Mock Version: 1.4.9
Mock Version: 1.4.9
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/clustal-omega.spec'], chrootPath='/var/lib/mock/f29-build-26494-13757/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': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x2001fdb8d0>timeout=345600uid=998gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --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': 'en_US.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
Wrote: /builddir/build/SRPMS/clustal-omega-1.2.4-7.fc29.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/clustal-omega.spec'], chrootPath='/var/lib/mock/f29-build-26494-13757/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': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x2001fdb8d0>timeout=345600uid=998gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --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': 'en_US.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.X80DZ6
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf clustal-omega-1.2.4
+ /usr/bin/gzip -dc /builddir/build/SOURCES/clustal-omega-1.2.4.tar.gz
+ /usr/bin/tar -xof -
+ 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
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.PR2d12
+ umask 022
+ cd /builddir/build/BUILD
+ cd clustal-omega-1.2.4
+ export 'CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' 'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ LDFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export LDFLAGS
+ '[' 1 = 1 ']'
BUILDSTDERR: +++ dirname ./configure
BUILDSTDERR: ++ find . -name config.guess -o -name config.sub
+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
BUILDSTDERR: ++ basename ./config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./config.sub
BUILDSTDERR: ++ 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)
BUILDSTDERR: ++ basename ./config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./config.guess
BUILDSTDERR: ++ 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' ']'
BUILDSTDERR: ++ 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
+ ./configure --build=riscv64-redhat-linux-gnu --host=riscv64-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 riscv64-redhat-linux-gnu-gcc... no
checking for 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... riscv64-redhat-linux-gnu
checking host system type... riscv64-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
checking for riscv64-redhat-linux-gnu-objdump... no
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for riscv64-redhat-linux-gnu-ar... no
checking for ar... ar
checking for riscv64-redhat-linux-gnu-strip... no
checking for strip... strip
checking for riscv64-redhat-linux-gnu-ranlib... no
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for a BSD-compatible install... /usr/bin/install -c
checking for riscv64-redhat-linux-gnu-gcc... gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) none
checking how to run the C preprocessor... gcc -E
checking for riscv64-redhat-linux-gnu-g++... no
checking for riscv64-redhat-linux-gnu-c++... no
checking for riscv64-redhat-linux-gnu-gpp... no
checking for riscv64-redhat-linux-gnu-aCC... no
checking for riscv64-redhat-linux-gnu-CC... no
checking for riscv64-redhat-linux-gnu-cxx... no
checking for riscv64-redhat-linux-gnu-cc++... no
checking for riscv64-redhat-linux-gnu-cl.exe... no
checking for riscv64-redhat-linux-gnu-FCC... no
checking for riscv64-redhat-linux-gnu-KCC... no
checking for riscv64-redhat-linux-gnu-RCC... no
checking for riscv64-redhat-linux-gnu-xlC_r... no
checking for riscv64-redhat-linux-gnu-xlC... no
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking how to run the C++ preprocessor... g++ -E
checking for ANSI C header files... (cached) yes
checking assert.h usability... yes
checking assert.h presence... yes
checking for assert.h... yes
checking ctype.h usability... yes
checking ctype.h presence... yes
checking for ctype.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking for memory.h... (cached) yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for inline... inline
checking for log in -lm... yes
checking for log2 in -lm... yes
checking argtable2.h usability... yes
checking argtable2.h presence... yes
checking for argtable2.h... yes
checking for arg_parse in -largtable2... yes
