Mock Version: 6.0 Mock Version: 6.0 Mock Version: 6.0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target aarch64 --nodeps /builddir/build/SPECS/R-rtracklayer.spec'], chrootPath='/var/lib/mock/f42-build-56976098-6547421/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.010w3ion:/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.010w3ion:/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', '816e45037aef45069c38a8452734ba75', '-D', '/var/lib/mock/f42-build-56976098-6547421/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.010w3ion:/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 aarch64 --nodeps /builddir/build/SPECS/R-rtracklayer.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: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721174400 Wrote: /builddir/build/SRPMS/R-rtracklayer-1.62.0-2.fc42.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target aarch64 --nodeps /builddir/build/SPECS/R-rtracklayer.spec'], chrootPath='/var/lib/mock/f42-build-56976098-6547421/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.010w3ion:/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.010w3ion:/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', 'e826c12ae0b24372a83840c39f558259', '-D', '/var/lib/mock/f42-build-56976098-6547421/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.010w3ion:/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 aarch64 --nodeps /builddir/build/SPECS/R-rtracklayer.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: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721174400 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.sAc8HU + umask 022 + cd /builddir/build/BUILD/R-rtracklayer-1.62.0-build + test -d /builddir/build/BUILD/R-rtracklayer-1.62.0-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/R-rtracklayer-1.62.0-build + /usr/bin/rm -rf /builddir/build/BUILD/R-rtracklayer-1.62.0-build + /usr/bin/mkdir -p /builddir/build/BUILD/R-rtracklayer-1.62.0-build + /usr/bin/mkdir -p /builddir/build/BUILD/R-rtracklayer-1.62.0-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.uZ5B6P + umask 022 + cd /builddir/build/BUILD/R-rtracklayer-1.62.0-build + cd /builddir/build/BUILD/R-rtracklayer-1.62.0-build + rm -rf rtracklayer + /usr/bin/mkdir -p rtracklayer + cd rtracklayer + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/rtracklayer_1.62.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + sed -i -e 's|zlibbioc,||' rtracklayer/DESCRIPTION + sed -i -e 's|import(zlibbioc)||' rtracklayer/NAMESPACE + pushd rtracklayer ~/build/BUILD/R-rtracklayer-1.62.0-build/rtracklayer/rtracklayer ~/build/BUILD/R-rtracklayer-1.62.0-build/rtracklayer Patch #0 (0001-fix-format-security.patch): + echo 'Patch #0 (0001-fix-format-security.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file src/handlers.c + popd ~/build/BUILD/R-rtracklayer-1.62.0-build/rtracklayer + cp /builddir/build/SOURCES/rtracklayer_jimkent_license.txt . + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.iyewXm + umask 022 + cd /builddir/build/BUILD/R-rtracklayer-1.62.0-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --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 rtracklayer + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.29e1Qi + umask 022 + cd /builddir/build/BUILD/R-rtracklayer-1.62.0-build + '[' /builddir/build/BUILD/R-rtracklayer-1.62.0-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/R-rtracklayer-1.62.0-build/BUILDROOT ++ dirname /builddir/build/BUILD/R-rtracklayer-1.62.0-build/BUILDROOT + mkdir -p /builddir/build/BUILD/R-rtracklayer-1.62.0-build + mkdir /builddir/build/BUILD/R-rtracklayer-1.62.0-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --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 rtracklayer + mkdir -p /builddir/build/BUILD/R-rtracklayer-1.62.0-build/BUILDROOT/usr/lib64/R/library + /usr/bin/R CMD INSTALL rtracklayer -l /builddir/build/BUILD/R-rtracklayer-1.62.0-build/BUILDROOT/usr/lib64/R/library * installing *source* package ‘rtracklayer’ ... ** using staged installation checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for OPENSSL... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (GCC) 15.0.1 20250201 (Red Hat 15.0.1-0)’ gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c XVector_stubs.c -o XVector_stubs.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c R_init_rtracklayer.c -o R_init_rtracklayer.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c readGFF.c -o readGFF.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c bbiHelper.c -o bbiHelper.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c bigWig.c -o bigWig.o bigWig.c: In function ‘BWGFile_query’: bigWig.c:268:11: warning: ‘ans_nhits’ may be used uninitialized [-Wmaybe-uninitialized] 268 | INTEGER(ans_nhits)[i] = nqhits; | ^~~~~~~~~~~~~~~~~~ bigWig.c:231:58: note: ‘ans_nhits’ was declared here 231 | SEXP ans, ans_start, ans_width, ans_score, ans_ranges, ans_nhits; | ^~~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c bigBedHelper.c -o bigBedHelper.o In file included from /usr/include/string.h:548, from ucsc/common.h:33, from bigBedHelper.h:5, from bigBedHelper.c:1: In function ‘strncpy’, inlined from ‘bbNamedFileChunkKey’ at bigBedHelper.c:148:3: /usr/include/bits/string_fortified.h:100:10: warning: ‘strncpy’ destination unchanged after copying no bytes [-Wstringop-truncation] 100 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c bigBed.c -o bigBed.o bigBed.c: In function ‘BBDFile_write’: bigBed.c:338:10: warning: variable ‘extraIndexListEndOffset’ set but not used [-Wunused-but-set-variable] 338 | bits64 extraIndexListEndOffset = 0; | ^~~~~~~~~~~~~~~~~~~~~~~ bigBed.c: In function ‘BBDFile_query’: bigBed.c:195:7: warning: ‘name’ may be used uninitialized [-Wmaybe-uninitialized] 195 | SET_STRING_ELT(name, i, mkChar(bed->name)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigBed.c:74:54: note: ‘name’ was declared here 74 | SEXP ans, n_qhits, ranges, chromStart, chromWidth, name, score, | ^~~~ bigBed.c:198:7: warning: ‘score’ may be used uninitialized [-Wmaybe-uninitialized] 198 | INTEGER(score)[i] = bed->score; | ^~~~~~~~~~~~~~ bigBed.c:74:60: note: ‘score’ was declared here 74 | SEXP ans, n_qhits, ranges, chromStart, chromWidth, name, score, | ^~~~~ bigBed.c:205:7: warning: ‘thickStart’ may be used uninitialized [-Wmaybe-uninitialized] 205 | INTEGER(thickStart)[i] = bed->thickStart; | ^~~~~~~~~~~~~~~~~~~ bigBed.c:75:26: note: ‘thickStart’ was declared here 75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks, | ^~~~~~~~~~ bigBed.c:204:7: warning: ‘thickWidth’ may be used uninitialized [-Wmaybe-uninitialized] 204 | INTEGER(thickWidth)[i] = bed->thickEnd - bed->thickStart + 1; | ^~~~~~~~~~~~~~~~~~~ bigBed.c:75:38: note: ‘thickWidth’ was declared here 75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks, | ^~~~~~~~~~ bigBed.c:209:7: warning: ‘itemRgb’ may be used uninitialized [-Wmaybe-uninitialized] 209 | SET_STRING_ELT(itemRgb, i, mkChar(rgbBuf)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigBed.c:75:50: note: ‘itemRgb’ was declared here 75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks, | ^~~~~~~ bigBed.c:218:7: warning: ‘blocks’ may be used uninitialized [-Wmaybe-uninitialized] 218 | SET_VECTOR_ELT(blocks, i, new_IRanges("IRanges", bstart, bwidth, R_NilValue)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigBed.c:75:59: note: ‘blocks’ was declared here 75 | strand = R_NilValue, thickStart, thickWidth, itemRgb, blocks, | ^~~~~~ bigBed.c:236:13: warning: ‘lengthIndex’ may be used uninitialized [-Wmaybe-uninitialized] 236 | INTEGER(lengthIndex)[efIndex] = index + 1; | ^~~~~~~~~~~~~~~~~~~~ bigBed.c:76:31: note: ‘lengthIndex’ was declared here 76 | extraFields = R_NilValue, lengthIndex; | ^~~~~~~~~~~ bigBed.c:226:22: warning: ‘typeId’ may be used uninitialized [-Wmaybe-uninitialized] 226 | switch(typeId[efIndex]) { | ^ bigBed.c:141:13: note: ‘typeId’ was declared here 141 | SEXPTYPE *typeId; | ^~~~~~ gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c chain_io.c -o chain_io.