Mock Version: 3.3
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target x86_64 --nodeps /builddir/build/SPECS/clustal-omega.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1667513711.783483/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f00948c5fc0>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.ldglz9lk:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--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=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.ldglz9lk:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--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', 'c206ecf5ea94475db153b8659ee081cc', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1667513711.783483/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.ldglz9lk:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target x86_64 --nodeps /builddir/build/SPECS/clustal-omega.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1658275200
Wrote: /builddir/build/SRPMS/clustal-omega-1.2.4-15.fc38.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target x86_64 --nodeps /builddir/build/SPECS/clustal-omega.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1667513711.783483/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f00948c5fc0>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.ldglz9lk:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--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=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.ldglz9lk:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--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', 'b8b6809a035b4fe18aa4113f4cd0b656', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1667513711.783483/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.ldglz9lk:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target x86_64 --nodeps /builddir/build/SPECS/clustal-omega.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1658275200
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.YNghJ9
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf clustal-omega-1.2.4
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/clustal-omega-1.2.4.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd clustal-omega-1.2.4
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ sed -i 's/\r$//' README
+ sed -i s/mktemp/mkstemp/g src/clustal-omega.c
+ sed -i 's/\${AM_CFLAGS} -O3/${AM_CFLAGS}/g' configure
+ sed -i 's/\${AM_CXXFLAGS} -O3/${AM_CXXFLAGS}/g' configure
+ sed -i '/inline float log/d' src/hhalign/util-C.h
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.ic20og
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-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 -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 clustal-omega-1.2.4
+ export 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'LDFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ LDFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ 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
+ mv ./configure.backup ./configure
+ /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
--- ./configure.backup	2022-11-03 22:16:41.098830420 +0000
+++ ./configure	2022-11-03 22:16:41.169828038 +0000
@@ -22020,7 +22020,7 @@
 compiler='`$ECHO "X$compiler" | $Xsed -e "$delay_single_quote_subst"`'
 GCC='`$ECHO "X$GCC" | $Xsed -e "$delay_single_quote_subst"`'
 lt_cv_sys_global_symbol_pipe='`$ECHO "X$lt_cv_sys_global_symbol_pipe" | $Xsed -e "$delay_single_quote_subst"`'
-lt_cv_sys_global_symbol_to_cdecl='`$ECHO "X$lt_cv_sys_global_symbol_to_cdecl" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
 lt_cv_sys_global_symbol_to_c_name_address='`$ECHO "X$lt_cv_sys_global_symbol_to_c_name_address" | $Xsed -e "$delay_single_quote_subst"`'
 lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='`$ECHO "X$lt_cv_sys_global_symbol_to_c_name_address_lib_prefix" | $Xsed -e "$delay_single_quote_subst"`'
 objdir='`$ECHO "X$objdir" | $Xsed -e "$delay_single_quote_subst"`'
+ '[' 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.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./config.sub
++ basename ./config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub
'/usr/lib/rpm/redhat/config.sub' -> './config.sub'
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
++ basename ./config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./config.guess
++ basename ./config.guess
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess
'/usr/lib/rpm/redhat/config.guess' -> './config.guess'
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
+ for i in $(find . -name ltmain.sh)
+ /usr/bin/sed -i.backup -e 's~compiler_flags=$~compiler_flags="-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld"~' ./ltmain.sh
++ grep -q runstatedir=DIR ./configure
+ ./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 --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --disable-static
configure:
    Welcome to Clustal Omega - version 1.2.4 (AndreaGiacomo)
                       +NMMMMMMMMMS=
                    MMMMM?      :MMMMM8
                  IMMMMS           MMMMM,
                ~MMMMN              ,MMMMM
               =MMMMM                 MMMMM
              ?MMMMM                  +MMMMM
              MMMMMS                   MMMMM
              MMMMM                    MMMMM:
              MMMMM                    MMMMM+
              MMMMM                    MMMMM~
              MMMMM                    MMMMM
              MMMMMZ                   MMMMM
               MMMMM                  ,MMMMZ
                MMMM8                 MMMM+
                 MMMMS               MMMM,
                   MMMMO           MMMM
            ,N       SMMM        MMM8       +8
            ,M7         M+       M+        :M8
            ,MMMMMMMMMMMMI       MMMMMMMMMMMM8
            ,MMMMMMMMMMMM8       MMMMMMMMMMMM8
            ,MMMMMMMMMMMMN       MMMMMMMMMMMM8
              
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking for x86_64-redhat-linux-gnu-gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking build system type... x86_64-redhat-linux-gnu
checking host system type... x86_64-redhat-linux-gnu
