Mock Version: 6.5 Mock Version: 6.5 Mock Version: 6.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-ape.spec'], chrootPath='/var/lib/mock/f45-build-5992-345/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=864000uid=995gid=135user='mockbuild'unshare_net=TrueprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.tvsynko9:/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.tvsynko9:/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', 'eadcc2017b634c23a03b86b61e2ca5de', '-D', '/var/lib/mock/f45-build-5992-345/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.tvsynko9:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-ape.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1784073600 Wrote: /builddir/build/SRPMS/R-ape-5.8.1-5.fc45.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -br --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-ape.spec'], chrootPath='/var/lib/mock/f45-build-5992-345/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=864000uid=995gid=135user='mockbuild'unshare_net=TrueraiseExc=FalseprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.tvsynko9:/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.tvsynko9:/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', '404e2d45f33f417c87bc80f9b62ed787', '-D', '/var/lib/mock/f45-build-5992-345/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.tvsynko9:/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 -br --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-ape.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1784073600 Executing(mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.VSAqWs Creating(rpmbuild.env): /builddir/build/BUILD/R-ape-5.8.1-build/rpmbuild.env RPM_SOURCE_DIR="/builddir/build/SOURCES" RPM_BUILD_DIR="/builddir/build/BUILD/R-ape-5.8.1-build" RPM_OPT_FLAGS="-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer" RPM_LD_FLAGS="-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes " RPM_ARCH="riscv64" RPM_OS="linux" RPM_BUILD_NCPUS="8" RPM_SPECPARTS_DIR="/builddir/build/BUILD/R-ape-5.8.1-build/SPECPARTS" export RPM_SOURCE_DIR RPM_BUILD_DIR RPM_OPT_FLAGS RPM_ARCH RPM_OS RPM_BUILD_NCPUS RPM_SPECPARTS_DIR RPM_LD_FLAGS RPM_DOC_DIR="/usr/share/doc" export RPM_DOC_DIR RPM_PACKAGE_NAME="R-ape" RPM_PACKAGE_VERSION="5.8.1" RPM_PACKAGE_RELEASE="5.fc45" export RPM_PACKAGE_NAME RPM_PACKAGE_VERSION RPM_PACKAGE_RELEASE LANG=C.UTF-8 export LANG unset CDPATH DISPLAY ||: unset DEBUGINFOD_URLS ||: unset RPM_CONFIG_DIR ||: RPM_BUILD_ROOT="/builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT" export RPM_BUILD_ROOT PKG_CONFIG_PATH="${PKG_CONFIG_PATH}:/usr/lib64/pkgconfig:/usr/share/pkgconfig" export PKG_CONFIG_PATH CONFIG_SITE=${CONFIG_SITE:-NONE} export CONFIG_SITE Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.aQiWlQ + umask 022 + cd /builddir/build/BUILD/R-ape-5.8.1-build + cd /builddir/build/BUILD/R-ape-5.8.1-build + rm -rf R-ape-5.8.1 + /usr/bin/mkdir -p R-ape-5.8.1 + cd R-ape-5.8.1 + /usr/bin/rpmuncompress -x /builddir/build/SOURCES/ape_5.8-1.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + RPM_EC=0 ++ jobs -p + exit 0 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.aqPtWA + umask 022 + cd /builddir/build/BUILD/R-ape-5.8.1-build + cd R-ape-5.8.1 + echo ape/DESCRIPTION + /usr/lib/rpm/R-deps.R LinkingTo Depends Imports + echo ape/DESCRIPTION + /usr/lib/rpm/R-deps.R Suggests + grep -E 'testthat|tinytest|RUnit|testit' + true + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/R-ape-5.8.1-5.fc45.buildreqs.nosrc.rpm Child return code was: 11 Dynamic buildrequires detected Going to install missing buildrequires. See root.log for details. ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -br --noprep --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-ape.spec'], chrootPath='/var/lib/mock/f45-build-5992-345/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=864000uid=995gid=135user='mockbuild'unshare_net=TrueraiseExc=FalseprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.tvsynko9:/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.tvsynko9:/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', '3c098392696f468fb08cf065c5a86027', '-D', '/var/lib/mock/f45-build-5992-345/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.tvsynko9:/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 -br --noprep --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-ape.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1784073600 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.bYmKTA + umask 022 + cd /builddir/build/BUILD/R-ape-5.8.1-build + cd R-ape-5.8.1 + echo ape/DESCRIPTION + /usr/lib/rpm/R-deps.R LinkingTo Depends Imports + echo ape/DESCRIPTION + /usr/lib/rpm/R-deps.R Suggests + grep -E 'testthat|tinytest|RUnit|testit' + true + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/R-ape-5.8.1-5.fc45.buildreqs.nosrc.rpm Child return code was: 11 Dynamic buildrequires detected Going to install missing buildrequires. See root.log for details. ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -ba --noprep --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-ape.spec'], chrootPath='/var/lib/mock/f45-build-5992-345/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=864000uid=995gid=135user='mockbuild'unshare_net=TrueprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.tvsynko9:/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.tvsynko9:/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', 'fc0d4a9ff3a94e9ba99789e93e23ba56', '-D', '/var/lib/mock/f45-build-5992-345/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.tvsynko9:/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 -ba --noprep --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-ape.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1784073600 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.yyQdEF + umask 022 + cd /builddir/build/BUILD/R-ape-5.8.1-build + cd R-ape-5.8.1 + echo ape/DESCRIPTION + /usr/lib/rpm/R-deps.R LinkingTo Depends Imports + echo ape/DESCRIPTION + /usr/lib/rpm/R-deps.R Suggests + grep -E 'testthat|tinytest|RUnit|testit' + true + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.1YCWYR + umask 022 + cd /builddir/build/BUILD/R-ape-5.8.1-build + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 R-ape-5.8.1 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.oKQLJF + umask 022 + cd /builddir/build/BUILD/R-ape-5.8.1-build + '[' /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT ++ dirname /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT + mkdir -p /builddir/build/BUILD/R-ape-5.8.1-build + mkdir /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 R-ape-5.8.1 + mkdir -p /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT/usr/lib64/R/library ++ date --utc --date=@1784073600 -R + builddate='Wed, 15 Jul 2026 00:00:00 +0000' + set -o pipefail + /usr/bin/R CMD INSTALL '--built-timestamp=Wed, 15 Jul 2026 00:00:00 +0000' -l /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT/usr/lib64/R/library ape + tee install.log * installing *source* package ‘ape’ ... ** package ‘ape’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (GCC) 16.1.1 20260703 (Red Hat 16.1.1-4)’ using C++ compiler: ‘g++ (GCC) 16.1.1 20260703 (Red Hat 16.1.1-4)’ gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c BIONJ.c -o BIONJ.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c NNI.c -o NNI.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c RcppExports.cpp -o RcppExports.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c SPR.c -o SPR.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c additive.c -o additive.o additive.c: In function ‘C_additive’: additive.c:13:9: warning: variable ‘m’ set but not used [-Wunused-but-set-variable=] 13 | int m=*mp; | ^ gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c ape.c -o ape.