dh build dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:133: installing './compile' configure.ac:115: installing './install-sh' configure.ac:115: installing './missing' Makefile.am: installing './INSTALL' src/Makefile.am: installing './depcomp' dh_auto_configure ./configure --build=s390x-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/s390x-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking 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... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether 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 whether gcc understands -c and -o together... yes 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... s390x-ibm-linux-gnu checking host system type... s390x-ibm-linux-gnu checking whether make sets $(MAKE)... (cached) yes checking how to print strings... printf 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 how to convert s390x-ibm-linux-gnu file names to s390x-ibm-linux-gnu format... func_convert_file_noop checking how to convert s390x-ibm-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no 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... yes 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 -m elf64_s390) 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... yes checking for gcc... (cached) 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 whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking how to run the C preprocessor... gcc -E 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 how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf64_s390 checking if the linker (/usr/bin/ld -m elf64_s390) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf64_s390) 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... yes 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 -m elf64_s390) supports shared libraries... yes checking dynamic linker characteristics... (cached) 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... yes configure: WARNING: Clustal Omega hasn't been tested on Big-Endian machines...expecting trouble! 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 checking that generated files are newer than configure... done 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 debian/rules override_dh_auto_build-indep make[1]: Entering directory '/root/clustalo-1.2.4' # nothing to do here make[1]: Leaving directory '/root/clustalo-1.2.4' dh_auto_build -Nlibclustalo-doc make -j1 make[1]: Entering directory '/root/clustalo-1.2.4' Making all in src make[2]: Entering directory '/root/clustalo-1.2.4/src' make all-recursive make[3]: Entering directory '/root/clustalo-1.2.4/src' Making all in hhalign make[4]: Entering directory '/root/clustalo-1.2.4/src/hhalign' /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o hhalign.lo hhalign.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong 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all in squid make[4]: Entering directory '/root/clustalo-1.2.4/src/squid' /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o a2m.lo a2m.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c a2m.c -fPIC -DPIC -o .libs/a2m.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c a2m.c -o a2m.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o aligneval.lo aligneval.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c aligneval.c -fPIC -DPIC -o .libs/aligneval.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c aligneval.c -o aligneval.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o alignio.lo alignio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g 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-I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o dayhoff.lo dayhoff.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c dayhoff.c -fPIC -DPIC -o .libs/dayhoff.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c dayhoff.c -o dayhoff.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o eps.lo eps.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c eps.c -fPIC -DPIC -o .libs/eps.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c eps.c -o eps.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o file.lo file.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c file.c -fPIC -DPIC -o .libs/file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c file.c -o file.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o getopt.lo getopt.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c getopt.c -fPIC -DPIC -o .libs/getopt.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c getopt.c -o getopt.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o gki.lo gki.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c gki.c -fPIC -DPIC -o .libs/gki.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c gki.c -o gki.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o gsi.lo gsi.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c gsi.c -fPIC -DPIC -o .libs/gsi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c gsi.c -o gsi.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o gsi64.lo gsi64.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c gsi64.c -fPIC -DPIC -o .libs/gsi64.o libtool: compile: gcc 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-I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o weights.lo weights.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c weights.c -fPIC -DPIC -o .libs/weights.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c weights.c -o weights.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=link gcc -fopenmp -O3 -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 cr .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[4]: Leaving directory '/root/clustalo-1.2.4/src/clustal' make[4]: Entering directory '/root/clustalo-1.2.4/src' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o main.o main.cpp gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o mymain.o mymain.