checking for OpenMP flag of C compiler... -fopenmp
checking whether byte ordering is bigendian... no
checking for ntohs... yes
checking for ntohl... yes
checking for ntons... no
checking for ntonl... no
checking size of unsigned short... 2
checking size of unsigned int... 4
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking for stroul... no
checking for strtoull... yes
checking for ftello... yes
checking for fseeko... yes
checking for ftello64... yes
checking for fseeko64... yes
checking for ftell64... no
checking for fseek64... no
checking for off_t... yes
checking size of fpos_t... 16
checking if malloc debugging is wanted... no
checking whether to build with debug information... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating clustalo.pc
config.status: creating Doxyfile
config.status: creating src/clustal/Makefile
config.status: creating src/hhalign/Makefile
config.status: creating src/kmpp/Makefile
config.status: creating src/squid/Makefile
config.status: creating src/config.h
config.status: executing src/clustal-omega-config.h commands
config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines
config.status: src/clustal-omega-config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
+ make V=1 -j4
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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c hhalign.cpp -fPIC -DPIC -o .libs/hhalign.o
BUILDSTDERR: In file included from hhalign.cpp:70:
BUILDSTDERR: hhhmm-C.h: In member function 'int HMM::ReadHMMer3(FILE*, char*)':
BUILDSTDERR: hhhmm-C.h:1141:12: warning: variable 'dAlphaInv' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: double dAlphaInv = 1.00 / (double)(iAlpha); /* weight of AA */
BUILDSTDERR: ^~~~~~~~~
BUILDSTDERR: hhhmm-C.h: In member function 'void HMM::WriteToFileHMMER(char*)':
BUILDSTDERR: hhhmm-C.h:2206:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR: for (i=0; i<=par.argc-1; ++i) fprintf(outf,"%s ",par.argv[i]); fprintf(outf,"\n");
BUILDSTDERR: ^~~
BUILDSTDERR: hhhmm-C.h:2206:66: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
BUILDSTDERR: for (i=0; i<=par.argc-1; ++i) fprintf(outf,"%s ",par.argv[i]); fprintf(outf,"\n");
BUILDSTDERR: ^~~~~~~
BUILDSTDERR: In file included from hhalign.cpp:71:
BUILDSTDERR: hhalignment-C.h: In member function 'void Alignment::Read(FILE*, char*, char*)':
BUILDSTDERR: hhalignment-C.h:250:32: warning: variable 'ptr2' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: char *ptr1, *ptr2;
BUILDSTDERR: ^~~~
BUILDSTDERR: hhalignment-C.h: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM&)':
BUILDSTDERR: hhalignment-C.h:1473:19: warning: variable 'score_M' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: float score_M=0.0;
BUILDSTDERR: ^~~~~~~
BUILDSTDERR: hhalignment-C.h:1474:19: warning: variable 'score_prev' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: float score_prev=0.0;
BUILDSTDERR: ^~~~~~~~~~
BUILDSTDERR: hhalignment-C.h: In member function 'void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM&, char*)':
BUILDSTDERR: hhalignment-C.h:1981:18: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
BUILDSTDERR: if (ncol<NCOLMIN)
BUILDSTDERR: ^
BUILDSTDERR: hhalignment-C.h: In member function 'void Alignment::Transitions_from_I_state(HMM&, char*)':
BUILDSTDERR: hhalignment-C.h:2248:28: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
BUILDSTDERR: if (ncol>=NCOLMIN)
BUILDSTDERR: ^
BUILDSTDERR: hhalignment-C.h: In member function 'void Alignment::Transitions_from_D_state(HMM&, char*)':
BUILDSTDERR: hhalignment-C.h:2485:20: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
BUILDSTDERR: if (ncol<NCOLMIN)
BUILDSTDERR: ^
BUILDSTDERR: In file included from hhalign.cpp:75:
BUILDSTDERR: hhhitlist-C.h: In member function 'void HitList::TransitiveScoring()':
BUILDSTDERR: hhhitlist-C.h:1257:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: size_t unused; /* disable fread gcc warning */
BUILDSTDERR: ^~~~~~
BUILDSTDERR: hhhitlist-C.h: In member function 'void HitList::TransitiveScoring2()':
BUILDSTDERR: hhhitlist-C.h:1622:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: size_t unused; /* disable fread gcc warning */
BUILDSTDERR: ^~~~~~
BUILDSTDERR: hhhitlist-C.h: In member function 'void HitList::TransitiveScoring3()':
