib/mock/f40-build-789414-135700/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=604800uid=982gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.1x_qzwzx:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.1x_qzwzx:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'e170d85895fb4cdeb822ddf2ff9ff41d', '-D', '/var/lib/mock/f40-build-789414-135700/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.1x_qzwzx:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-Rsamtools.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 Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1705881600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.sgYeuI + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf Rsamtools + /usr/bin/mkdir -p Rsamtools + cd Rsamtools + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/Rsamtools_2.12.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + rm -rf /builddir/build/BUILD/Rsamtools-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/Rsamtools-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + sed -i 's|zlibbioc, ||g' Rsamtools/DESCRIPTION + sed -i '/import(zlibbioc)/d' Rsamtools/NAMESPACE + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.uexxKW + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 Rsamtools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.O62hEV + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-Rsamtools-2.12.0-6.fc40.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-Rsamtools-2.12.0-6.fc40.riscv64 ++ dirname /builddir/build/BUILDROOT/R-Rsamtools-2.12.0-6.fc40.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-Rsamtools-2.12.0-6.fc40.riscv64 + CFLAGS='-O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 Rsamtools + mkdir -p /builddir/build/BUILDROOT/R-Rsamtools-2.12.0-6.fc40.riscv64/usr/lib64/R/library + R CMD INSTALL -l /builddir/build/BUILDROOT/R-Rsamtools-2.12.0-6.fc40.riscv64/usr/lib64/R/library Rsamtools * installing *source* package ‘Rsamtools’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 14.0.1 20240217 (Red Hat 14.0.1-0)’ using C++ compiler: ‘g++ (GCC) 14.0.1 20240217 (Red Hat 14.0.1-0)’ gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c IRanges_stubs.c -o IRanges_stubs.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c PileupBuffer.cpp -o PileupBuffer.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c PosCacheColl.cpp -o PosCacheColl.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c R_init_Rsamtools.c -o R_init_Rsamtools.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c ResultManager.cpp -o ResultManager.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c XVector_stubs.c -o XVector_stubs.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c as_bam.c -o as_bam.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c bam.c -o bam.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c bam_data.c -o bam_data.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c bam_mate_iter.cpp -o bam_mate_iter.o In file included from /usr/lib64/R/library/Rhtslib/include/sam.h:29, from Template.h:9, from BamIterator.h:10, from BamRangeIterator.h:7, from bam_mate_iter.cpp:2: BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’: /usr/lib64/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) | ~~~~~~~~~^~~~~~~~~~~~~~ BamRangeIterator.h:138:16: note: in expansion of macro ‘bam_seek’ 138 | (void) bam_seek(bfile, pos, SEEK_SET); | ^~~~~~~~ BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’: /usr/lib64/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) | ~~~~~~~~~^~~~~~~~~~~~~~ BamIterator.h:87:16: note: in expansion of macro ‘bam_seek’ 87 | (void) bam_seek(bfile, 0, 0); | ^~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c bam_plbuf.c -o bam_plbuf.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c bam_sort.c -o bam_sort.o In file included from /usr/include/string.h:548, from /usr/lib64/R/library/Rhtslib/include/bam_sort.c:34, from bam_sort.c:1: In function ‘memcpy’, inlined from ‘kputsn’ at /usr/lib64/R/library/Rhtslib/include/htslib/kstring.h:148:2, inlined from ‘kputs’ at /usr/lib64/R/library/Rhtslib/include/htslib/kstring.h:156:9, inlined from ‘trans_rg_pg.isra’ at /usr/lib64/R/library/Rhtslib/include/bam_sort.c:625:17: /usr/include/bits/string_fortified.h:29:10: warning: ‘__builtin_memcpy’ specified bound 18446744073709551614 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib64/R/library/Rhtslib/include/bam_sort.c: In function ‘bam_sort_core_ext’: /usr/lib64/R/library/Rhtslib/include/bam_sort.c:2065:9: warning: ‘__builtin_strncpy’ specified bound 2 equals destination size [-Wstringop-truncation] 2065 | strncpy(g_sort_tag, sort_by_tag, 2); | ^ gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c bambuffer.c -o bambuffer.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c bamfile.c -o bamfile.o bamfile.c: In function ‘bamfile_isincomplete’: bamfile.c:168:20: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 168 | (void) bgzf_seek(bfile->file->x.bam, offset, SEEK_SET); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘_bam_tryindexload’, inlined from ‘_bamfile_open_r’ at bamfile.c:89:24, inlined from ‘bamfile_open’ at bamfile.c:127:17: bamfile.c:29:17: warning: ‘cfile’ may be used uninitialized [-Wmaybe-uninitialized] 29 | index = hts_idx_load2(file, indexname); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bamfile.c: In function ‘bamfile_open’: bamfile.c:73:17: note: ‘cfile’ was declared here 73 | const char *cfile; | ^~~~~ gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c bcffile.c -o bcffile.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c encode.c -o encode.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c fafile.c -o fafile.