Mock Version: 5.5 Mock Version: 5.5 Mock Version: 5.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target x86_64 --nodeps /builddir/build/SPECS/bfast.spec'], chrootPath='/var/lib/mock/f40-build-50539957-6051664/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'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.em_egfhk:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.em_egfhk:/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', 'be6b32a837774050a2f7a658554c2602', '-D', '/var/lib/mock/f40-build-50539957-6051664/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.em_egfhk:/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 x86_64 --nodeps /builddir/build/SPECS/bfast.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 warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1689724800 Wrote: /builddir/build/SRPMS/bfast-0.7.0a-32.fc40.src.rpm RPM build warnings: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target x86_64 --nodeps /builddir/build/SPECS/bfast.spec'], chrootPath='/var/lib/mock/f40-build-50539957-6051664/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'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.em_egfhk:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.em_egfhk:/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', '0fd4b70cfcde4d8b926bb38f9875af38', '-D', '/var/lib/mock/f40-build-50539957-6051664/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.em_egfhk:/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 x86_64 --nodeps /builddir/build/SPECS/bfast.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 warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1689724800 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.0fzVFi + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf bfast-0.7.0a + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/bfast-0.7.0a.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd bfast-0.7.0a + rm -rf /builddir/build/BUILD/bfast-0.7.0a-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/bfast-0.7.0a-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (bfast-pthread-new.patch): + echo 'Patch #0 (bfast-pthread-new.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file bfast/Makefile.am patching file bfast/Makefile.in patching file butil/Makefile.am patching file butil/Makefile.in patching file scripts/Makefile.am patching file scripts/Makefile.in patching file tests/Makefile.in + sed -i -e 's,^\(CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"\),# \1,' configure.ac + autoreconf -fi configure.ac:23: warning: The macro `AC_GNU_SOURCE' is obsolete. configure.ac:23: You should run autoupdate. ./lib/autoconf/specific.m4:312: AC_GNU_SOURCE is expanded from... configure.ac:23: the top level configure.ac:87: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:87: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:87: the top level parallel-tests: installing 'config/test-driver' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.7WnBI5 + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bfast-0.7.0a + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure --- ./configure.backup 2024-04-26 17:10:08.688129800 +0000 +++ ./configure 2024-04-26 17:10:09.578211308 +0000 @@ -1692,7 +1692,7 @@ #ifdef __cplusplus extern "C" #endif -char $2 (); +__attribute__ ((used)) char $2 (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config/config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./config/config.guess ++ basename ./config/config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config/config.guess '/usr/lib/rpm/redhat/config.guess' -> './config/config.guess' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config/config.sub ++ basename ./config/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config/config.sub '/usr/lib/rpm/redhat/config.sub' -> './config/config.sub' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure ++ echo --runstatedir=/run + ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline' checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-redhat-linux-gnu checking for x86_64-redhat-linux-gnu-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no ./configure: line 4851: git: command not found checking for bzlib.h... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for an ANSI C-conforming const... yes checking host system type... x86_64-redhat-linux-gnu checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for pow in -lm... yes checking for gzread in -lz... yes checking for floor... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking for strdup... yes checking for strpbrk... yes checking for strstr... yes checking for strtok_r... yes checking for _LARGEFILE_SOURCE value needed for large files... no checking for int8_t... yes checking for int32_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint32_t... yes checking for uint64_t... yes checking size of short int... 2 checking size of int... 4 checking size of long int... 8 checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for limits.