Mock Version: 6.1
Mock Version: 6.1
Mock Version: 6.1
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target ppc64le --nodeps /builddir/build/SPECS/R-Rsamtools.spec'], chrootPath='/var/lib/mock/f41-build-58525456-6566153/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fffb8641370>timeout=201600uid=1000gid=425user='mockbuild'unshare_net=TrueprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.pyy4togv:/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'])
Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.pyy4togv:/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', 'c4e4a0a71dda49a1804c5e9c642aa8c2', '-D', '/var/lib/mock/f41-build-58525456-6566153/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.pyy4togv:/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;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target ppc64le --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;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1721174400
Wrote: /builddir/build/SRPMS/R-Rsamtools-2.18.0-2.fc41.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target ppc64le --nodeps /builddir/build/SPECS/R-Rsamtools.spec'], chrootPath='/var/lib/mock/f41-build-58525456-6566153/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fffb8641370>timeout=201600uid=1000gid=425user='mockbuild'unshare_net=TrueprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.pyy4togv:/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'])
Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.pyy4togv:/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', '35c661da9c90431dae3046df39c28ac5', '-D', '/var/lib/mock/f41-build-58525456-6566153/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.pyy4togv:/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;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target ppc64le --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;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1721174400
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.04sAwJ
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.lfTStg
+ umask 022
+ cd /builddir/build/BUILD/R-Rsamtools-2.18.0-build
+ cd /builddir/build/BUILD/R-Rsamtools-2.18.0-build
+ rm -rf Rsamtools
+ /usr/bin/mkdir -p Rsamtools
+ cd Rsamtools
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/Rsamtools_2.18.0.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ pushd Rsamtools
~/build/BUILD/R-Rsamtools-2.18.0-build/Rsamtools/Rsamtools ~/build/BUILD/R-Rsamtools-2.18.0-build/Rsamtools
Patch #0 (0001-format-security-fix.patch):
+ echo 'Patch #0 (0001-format-security-fix.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0
patching file src/samtools_patch.c
patching file src/zip_compression.c
+ popd
~/build/BUILD/R-Rsamtools-2.18.0-build/Rsamtools
+ 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.lkzI9b
+ umask 022
+ cd /builddir/build/BUILD/R-Rsamtools-2.18.0-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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection '
+ 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 Rsamtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.pJALfQ
+ umask 022
+ cd /builddir/build/BUILD/R-Rsamtools-2.18.0-build
+ '[' /builddir/build/BUILD/R-Rsamtools-2.18.0-build/BUILDROOT '!=' / ']'
+ rm -rf /builddir/build/BUILD/R-Rsamtools-2.18.0-build/BUILDROOT
++ dirname /builddir/build/BUILD/R-Rsamtools-2.18.0-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/R-Rsamtools-2.18.0-build
+ mkdir /builddir/build/BUILD/R-Rsamtools-2.18.0-build/BUILDROOT
+ 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection '
+ 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 Rsamtools
+ mkdir -p /builddir/build/BUILD/R-Rsamtools-2.18.0-build/BUILDROOT/usr/lib64/R/library
+ R CMD INSTALL -l /builddir/build/BUILD/R-Rsamtools-2.18.0-build/BUILDROOT/usr/lib64/R/library Rsamtools
* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 14.2.1 20250110 (Red Hat 14.2.1-7)’
using C++ compiler: ‘g++ (GCC) 14.2.1 20250110 (Red Hat 14.2.1-7)’
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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included 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/samtools-1.7-compat.h:14:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
14 | #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/samtools-1.7-compat.h:14:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
14 | #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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -c bam_sort.c -o bam_sort.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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -c bedidx.c -o bedidx.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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -c idxstats.c -o idxstats.o
In file included from bamfile.h:5,
from idxstats.c:1:
idxstats.c: In function ‘idxstats_bamfile’:
/usr/lib64/R/library/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
14 | #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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -c io_sam.c -o io_sam.o
In file included from io_sam.c:2:
io_sam.c: In function ‘_scan_bam_all’:
/usr/lib64/R/library/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
| ^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:307:12: note: in expansion of macro ‘bam_seek’
307 | (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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -c sam_opts.c -o sam_opts.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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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:270:9: note: declared here
270 | 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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -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,pack-relative-relocs -Wl,-z,now -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_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o bedidx.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.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 -lbz2 -llzma -lz -L/usr/lib64/R/lib -lR
installing to /builddir/build/BUILD/R-Rsamtools-2.18.0-build/BUILDROOT/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_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o bedidx.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.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/BUILD/R-Rsamtools-2.18.0-build/BUILDROOT/usr/lib64/R/library/R.css
+ /usr/bin/find-debuginfo -j8 --strict-build-id -m -i --build-id-seed 2.18.0-2.fc41 --unique-debug-suffix -2.18.0-2.fc41.ppc64le --unique-debug-src-base R-Rsamtools-2.18.0-2.fc41.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/R-Rsamtools-2.18.0-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-2.18.0-2.fc41.ppc64le
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 -j8
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-determinism --brp -j8 /builddir/build/BUILD/R-Rsamtools-2.18.0-build/BUILDROOT
Scanned 30 directories and 531 files,
processed 364 inodes,
0 modified (0 replaced + 0 rewritten),
0 unsupported format, 0 errors
Reading /builddir/build/BUILD/R-Rsamtools-2.18.0-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.5heiMn
+ umask 022
+ cd /builddir/build/BUILD/R-Rsamtools-2.18.0-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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection '
+ 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 Rsamtools
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: R-Rsamtools-2.18.0-2.fc41.ppc64le
Provides: R(Rsamtools) = 2.18.0 R-Rsamtools = 2.18.0-2.fc41 R-Rsamtools(ppc-64) = 2.18.0-2.fc41 R-Rsamtools-devel = 2.18.0-2.fc41
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) = 4.4 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 libR.so()(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libcurl.so.4()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.9)(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) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.3.3)(64bit) rtld(GNU_HASH)
Obsoletes: R-Rsamtools-devel <= 1.34.1
Suggests: R(GenomicAlignments) R(RUnit) R(knitr)
Processing files: R-Rsamtools-debugsource-2.18.0-2.fc41.ppc64le
Provides: R-Rsamtools-debugsource = 2.18.0-2.fc41 R-Rsamtools-debugsource(ppc-64) = 2.18.0-2.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: R-Rsamtools-debuginfo-2.18.0-2.fc41.ppc64le
Provides: R-Rsamtools-debuginfo = 2.18.0-2.fc41 R-Rsamtools-debuginfo(ppc-64) = 2.18.0-2.fc41 debuginfo(build-id) = e550edef9a674585748e0bf0a6f43f139c4af445
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: R-Rsamtools-debugsource(ppc-64) = 2.18.0-2.fc41
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/R-Rsamtools-2.18.0-build/BUILDROOT
Wrote: /builddir/build/RPMS/R-Rsamtools-debugsource-2.18.0-2.fc41.ppc64le.rpm
Wrote: /builddir/build/RPMS/R-Rsamtools-debuginfo-2.18.0-2.fc41.ppc64le.rpm
Wrote: /builddir/build/RPMS/R-Rsamtools-2.18.0-2.fc41.ppc64le.rpm
Child return code was: 0