+ exec + rm -rf /rpmbuild + mkdir -p /rpmbuild + su -c 'rpmbuild -ba /builddir/build/SPECS/exonerate.spec --define "debug_package %{nil}" --undefine _annotated_build --define "_missing_doc_files_terminate_build %{nil}" --define "_emacs_sitestartdir /usr/share/emacs/site-lisp/site-start.d" --define "_emacs_sitelispdir /usr/share/emacs/site-lisp" --nocheck ' mockbuild Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.ExNeys + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf exonerate-2.4.0 + /usr/bin/tar -xof - + /usr/bin/gzip -dc /builddir/build/SOURCES/exonerate-2.4.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd exonerate-2.4.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (exonerate-fix_nothread-compilation.patch):' Patch #0 (exonerate-fix_nothread-compilation.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file src/general/jobqueue.c + echo 'Patch #1 (exonerate-fix-nothread-concurrent-connections.patch):' Patch #1 (exonerate-fix-nothread-concurrent-connections.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file src/general/socket.c + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.JzD0Dk + umask 022 + cd /builddir/build/BUILD + cd exonerate-2.4.0 + 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 ' + 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 ' + 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 -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 -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + export LDFLAGS + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config.sub ++ basename ./config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub '/usr/lib/rpm/redhat/config.sub' -> './config.sub' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./config.guess ++ basename ./config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess '/usr/lib/rpm/redhat/config.guess' -> './config.guess' + '[' 1 = 1 ']' + '[' x '!=' x-specs=/usr/lib/rpm/redhat/redhat-hardened-ld ']' ++ find . -name 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 --enable-glib2 --disable-assert --enable-paranoia --disable-gprof --disable-gcov --enable-compiledmodels --enable-utilities --disable-pthreads --enable-largefile checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking whether make sets $(MAKE)... yes checking for working aclocal-1.4... missing checking for working autoconf... missing checking for working automake-1.4... missing checking for working autoheader... missing checking for working makeinfo... missing 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 for a BSD-compatible install... /usr/bin/install -c checking whether make sets $(MAKE)... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline 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 limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking errno.h usability... yes checking errno.h presence... yes checking for errno.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for strings.h... (cached) yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking for sys/stat.h... (cached) yes checking for sys/types.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 build system type... riscv64-redhat-linux-gnu checking host system type... riscv64-redhat-linux-gnu Set host to riscv64-redhat-linux-gnu riscv64-redhat-linux-gnu *** Unknown build platform: riscv64-redhat-linux-gnu *** Set source_root_dir to /builddir/build/BUILD/exonerate-2.4.0 ---------------------------------------------------------------- checking for socklen_t... yes checking for pkg-config... /usr/bin/pkg-config Using GLIB-2 Turning assertions off Turning PARANOID options on Not using options for profiling with gprof Not using options for analysis with gcov Adding support for LARGE FILES (>2Gb) for a 32 bit system Using COMPILED C4 MODELS Installing UTILITIES Not using pthreads ---------------------------------------------------------------- configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/man/Makefile config.status: creating doc/man/man1/Makefile config.status: creating src/Makefile config.status: creating src/general/Makefile config.status: creating src/sequence/Makefile config.status: creating src/database/Makefile config.status: creating src/struct/Makefile config.status: creating src/comparison/Makefile config.status: creating src/c4/Makefile config.status: creating src/bsdp/Makefile config.status: creating src/sdp/Makefile config.status: creating src/hub/Makefile config.status: creating src/model/Makefile config.status: creating src/program/Makefile config.status: creating src/util/Makefile config.status: creating test/Makefile config.status: creating test/util/Makefile config.status: creating test/ipcress/Makefile config.status: creating test/exonerate/Makefile config.status: creating test/data/Makefile config.status: creating test/data/cdna/Makefile config.status: creating test/data/protein/Makefile + export 'C4_COMPILED_MODELS=est2genome protein2genome cdna2genome coding2genome' + C4_COMPILED_MODELS='est2genome protein2genome cdna2genome coding2genome' ++ pkg-config --cflags glib-2.0 + make -j1 '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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include ' 'LDFLAGS=-Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now' Making all in doc make[1]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/doc' Making all in man make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man' Making all in man1 make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man/man1' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man/man1' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man' make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/doc' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/doc' make[1]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/doc' Making all in src make[1]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src' Making all in struct make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/struct' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fsm.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fsm.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c recyclebin.c recyclebin.c: In function 'RecycleBin_profile': recyclebin.c:146:9: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(global_recycle_bin_tree, ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:88:0, from recyclebin.h:23, from recyclebin.c:17: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fsm.test fsm.test.o fsm.o recyclebin.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c matrix.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c matrix.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o matrix.test matrix.test.o matrix.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c pqueue.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c pqueue.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o pqueue.test pqueue.test.o pqueue.o recyclebin.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c slist.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c slist.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o slist.test slist.test.o slist.o recyclebin.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c rangetree.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c rangetree.c rangetree.c: In function 'RangeTree_insert_recent': rangetree.c:151:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(rt->recent_data, RangeTree_insert_recent_collect, ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:88:0, from rangetree.h:23, from rangetree.c:18: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o rangetree.test rangetree.test.o rangetree.o recyclebin.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c vfsm.