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c -o clustal-omega.lo clustal-omega.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c clustal-omega.c -fPIC -DPIC -o .libs/clustal-omega.o clustal-omega.c: In function ‘PrintLongVersion’: clustal-omega.c:152:49: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 152 | PACKAGE_VERSION, PACKAGE_CODENAME, __DATE__); | ^~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -c clustal-omega.c -o clustal-omega.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -O3 -fopenmp -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -static -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o libclustalo.la -rpath /usr/lib/s390x-linux-gnu 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 "/root/clustalo-1.2.4/src/clustal/.libs/libclustal.a") libtool: link: (cd .libs/libclustalo.lax/libhhalign.a && ar x "/root/clustalo-1.2.4/src/hhalign/.libs/libhhalign.a") libtool: link: (cd .libs/libclustalo.lax/libsquid.a && ar x "/root/clustalo-1.2.4/src/squid/.libs/libsquid.a") libtool: link: (cd .libs/libclustalo.lax/libkmpp.a && ar x "/root/clustalo-1.2.4/src/kmpp/.libs/libkmpp.a") libtool: link: ar cr .libs/libclustalo.a clustal-omega.o .libs/libclustalo.lax/libclustal.a/hhalign_wrapper.o .libs/libclustalo.lax/libclustal.a/ktuple_pair.o .libs/libclustalo.lax/libclustal.a/list.o .libs/libclustalo.lax/libclustal.a/log.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/pair_dist.o .libs/libclustalo.lax/libclustal.a/progress.o .libs/libclustalo.lax/libclustal.a/seq.o .libs/libclustalo.lax/libclustal.a/symmatrix.o .libs/libclustalo.lax/libclustal.a/tree.o .libs/libclustalo.lax/libclustal.a/util.o .libs/libclustalo.lax/libclustal.a/weights.o .libs/libclustalo.lax/libhhalign.a/hhalign.o .libs/libclustalo.lax/libsquid.a/a2m.o .libs/libclustalo.lax/libsquid.a/aligneval.o .libs/libclustalo.lax/libsquid.a/alignio.o .libs/libclustalo.lax/libsquid.a/clustal.o .libs/libclustalo.lax/libsquid.a/cluster.o .libs/libclustalo.lax/libsquid.a/dayhoff.o .libs/libclustalo.lax/libsquid.a/eps.o .libs/libclustalo.lax/libsquid.a/file.o .libs/libclustalo.lax/libsquid.a/getopt.o .libs/libclustalo.lax/libsquid.a/gki.o .libs/libclustalo.lax/libsquid.a/gsi.o .libs/libclustalo.lax/libsquid.a/gsi64.o .libs/libclustalo.lax/libsquid.a/hsregex.o .libs/libclustalo.lax/libsquid.a/iupac.o .libs/libclustalo.lax/libsquid.a/msa.o .libs/libclustalo.lax/libsquid.a/msf.o .libs/libclustalo.lax/libsquid.a/phylip.o .libs/libclustalo.lax/libsquid.a/revcomp.o .libs/libclustalo.lax/libsquid.a/rk.o .libs/libclustalo.lax/libsquid.a/selex.o .libs/libclustalo.lax/libsquid.a/seqencode.o .libs/libclustalo.lax/libsquid.a/shuffle.o .libs/libclustalo.lax/libsquid.a/sqerror.o .libs/libclustalo.lax/libsquid.a/sqio.o .libs/libclustalo.lax/libsquid.a/squidcore.o .libs/libclustalo.lax/libsquid.a/sre_ctype.o .libs/libclustalo.lax/libsquid.a/sre_math.o .libs/libclustalo.lax/libsquid.a/sre_random.o .libs/libclustalo.lax/libsquid.a/sre_string.o .libs/libclustalo.lax/libsquid.a/ssi.o .libs/libclustalo.lax/libsquid.a/stack.o .libs/libclustalo.lax/libsquid.a/stockholm.o .libs/libclustalo.lax/libsquid.a/stopwatch.o .libs/libclustalo.lax/libsquid.a/translate.o .libs/libclustalo.lax/libsquid.a/types.o .libs/libclustalo.lax/libsquid.a/vectorops.o .libs/libclustalo.lax/libsquid.a/weight.o .libs/libclustalo.lax/libkmpp.a/KMeans.o .libs/libclustalo.lax/libkmpp.a/KmTree.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/bash ../libtool --tag=CXX --mode=link g++ -O3 -fopenmp -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm libtool: link: g++ -O3 -fopenmp -g -fdebug-prefix-map=/root/clustalo-1.2.4=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o clustalo main.o mymain.o ./.libs/libclustalo.a /usr/lib/s390x-linux-gnu/libargtable2.so -lm -fopenmp /usr/bin/ld: ./.libs/libclustalo.a(clustal-omega.o): in function `AlnToHHMFile': ./src/clustal-omega.c:393: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' make[4]: Leaving directory '/root/clustalo-1.2.4/src' make[3]: Leaving directory '/root/clustalo-1.2.4/src' make[2]: Leaving directory '/root/clustalo-1.2.4/src' make[2]: Entering directory '/root/clustalo-1.2.4' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/root/clustalo-1.2.4' make[1]: Leaving directory '/root/clustalo-1.2.4' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/root/clustalo-1.2.4' dh_auto_test -a make -j1 check VERBOSE=1 make[2]: Entering directory '/root/clustalo-1.2.4' Making check in src make[3]: Entering directory '/root/clustalo-1.2.4/src' Making check in hhalign make[4]: Entering directory '/root/clustalo-1.2.4/src/hhalign' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/root/clustalo-1.2.4/src/hhalign' Making check in squid make[4]: Entering directory '/root/clustalo-1.2.4/src/squid' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/root/clustalo-1.2.4/src/squid' Making check in kmpp make[4]: Entering directory '/root/clustalo-1.2.4/src/kmpp' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/root/clustalo-1.2.4/src/kmpp' Making check in clustal make[4]: Entering directory '/root/clustalo-1.2.4/src/clustal' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/root/clustalo-1.2.4/src/clustal' make[4]: Entering directory '/root/clustalo-1.2.4/src' make[4]: Nothing to be done for 'check-am'. make[4]: Leaving directory '/root/clustalo-1.2.4/src' make[3]: Leaving directory '/root/clustalo-1.2.4/src' make[3]: Entering directory '/root/clustalo-1.2.4' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/root/clustalo-1.2.4' make[2]: Leaving directory '/root/clustalo-1.2.4' # Run additional test from python-biopython package to verify that # this will work as well src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force make[1]: *** [debian/rules:36: override_dh_auto_test-arch] Segmentation fault (core dumped) make[1]: Leaving directory '/root/clustalo-1.2.4' make: *** [debian/rules:16: build] Error 2