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c bNNI.c -o bNNI.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c bionjs.c -o bionjs.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c bipartition.c -o bipartition.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c bitsplits.c -o bitsplits.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c delta_plot.c -o delta_plot.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c dist_dna.c -o dist_dna.o dist_dna.c: In function ‘distDNA_LogDet’: dist_dna.c:822:17: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized] 822 | case 40 : m += 8; break;\ | ~~^~~~ dist_dna.c:850:20: note: ‘m’ was declared here 850 | int i1, i2, k, m, s1, s2, target, L, Ntab[16], ndim = 4, info, ipiv[16]; | ^ dist_dna.c: In function ‘distDNA_LogDet_pairdel’: dist_dna.c:822:17: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized] 822 | case 40 : m += 8; break;\ | ~~^~~~ dist_dna.c:871:20: note: ‘m’ was declared here 871 | int i1, i2, k, m, s1, s2, target, L, Ntab[16], ndim = 4, info, ipiv[16]; | ^ dist_dna.c: In function ‘distDNA_BH87’: dist_dna.c:822:17: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized] 822 | case 40 : m += 8; break;\ | ~~^~~~ dist_dna.c:896:32: note: ‘m’ was declared here 896 | int i1, i2, k, kb, s1, s2, m, Ntab[16], ROWsums[4]; | ^ dist_dna.c: In function ‘distDNA_ParaLin’: dist_dna.c:822:17: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized] 822 | case 40 : m += 8; break;\ | ~~^~~~ dist_dna.c:973:28: note: ‘m’ was declared here 973 | int i1, i2, k, s1, s2, m, target, L, Ntab[16], ndim = 4, info, ipiv[16]; | ^ dist_dna.c: In function ‘distDNA_ParaLin_pairdel’: dist_dna.c:822:17: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized] 822 | case 40 : m += 8; break;\ | ~~^~~~ dist_dna.c:1012:28: note: ‘m’ was declared here 1012 | int i1, i2, k, s1, s2, m, target, L, Ntab[16], ndim = 4, info, ipiv[16]; | ^ dist_dna.c: In function ‘dist_dna’: dist_dna.c:1342:13: warning: ‘var’ may be used uninitialized [-Wmaybe-uninitialized] 1342 | distDNA_ParaLin(x, n, s, d, variance, var); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dist_dna.c:1233:29: note: ‘var’ was declared here 1233 | double *BF, alpha, *d, *var; | ^~~ dist_dna.c:1318:13: warning: ‘alpha’ may be used uninitialized [-Wmaybe-uninitialized] 1318 | distDNA_TN93(x, n, s, d, BF, variance, var, gamma, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dist_dna.c:1233:17: note: ‘alpha’ was declared here 1233 | double *BF, alpha, *d, *var; | ^~~~~ gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c dist_nodes.c -o dist_nodes.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c ewLasso.c -o ewLasso.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c heap.c -o heap.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c mat_expo.c -o mat_expo.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c me.c -o me.o me.c: In function ‘detrifurcate’: me.c:295:11: warning: ‘w’ may be used uninitialized [-Wmaybe-uninitialized] 295 | T->root = w; | ~~~~~~~~^~~ me.c:275:13: note: ‘w’ was declared here 275 | node *v, *w; | ^ gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c me_balanced.c -o me_balanced.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c me_ols.c -o me_ols.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c mvr.c -o mvr.o mvr.c: In function ‘C_mvr’: mvr.c:97:37: warning: ‘OTU1’ may be used uninitialized [-Wmaybe-uninitialized] 97 | edge2[k] = otu_label[OTU1]; | ^ mvr.c:13:39: note: ‘OTU1’ was declared here 13 | int n, i, j, k, ij, smallest, OTU1, OTU2, cur_nod, o_l, *otu_label; | ^~~~ mvr.c:98:41: warning: ‘OTU2’ may be used uninitialized [-Wmaybe-uninitialized] 98 | edge2[k + 1] = otu_label[OTU2]; | ^ mvr.c:13:45: note: ‘OTU2’ was declared here 13 | int n, i, j, k, ij, smallest, OTU1, OTU2, cur_nod, o_l, *otu_label; | ^~~~ gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c mvrs.c -o mvrs.