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 i686 --nodeps /builddir/build/SPECS/R-Rsamtools.spec'], chrootPath='/var/lib/mock/f43-build-side-110352-58923970-6569299/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=201600uid=1000gid=425user='mockbuild'unshare_net=TrueprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.m803qg3z:/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.m803qg3z:/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', '76f174896f21400ebf72d64293a6330b', '-D', '/var/lib/mock/f43-build-side-110352-58923970-6569299/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.m803qg3z:/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 i686 --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: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1745020800 Wrote: /builddir/build/SRPMS/R-Rsamtools-2.24.0-2.fc43.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target i686 --nodeps /builddir/build/SPECS/R-Rsamtools.spec'], chrootPath='/var/lib/mock/f43-build-side-110352-58923970-6569299/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=201600uid=1000gid=425user='mockbuild'unshare_net=TrueprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.m803qg3z:/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.m803qg3z:/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', 'dad7efbe68a547298bf71d5750047464', '-D', '/var/lib/mock/f43-build-side-110352-58923970-6569299/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.m803qg3z:/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 i686 --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: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1745020800 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.Y5ivhH Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.mAd5bC + umask 022 + cd /builddir/build/BUILD/R-Rsamtools-2.24.0-build + cd /builddir/build/BUILD/R-Rsamtools-2.24.0-build + rm -rf Rsamtools + /usr/bin/mkdir -p Rsamtools + cd Rsamtools + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/Rsamtools_2.24.0.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-2.24.0-build/Rsamtools/Rsamtools ~/build/BUILD/R-Rsamtools-2.24.0-build/Rsamtools ~/build/BUILD/R-Rsamtools-2.24.0-build/Rsamtools + popd + 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.R7oNs2 + umask 022 + cd /builddir/build/BUILD/R-Rsamtools-2.24.0-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib/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/lib: + 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.aPGUYC + umask 022 + cd /builddir/build/BUILD/R-Rsamtools-2.24.0-build + '[' /builddir/build/BUILD/R-Rsamtools-2.24.0-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/R-Rsamtools-2.24.0-build/BUILDROOT ++ dirname /builddir/build/BUILD/R-Rsamtools-2.24.0-build/BUILDROOT + mkdir -p /builddir/build/BUILD/R-Rsamtools-2.24.0-build + mkdir /builddir/build/BUILD/R-Rsamtools-2.24.0-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib/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/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd Rsamtools + mkdir -p /builddir/build/BUILD/R-Rsamtools-2.24.0-build/BUILDROOT/usr/lib/R/library + R CMD INSTALL -l /builddir/build/BUILD/R-Rsamtools-2.24.0-build/BUILDROOT/usr/lib/R/library Rsamtools * installing *source* package ‘Rsamtools’ ... ** this is package ‘Rsamtools’ version ‘2.24.0’ ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.0.1 20250417 (Red Hat 15.0.1-0)’ using C++ compiler: ‘g++ (GCC) 15.0.1 20250417 (Red Hat 15.0.1-0)’ gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c PosCacheColl.cpp -o PosCacheColl.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c ResultManager.cpp -o ResultManager.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c XVector_stubs.c -o XVector_stubs.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c as_bam.c -o as_bam.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c bam.c -o bam.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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:1: BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’: /usr/lib/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/lib/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 -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c bam_plbuf.c -o bam_plbuf.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c bam_sort.c -o bam_sort.