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for float.h... yes checking for zlib.h... yes checking for fcntl.h... yes checking for inline... inline checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bfast/Makefile config.status: creating butil/Makefile config.status: creating scripts/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands + /usr/bin/make -O -j6 V=1 VERBOSE=1 /usr/bin/make all-recursive Making all in bfast make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline -c -o BError.o BError.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline -c -o AlignedRead.o AlignedRead.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline -c -o AlignedEnd.o AlignedEnd.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline -c -o AlignedEntry.o AlignedEntry.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline -c -o RGBinary.o RGBinary.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' RGBinary.c: In function ‘RGBinaryReadBinaryHeader’: RGBinary.c:260:17: warning: variable ‘numCharsPerByte’ set but not used [-Wunused-but-set-variable] 260 | int32_t numCharsPerByte; | ^~~~~~~~~~~~~~~ RGBinary.c: In function ‘RGBinaryWriteBinaryHeader’: RGBinary.c:387:17: warning: variable ‘numCharsPerByte’ set but not used [-Wunused-but-set-variable] 387 | int32_t numCharsPerByte; | ^~~~~~~~~~~~~~~ RGBinary.c: In function ‘RGBinaryWriteBinary’: RGBinary.c:421:17: warning: variable ‘numCharsPerByte’ set but not used [-Wunused-but-set-variable] 421 | int32_t numCharsPerByte; | ^~~~~~~~~~~~~~~ RGBinary.c: In function ‘RGBinaryGetFourBit’: RGBinary.c:820:14: warning: variable ‘curChar’ set but not used [-Wunused-but-set-variable] 820 | char curChar; | ^~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline -c -o AlignedReadConvert.o AlignedReadConvert.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline -c -o RGIndexExons.o RGIndexExons.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline -c -o RGIndexLayout.o RGIndexLayout.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline -c -o RGMatch.o RGMatch.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' RGMatch.c: In function ‘RGMatchRead’: RGMatch.c:23:25: error: passing argument 1 of ‘feof’ from incompatible pointer type [-Wincompatible-pointer-types] 23 | if(feof(fp) != 0) { | ^~ | | | gzFile {aka struct gzFile_s *} In file included from RGMatch.c:2: /usr/include/stdio.h:862:24: note: expected ‘FILE *’ but argument is of type ‘gzFile’ {aka ‘struct gzFile_s *’} 862 | extern int feof (FILE *__stream) __THROW __wur __nonnull ((1)); | ~~~~~~^~~~~~~~ make[2]: *** [Makefile:472: RGMatch.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline -c -o RGRanges.o RGRanges.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline -c -o BLib.o BLib.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline -c -o RGIndexAccuracy.o RGIndexAccuracy.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline -c -o RGMatches.o RGMatches.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' make[2]: Entering directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' gcc -DHAVE_CONFIG_H -I. -I.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fgnu89-inline -c -o RGIndex.o RGIndex.c make[2]: Leaving directory '/builddir/build/BUILD/bfast-0.7.0a/bfast' RGIndex.c: In function ‘RGIndexCreateHelper’: RGIndex.c:463:31: warning: variable ‘keyEndPos’ set but not used [-Wunused-but-set-variable] 463 | uint32_t keyStartPos, keyEndPos; | ^~~~~~~~~ RGIndex.c: In function ‘RGIndexCompareContigPos’: RGIndex.c:2428:25: warning: variable ‘length’ set but not used [-Wunused-but-set-variable] 2428 | int32_t length; | ^~~~~~ make[1]: *** [Makefile:435: all-recursive] Error 1 make: *** [Makefile:355: all] Error 2 error: Bad exit status from /var/tmp/rpm-tmp.7WnBI5 (%build) RPM build warnings: RPM build errors: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N) Bad exit status from /var/tmp/rpm-tmp.7WnBI5 (%build) Child return code was: 1 EXCEPTION: [Error('Command failed: \n # /usr/bin/systemd-nspawn -q -M 0fd4b70cfcde4d8b926bb38f9875af38 -D /var/lib/mock/f40-build-50539957-6051664/root -a -u mockbuild --capability=cap_ipc_lock --bind=/tmp/mock-resolv.em_egfhk:/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 x86_64 --nodeps /builddir/build/SPECS/bfast.spec\'\n', 1)] Traceback (most recent call last): File "/usr/lib/python3.12/site-packages/mockbuild/trace_decorator.py", line 93, in trace result = func(*args, **kw) ^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/site-packages/mockbuild/util.py", line 612, 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 0fd4b70cfcde4d8b926bb38f9875af38 -D /var/lib/mock/f40-build-50539957-6051664/root -a -u mockbuild --capability=cap_ipc_lock --bind=/tmp/mock-resolv.em_egfhk:/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 x86_64 --nodeps /builddir/build/SPECS/bfast.spec'