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c nj.c -o nj.o nj.c: In function ‘C_nj’: nj.c:114:36: warning: ‘OTU1’ may be used uninitialized [-Wmaybe-uninitialized] 114 | edge[k + Nedge] = otu_label[OTU1]; | ^ nj.c:66:49: note: ‘OTU1’ was declared here 66 | int n, i, j, k, *edge, cur_nod, *otu_label, OTU1, OTU2, Nedge; | ^~~~ nj.c:115:40: warning: ‘OTU2’ may be used uninitialized [-Wmaybe-uninitialized] 115 | edge[k + 1 + Nedge] = otu_label[OTU2]; | ^ nj.c:66:55: note: ‘OTU2’ was declared here 66 | int n, i, j, k, *edge, cur_nod, *otu_label, OTU1, OTU2, Nedge; | ^~~~ nj.c:123:14: warning: ‘smallest’ may be used uninitialized [-Wmaybe-uninitialized] 123 | A = D[smallest]; | ^ nj.c:67:14: note: ‘smallest’ was declared here 67 | long ij, smallest; | ^~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c njs.c -o njs.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c pic.c -o pic.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c plot_phylo.c -o plot_phylo.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c prop_part.cpp -o prop_part.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c rTrait.c -o rTrait.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c read_dna.c -o read_dna.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c reorder_Rcpp.cpp -o reorder_Rcpp.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c reorder_phylo.c -o reorder_phylo.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c treePop.c -o treePop.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c tree_build.c -o tree_build.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c tree_phylo.c -o tree_phylo.o gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c triangMtd.c -o triangMtd.o triangMtd.c: In function ‘C_triangMtd’: triangMtd.c:89:9: warning: variable ‘ij’ set but not used [-Wunused-but-set-variable=] 89 | int ij=-1; | ^~ gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c triangMtds.c -o triangMtds.o triangMtds.c: In function ‘C_triangMtds’: triangMtds.c:47:11: warning: ‘(*m.0_252)[1]’ may be used uninitialized [-Wmaybe-uninitialized] 47 | while(m[ij]==n){ij++;} | ~^~~~ gcc -I"/usr/include/R" -DNDEBUG -I'/usr/lib64/R/library/Rcpp/include' -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c ultrametric.c -o ultrametric.o ultrametric.c: In function ‘C_ultrametric’: ultrametric.c:13:9: warning: variable ‘m’ set but not used [-Wunused-but-set-variable=] 13 | int m=*mp; | ^ g++ -std=gnu++17 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -o ape.so BIONJ.o NNI.o RcppExports.o SPR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o prop_part.o rTrait.o read_dna.o reorder_Rcpp.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o -lflexiblas -L -L -lgfortran -lm -L/usr/lib64/R/lib -lR installing to /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT/usr/lib64/R/library/00LOCK-ape/00new/ape/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘ape’ finding HTML links ... done AAbin html CADM.global html DNAbin html DNAbin2indel html Initialize.corPhyl html LTT html MPR html MoranI html SDM html ace html add.scale.bar html additive html alex html all.equal.DNAbin html all.equal.phylo html alview html ape-internal html ape-package html apetools html as.alignment html as.bitsplits html as.matching html as.phylo html as.phylo.formula html axisPhylo html balance html base.freq html bd.ext html bd.time html binaryPGLMM html bind.tree html bionj html bird.families html bird.orders html birthdeath html boot.phylo html branching.times html c.phylo html carnivora html checkAlignment html checkLabel html checkValidPhylo html cherry html chiroptera html chronoMPL html chronopl html chronos html clustal html coalescent.intervals html collapse.singles html collapsed.intervals html compar.cheverud html compar.gee html compar.lynch html compar.ou html comparePhylo html compute.brlen html compute.brtime html consensus html cophenetic.phylo html cophyloplot html corBlomberg html corBrownian html corClasses