BUILDSTDERR: hhhitlist-C.h:1992:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: size_t unused; /* disable fread gcc warning */
BUILDSTDERR: ^~~~~~
BUILDSTDERR: hhhitlist-C.h: In member function 'void HitList::TransitiveScoring4()':
BUILDSTDERR: hhhitlist-C.h:2357:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: size_t unused; /* disable fread gcc warning */
BUILDSTDERR: ^~~~~~
BUILDSTDERR: 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*)':
BUILDSTDERR: hhalign.cpp:714:9: warning: variable 'Nali' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: int Nali; /* number of normally backtraced alignments
BUILDSTDERR: ^~~~
/bin/sh ../../libtool --tag=CXX --mode=link g++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o a2m.lo a2m.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o aligneval.lo aligneval.c
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/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o clustal.lo clustal.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c aligneval.c -fPIC -DPIC -o .libs/aligneval.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c clustal.c -fPIC -DPIC -o .libs/clustal.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c alignio.c -fPIC -DPIC -o .libs/alignio.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c a2m.c -fPIC -DPIC -o .libs/a2m.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o cluster.lo cluster.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c cluster.c -fPIC -DPIC -o .libs/cluster.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o dayhoff.lo dayhoff.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o eps.lo eps.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c dayhoff.c -fPIC -DPIC -o .libs/dayhoff.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o file.lo file.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o getopt.lo getopt.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o gki.lo gki.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o gsi.lo gsi.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c gki.c -fPIC -DPIC -o .libs/gki.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o gsi64.lo gsi64.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o hsregex.lo hsregex.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o iupac.lo iupac.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o msa.lo msa.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c iupac.c -fPIC -DPIC -o .libs/iupac.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o msf.lo msf.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o phylip.lo phylip.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c msf.c -fPIC -DPIC -o .libs/msf.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c phylip.c -fPIC -DPIC -o .libs/phylip.o
BUILDSTDERR: msf.c: In function 'ReadMSF':
BUILDSTDERR: msf.c:85:11: warning: variable 'alleged_checksum' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: int alleged_checksum = 0;
BUILDSTDERR: ^~~~~~~~~~~~~~~~
BUILDSTDERR: msf.c:83:11: warning: variable 'alleged_alen' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: int alleged_alen = 0;
BUILDSTDERR: ^~~~~~~~~~~~
BUILDSTDERR: phylip.c: In function 'ReadPhylip':
BUILDSTDERR: phylip.c:78:15: warning: variable 'alen' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: int nseq, alen;
BUILDSTDERR: ^~~~
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o revcomp.lo revcomp.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c revcomp.c -fPIC -DPIC -o .libs/revcomp.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o rk.lo rk.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o selex.lo selex.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c rk.c -fPIC -DPIC -o .libs/rk.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o seqencode.lo seqencode.c