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c twoBit.c -o twoBit.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c handlers.c -o handlers.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c utils.c -o utils.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/memgfx.c -o ucsc/memgfx.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/aliType.c -o ucsc/aliType.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/binRange.c -o ucsc/binRange.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/htmlColor.c -o ucsc/htmlColor.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/sqlList.c -o ucsc/sqlList.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/tokenizer.c -o ucsc/tokenizer.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/asParse.c -o ucsc/asParse.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/basicBed.c -o ucsc/basicBed.o ucsc/basicBed.c: In function ‘bedParseRgb’: ucsc/basicBed.c:997:1: warning: ‘strncpy’ specified bound 64 equals destination size [-Wstringop-truncation] 997 | strncpy(dupe, itemRgb, sizeof(dupe)); | ^ gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/bigBed.c -o ucsc/bigBed.o ucsc/bigBed.c: In function ‘extractField’: ucsc/bigBed.c:314:52: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 314 | warn("Not enough fields in extractField of %s", line); | ^~ gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/bbiRead.c -o ucsc/bbiRead.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o ucsc/bwgQuery.c: In function ‘bigWigIntervalQuery’: ucsc/bwgQuery.c:187:25: warning: variable ‘blockEnd’ set but not used [-Wunused-but-set-variable] 187 | char *blockPt, *blockEnd; | ^~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/cirTree.c -o ucsc/cirTree.o gcc -I"/usr/include/R" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ucsc/common.c -o ucsc/common.o ucsc/common.c: In function ‘slUniqify’: ucsc/common.c:360:9: error: too many arguments to function ‘free’; expected 0, have 1 360 | free(el); | ^~~~ ~~ make: *** [/usr/lib64/R/etc/Makeconf:195: ucsc/common.o] Error 1 ERROR: compilation failed for package ‘rtracklayer’ * removing ‘/builddir/build/BUILD/R-rtracklayer-1.62.0-build/BUILDROOT/usr/lib64/R/library/rtracklayer’ RPM build errors: error: Bad exit status from /var/tmp/rpm-tmp.29e1Qi (%install) Bad exit status from /var/tmp/rpm-tmp.29e1Qi (%install) Child return code was: 1 EXCEPTION: [Error('Command failed: \n # /usr/bin/systemd-nspawn -q -M e826c12ae0b24372a83840c39f558259 -D /var/lib/mock/f42-build-56976098-6547421/root -a -u mockbuild --capability=cap_ipc_lock --bind=/tmp/mock-resolv.010w3ion:/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 aarch64 --nodeps /builddir/build/SPECS/R-rtracklayer.spec\'\n', 1)] Traceback (most recent call last): File "/usr/lib/python3.13/site-packages/mockbuild/trace_decorator.py", line 93, in trace result = func(*args, **kw) File "/usr/lib/python3.13/site-packages/mockbuild/util.py", line 610, in do_with_status raise exception.Error("Command failed: \n # %s\n%s" % (cmd_pretty(command, env), output), child.returncode) mockbuild.exception.Error: Command failed: # /usr/bin/systemd-nspawn -q -M e826c12ae0b24372a83840c39f558259 -D /var/lib/mock/f42-build-56976098-6547421/root -a -u mockbuild --capability=cap_ipc_lock --bind=/tmp/mock-resolv.010w3ion:/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 aarch64 --nodeps /builddir/build/SPECS/R-rtracklayer.spec'