html corGrafen html corMartins html corPagel html corphylo html correlogram.formula html cynipids html dbd html def html degree html del.gaps html delta.plot html dist.dna html dist.gene html dist.topo html diversi.gof html diversi.time html diversity.contrast.test html dnds html drop.tip html edges html evonet html ewLasso html fastme html gammaStat html getAnnotationsGenBank html hivtree html howmanytrees html identify.phylo html image.DNAbin html is.binary.tree html is.compatible html is.monophyletic html is.ultrametric html kronoviz html label2table html ladderize html latag2n html lmorigin html ltt.plot html makeLabel html makeNodeLabel html mantel.test html mat3 html mat5M3ID html mat5Mrand html matexpo html mcconwaysims.test html mcmc.popsize html mixedFontLabel html mrca html mst html multi2di html multiphylo html mvr html nj html njs html node.dating html node.depth html nodelabels html nodepath html parafit html pcoa html phydataplot html phymltest html pic html pic.ortho html plot.correlogram html plot.phylo html plot.phyloExtra html plot.varcomp html plotTreeTime html print.phylo html rDNAbin html rTraitCont html rTraitDisc html rTraitMult html read.GenBank html read.caic html read.dna html read.gff html read.nexus html read.nexus.data html read.tree html reconstruct html reorder.phylo html richness.yule.test html rlineage html root html rotate html rtree html rtt html seg.sites html skyline html skylineplot html slowinskiguyer.test html solveAmbiguousBases html speciesTree html stree html subtreeplot html subtrees html summary.phylo html trans html treePop html trex html triangMtd html unique.multiPhylo html updateLabel html varCompPhylip html varcomp html vcv.phylo html vcv2phylo html weight.taxo html where html which.edge html woodmouse html write.dna html write.nexus html write.nexus.data html write.phyloXML html write.tree html yule html yule.cov html yule.time html zoom html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ape) + rm -f ape/src/BIONJ.o ape/src/NNI.o ape/src/RcppExports.o ape/src/SPR.o ape/src/additive.o ape/src/ape.o ape/src/bNNI.o ape/src/bionjs.o ape/src/bipartition.o ape/src/bitsplits.o ape/src/delta_plot.o ape/src/dist_dna.o ape/src/dist_nodes.o ape/src/ewLasso.o ape/src/heap.o ape/src/mat_expo.o ape/src/me.o ape/src/me_balanced.o ape/src/me_ols.o ape/src/mvr.o ape/src/mvrs.o ape/src/nj.o ape/src/njs.o ape/src/pic.o ape/src/plot_phylo.o ape/src/prop_part.o ape/src/rTrait.o ape/src/read_dna.o ape/src/reorder_Rcpp.o ape/src/reorder_phylo.o ape/src/treePop.o ape/src/tree_build.o ape/src/tree_phylo.o ape/src/triangMtd.o ape/src/triangMtds.o ape/src/ultrametric.o ape/src/ape.so /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT/usr/lib64/R/library/R.css + IS_NOARCH=1 + '[' riscv64 = noarch ']' + IS_NOARCH=0 + LIB_FOUND=1 + find /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT/usr/lib64/R/library/ape/libs -name '*.so' + grep -q '^' + case $(($IS_NOARCH + $LIB_FOUND)) in + /usr/lib/rpm/R-files.R -b /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT -p /usr/lib64/R/library/ape + /usr/bin/find-debuginfo -j8 --strict-build-id -m -i --build-id-seed 5.8.1-5.fc45 --unique-debug-suffix -5.8.1-5.fc45.riscv64 --unique-debug-src-base R-ape-5.8.1-5.fc45.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/R-ape-5.8.1-build/R-ape-5.8.1 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-ape-5.8.1-5.fc45.riscv64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + COMPRESS='gzip -9 -n' + COMPRESS_EXT=.gz + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /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 -j8 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-det --brp -j8 /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT Scanned 26 directories and 744 files, processed 659 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors + /usr/bin/linkdupes --brp /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT/usr