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c vfsm.c In file included from /usr/include/glib-2.0/glib.h:62:0, from vfsm.h:19, from vfsm.c:25: vfsm.c: In function 'VFSM_info': vfsm.c:83:15: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 9 has type 'VFSM_Int {aka long unsigned int}' [-Wformat=] g_message("VFSM info:\n" ^ vfsm.c:99:12: vfsm->prs, ~~~~~~~ /usr/include/glib-2.0/glib/gmessages.h:333:32: note: in definition of macro 'g_message' __VA_ARGS__) ^~~~~~~~~~~ vfsm.c:83:15: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 10 has type 'VFSM_Int {aka long unsigned int}' [-Wformat=] g_message("VFSM info:\n" ^ vfsm.c:100:12: vfsm->prw, ~~~~~~~ /usr/include/glib-2.0/glib/gmessages.h:333:32: note: in definition of macro 'g_message' __VA_ARGS__) ^~~~~~~~~~~ vfsm.c:83:15: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 11 has type 'VFSM_Int {aka long unsigned int}' [-Wformat=] g_message("VFSM info:\n" ^ vfsm.c:101:12: vfsm->lrs, ~~~~~~~ /usr/include/glib-2.0/glib/gmessages.h:333:32: note: in definition of macro 'g_message' __VA_ARGS__) ^~~~~~~~~~~ vfsm.c:83:15: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'VFSM_Int {aka long unsigned int}' [-Wformat=] g_message("VFSM info:\n" ^ vfsm.c:102:12: vfsm->lrw, ~~~~~~~ /usr/include/glib-2.0/glib/gmessages.h:333:32: note: in definition of macro 'g_message' __VA_ARGS__) ^~~~~~~~~~~ vfsm.c:83:15: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 13 has type 'VFSM_Int {aka long unsigned int}' [-Wformat=] g_message("VFSM info:\n" ^ vfsm.c:103:12: vfsm->total ~~~~~~~ /usr/include/glib-2.0/glib/gmessages.h:333:32: note: in definition of macro 'g_message' __VA_ARGS__) ^~~~~~~~~~~ vfsm.c:107:17: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'VFSM_Int {aka long unsigned int}' [-Wformat=] g_print(" branch_size [%d] [%" VFSM_PRINT_FORMAT "]\n", ^~~~~~~~~~~~~~~~~~~~~~~ i, vfsm->branch_size[i]); ~~~~~~~~~~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o vfsm.test vfsm.test.o vfsm.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c recyclebin.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o recyclebin.test recyclebin.test.o recyclebin.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sparsecache.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sparsecache.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o sparsecache.test sparsecache.test.o sparsecache.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c dejavu.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c dejavu.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o dejavu.test dejavu.test.o dejavu.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c bitarray.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c bitarray.c bitarray.c: In function 'BitArray_read': bitarray.c:83:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(ba->data, sizeof(guchar), size, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bitarray.c: In function 'BitArray_read_int': bitarray.c:189:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&num, sizeof(guint64), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o bitarray.test bitarray.test.o bitarray.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c splaytree.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c splaytree.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o splaytree.test splaytree.test.o splaytree.o recyclebin.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c noitree.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c noitree.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o noitree.test noitree.test.o noitree.o recyclebin.o splaytree.o -lglib-2.0 make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/struct' Making all in general make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/general' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c argument.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c argument.c argument.c: In function 'ArgumentParse_boolean': argument.c:138:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(arg_string, true_string[i])) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ argument.c:140:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(arg_string, false_string[i])) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ argument.c: In function 'Argument_process': argument.c:502:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(arg->option_registry, Argument_set_env_var_func, ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:88:0, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ argument.c:559:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(arg->option_registry, ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:88:0, from argument.h:26, from argument.c:16: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o argument.test argument.test.o argument.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c lineparse.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c lineparse.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o lineparse.test lineparse.test.o lineparse.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c compoundfile.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c compoundfile.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o compoundfile.test compoundfile.test.o compoundfile.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c socket.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c socket.c socket.c: In function 'SocketServer_listen': socket.c:341:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] while (msgsock = accept(server->connection->sock, ^~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o socket.test socket.test.o socket.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c jobqueue.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c jobqueue.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o jobqueue.test jobqueue.test.o jobqueue.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c threadref.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c threadref.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o threadref.test threadref.test.o threadref.o -lpthread -lglib-2.0 make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/general' Making all in sequence make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/sequence' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sequence.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sequence.c sequence.c: In function 'Sequence_destroy_annotation_tree': sequence.c:97:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(tree, Sequence_destroy_annotation_data, ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:88:0, from sequence.h:24, from sequence.c:21: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ sequence.c: In function 'Sequence_lock': sequence.c:813:24: warning: unused variable 'revcomp' [-Wunused-variable] register Sequence *revcomp; ^~~~~~~ sequence.c:812:36: warning: unused variable 'translation' [-Wunused-variable] register Sequence_Translation *translation; ^~~~~~~~~~~ sequence.c:811:31: warning: unused variable 'filter' [-Wunused-variable] register Sequence_Filter *filter; ^~~~~~ sequence.c:810:31: warning: unused variable 'subseq' [-Wunused-variable] register Sequence_Subseq *subseq; ^~~~~~ sequence.c: In function 'Sequence_unlock': sequence.c:852:24: warning: unused variable 'revcomp' [-Wunused-variable] register Sequence *revcomp; ^~~~~~~ sequence.c:851:36: warning: unused variable 'translation' [-Wunused-variable] register Sequence_Translation *translation; ^~~~~~~~~~~ sequence.c:850:31: warning: unused variable 'filter' [-Wunused-variable] register Sequence_Filter *filter; ^~~~~~ sequence.c:849:31: warning: unused variable 'subseq' [-Wunused-variable] register Sequence_Subseq *subseq; ^~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c alphabet.c alphabet.c: In function 'Alphabet_name_get_type': alphabet.c:317:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, dna_string[i])) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from alphabet.h:24, from alphabet.