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c seqencode.c -fPIC -DPIC -o .libs/seqencode.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sqerror.c -fPIC -DPIC -o .libs/sqerror.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c squidcore.c -fPIC -DPIC -o .libs/squidcore.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sre_math.c -fPIC -DPIC -o .libs/sre_math.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sre_random.c -fPIC -DPIC -o .libs/sre_random.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c sre_string.c -fPIC -DPIC -o .libs/sre_string.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ssi.c -fPIC -DPIC -o .libs/ssi.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c stack.c -fPIC -DPIC -o .libs/stack.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c stockholm.c -fPIC -DPIC -o .libs/stockholm.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c stopwatch.c -fPIC -DPIC -o .libs/stopwatch.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c types.c -fPIC -DPIC -o .libs/types.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c weight.c -fPIC -DPIC -o .libs/weight.o
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Making all in kmpp
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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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o ktuple_pair.lo ktuple_pair.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o list.lo list.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o log.lo log.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c list.c -fPIC -DPIC -o .libs/list.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ktuple_pair.c -fPIC -DPIC -o .libs/ktuple_pair.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c hhalign_wrapper.c -fPIC -DPIC -o .libs/hhalign_wrapper.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o muscle_upgma.lo muscle_upgma.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o muscle_tree.lo muscle_tree.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c muscle_tree.c -fPIC -DPIC -o .libs/muscle_tree.o
BUILDSTDERR: hhalign_wrapper.c: In function 'ReAttachLeadingGaps':
BUILDSTDERR: hhalign_wrapper.c:259:9: warning: variable 'iSize2' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: int iSize2 = 0; /* #seqs in 2nd profile */
BUILDSTDERR: ^~~~~~
BUILDSTDERR: hhalign_wrapper.c:258:9: warning: variable 'iSize1' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: int iSize1 = 0; /* #seqs in 1st profile */
BUILDSTDERR: ^~~~~~
BUILDSTDERR: hhalign_wrapper.c: In function 'PileUp':
BUILDSTDERR: hhalign_wrapper.c:633:9: warning: variable 'iHHret' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: int iHHret = -1; /* return value of hhalign() */
BUILDSTDERR: ^~~~~~
BUILDSTDERR: hhalign_wrapper.c:621:9: warning: variable 'iCountPro' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: int iCountPro = 0; /* count how many sequences are already in profile */
BUILDSTDERR: ^~~~~~~~~
BUILDSTDERR: hhalign_wrapper.c: In function 'HHalignWrapper':
BUILDSTDERR: hhalign_wrapper.c:1556:29: warning: operation on '*(ppiLeafList + (sizetype)((long unsigned int)iL * 8))' may be undefined [-Wsequence-point]
BUILDSTDERR: ppiLeafList[iL] = CKFREE(ppiLeafList[iL]);
BUILDSTDERR: hhalign_wrapper.c:1557:29: warning: operation on '*(ppiLeafList + (sizetype)((long unsigned int)iR * 8))' may be undefined [-Wsequence-point]
BUILDSTDERR: ppiLeafList[iR] = CKFREE(ppiLeafList[iR]);
BUILDSTDERR: muscle_tree.c:42:21: warning: 'VERY_NEGATIVE_DOUBLE' defined but not used [-Wunused-const-variable=]
BUILDSTDERR: static const double VERY_NEGATIVE_DOUBLE = -9e29;
BUILDSTDERR: ^~~~~~~~~~~~~~~~~~~~
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o mbed.lo mbed.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c mbed.c -fPIC -DPIC -o .libs/mbed.o
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o pair_dist.lo pair_dist.c
BUILDSTDERR: mbed.c: In function 'BisectingKmeans':
BUILDSTDERR: mbed.c:788:16: warning: variable 'dCost' set but not used [-Wunused-but-set-variable]
BUILDSTDERR: double dCost = -1.0;
BUILDSTDERR: ^~~~~
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c pair_dist.c -fPIC -DPIC -o .libs/pair_dist.o
BUILDSTDERR: At top level:
BUILDSTDERR: mbed.c:69:18: warning: 'MAX_ALLOWED_SEQ_PER_PRECLUSTER' defined but not used [-Wunused-const-variable=]
BUILDSTDERR: static const int MAX_ALLOWED_SEQ_PER_PRECLUSTER = 100;
BUILDSTDERR: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o progress.lo progress.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o seq.lo seq.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o symmatrix.lo symmatrix.c
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o tree.lo tree.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c symmatrix.c -fPIC -DPIC -o .libs/symmatrix.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c tree.c -fPIC -DPIC -o .libs/tree.o