Scanned 25 directories and 744 files, considered 744 files, read 470 files, linked 279 files, 0 errors sum of sizes of linked files: 42116 bytes Reading /builddir/build/BUILD/R-ape-5.8.1-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.jenms0 + umask 022 + cd /builddir/build/BUILD/R-ape-5.8.1-build + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=rva23u64 -mabi=lp64d -fasynchronous-unwind-tables -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 R-ape-5.8.1 + export LANG=C.UTF-8 + LANG=C.UTF-8 + export _R_CHECK_FORCE_SUGGESTS_=0 + _R_CHECK_FORCE_SUGGESTS_=0 + /usr/bin/R CMD check -l /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT/usr/lib64/R/library --install=check:install.log --no-manual --ignore-vignettes ape --no-examples * using log directory ‘/builddir/build/BUILD/R-ape-5.8.1-build/R-ape-5.8.1/ape.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: riscv64-koji-linux-gnu * R was compiled by gcc (GCC) 15.0.1 20250114 (Red Hat 15.0.1-0) GNU Fortran (GCC) 15.0.1 20250114 (Red Hat 15.0.1-0) * running under: Fedora Linux 45 (Forty Five Prerelease) * using session charset: UTF-8 * using options ‘--no-examples --no-manual --ignore-vignettes’ * checking for file ‘ape/DESCRIPTION’ ... OK * this is package ‘ape’ version ‘5.8-1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.20/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.20/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.20/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.20/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.20/data/experiment/src/contrib/PACKAGES' NOTE Packages suggested but not available for checking: 'gee', 'expm', 'igraph', 'phangorn', 'xml2' * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ape’ can be installed ... OK * used C compiler: ‘gcc (GCC) 16.1.1 20260703 (Red Hat 16.1.1-4)’ * used C++ compiler: ‘g++ (GCC) 16.1.1 20260703 (Red Hat 16.1.1-4)’ * checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: R 1.9Mb help 1.8Mb html 1.2Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown packages ‘phangorn’, ‘expm’ in Rd xrefs * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE /usr/bin/nm: /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT/usr/lib64/R/library/ape/libs/ape.so: no symbols Note: information on .o files is not available /usr/bin/nm: /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT/usr/lib64/R/library/ape/libs/ape.so: no symbols See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... SKIPPED * checking examples ... SKIPPED * DONE Status: 4 NOTEs See ‘/builddir/build/BUILD/R-ape-5.8.1-build/R-ape-5.8.1/ape.Rcheck/00check.log’ for details. + RPM_EC=0 ++ jobs -p + exit 0 Processing files: R-ape-5.8.1-5.fc45.riscv64 Provides: R(ape) = 5.8.1 R-ape = 5.8.1-5.fc45 R-ape(riscv-64) = 5.8.1-5.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: R(ABI) = 4.4 R(Rcpp) >= 0.12.0 R(digest) R(graphics) R(lattice) R(methods) R(nlme) R(parallel) R(stats) R(utils) R-core >= 3.2.0 ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libflexiblas.so.3()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH) Processing files: R-ape-debugsource-5.8.1-5.fc45.riscv64 Provides: R-ape-debugsource = 5.8.1-5.fc45 R-ape-debugsource(riscv-64) = 5.8.1-5.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-ape-debuginfo-5.8.1-5.fc45.riscv64 Provides: R-ape-debuginfo = 5.8.1-5.fc45 R-ape-debuginfo(riscv-64) = 5.8.1-5.fc45 debuginfo(build-id) = 0a9683b72a661f2647cc99750ee51d3db7383451 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-ape-debugsource(riscv-64) = 5.8.1-5.fc45 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/R-ape-5.8.1-build/BUILDROOT Wrote: /builddir/build/SRPMS/R-ape-5.8.1-5.fc45.src.rpm Wrote: /builddir/build/RPMS/R-ape-debugsource-5.8.1-5.fc45.riscv64.rpm Wrote: /builddir/build/RPMS/R-ape-debuginfo-5.8.1-5.fc45.riscv64.rpm Wrote: /builddir/build/RPMS/R-ape-5.8.1-5.fc45.riscv64.rpm Child return code was: 0