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
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configure: creating ./config.status
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+ make V=1 -j2
Making all in src
make[1]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src'
make  all-recursive
make[2]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src'
Making all in hhalign
make[3]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/hhalign'
/bin/sh ../../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src    -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o hhalign.lo hhalign.cpp
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c hhalign.cpp  -fPIC -DPIC -o .libs/hhalign.o
In file included from hhalign.cpp:70:
hhhmm-C.h: In member function 'int HMM::ReadHMMer3(FILE*, char*)':
hhhmm-C.h:1141:12: warning: variable 'dAlphaInv' set but not used [-Wunused-but-set-variable]
 1141 |     double dAlphaInv = 1.00 / (double)(iAlpha); /* weight of AA */
      |            ^~~~~~~~~
hhhmm-C.h: In member function 'void HMM::WriteToFileHMMER(char*)':
hhhmm-C.h:2206:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 2206 |   for (i=0; i<=par.argc-1; ++i) fprintf(outf,"%s ",par.argv[i]); fprintf(outf,"\n");
      |   ^~~
hhhmm-C.h:2206:66: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 2206 |   for (i=0; i<=par.argc-1; ++i) fprintf(outf,"%s ",par.argv[i]); fprintf(outf,"\n");
      |                                                                  ^~~~~~~
In file included from hhalign.cpp:71:
hhalignment-C.h: In member function 'void Alignment::Read(FILE*, char*, char*)':
hhalignment-C.h:250:32: warning: variable 'ptr2' set but not used [-Wunused-but-set-variable]
  250 |                   char *ptr1, *ptr2;
      |                                ^~~~
hhalignment-C.h: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM&)':
hhalignment-C.h:1473:19: warning: variable 'score_M' set but not used [-Wunused-but-set-variable]
 1473 |             float score_M=0.0;
      |                   ^~~~~~~
hhalignment-C.h:1474:19: warning: variable 'score_prev' set but not used [-Wunused-but-set-variable]
 1474 |             float score_prev=0.0;
      |                   ^~~~~~~~~~
hhalignment-C.h: In member function 'void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM&, char*)':
hhalignment-C.h:1981:18: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
 1981 |               if (ncol<NCOLMIN)
      |                  ^
hhalignment-C.h: In member function 'void Alignment::Transitions_from_I_state(HMM&, char*)':
hhalignment-C.h:2248:28: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
 2248 |                         if (ncol>=NCOLMIN)
      |                            ^
hhalignment-C.h: In member function 'void Alignment::Transitions_from_D_state(HMM&, char*)':
hhalignment-C.h:2485:20: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
 2485 |                 if (ncol<NCOLMIN)
      |                    ^
In file included from hhalign.cpp:75:
hhhitlist-C.h: In member function 'void HitList::MaxLikelihoodEVD(HMM&, int)':
hhhitlist-C.h:661:9: warning: the address of 'HMM::fam' will never be NULL [-Waddress]
  661 |   if (q.fam && q.fam[0]>='a' && q.fam[0]<='k' && q.fam[1]=='.')
      |       ~~^~~
In file included from hhalign.cpp:64:
hhhmm.h:53:8: note: 'HMM::fam' declared here
   53 |   char fam[NAMELEN];        // family ID (derived from name) (FAM field)
      |        ^~~
hhhitlist-C.h: In member function 'void HitList::CalculateHHblastCorrelation(HMM&)':
hhhitlist-C.h:838:9: warning: the address of 'HMM::fam' will never be NULL [-Waddress]
  838 |   if (q.fam && q.fam[0]>='a' && q.fam[0]<='k' && q.fam[1]=='.')
      |       ~~^~~
hhhmm.h:53:8: note: 'HMM::fam' declared here
   53 |   char fam[NAMELEN];        // family ID (derived from name) (FAM field)
      |        ^~~
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring()':
hhhitlist-C.h:1257:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
 1257 |   size_t unused; /* disable fread gcc warning */
      |          ^~~~~~
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring2()':
hhhitlist-C.h:1622:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
 1622 |   size_t unused; /* disable fread gcc warning */
      |          ^~~~~~
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring3()':
hhhitlist-C.h:1992:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
 1992 |   size_t unused; /* disable fread gcc warning */
      |          ^~~~~~
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring4()':
hhhitlist-C.h:2357:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
 2357 |   size_t unused; /* disable fread gcc warning */
      |          ^~~~~~
hhalign.cpp: In function 'int hhalign(char**, int, double*, char**, int, double*, double*, hmm_light*, hmm_light*, char*, char*, char*, char*, hhalign_para, hhalign_scores*, int, int, char*, char*)':
hhalign.cpp:714:9: warning: variable 'Nali' set but not used [-Wunused-but-set-variable]
  714 |     int Nali;                    /* number of normally backtraced alignments
      |         ^~~~
hhhmm-C.h: In member function 'HMM::Read(_IO_FILE*, char*)':
hhhmm-C.h:294:20: warning: '__strncat_chk' output may be truncated copying between 0 and 510 bytes from a string of length 262139 [-Wstringop-truncation]
  294 |             strncat(file,ptr,NAMELEN-1-strlen(file));   // append file name read from file to path
      |                    ^
hhhmm-C.h:285:27: warning: 'strncpy' output may be truncated copying 254 bytes from a string of length 262140 [-Wstringop-truncation]
  285 |           if (ptr) strncpy(fam,ptr,IDLEN-1); else strcpy(fam,""); //copy family name to basename
      |                           ^
hhhmm-C.h:269:22: warning: 'strncpy' output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation]
  269 |               strncpy(longname,ptr,DESCLEN-1); //copy full name to longname
      |                      ^
hhhmm-C.h:271:22: warning: 'strncpy' output may be truncated copying 510 bytes from a string of length 262139 [-Wstringop-truncation]
  271 |               strncpy(name,ptr,NAMELEN-1);     //copy longname to name...