BUILDSTDERR: seq.c: In function 'FreeMSeq':
BUILDSTDERR: seq.c:826:27: warning: operation on '(*mseq)->filename' may be undefined [-Wsequence-point]
BUILDSTDERR: (*mseq)->filename = CKFREE((*mseq)->filename);
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o util.lo util.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o weights.lo weights.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c weights.c -fPIC -DPIC -o .libs/weights.o
/bin/sh ../../libtool --tag=CC --mode=link gcc -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o clustal-omega.lo clustal-omega.c
g++ -DHAVE_CONFIG_H -I. -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o main.o main.cpp
gcc -DHAVE_CONFIG_H -I. -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c mymain.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c clustal-omega.c -fPIC -DPIC -o .libs/clustal-omega.o
BUILDSTDERR: clustal-omega.c: In function 'AlnToHHMFile':
BUILDSTDERR: clustal-omega.c:393:14: warning: comparison between pointer and integer
BUILDSTDERR: if (NULL == mkstemp(tmp_aln)) {
BUILDSTDERR: ^~
BUILDSTDERR: clustal-omega.c: In function 'AlnToHMMFile':
BUILDSTDERR: clustal-omega.c:479:14: warning: comparison between pointer and integer
BUILDSTDERR: if (NULL == mkstemp(tmp_aln)) {
BUILDSTDERR: ^~
BUILDSTDERR: clustal-omega.c:502:18: warning: comparison between pointer and integer
BUILDSTDERR: if (NULL == mkstemp(tmp_hmm)) {
BUILDSTDERR: ^~
BUILDSTDERR: clustal-omega.c: In function 'AlnToHMM':
BUILDSTDERR: clustal-omega.c:573:14: warning: comparison between pointer and integer
BUILDSTDERR: if (NULL == mkstemp(pcHMM)) {
BUILDSTDERR: ^~
BUILDSTDERR: At top level:
BUILDSTDERR: clustal-omega.c:134:18: warning: 'ITERATION_SCORE_IMPROVEMENT_THRESHOLD' defined but not used [-Wunused-const-variable=]
BUILDSTDERR: static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01;
BUILDSTDERR: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -static -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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/hhalign_wrapper.o .libs/libclustalo.lax/libclustal.a/ktuple_pair.o .libs/libclustalo.lax/libclustal.a/muscle_tree.o .libs/libclustalo.lax/libclustal.a/list.o .libs/libclustalo.lax/libclustal.a/tree.o .libs/libclustalo.lax/libclustal.a/mbed.o .libs/libclustalo.lax/libclustal.a/weights.o .libs/libclustalo.lax/libclustal.a/pair_dist.o .libs/libclustalo.lax/libclustal.a/symmatrix.o .libs/libclustalo.lax/libclustal.a/util.o .libs/libclustalo.lax/libclustal.a/log.o .libs/libclustalo.lax/libclustal.a/progress.o .libs/libclustalo.lax/libclustal.a/seq.o .libs/libclustalo.lax/libclustal.a/muscle_upgma.o .libs/libclustalo.lax/libhhalign.a/hhalign.o .libs/libclustalo.lax/libsquid.a/dayhoff.o .libs/libclustalo.lax/libsquid.a/translate.o .libs/libclustalo.lax/libsquid.a/eps.o .libs/libclustalo.lax/libsquid.a/alignio.o .libs/libclustalo.lax/libsquid.a/cluster.o .libs/libclustalo.lax/libsquid.a/squidcore.o .libs/libclustalo.lax/libsquid.a/getopt.o .libs/libclustalo.lax/libsquid.a/rk.o .libs/libclustalo.lax/libsquid.a/gki.o .libs/libclustalo.lax/libsquid.a/shuffle.o .libs/libclustalo.lax/libsquid.a/seqencode.o .libs/libclustalo.lax/libsquid.a/sre_math.o .libs/libclustalo.lax/libsquid.a/sqio.o .libs/libclustalo.lax/libsquid.a/stack.o .libs/libclustalo.lax/libsquid.a/clustal.o .libs/libclustalo.lax/libsquid.a/msf.o .libs/libclustalo.lax/libsquid.a/gsi64.o .libs/libclustalo.lax/libsquid.a/selex.o .libs/libclustalo.lax/libsquid.a/stopwatch.o .libs/libclustalo.lax/libsquid.a/file.o .libs/libclustalo.lax/libsquid.a/sre_ctype.o .libs/libclustalo.lax/libsquid.a/iupac.o .libs/libclustalo.lax/libsquid.a/sqerror.o .libs/libclustalo.lax/libsquid.a/msa.o .libs/libclustalo.lax/libsquid.a/stockholm.o .libs/libclustalo.lax/libsquid.a/weight.o .libs/libclustalo.lax/libsquid.a/sre_string.o .libs/libclustalo.lax/libsquid.a/ssi.o .libs/libclustalo.lax/libsquid.a/phylip.o .libs/libclustalo.lax/libsquid.a/types.o .libs/libclustalo.lax/libsquid.a/aligneval.o .libs/libclustalo.lax/libsquid.a/hsregex.o .libs/libclustalo.lax/libsquid.a/a2m.o .libs/libclustalo.lax/libsquid.a/revcomp.o .libs/libclustalo.lax/libsquid.a/sre_random.o .libs/libclustalo.lax/libsquid.a/gsi.o .libs/libclustalo.lax/libsquid.a/vectorops.o .libs/libclustalo.lax/libkmpp.a/KmTree.o .libs/libclustalo.lax/libkmpp.a/KMeans.o .libs/libclustalo.lax/libkmpp.a/KmUtils.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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm