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c bambuffer.c -o bambuffer.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c bcffile.c -o bcffile.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c bedidx.c -o bedidx.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c encode.c -o encode.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c fafile.c -o fafile.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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/lib/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 -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c io_sam.c -o io_sam.o In file included from io_sam.c:3: io_sam.c: In function ‘_scan_bam_all’: /usr/lib/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:302:12: note: in expansion of macro ‘bam_seek’ 302 | (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/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c pileup.cpp -o pileup.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c pileupbam.c -o pileupbam.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c sam_opts.c -o sam_opts.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c sam_utils.c -o sam_utils.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c samtools_patch.c -o samtools_patch.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c scan_bam_data.c -o scan_bam_data.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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/lib/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 -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c tagfilter.c -o tagfilter.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c utilities.c -o utilities.o gcc -std=gnu23 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/library/Rhtslib/include' -I'/usr/lib/R/library/S4Vectors/include' -I'/usr/lib/R/library/IRanges/include' -I'/usr/lib/R/library/XVector/include' -I'/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -c zip_compression.c -o zip_compression.o g++ -std=gnu++17 -shared -L/usr/lib/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.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/lib/R/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/usr/lib/R/lib -lR installing to /builddir/build/BUILD/R-Rsamtools-2.24.0-build/BUILDROOT/usr/lib/R/library/00LOCK-Rsamtools/00new/Rsamtools/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning messages: 1: multiple methods tables found for ‘intersect’ 2: multiple methods tables found for ‘union’ 3: multiple methods tables found for ‘intersect’ 4: multiple methods tables found for ‘setdiff’ 5: multiple methods tables found for ‘intersect’ ** help *** installing help indices converting help for package ‘Rsamtools’ finding HTML links ... done ApplyPileupsParam-class html BamFile-class html Rd warning: BamFile-class.Rd:178: missing link ‘FilterRules’ Rd warning: BamFile-class.Rd:258: missing link ‘SimpleList’ Rd warning: BamFile-class.Rd:305: missing link ‘Seqinfo-class’ BamViews-class html Rd warning: BamViews-class.Rd:88: missing link ‘DataFrame-class’ Rd warning: BamViews-class.Rd:92: missing link ‘GRanges-class’ Rd warning: BamViews-class.Rd:143: missing link ‘DataFrame-class’ Rd warning: BamViews-class.Rd:147: missing link ‘GRanges-class’ Rd warning: BamViews-class.Rd:176: missing link ‘DataFrame-class’ Rd warning: BamViews-class.Rd:180: missing link ‘DataFrame-class’ Rd warning: BamViews-class.Rd:184: missing link ‘GRanges-class’ Rd warning: BamViews-class.Rd:188: missing link ‘GRanges-class’ BcfFile-class html Rd warning: BcfFile-class.Rd:97: missing link ‘SimpleList’ FaFile-class html Rd warning: FaFile-class.Rd:98: missing link ‘GRanges-class’ Rd warning: FaFile-class.Rd:99: missing link ‘IntegerRangesList-class’ Rd warning: FaFile-class.Rd:149: missing link ‘SimpleList’ Rd warning: FaFile-class.Rd:181: missing link ‘GRanges-class’ Rd warning: FaFile-class.Rd:189: missing link ‘DNAStringSet-class’ PileupFiles-class html Rsamtools-package html RsamtoolsFile-class html RsamtoolsFileList-class html Rd warning: RsamtoolsFileList-class.Rd:62: missing link ‘SimpleList’ ScanBamParam-class html Rd warning: ScanBamParam-class.Rd:151: missing link ‘GRanges-class’ Rd warning: ScanBamParam-class.Rd:152: missing link ‘IntegerRangesList-class’ ScanBcfParam-class html TabixFile-class html Rd warning: TabixFile-class.Rd:115: missing