      |                      ^
hhhmm-C.h: In member function 'HMM::ReadHMMer(_IO_FILE*, char*)':
hhhmm-C.h:668:18: warning: 'strncpy' output may be truncated copying 510 bytes from a string of length 262139 [-Wstringop-truncation]
  668 |           strncpy(name,ptr,NAMELEN-1);    // copy full name to name
      |                  ^
hhhmm-C.h:676:18: warning: 'strncpy' output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation]
  676 |           strncpy(longname,ptr,DESCLEN-1); // copy Accession id to longname...
      |                  ^
hhhmm-C.h:1006:10: warning: 'strncat' output may be truncated copying between 0 and 32764 bytes from a string of length 32764 [-Wstringop-truncation]
 1006 |   strncat(longname,desc,DESCLEN-strlen(longname)-1);
      |          ^
hhhmm-C.h: In member function 'HMM::ReadHMMer3(_IO_FILE*, char*)':
hhhmm-C.h:1167:25: warning: 'strncpy' output may be truncated copying 510 bytes from a string of length 262139 [-Wstringop-truncation]
 1167 |                  strncpy(name,ptr,NAMELEN-1);    // copy full name to name
      |                         ^
hhhmm-C.h:1175:25: warning: 'strncpy' output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation]
 1175 |                  strncpy(longname,ptr,DESCLEN-1); // copy Accession id to longname...
      |                         ^
hhhmm-C.h:1500:9: warning: 'strncat' output may be truncated copying between 0 and 32764 bytes from a string of length 32764 [-Wstringop-truncation]
 1500 |  strncat(longname,desc,DESCLEN-strlen(longname)-1);
      |         ^
hhhmm-C.h: In member function 'HMM::UseSecStrucDependentGapPenalties()':
hhhmm-C.h:1748:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
 1748 |   iis[0]=iis[L]=0;
      |          ~~~~~~^~
hhhmm-C.h:1734:17: note: at offset [-2147483648, -1] into destination object 'iis' of size [0, 2147483647]
 1734 |   unsigned char iis[par.maxResLen]; // inside-integer array
      |                 ^~~
hhalignment-C.h: In member function 'Alignment::Read(_IO_FILE*, char*, char*)':
hhalignment-C.h:252:26: warning: 'strncpy' output may be truncated copying 32764 bytes from a string of length 262142 [-Wstringop-truncation]
  252 |                   strncpy(longname,ptr1,DESCLEN-1); // copy whole commentary line after '# ' into longname
      |                          ^
/bin/sh ../../libtool --tag=CXX   --mode=link g++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -o libhhalign.la  hhalign.lo  -largtable2 -lm 
libtool: link: ar cru .libs/libhhalign.a .libs/hhalign.o 
libtool: link: ranlib .libs/libhhalign.a
libtool: link: ( cd ".libs" && rm -f "libhhalign.la" && ln -s "../libhhalign.la" "libhhalign.la" )
make[3]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/hhalign'
Making all in squid
make[3]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/squid'
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o a2m.lo a2m.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o aligneval.lo aligneval.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c a2m.c  -fPIC -DPIC -o .libs/a2m.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c aligneval.c  -fPIC -DPIC -o .libs/aligneval.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o alignio.lo alignio.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c alignio.c  -fPIC -DPIC -o .libs/alignio.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o clustal.lo clustal.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c clustal.c  -fPIC -DPIC -o .libs/clustal.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o cluster.lo cluster.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o dayhoff.lo dayhoff.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c cluster.c  -fPIC -DPIC -o .libs/cluster.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dayhoff.c  -fPIC -DPIC -o .libs/dayhoff.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o eps.lo eps.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c eps.c  -fPIC -DPIC -o .libs/eps.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o file.lo file.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c file.c  -fPIC -DPIC -o .libs/file.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o getopt.lo getopt.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c getopt.c  -fPIC -DPIC -o .libs/getopt.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o gki.lo gki.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c gki.c  -fPIC -DPIC -o .libs/gki.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o gsi.lo gsi.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c gsi.c  -fPIC -DPIC -o .libs/gsi.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o gsi64.lo gsi64.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c gsi64.c  -fPIC -DPIC -o .libs/gsi64.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o hsregex.lo hsregex.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c hsregex.c  -fPIC -DPIC -o .libs/hsregex.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o iupac.lo iupac.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c iupac.c  -fPIC -DPIC -o .libs/iupac.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o msa.lo msa.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c msa.c  -fPIC -DPIC -o .libs/msa.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o msf.lo msf.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c msf.c  -fPIC -DPIC -o .libs/msf.o