libtool: link: g++ -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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'
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.ZcxhoZ
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64
BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64
+ cd clustal-omega-1.2.4
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64 '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-1.2.4-7.fc29.riscv64/usr/include/clustalo/hhalign"
/usr/bin/install -p -m 644 'general.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/hhalign/general.h'
/usr/bin/install -p -m 644 'hhfunc.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/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-1.2.4-7.fc29.riscv64/usr/include/clustalo/squid"
/usr/bin/install -p -m 644 'gki.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/squid/gki.h'
/usr/bin/install -p -m 644 'gsi64.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/squid/gsi64.h'
/usr/bin/install -p -m 644 'msa.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/squid/msa.h'
/usr/bin/install -p -m 644 'rk.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/squid/rk.h'
/usr/bin/install -p -m 644 'squid.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/squid/squid.h'
/usr/bin/install -p -m 644 'stopwatch.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/squid/stopwatch.h'
/usr/bin/install -p -m 644 'sqfuncs.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/squid/sqfuncs.h'
/usr/bin/install -p -m 644 'sre_random.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/squid/sre_random.h'
/usr/bin/install -p -m 644 'ssi.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/squid/ssi.h'
/usr/bin/install -p -m 644 'stockholm.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/squid/stockholm.h'
/usr/bin/install -p -m 644 'vectorops.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/squid/vectorops.h'
/usr/bin/install -p -m 644 'version.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/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-1.2.4-7.fc29.riscv64/usr/include/clustalo/clustal"
/usr/bin/install -p -m 644 'hhalign_wrapper.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/clustal/hhalign_wrapper.h'
/usr/bin/install -p -m 644 'ktuple_pair.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/clustal/ktuple_pair.h'
/usr/bin/install -p -m 644 'log.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/clustal/log.h'
/usr/bin/install -p -m 644 'mbed.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/clustal/mbed.h'
/usr/bin/install -p -m 644 'muscle_tree.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/clustal/muscle_tree.h'
/usr/bin/install -p -m 644 'pair_dist.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/clustal/pair_dist.h'
/usr/bin/install -p -m 644 'progress.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/clustal/progress.h'
/usr/bin/install -p -m 644 'seq.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/clustal/seq.h'
/usr/bin/install -p -m 644 'symmatrix.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/clustal/symmatrix.h'
/usr/bin/install -p -m 644 'tree.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/clustal/tree.h'
/usr/bin/install -p -m 644 'util.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/clustal/util.h'
/usr/bin/install -p -m 644 'weights.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/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-1.2.4-7.fc29.riscv64/usr/lib64"
/bin/sh ../libtool --mode=install /usr/bin/install -p 'libclustalo.la' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/lib64/libclustalo.la'
libtool: install: /usr/bin/install -p .libs/libclustalo.lai /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/lib64/libclustalo.la
libtool: install: /usr/bin/install -p .libs/libclustalo.a /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/lib64/libclustalo.a
libtool: install: chmod 644 /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/lib64/libclustalo.a