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ alphabet.c:320:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, protein_string[i])) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from alphabet.h:24, from alphabet.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ alphabet.c:323:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name, unknown_string[i])) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from alphabet.h:24, from alphabet.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c translate.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c splice.c splice.c: In function 'SplicePredictor_parse_data': splice.c:146:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(word, "splice")) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from splice.h:23, from splice.c:22: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_5SS_data': splice.c:195:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from splice.h:23, from splice.c:22: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ splice.c: In function 'SplicePredictor_add_3SS_data': splice.c:203:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!path) || (!strlen(path)) || (!g_strcasecmp(path, "primate"))) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from splice.h:23, from splice.c:22: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o sequence.test sequence.test.o sequence.o alphabet.o translate.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c submat.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c submat.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o submat.test submat.test.o submat.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c translate.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o translate.test translate.test.o translate.o ../../src/general/argument.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c splice.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o splice.test splice.test.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c alphabet.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o alphabet.test alphabet.test.o alphabet.o ../../src/general/argument.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c codonsubmat.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c codonsubmat.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o codonsubmat.test codonsubmat.test.o codonsubmat.o ../../src/general/argument.o -lm -lglib-2.0 make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/sequence' Making all in comparison make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/comparison' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c wordhood.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c wordhood.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o wordhood.test wordhood.test.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c hspset.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c hspset.c hspset.c: In function 'HSP_Display_insert': hspset.c:637:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(query_str); ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ hspset.c:638:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(target_str); ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ hspset.c:640:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(query_str); ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ hspset.c:641:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(target_str); ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from hspset.h:26, from hspset.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ hspset.c: In function 'HSPset_seed_all_hsps': hspset.c:1098:25: warning: variable 'tpos' set but not used [-Wunused-but-set-variable] register gint qpos, tpos; ^~~~ hspset.c:1098:19: warning: variable 'qpos' set but not used [-Wunused-but-set-variable] register gint qpos, tpos; ^~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c match.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o hspset.test hspset.test.o hspset.o match.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c pcr.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c pcr.c pcr.c: In function 'PCR_Match_allocate': pcr.c:31:9: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] pcr_match = g_chunk_new(PCR_Match, pcr->match_mem_chunk); ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:103:0, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_create': pcr.c:59:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] register PCR_Probe *pcr_probe = g_chunk_new(PCR_Probe, ^~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:103:0, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Probe_destroy': pcr.c:69:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] g_mem_chunk_free(pcr->probe_mem_chunk, pcr_probe); ^~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:103:0, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here void g_mem_chunk_free (GMemChunk *mem_chunk, ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_create': pcr.c:155:5: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] register PCR_Sensor *pcr_sensor = g_chunk_new(PCR_Sensor, ^~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:103:0, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:50:17: note: declared here gpointer g_mem_chunk_alloc (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Sensor_destroy': pcr.c:174:5: warning: 'g_mem_chunk_free' is deprecated [-Wdeprecated-declarations] g_mem_chunk_free(pcr->sensor_mem_chunk, pcr_sensor); ^~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:103:0, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:54:17: note: declared here void g_mem_chunk_free (GMemChunk *mem_chunk, ^~~~~~~~~~~~~~~~ pcr.c: In function 'PCR_Primer_create': pcr.c:252:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(pcr_primer->forward); ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ pcr.c:253:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(pcr_primer->revcomp); ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ pcr.c: In function 'PCR_create': pcr.c:357:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->sensor_mem_chunk = g_mem_chunk_new("PCR_Sensor", ^~~ In file included from /usr/include/glib-2.0/glib.h:103:0, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c:363:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->probe_mem_chunk = g_mem_chunk_new("PCR_Probe", ^~~ In file included from /usr/include/glib-2.0/glib.h:103:0, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c:366:5: warning: 'g_mem_chunk_new' is deprecated [-Wdeprecated-declarations] pcr->match_mem_chunk = g_mem_chunk_new("PCR_Match", ^~~ In file included from /usr/include/glib-2.0/glib.h:103:0, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:43:17: note: declared here GMemChunk * g_mem_chunk_new (const gchar *name, ^~~~~~~~~~~~~~~ pcr.c: In function 'PCR_destroy': pcr.c:381:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->sensor_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:103:0, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ pcr.c:383:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->probe_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:103:0, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ pcr.c:384:5: warning: 'g_mem_chunk_destroy' is deprecated [-Wdeprecated-declarations] g_mem_chunk_destroy(pcr->match_mem_chunk); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:103:0, from pcr.h:23, from pcr.c:16: /usr/include/glib-2.0/glib/deprecated/gallocator.h:48:17: note: declared here void g_mem_chunk_destroy (GMemChunk *mem_chunk); ^~~~~~~~~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o pcr.test pcr.test.o pcr.