link ‘SimpleList’ applyPileups html defunct html deprecated html headerTabix html indexTabix html pileup html quickBamFlagSummary html readPileup html scanBam html Rd warning: scanBam.Rd:100: missing link ‘FilterRules’ scanBcf html scanFa html Rd warning: scanFa.Rd:51: missing link ‘GRanges-class’ Rd warning: scanFa.Rd:52: missing link ‘IntegerRangesList-class’ Rd warning: scanFa.Rd:71: missing link ‘GRanges-class’ Rd warning: scanFa.Rd:76: missing link ‘DNAStringSet-class’ Rd warning: scanFa.Rd:76: missing link ‘RNAStringSet-class’ Rd warning: scanFa.Rd:77: missing link ‘AAStringSet-class’ scanTabix html seqnamesTabix html testPairedEndBam html zip html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: multiple methods tables found for ‘intersect’ Warning: multiple methods tables found for ‘union’ Warning: multiple methods tables found for ‘intersect’ Warning: multiple methods tables found for ‘setdiff’ Warning: multiple methods tables found for ‘intersect’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: multiple methods tables found for ‘intersect’ Warning: multiple methods tables found for ‘union’ Warning: multiple methods tables found for ‘intersect’ Warning: multiple methods tables found for ‘setdiff’ Warning: multiple methods tables found for ‘intersect’ ** 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 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-2.24.0-build/BUILDROOT/usr/lib/R/library/R.css + /usr/bin/find-debuginfo -j6 --strict-build-id -m -i --build-id-seed 2.24.0-2.fc43 --unique-debug-suffix -2.24.0-2.fc43.i386 --unique-debug-src-base R-Rsamtools-2.24.0-2.fc43.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/R-Rsamtools-2.24.0-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-2.24.0-2.fc43.i386 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/lib/R/library/Rsamtools/scripts/update-samtools.sh from /bin/sh to #!/usr/bin/sh + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j6 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j6 /builddir/build/BUILD/R-Rsamtools-2.24.0-build/BUILDROOT Scanned 29 directories and 532 files, processed 370 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/R-Rsamtools-2.24.0-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.QW2kxR + umask 022 + cd /builddir/build/BUILD/R-Rsamtools-2.24.0-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib/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/lib: + 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-2.24.0-2.fc43.i686 Provides: R(Rsamtools) = 2.24.0 R-Rsamtools = 2.24.0-2.fc43 R-Rsamtools(x86-32) = 2.24.0-2.fc43 R-Rsamtools-devel = 2.24.0-2.fc43 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) = 4.5 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 libbz2.so.1 libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.2) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.33) libc.so.6(GLIBC_2.34) libc.so.6(GLIBC_2.38) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_ABI_DT_RELR) libcurl.so.4 libgcc_s.so.1 libgcc_s.so.1(GCC_3.0) libgcc_s.so.1(GCC_3.3.1) libgcc_s.so.1(GCC_7.0.0) libgcc_s.so.1(GLIBC_2.0) liblzma.so.5 liblzma.so.5(XZ_5.0) libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.29) libstdc++.so.6 libstdc++.so.6(CXXABI_1.3) libstdc++.so.6(CXXABI_1.3.9) libstdc++.so.6(GLIBCXX_3.4) libstdc++.so.6(GLIBCXX_3.4.15) libstdc++.so.6(GLIBCXX_3.4.20) libstdc++.so.6(GLIBCXX_3.4.30) libz.so.1 libz.so.1(ZLIB_1.2.3.3) rtld(GNU_HASH) Obsoletes: R-Rsamtools-devel <= 1.34.1 Suggests: R(GenomicAlignments) R(RUnit) R(knitr) Processing files: R-Rsamtools-debugsource-2.24.0-2.fc43.i686 Provides: R-Rsamtools-debugsource = 2.24.0-2.fc43 R-Rsamtools-debugsource(x86-32) = 2.24.0-2.fc43 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-Rsamtools-debuginfo-2.24.0-2.fc43.i686 Provides: R-Rsamtools-debuginfo = 2.24.0-2.fc43 R-Rsamtools-debuginfo(x86-32) = 2.24.0-2.fc43 debuginfo(build-id) = 9a769ac1ad492f41307477688053e5ac608c23a8 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-Rsamtools-debugsource(x86-32) = 2.24.0-2.fc43 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/R-Rsamtools-2.24.0-build/BUILDROOT Wrote: /builddir/build/RPMS/R-Rsamtools-debugsource-2.24.0-2.fc43.i686.rpm Wrote: /builddir/build/RPMS/R-Rsamtools-debuginfo-2.24.0-2.fc43.i686.rpm Wrote: /builddir/build/RPMS/R-Rsamtools-2.24.0-2.fc43.i686.rpm Child return code was: 0