libtool: install: ranlib /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/lib64/libclustalo.a
BUILDSTDERR: libtool: install: warning: remember to run `libtool --finish /usr/lib64'
test -z "/usr/bin" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/bin"
/bin/sh ../libtool --mode=install /usr/bin/install -p 'clustalo' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/bin/clustalo'
libtool: install: /usr/bin/install -p clustalo /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/bin/clustalo
test -z "/usr/include/clustalo/" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo/"
/usr/bin/install -p -m 644 'clustal-omega-config.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/include/clustalo//clustal-omega-config.h'
/usr/bin/install -p -m 644 'clustal-omega.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/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-1.2.4-7.fc29.riscv64/usr/share/doc/clustal-omega"
/usr/bin/install -p -m 644 'README' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/share/doc/clustal-omega/README'
test -z "/usr/lib64/pkgconfig" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/lib64/pkgconfig"
/usr/bin/install -p -m 644 'clustalo.pc' '/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/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-1.2.4-7.fc29.riscv64/usr/lib64/libclustalo.la /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/lib64/libclustalo.a
+ /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.2.4-7.fc29 --unique-debug-suffix -1.2.4-7.fc29.riscv64 --unique-debug-src-base clustal-omega-1.2.4-7.fc29.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/clustal-omega-1.2.4
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/bin/clustalo
extracting debug info from /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/bin/clustalo
/usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
BUILDSTDERR: 3429 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
BUILDSTDERR: /sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 1
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
Processing files: clustal-omega-1.2.4-7.fc29.riscv64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.j074AZ
+ umask 022
+ cd /builddir/build/BUILD
+ cd clustal-omega-1.2.4
+ DOCDIR=/builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/share/doc/clustal-omega
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/share/doc/clustal-omega
+ cp -pr COPYING /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/share/doc/clustal-omega
+ cp -pr README /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64/usr/share/doc/clustal-omega
+ exit 0
Provides: bundled(squid) = 1.9 clustal-omega = 1.2.4-7.fc29 clustal-omega(riscv-64) = 1.2.4-7.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libargtable2.so.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(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(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libpthread.so.0()(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_3.4.9)(64bit) rtld(GNU_HASH)
Processing files: clustal-omega-devel-1.2.4-7.fc29.riscv64
Provides: clustal-omega-devel = 1.2.4-7.fc29 clustal-omega-devel(riscv-64) = 1.2.4-7.fc29 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-1.2.4-7.fc29.riscv64
Provides: clustal-omega-debugsource = 1.2.4-7.fc29 clustal-omega-debugsource(riscv-64) = 1.2.4-7.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: clustal-omega-debuginfo-1.2.4-7.fc29.riscv64
Provides: clustal-omega-debuginfo = 1.2.4-7.fc29 clustal-omega-debuginfo(riscv-64) = 1.2.4-7.fc29 debuginfo(build-id) = a53ac89254a1d55bd49a8262a00c544651484e98
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: clustal-omega-debugsource(riscv-64) = 1.2.4-7.fc29
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64
Wrote: /builddir/build/RPMS/clustal-omega-1.2.4-7.fc29.riscv64.rpm
Wrote: /builddir/build/RPMS/clustal-omega-devel-1.2.4-7.fc29.riscv64.rpm
Wrote: /builddir/build/RPMS/clustal-omega-debugsource-1.2.4-7.fc29.riscv64.rpm
Wrote: /builddir/build/RPMS/clustal-omega-debuginfo-1.2.4-7.fc29.riscv64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.jTMfFG
+ umask 022
+ cd /builddir/build/BUILD
+ cd clustal-omega-1.2.4
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/clustal-omega-1.2.4-7.fc29.riscv64
+ exit 0
Child return code was: 0