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/fsm.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c comparison.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c comparison.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o comparison.test comparison.test.o comparison.o hspset.o match.o wordhood.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/recyclebin.o ../../src/struct/pqueue.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c match.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o match.test match.test.o match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c seeder.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c seeder.c seeder.c: In function 'Seeder_decide_fsm_type': seeder.c:268:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "none")) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from seeder.h:23, from seeder.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ seeder.c:273:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "normal")) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from seeder.h:23, from seeder.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ seeder.c:275:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_fsm, "compact")) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from seeder.h:23, from seeder.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o seeder.test seeder.test.o seeder.o wordhood.o hspset.o match.o comparison.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/recyclebin.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/comparison' Making all in database make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/database' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastadb.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastadb.c fastadb.c: In function 'FastaDB_SparseCache_fill_func': fastadb.c:1006:29: warning: variable 'db_end' set but not used [-Wunused-but-set-variable] register gint db_start, db_end; ^~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastadb.test fastadb.test.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastapipe.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastapipe.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastapipe.test fastapipe.test.o fastapipe.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c dataset.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c dataset.c dataset.c: In function 'Dataset_info': dataset.c:305:13: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'guint64 {aka long unsigned int}' [-Wformat=] g_print("Sequence Dataset:\n" ^~~~~~~~~~~~~~~~~~~~~ dataset.c:316:13: dataset->header->number_of_seqs, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dataset.c:310:39: note: format string is defined here " number of sequences: %lld\n" ~~~^ %ld dataset.c:305:13: warning: format '%lld' expects argument of type 'long long int', but argument 7 has type 'guint64 {aka long unsigned int}' [-Wformat=] g_print("Sequence Dataset:\n" ^~~~~~~~~~~~~~~~~~~~~ dataset.c:317:13: dataset->header->max_seq_len); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dataset.c:311:39: note: format string is defined here " longest sequence: %lld\n\n", ~~~^ %ld gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o dataset.test dataset.test.o dataset.o fastadb.o ../../src/general/compoundfile.o ../../src/struct/bitarray.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c index.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/struct -I../../src/general -I../../src/comparison -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c index.c index.c: In function 'Index_visit_words': index.c:304:32: warning: variable 'dataset_seq' set but not used [-Wunused-but-set-variable] register Dataset_Sequence *dataset_seq; ^~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:62:0, from index.h:24, from index.c:21: index.c: In function 'Index_desaturate': index.c:377:15: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'gint64 {aka long int}' [-Wformat=] g_message("Removed [%" CUSTOM_GUINT64_FORMAT ^ /usr/include/glib-2.0/glib/gmessages.h:333:32: note: in definition of macro 'g_message' __VA_ARGS__) ^~~~~~~~~~~ index.c:377:15: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'gint64 {aka long int}' [-Wformat=] g_message("Removed [%" CUSTOM_GUINT64_FORMAT ^ /usr/include/glib-2.0/glib/gmessages.h:333:32: note: in definition of macro 'g_message' __VA_ARGS__) ^~~~~~~~~~~ index.c: In function 'Index_report_words_visit': index.c:584:26: warning: variable 'index_word' set but not used [-Wunused-but-set-variable] register Index_Word *index_word; ^~~~~~~~~~ index.c: In function 'Index_open': index.c:943:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(index->dataset_path, sizeof(gchar), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ index->header->dataset_path_len, index->fp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o index.test index.test.o index.o fastadb.o dataset.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/struct/bitarray.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/struct/splaytree.o ../../src/struct/noitree.o ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/database' Making all in c4 make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/c4' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c region.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c region.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o region.test region.test.o region.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c c4.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c c4.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o c4.test c4.test.o c4.o region.o ../../src/struct/matrix.o ../../src/general/threadref.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c alignment.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c alignment.c alignment.c: In function 'AlignmentView_add_SPLICE_SITE': alignment.c:660:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(qy_seq_string); ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:667:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(tg_seq_string); ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:677:13: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(qy_seq_string); ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c:690:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] g_strdown(tg_seq_string); ^~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:208:23: note: declared here gchar* g_strdown (gchar *string); ^~~~~~~~~ alignment.c: In function 'AlignmentView_add_SPLIT_CODON': alignment.c:987:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(qy_codon); ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ alignment.c:988:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(tg_codon); ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/comparison/match.h:23, from alignment.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o alignment.test alignment.test.o alignment.o c4.o region.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c codegen.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c codegen.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o codegen.test codegen.test.o codegen.o ../../src/general/argument.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c optimal.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c optimal.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c layout.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c viterbi.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c subopt.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c cgutil.