msf.c: In function 'ReadMSF':
msf.c:85:11: warning: variable 'alleged_checksum' set but not used [-Wunused-but-set-variable]
   85 |   int     alleged_checksum = 0;
      |           ^~~~~~~~~~~~~~~~
msf.c:83:11: warning: variable 'alleged_alen' set but not used [-Wunused-but-set-variable]
   83 |   int     alleged_alen = 0;
      |           ^~~~~~~~~~~~
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o phylip.lo phylip.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c phylip.c  -fPIC -DPIC -o .libs/phylip.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o revcomp.lo revcomp.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c revcomp.c  -fPIC -DPIC -o .libs/revcomp.o
phylip.c: In function 'ReadPhylip':
phylip.c:78:15: warning: variable 'alen' set but not used [-Wunused-but-set-variable]
   78 |   int   nseq, alen;
      |               ^~~~
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o rk.lo rk.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o selex.lo selex.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rk.c  -fPIC -DPIC -o .libs/rk.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c selex.c  -fPIC -DPIC -o .libs/selex.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o seqencode.lo seqencode.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c seqencode.c  -fPIC -DPIC -o .libs/seqencode.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o shuffle.lo shuffle.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c shuffle.c  -fPIC -DPIC -o .libs/shuffle.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o sqerror.lo sqerror.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c sqerror.c  -fPIC -DPIC -o .libs/sqerror.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o sqio.lo sqio.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c sqio.c  -fPIC -DPIC -o .libs/sqio.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o squidcore.lo squidcore.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c squidcore.c  -fPIC -DPIC -o .libs/squidcore.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o sre_ctype.lo sre_ctype.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c sre_ctype.c  -fPIC -DPIC -o .libs/sre_ctype.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o sre_math.lo sre_math.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c sre_math.c  -fPIC -DPIC -o .libs/sre_math.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o sre_random.lo sre_random.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c sre_random.c  -fPIC -DPIC -o .libs/sre_random.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o sre_string.lo sre_string.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c sre_string.c  -fPIC -DPIC -o .libs/sre_string.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o ssi.lo ssi.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c ssi.c  -fPIC -DPIC -o .libs/ssi.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o stack.lo stack.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c stack.c  -fPIC -DPIC -o .libs/stack.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o stockholm.lo stockholm.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c stockholm.c  -fPIC -DPIC -o .libs/stockholm.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o stopwatch.lo stopwatch.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o translate.lo translate.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c stopwatch.c  -fPIC -DPIC -o .libs/stopwatch.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c translate.c  -fPIC -DPIC -o .libs/translate.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o types.lo types.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o vectorops.lo vectorops.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c types.c  -fPIC -DPIC -o .libs/types.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c vectorops.c  -fPIC -DPIC -o .libs/vectorops.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o weight.lo weight.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c weight.c  -fPIC -DPIC -o .libs/weight.o
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -o libsquid.la  a2m.lo aligneval.lo alignio.lo clustal.lo cluster.lo dayhoff.lo eps.lo file.lo getopt.lo gki.lo gsi.lo gsi64.lo hsregex.lo iupac.lo msa.lo msf.lo phylip.lo revcomp.lo rk.lo selex.lo seqencode.lo shuffle.lo sqerror.lo sqio.lo squidcore.lo sre_ctype.lo sre_math.lo sre_random.lo sre_string.lo ssi.lo stack.lo stockholm.lo stopwatch.lo translate.lo types.lo vectorops.lo weight.lo  -largtable2 -lm 
libtool: link: ar cru .libs/libsquid.a .libs/a2m.o .libs/aligneval.o .libs/alignio.o .libs/clustal.o .libs/cluster.o .libs/dayhoff.o .libs/eps.o .libs/file.o .libs/getopt.o .libs/gki.o .libs/gsi.o .libs/gsi64.o .libs/hsregex.o .libs/iupac.o .libs/msa.o .libs/msf.o .libs/phylip.o .libs/revcomp.o .libs/rk.o .libs/selex.o .libs/seqencode.o .libs/shuffle.o .libs/sqerror.o .libs/sqio.o .libs/squidcore.o .libs/sre_ctype.o .libs/sre_math.o .libs/sre_random.o .libs/sre_string.o .libs/ssi.o .libs/stack.o .libs/stockholm.o .libs/stopwatch.o .libs/translate.o .libs/types.o .libs/vectorops.o .libs/weight.o 