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c idxstats.c -o idxstats.o In file included from /usr/lib64/R/library/Rhtslib/include/sam.h:29, from bamfile.h:5, from idxstats.c:1: idxstats.c: In function ‘idxstats_bamfile’: /usr/lib64/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) | ^~~~~~~~~~~~~~~~~~~~~~~ idxstats.c:20:12: note: in expansion of macro ‘bam_seek’ 20 | (void) bam_seek(fp, 0, 0); | ^~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c io_sam.c -o io_sam.o In file included from /usr/lib64/R/library/Rhtslib/include/sam.h:29, from io_sam.c:2: io_sam.c: In function ‘_scan_bam_all’: /usr/lib64/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) | ^~~~~~~~~~~~~~~~~~~~~~~ io_sam.c:304:12: note: in expansion of macro ‘bam_seek’ 304 | (void) bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET); | ^~~~~~~~ g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c pileup.cpp -o pileup.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c pileupbam.c -o pileupbam.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c sam.c -o sam.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c sam_opts.c -o sam_opts.o In file included from sam_opts.c:1: /usr/lib64/R/library/Rhtslib/include/sam_opts.c: In function ‘parse_sam_global_opt’: /usr/lib64/R/library/Rhtslib/include/sam_opts.c:85:52: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 85 | fprintf(stderr, "Unexpected global option: %s\n", lopt->name); | ^~ gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c sam_utils.c -o sam_utils.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c samtools_patch.c -o samtools_patch.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c scan_bam_data.c -o scan_bam_data.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c tabixfile.c -o tabixfile.o tabixfile.c: In function ‘index_tabix’: tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations] 190 | if (bgzf_is_bgzf(fn) != 1) | ^~ In file included from tabixfile.c:3: /usr/lib64/R/library/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here 243 | int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead"); | ^~~~~~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c tagfilter.c -o tagfilter.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c utilities.c -o utilities.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -I/usr/local/include -fpic -O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c zip_compression.c -o zip_compression.o g++ -std=gnu++17 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -o Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o /usr/lib64/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/usr/lib64/R/lib -lR installing to /builddir/build/BUILDROOT/R-Rsamtools-2.12.0-6.fc40.riscv64/usr/lib64/R/library/00LOCK-Rsamtools/00new/Rsamtools/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘Rsamtools’ finding HTML links ... done ApplyPileupsParam-class html BamFile-class html finding level-2 HTML links ... done BamViews-class html BcfFile-class html FaFile-class html PileupFiles-class html Rsamtools-package html RsamtoolsFile-class html RsamtoolsFileList-class html ScanBamParam-class html ScanBcfParam-class html TabixFile-class html applyPileups html defunct html deprecated html headerTabix html indexTabix html pileup html quickBamFlagSummary html readPileup html scanBam html scanBcf html scanFa html scanTabix html seqnamesTabix html testPairedEndBam html zip 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 (Rsamtools) + test -d Rsamtools/src + cd Rsamtools/src + rm -f Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o Rsamtools.so + rm -f /builddir/build/BUILDROOT/R-Rsamtools-2.12.0-6.fc40.riscv64/usr/lib64/R/library/R.css + /usr/bin/find-debuginfo -j64 --strict-build-id -m -i --build-id-seed 2.12.0-6.fc40 --unique-debug-suffix -2.12.0-6.fc40.riscv64 --unique-debug-src-base R-Rsamtools-2.12.0-6.fc40.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/Rsamtools find-debuginfo: starting Extracting debug info from 1 files DWARF-compressing 1 files sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/R-Rsamtools-2.12.0-6.fc40.riscv64 490 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs mangling shebang in /usr/lib64/R/library/Rsamtools/scripts/update-samtools.sh from /bin/sh to #!/usr/bin/sh + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j64 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.ngirKB + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 Rsamtools + RPM_EC=0 ++ jobs -p Processing files: R-Rsamtools-2.12.0-6.fc40.riscv64 + exit 0 Provides: R(Rsamtools) = 2.12.0 R-Rsamtools = 2.12.0-6.fc40 R-Rsamtools(riscv-64) = 2.12.0-6.fc40 R-Rsamtools-devel = 2.12.0-6.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/sh R(ABI) = 4.3 R(BiocGenerics) >= 0.25.1 R(BiocParallel) R(Biostrings) >= 2.47.6 R(GenomeInfoDb) >= 1.1.3 R(GenomicRanges) >= 1.31.8 R(IRanges) >= 2.13.12 R(S4Vectors) >= 0.17.25 R(XVector) >= 0.19.7 R(bitops) R(methods) R(stats) R(utils) R-core >= 3.5.0 ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libcurl.so.4()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.4)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) rtld(GNU_HASH) Obsoletes: R-Rsamtools-devel <= 1.34.1 Suggests: R(GenomicAlignments) R(RUnit) Processing files: R-Rsamtools-debugsource-2.12.0-6.fc40.riscv64 Provides: R-Rsamtools-debugsource = 2.12.0-6.fc40 R-Rsamtools-debugsource(riscv-64) = 2.12.0-6.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-Rsamtools-debuginfo-2.12.0-6.fc40.riscv64 Provides: R-Rsamtools-debuginfo = 2.12.0-6.fc40 R-Rsamtools-debuginfo(riscv-64) = 2.12.0-6.fc40 debuginfo(build-id) = a659401ec1f7c4e90f8d781abd6e1bf4045a4831 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-Rsamtools-debugsource(riscv-64) = 2.12.0-6.fc40 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-Rsamtools-2.12.0-6.fc40.riscv64 Wrote: /builddir/build/RPMS/R-Rsamtools-debugsource-2.12.0-6.fc40.riscv64.rpm Wrote: /builddir/build/RPMS/R-Rsamtools-debuginfo-2.12.0-6.fc40.riscv64.rpm Wrote: /builddir/build/RPMS/R-Rsamtools-2.12.0-6.fc40.riscv64.rpm Child return code was: 0