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o optimal.test optimal.test.o optimal.o c4.o alignment.o codegen.o region.o layout.o viterbi.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c layout.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o layout.test layout.test.o layout.o ../../src/struct/matrix.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c viterbi.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o viterbi.test viterbi.test.o viterbi.o c4.o region.o alignment.o codegen.o layout.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c opair.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c opair.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o opair.test opair.test.o opair.o optimal.o c4.o alignment.o codegen.o region.o layout.o viterbi.o subopt.o cgutil.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c subopt.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o subopt.test subopt.test.o subopt.o region.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c cgutil.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o cgutil.test cgutil.test.o cgutil.o codegen.o c4.o region.o ../../src/general/argument.o ../../src/struct/matrix.o ../../src/general/threadref.o -lglib-2.0 make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/c4' Making all in bsdp make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/bsdp' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c heuristic.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c heuristic.c heuristic.c: In function 'Heuristic_Pair_get_max_range': heuristic.c:759:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if((*max_query_join_range) < range); ^~ heuristic.c:760:12: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' (*max_query_join_range) = range; ^ heuristic.c:762:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if((*max_target_join_range) < range); ^~ heuristic.c:763:12: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' (*max_target_join_range) = range; ^ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o heuristic.test heuristic.test.o heuristic.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c bsdp.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c bsdp.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o bsdp.test bsdp.test.o bsdp.o ../../src/general/argument.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c hpair.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c hpair.c hpair.c: In function 'HPair_next_path': hpair.c:747:30: warning: variable 'src_node_data' set but not used [-Wunused-but-set-variable] *src_node_data, *dst_node_data; ^~~~~~~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sar.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o hpair.test hpair.test.o hpair.o heuristic.o bsdp.o sar.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sar.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o sar.test sar.test.o sar.o heuristic.o ../../src/struct/slist.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/bsdp' Making all in sdp make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/sdp' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sdp.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sdp.c sdp.c: In function 'Scheduler_Seed_Boundary_get_forward': sdp.c:264:24: warning: variable 'seed' set but not used [-Wunused-but-set-variable] register SDP_Seed *seed; ^~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c boundary.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c scheduler.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c lookahead.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c straceback.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o sdp.test sdp.test.o sdp.o boundary.o scheduler.o lookahead.o straceback.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c lookahead.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o lookahead.test lookahead.test.o lookahead.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c boundary.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o boundary.test boundary.test.o boundary.o ../../src/general/argument.o ../../src/c4/region.o -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c scheduler.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o scheduler.test scheduler.test.o scheduler.o lookahead.o boundary.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c straceback.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o straceback.test straceback.test.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/sdp' Making all in model make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/model' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c edit_distance.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c edit_distance.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o edit_distance.test edit_distance.test.o edit_distance.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c affine.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c affine.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c ungapped.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o affine.test affine.test.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c protein2dna.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c protein2dna.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c frameshift.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o protein2dna.test protein2dna.test.o protein2dna.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c ner.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c ner.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o ner.test ner.test.o ner.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c est2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c est2genome.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c intron.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o est2genome.test est2genome.test.o est2genome.o affine.o ungapped.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c ungapped.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o ungapped.test ungapped.test.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c intron.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o intron.test intron.test.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c protein2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c protein2genome.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c phase.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o protein2genome.test protein2genome.test.o protein2genome.o protein2dna.o ungapped.o intron.o affine.o frameshift.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c coding2coding.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c coding2coding.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o coding2coding.test coding2coding.test.o coding2coding.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c frameshift.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o frameshift.test frameshift.test.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c coding2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c coding2genome.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o coding2genome.test coding2genome.test.o coding2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c cdna2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c cdna2genome.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o cdna2genome.test cdna2genome.test.o cdna2genome.o affine.o ungapped.o frameshift.o intron.o phase.o coding2coding.o coding2genome.o est2genome.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c genome2genome.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c genome2genome.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o genome2genome.test genome2genome.test.o genome2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o coding2genome.o cdna2genome.o est2genome.