libtool: link: ranlib .libs/libsquid.a
libtool: link: ( cd ".libs" && rm -f "libsquid.la" && ln -s "../libsquid.la" "libsquid.la" )
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Making all in kmpp
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/bin/sh ../../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o KmTree.lo KmTree.cpp
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c KMeans.cpp  -fPIC -DPIC -o .libs/KMeans.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c KmTree.cpp  -fPIC -DPIC -o .libs/KmTree.o
/bin/sh ../../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o KmUtils.lo KmUtils.cpp
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c KmUtils.cpp  -fPIC -DPIC -o .libs/KmUtils.o
/bin/sh ../../libtool --tag=CXX   --mode=link g++ -DCLUSTALO   -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -o libkmpp.la  KMeans.lo KmTree.lo KmUtils.lo  -largtable2 -lm 
libtool: link: ar cru .libs/libkmpp.a .libs/KMeans.o .libs/KmTree.o .libs/KmUtils.o 
libtool: link: ranlib .libs/libkmpp.a
libtool: link: ( cd ".libs" && rm -f "libkmpp.la" && ln -s "../libkmpp.la" "libkmpp.la" )
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Making all in clustal
make[3]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/clustal'
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o hhalign_wrapper.lo hhalign_wrapper.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o ktuple_pair.lo ktuple_pair.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c hhalign_wrapper.c  -fPIC -DPIC -o .libs/hhalign_wrapper.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c ktuple_pair.c  -fPIC -DPIC -o .libs/ktuple_pair.o
hhalign_wrapper.c: In function 'ReAttachLeadingGaps':
hhalign_wrapper.c:259:9: warning: variable 'iSize2' set but not used [-Wunused-but-set-variable]
  259 |     int iSize2 = 0; /* #seqs in 2nd profile */
      |         ^~~~~~
hhalign_wrapper.c:258:9: warning: variable 'iSize1' set but not used [-Wunused-but-set-variable]
  258 |     int iSize1 = 0; /* #seqs in 1st profile */
      |         ^~~~~~
hhalign_wrapper.c: In function 'PileUp':
hhalign_wrapper.c:633:9: warning: variable 'iHHret' set but not used [-Wunused-but-set-variable]
  633 |     int iHHret = -1; /* return value of hhalign() */
      |         ^~~~~~
hhalign_wrapper.c:621:9: warning: variable 'iCountPro' set but not used [-Wunused-but-set-variable]
  621 |     int iCountPro = 0; /* count how many sequences are already in profile */
      |         ^~~~~~~~~
hhalign_wrapper.c: In function 'HHalignWrapper':
hhalign_wrapper.c:1556:29: warning: operation on '*(ppiLeafList + (sizetype)((long unsigned int)iL * 8))' may be undefined [-Wsequence-point]
 1556 |             ppiLeafList[iL] = CKFREE(ppiLeafList[iL]);
hhalign_wrapper.c:1557:29: warning: operation on '*(ppiLeafList + (sizetype)((long unsigned int)iR * 8))' may be undefined [-Wsequence-point]
 1557 |             ppiLeafList[iR] = CKFREE(ppiLeafList[iR]);
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o list.lo list.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c list.c  -fPIC -DPIC -o .libs/list.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o log.lo log.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c log.c  -fPIC -DPIC -o .libs/log.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o muscle_upgma.lo muscle_upgma.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c muscle_upgma.c  -fPIC -DPIC -o .libs/muscle_upgma.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o muscle_tree.lo muscle_tree.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c muscle_tree.c  -fPIC -DPIC -o .libs/muscle_tree.o
muscle_tree.c:42:21: warning: 'VERY_NEGATIVE_DOUBLE' defined but not used [-Wunused-const-variable=]
   42 | static const double VERY_NEGATIVE_DOUBLE = -9e29;
      |                     ^~~~~~~~~~~~~~~~~~~~
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o mbed.lo mbed.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c mbed.c  -fPIC -DPIC -o .libs/mbed.o
mbed.c: In function 'BisectingKmeans':
mbed.c:788:16: warning: variable 'dCost' set but not used [-Wunused-but-set-variable]
  788 |         double dCost = -1.0;
      |                ^~~~~
mbed.c: At top level:
mbed.c:69:18: warning: 'MAX_ALLOWED_SEQ_PER_PRECLUSTER' defined but not used [-Wunused-const-variable=]
   69 | static const int MAX_ALLOWED_SEQ_PER_PRECLUSTER = 100;
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o pair_dist.lo pair_dist.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pair_dist.c  -fPIC -DPIC -o .libs/pair_dist.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o progress.lo progress.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c progress.c  -fPIC -DPIC -o .libs/progress.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o seq.lo seq.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c seq.c  -fPIC -DPIC -o .libs/seq.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o symmatrix.lo symmatrix.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c symmatrix.c  -fPIC -DPIC -o .libs/symmatrix.o
seq.c: In function 'FreeMSeq':
seq.c:826:27: warning: operation on '(*mseq)->filename' may be undefined [-Wsequence-point]
  826 |         (*mseq)->filename = CKFREE((*mseq)->filename);
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o tree.lo tree.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c tree.c  -fPIC -DPIC -o .libs/tree.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util.lo util.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util.c  -fPIC -DPIC -o .libs/util.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o weights.lo weights.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c weights.c  -fPIC -DPIC -o .libs/weights.o
/bin/sh ../../libtool --tag=CC   --mode=link gcc -fopenmp  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -o libclustal.la  hhalign_wrapper.lo ktuple_pair.lo list.lo log.lo muscle_upgma.lo muscle_tree.lo mbed.lo pair_dist.lo progress.lo seq.lo symmatrix.lo tree.lo util.lo weights.lo  -largtable2 -lm 
libtool: link: ar cru .libs/libclustal.a .libs/hhalign_wrapper.o .libs/ktuple_pair.o .libs/list.o .libs/log.o .libs/muscle_upgma.o .libs/muscle_tree.o .libs/mbed.o .libs/pair_dist.o .libs/progress.o .libs/seq.o .libs/symmatrix.o .libs/tree.o .libs/util.o .libs/weights.o 
libtool: link: ranlib .libs/libclustal.a
libtool: link: ( cd ".libs" && rm -f "libclustal.la" && ln -s "../libclustal.la" "libclustal.la" )
make[3]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/clustal'
make[3]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src'
/bin/sh ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.    -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o clustal-omega.lo clustal-omega.c
g++ -DHAVE_CONFIG_H -I.    -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o main.o main.cpp
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c clustal-omega.c  -fPIC -DPIC -o .libs/clustal-omega.o
clustal-omega.c: In function 'AlnToHHMFile':
clustal-omega.c:393:14: warning: comparison between pointer and integer
  393 |     if (NULL == mkstemp(tmp_aln)) {
      |              ^~
clustal-omega.c: In function 'AlnToHMMFile':
clustal-omega.c:479:14: warning: comparison between pointer and integer
  479 |     if (NULL == mkstemp(tmp_aln)) {
      |              ^~
clustal-omega.c:502:18: warning: comparison between pointer and integer
  502 |         if (NULL == mkstemp(tmp_hmm)) {
      |                  ^~
clustal-omega.c: In function 'AlnToHMM':
clustal-omega.c:573:14: warning: comparison between pointer and integer
  573 |     if (NULL == mkstemp(pcHMM)) {
      |              ^~
clustal-omega.c: At top level:
clustal-omega.c:134:18: warning: 'ITERATION_SCORE_IMPROVEMENT_THRESHOLD' defined but not used [-Wunused-const-variable=]
  134 | static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01;
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I.    -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c mymain.c
/bin/sh ../libtool --tag=CC   --mode=link gcc -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -static -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -o libclustalo.la -rpath /usr/lib64 clustal-omega.lo clustal/libclustal.la hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la  -largtable2 -lm 
libtool: link: (cd .libs/libclustalo.lax/libclustal.a && ar x "/builddir/build/BUILD/clustal-omega-1.2.4/src/clustal/.libs/libclustal.a")
libtool: link: (cd .libs/libclustalo.lax/libhhalign.a && ar x "/builddir/build/BUILD/clustal-omega-1.2.4/src/hhalign/.libs/libhhalign.a")
libtool: link: (cd .libs/libclustalo.lax/libsquid.a && ar x "/builddir/build/BUILD/clustal-omega-1.2.4/src/squid/.libs/libsquid.a")
libtool: link: (cd .libs/libclustalo.lax/libkmpp.a && ar x "/builddir/build/BUILD/clustal-omega-1.2.4/src/kmpp/.libs/libkmpp.a")
libtool: link: ar cru .libs/libclustalo.a  .libs/clustal-omega.o  .libs/libclustalo.lax/libclustal.a/weights.o .libs/libclustalo.lax/libclustal.a/util.o .libs/libclustalo.lax/libclustal.a/tree.o .libs/libclustalo.lax/libclustal.a/symmatrix.o .libs/libclustalo.lax/libclustal.a/seq.o .libs/libclustalo.lax/libclustal.a/progress.o .libs/libclustalo.lax/libclustal.a/pair_dist.o .libs/libclustalo.lax/libclustal.a/mbed.o .libs/libclustalo.lax/libclustal.a/muscle_tree.o .libs/libclustalo.lax/libclustal.a/muscle_upgma.o .libs/libclustalo.lax/libclustal.a/log.o .libs/libclustalo.lax/libclustal.a/list.o .libs/libclustalo.lax/libclustal.a/ktuple_pair.o .libs/libclustalo.lax/libclustal.a/hhalign_wrapper.o  .libs/libclustalo.lax/libhhalign.a/hhalign.o  .libs/libclustalo.lax/libsquid.a/weight.o .libs/libclustalo.lax/libsquid.a/vectorops.o .libs/libclustalo.lax/libsquid.a/types.o .libs/libclustalo.lax/libsquid.a/translate.o .libs/libclustalo.lax/libsquid.a/stopwatch.o .libs/libclustalo.lax/libsquid.a/stockholm.o .libs/libclustalo.lax/libsquid.a/stack.o .libs/libclustalo.lax/libsquid.a/ssi.o .libs/libclustalo.lax/libsquid.a/sre_string.o .libs/libclustalo.lax/libsquid.a/sre_random.o .libs/libclustalo.lax/libsquid.a/sre_math.o .libs/libclustalo.lax/libsquid.a/sre_ctype.o .libs/libclustalo.lax/libsquid.a/squidcore.o .libs/libclustalo.lax/libsquid.a/sqio.o .libs/libclustalo.lax/libsquid.a/sqerror.o .libs/libclustalo.lax/libsquid.a/shuffle.o .libs/libclustalo.lax/libsquid.a/seqencode.o .libs/libclustalo.lax/libsquid.a/selex.o .libs/libclustalo.lax/libsquid.a/rk.o .libs/libclustalo.lax/libsquid.a/revcomp.o .libs/libclustalo.lax/libsquid.a/phylip.o .libs/libclustalo.lax/libsquid.a/msf.o .libs/libclustalo.lax/libsquid.a/msa.o .libs/libclustalo.lax/libsquid.a/iupac.o .libs/libclustalo.lax/libsquid.a/hsregex.o .libs/libclustalo.lax/libsquid.a/gsi64.o .libs/libclustalo.lax/libsquid.a/gsi.o .libs/libclustalo.lax/libsquid.a/gki.o .libs/libclustalo.lax/libsquid.a/getopt.o .libs/libclustalo.lax/libsquid.a/file.o .libs/libclustalo.lax/libsquid.a/eps.o .libs/libclustalo.lax/libsquid.a/dayhoff.o .libs/libclustalo.lax/libsquid.a/cluster.o .libs/libclustalo.lax/libsquid.a/clustal.o .libs/libclustalo.lax/libsquid.a/alignio.o .libs/libclustalo.lax/libsquid.a/aligneval.o .libs/libclustalo.lax/libsquid.a/a2m.o  .libs/libclustalo.lax/libkmpp.a/KmUtils.o .libs/libclustalo.lax/libkmpp.a/KmTree.o .libs/libclustalo.lax/libkmpp.a/KMeans.o 
libtool: link: ranlib .libs/libclustalo.a
libtool: link: rm -fr .libs/libclustalo.lax
libtool: link: ( cd ".libs" && rm -f "libclustalo.la" && ln -s "../libclustalo.la" "libclustalo.la" )
/bin/sh ../libtool --tag=CXX   --mode=link g++ -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm 
libtool: link: g++ -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -o clustalo main.o mymain.o  ./.libs/libclustalo.a -largtable2 -lm
make[3]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src'
make[2]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src'
make[1]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src'
make[1]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4'
make[1]: Nothing to be done for 'all-am'.
make[1]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4'
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.EmizYe
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64
++ dirname /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-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 -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 clustal-omega-1.2.4
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64 'INSTALL=/usr/bin/install -p'
Making install in src
make[1]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src'
Making install in hhalign
make[2]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/hhalign'
make[3]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/hhalign'
make[3]: Nothing to be done for 'install-exec-am'.
test -z "/usr/include/clustalo/hhalign" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/hhalign"
 /usr/bin/install -p -m 644 'general.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/hhalign/general.h'
 /usr/bin/install -p -m 644 'hhfunc.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/hhalign/hhfunc.h'
make[3]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/hhalign'
make[2]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/hhalign'
Making install in squid
make[2]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/squid'
make[3]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/squid'
make[3]: Nothing to be done for 'install-exec-am'.
test -z "/usr/include/clustalo/squid" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/squid"
 /usr/bin/install -p -m 644 'gki.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/squid/gki.h'
 /usr/bin/install -p -m 644 'gsi64.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/squid/gsi64.h'
 /usr/bin/install -p -m 644 'msa.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/squid/msa.h'
 /usr/bin/install -p -m 644 'rk.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/squid/rk.h'
 /usr/bin/install -p -m 644 'squid.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/squid/squid.h'
 /usr/bin/install -p -m 644 'stopwatch.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/squid/stopwatch.h'
 /usr/bin/install -p -m 644 'sqfuncs.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/squid/sqfuncs.h'
 /usr/bin/install -p -m 644 'sre_random.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/squid/sre_random.h'
 /usr/bin/install -p -m 644 'ssi.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/squid/ssi.h'
 /usr/bin/install -p -m 644 'stockholm.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/squid/stockholm.h'
 /usr/bin/install -p -m 644 'vectorops.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/squid/vectorops.h'
 /usr/bin/install -p -m 644 'version.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/squid/version.h'
make[3]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/squid'
make[2]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/squid'
Making install in kmpp
make[2]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/kmpp'
make[3]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/kmpp'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/kmpp'
make[2]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/kmpp'
Making install in clustal
make[2]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/clustal'
make[3]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/clustal'
make[3]: Nothing to be done for 'install-exec-am'.