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c phase.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o phase.test phase.test.o phase.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c modeltype.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c modeltype.c modeltype.c: In function 'Model_Type_from_string': modeltype.c:121:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name[i], str)) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ modeltype.c:124:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(short_name[i], str)) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/c4/c4.h:23, from modeltype.h:23, from modeltype.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o modeltype.test modeltype.test.o modeltype.o ungapped.o affine.o est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o coding2genome.o genome2genome.o cdna2genome.o frameshift.o phase.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include \"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c bootstrapper.c bootstrapper.c: In function 'Argument_main': bootstrapper.c:421:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if((!models) || (!g_strcasecmp(models, "all"))) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/c4/c4.h:23, from ungapped.h:23, from bootstrapper.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o bootstrapper bootstrapper.o modeltype.o ungapped.o affine.o est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o coding2genome.o genome2genome.o cdna2genome.o frameshift.o intron.o phase.o ../../src/struct/pqueue.o ../../src/comparison/comparison.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/bsdp/heuristic.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/sdp/boundary.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/model' Making all in hub make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/hub' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c gam.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c gam.c gam.c: In function 'GAM_Refinement_from_string': gam.c:68:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(name[i], str)) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gam.c: In function 'GAM_bestn_tree_destroy': gam.c:526:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(bestn_tree, GAM_tree_collect_values, ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:88:0, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_percent_threshold_tree_destroy': gam.c:539:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(percent_threshold_tree, GAM_tree_collect_values, ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:88:0, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gam.c: In function 'GAM_report': gam.c:589:9: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] g_tree_traverse(gam->bestn_tree, GAM_bestn_tree_report_traverse, ^~~~~~~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:88:0, from gam.h:23, from gam.c:21: /usr/include/glib-2.0/glib/gtree.h:88:10: note: declared here void g_tree_traverse (GTree *tree, ^~~~~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o gam.test gam.test.o gam.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c analysis.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c analysis.c analysis.c: In function 'Analysis_decide_scan_query': analysis.c:329:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(force_scan, "none")){ ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:336:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] } else if((!g_strcasecmp(force_scan, "query")) ^ In file included from /usr/include/glib-2.0/glib.h:79:0, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:337:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] || (!g_strcasecmp(force_scan, "q"))){ ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:339:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] } else if((!g_strcasecmp(force_scan, "target")) ^ In file included from /usr/include/glib-2.0/glib.h:79:0, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c:340:12: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] || (!g_strcasecmp(force_scan, "t"))){ ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from analysis.h:23, from analysis.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ analysis.c: In function 'Analysis_Client_get_Sequence': analysis.c:781:24: warning: variable 'checksum' set but not used [-Wunused-but-set-variable] register gint len, checksum; ^~~~~~~~ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c bsam.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o analysis.test analysis.test.o analysis.o gam.o bsam.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/comparison/seeder.o ../../src/comparison/comparison.o ../../src/database/fastapipe.o ../../src/database/fastadb.o ../../src/struct/dejavu.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/socket.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/general -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c bsam.test.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o bsam.test bsam.test.o bsam.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/sequence/splice.o ../../src/struct/dejavu.o ../../src/struct/pqueue.o ../../src/struct/sparsecache.o ../../src/struct/recyclebin.o ../../src/struct/matrix.o -lm -lglib-2.0 make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/hub' Making all in program make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/program' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c exonerate.c ../../src/model/bootstrapper --compiled no ** (process:2627): WARNING **: 04:15:35.949: Compiled with assertion checking - will run slowly ** Message: 04:15:36.007: Starting building bootstrapping components ** Message: 04:15:36.037: Processing model [est2genome] ** Message: 04:15:36.084: Bootstrapper processing model [est2genome] ** Message: 04:15:36.085: Process optimal [optimal:est2genome] ** (process:2627): WARNING **: 04:15:36.089: Creating codegen directory [/builddir/build/BUILD/exonerate-2.4.0/codegen] ** (process:2627): WARNING **: 04:15:36.092: Creating codegen directory [/builddir/build/BUILD/exonerate-2.4.0/codegen] ** (process:2627): WARNING **: 04:15:36.094: Creating codegen directory [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu] ** (process:2627): WARNING **: 04:15:36.099: Creating codegen directory [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu] ** Message: 04:15:36.157: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.c ** Message: 04:16:06.635: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.c ** Message: 04:16:51.147: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.c ** Message: 04:17:31.137: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.c: In function 'optimal_58_est2genome_32_find_32_checkpoint': /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.c:35:29: warning: variable 'transition' set but not used [-Wunused-but-set-variable] register C4_Transition *transition; ^~~~~~~~~~ ** Message: 04:19:00.838: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.c ** Message: 04:20:56.157: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] ** Message: 04:20:56.160: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] to archive ar -cSq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o ** Message: 04:20:56.355: Adding function [optimal_58_est2genome_32_find_32_score] ** Message: 04:20:56.357: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] ** Message: 04:20:56.358: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o ** Message: 04:20:56.593: Adding function [optimal_58_est2genome_32_find_32_path] ** Message: 04:20:56.596: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] ** Message: 