test -z "/usr/include/clustalo/clustal" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/clustal"
 /usr/bin/install -p -m 644 'hhalign_wrapper.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/clustal/hhalign_wrapper.h'
 /usr/bin/install -p -m 644 'ktuple_pair.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/clustal/ktuple_pair.h'
 /usr/bin/install -p -m 644 'log.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/clustal/log.h'
 /usr/bin/install -p -m 644 'mbed.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/clustal/mbed.h'
 /usr/bin/install -p -m 644 'muscle_tree.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/clustal/muscle_tree.h'
 /usr/bin/install -p -m 644 'pair_dist.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/clustal/pair_dist.h'
 /usr/bin/install -p -m 644 'progress.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/clustal/progress.h'
 /usr/bin/install -p -m 644 'seq.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/clustal/seq.h'
 /usr/bin/install -p -m 644 'symmatrix.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/clustal/symmatrix.h'
 /usr/bin/install -p -m 644 'tree.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/clustal/tree.h'
 /usr/bin/install -p -m 644 'util.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/clustal/util.h'
 /usr/bin/install -p -m 644 'weights.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/clustal/weights.h'
make[3]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/clustal'
make[2]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src/clustal'
make[2]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src'
make[3]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4/src'
test -z "/usr/lib64" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/lib64"
 /bin/sh ../libtool   --mode=install /usr/bin/install -p  'libclustalo.la' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/lib64/libclustalo.la'
libtool: install: /usr/bin/install -p .libs/libclustalo.lai /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/lib64/libclustalo.la
libtool: install: /usr/bin/install -p .libs/libclustalo.a /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/lib64/libclustalo.a
libtool: install: chmod 644 /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/lib64/libclustalo.a
libtool: install: ranlib /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/lib64/libclustalo.a
libtool: install: warning: remember to run `libtool --finish /usr/lib64'
test -z "/usr/bin" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/bin"
  /bin/sh ../libtool   --mode=install /usr/bin/install -p 'clustalo' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/bin/clustalo'
libtool: install: /usr/bin/install -p clustalo /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/bin/clustalo
test -z "/usr/include/clustalo/" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo/"
 /usr/bin/install -p -m 644 'clustal-omega-config.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo//clustal-omega-config.h'
 /usr/bin/install -p -m 644 'clustal-omega.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/include/clustalo//clustal-omega.h'
make[3]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src'
make[2]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src'
make[1]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4/src'
make[1]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4'
make[2]: Entering directory '/builddir/build/BUILD/clustal-omega-1.2.4'
make[2]: Nothing to be done for 'install-exec-am'.
test -z "/usr/share/doc/clustal-omega" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/share/doc/clustal-omega"
 /usr/bin/install -p -m 644 'README' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/share/doc/clustal-omega/README'
test -z "/usr/lib64/pkgconfig" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/lib64/pkgconfig"
 /usr/bin/install -p -m 644 'clustalo.pc' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/lib64/pkgconfig/clustalo.pc'
make[2]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4'
make[1]: Leaving directory '/builddir/build/BUILD/clustal-omega-1.2.4'
+ rm -f /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/lib64/libclustalo.la /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/lib64/libclustalo.a
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.2.4-15.fc38 --unique-debug-suffix -1.2.4-15.fc38.x86_64 --unique-debug-src-base clustal-omega-1.2.4-15.fc38.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/clustal-omega-1.2.4
extracting debug info from /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/bin/clustalo
original debug info size: 1660kB, size after compression: 1516kB
/usr/bin/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
3429 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/redhat/brp-python-hardlink
Processing files: clustal-omega-1.2.4-15.fc38.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.ZffZIj
+ umask 022
+ cd /builddir/build/BUILD
+ cd clustal-omega-1.2.4
+ DOCDIR=/builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/share/doc/clustal-omega
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/share/doc/clustal-omega
+ cp -pr COPYING /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/share/doc/clustal-omega
+ cp -pr README /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64/usr/share/doc/clustal-omega
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: bundled(squid) = 1.9 clustal-omega = 1.2.4-15.fc38 clustal-omega(x86-64) = 1.2.4-15.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libargtable2.so.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(GOMP_4.5)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.27)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(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_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH)
Processing files: clustal-omega-devel-1.2.4-15.fc38.x86_64
Provides: clustal-omega-devel = 1.2.4-15.fc38 clustal-omega-devel(x86-64) = 1.2.4-15.fc38 pkgconfig(clustalo) = 1.2.4
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/pkg-config
Processing files: clustal-omega-debugsource-1.2.4-15.fc38.x86_64
Provides: clustal-omega-debugsource = 1.2.4-15.fc38 clustal-omega-debugsource(x86-64) = 1.2.4-15.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: clustal-omega-debuginfo-1.2.4-15.fc38.x86_64
Provides: clustal-omega-debuginfo = 1.2.4-15.fc38 clustal-omega-debuginfo(x86-64) = 1.2.4-15.fc38 debuginfo(build-id) = 73ba8f83662d61e3297f0e140ba7d0261283a60d
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: clustal-omega-debugsource(x86-64) = 1.2.4-15.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64
Wrote: /builddir/build/RPMS/clustal-omega-debuginfo-1.2.4-15.fc38.x86_64.rpm
Wrote: /builddir/build/RPMS/clustal-omega-1.2.4-15.fc38.x86_64.rpm
Wrote: /builddir/build/RPMS/clustal-omega-debugsource-1.2.4-15.fc38.x86_64.rpm
Wrote: /builddir/build/RPMS/clustal-omega-devel-1.2.4-15.fc38.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.Vds5s8
+ umask 022
+ cd /builddir/build/BUILD
+ cd clustal-omega-1.2.4
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/clustal-omega-1.2.4-15.fc38.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.TcEXbQ
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf clustal-omega-1.2.4 clustal-omega-1.2.4.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0