04:20:56.598: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o ** Message: 04:20:56.886: Adding function [optimal_58_est2genome_32_find_32_region] ** Message: 04:20:56.889: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] ** Message: 04:20:56.891: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o ** Message: 04:20:57.277: Adding function [optimal_58_est2genome_32_find_32_checkpoint] ** Message: 04:20:57.279: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] ** Message: 04:20:57.282: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o ** Message: 04:20:57.817: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] ** Message: 04:20:58.114: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] ** Message: 04:20:58.200: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 04:21:40.255: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 04:22:46.814: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 04:22:46.821: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 04:22:47.604: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 04:22:47.606: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 04:22:47.610: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 04:22:48.430: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 04:22:48.455: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] ** Message: 04:22:48.548: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 04:23:17.589: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 04:23:53.652: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 04:23:53.655: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 04:23:54.429: Adding function [Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 04:23:54.431: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 04:23:54.434: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 04:23:55.254: Adding function [Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 04:23:55.272: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] ** Message: 04:23:55.383: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 04:24:38.154: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 04:25:41.166: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 04:25:41.170: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 04:25:42.090: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 04:25:42.093: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 04:25:42.094: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 04:25:43.029: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 04:25:43.044: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] ** Message: 04:25:43.127: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 04:26:09.287: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 04:26:44.925: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 04:26:44.928: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 04:26:46.018: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 04:26:46.021: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 04:26:46.022: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 04:26:47.265: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 04:26:47.267: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] ** Message: 04:26:47.405: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 04:28:01.253: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 04:29:53.559: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 04:29:53.563: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 04:29:54.804: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 04:29:54.808: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 04:29:54.809: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 04:29:56.193: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 04:29:56.194: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 04:29:56.249: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 04:30:25.305: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 04:31:03.777: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 04:31:03.779: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 04:31:05.208: Adding function [Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 04:31:05.210: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 04:31:05.212: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 04:31:06.753: Adding function [Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 04:31:06.756: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] ** Message: 04:31:06.930: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 04:32:45.898: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 04:32:45.901: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 04:32:47.609: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 04:32:47.611: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] ** Message: 04:32:47.738: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 04:33:35.162: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 04:34:43.437: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 04:34:43.440: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 04:34:45.326: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 04:34:45.329: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 04:34:45.330: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 04:34:47.433: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 04:34:47.435: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] ** Message: 04:34:47.706: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 04:36:16.038: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 04:38:16.741: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 04:38:16.744: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 04:38:18.673: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 04:38:18.675: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 04:38:18.677: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 04:38:20.766: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 04:38:20.785: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 04:38:20.839: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 04:38:49.156: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 04:39:27.179: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 04:39:27.182: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 04:39:29.191: Adding function [Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 04:39:29.210: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 04:39:29.213: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 04:39:31.318: Adding function [Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 04:39:31.321: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] ** Message: 04:39:31.473: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 04:41:13.221: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 04:41:13.223: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 04:41:15.442: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 04:41:15.446: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] ** Message: 04:41:15.541: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c ** Message: 04:42:02.910: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c ** Message: 04:43:13.766: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] ** Message: 04:43:13.769: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o ** Message: 04:43:16.942: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] ** Message: 04:43:16.963: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] ** Message: 04:43:16.964: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o ** Message: 04:43:19.594: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] ** Message: 04:43:19.714: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c: In function 'Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary': /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c:31:25: warning: unused variable 'shadow' [-Wunused-variable] register C4_Shadow *shadow; ^~~~~~ /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c:30:34: warning: unused variable 'span_data' [-Wunused-variable] register Scheduler_SpanData *span_data; ^~~~~~~~~ /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c:29:24: warning: unused variable 'span_seed' [-Wunused-variable] Scheduler_SpanSeed span_seed; ^~~~~~~~~ ** Message: 04:43:39.553: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.c ** Message: 04:44:00.670: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 04:44:00.674: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 04:44:03.110: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] ** Message: 04:44:03.125: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] ** Message: 04:44:03.129: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o ** Message: 04:44:05.557: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] ** Message: 04:44:05.566: Processing model [protein2genome] ** Message: 04:44:05.589: Bootstrapper processing model [protein2genome:local] ** Message: 04:44:05.590: Process optimal [optimal:protein2genome:local] ** Message: 04:44:05.663: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.c ** Message: 04:44:49.202: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.c ** Message: 04:45:49.673: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.c ** Message: 04:46:44.054: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c: In function 'optimal_58_protein2genome_58_local_32_find_32_checkpoint': /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c:35:29: warning: variable 'transition' set but not used [-Wunused-but-set-variable] register C4_Transition *transition; ^~~~~~~~~~ ** Message: 04:49:08.697: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.c ** Message: 04:52:19.914: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] ** Message: 04:52:19.931: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o ** Message: 04:52:22.402: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] ** Message: 04:52:22.405: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] ** Message: 04:52:22.407: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o ** Message: 04:52:25.070: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] ** Message: 04:52:25.074: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] ** Message: 04:52:25.075: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o ** Message: 04:52:27.862: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] ** Message: 04:52:27.868: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] ** Message: 04:52:27.869: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o ** Message: 04:52:30.878: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] ** Message: 04:52:30.893: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] ** Message: 04:52:30.895: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o ** Message: 04:52:34.068: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] ** Message: 04:52:35.085: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] ** Message: 04:52:35.319: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 04:54:59.077: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 04:58:58.173: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 04:58:58.176: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 04:59:01.278: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 04:59:01.280: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 04:59:01.281: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 04:59:04.765: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 04:59:04.768: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] ** Message: 04:59:04.897: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:00:22.327: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:02:14.205: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:02:14.208: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:02:17.580: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 05:02:17.582: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:02:17.585: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:02:21.285: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 05:02:21.289: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] ** Message: 05:02:21.670: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:07:36.894: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:16:20.847: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:16:20.857: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:16:25.077: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 05:16:25.079: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:16:25.082: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:16:29.542: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 05:16:29.546: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 05:16:29.679: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:17:52.253: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:19:56.301: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:19:56.305: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:20:00.932: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 05:20:00.935: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:20:00.940: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:20:05.779: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 05:20:05.781: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] ** Message: 05:20:06.126: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:27:20.345: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:27:20.348: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:27:25.390: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 05:27:25.395: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] ** Message: 05:27:25.615: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:29:52.374: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:34:05.238: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:34:05.242: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:34:10.084: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 05:34:10.087: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:34:10.089: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:34:15.095: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 05:34:15.099: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 05:34:15.233: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:35:39.884: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:37:43.222: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:37:43.228: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:37:48.534: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 05:37:48.537: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:37:48.539: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:37:53.577: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 05:37:53.590: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] ** Message: 05:37:53.933: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:45:03.486: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:45:03.489: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:45:09.216: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 05:45:09.219: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] ** Message: 05:45:09.449: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:47:43.177: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:51:38.596: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:51:38.599: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:51:44.694: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 05:51:44.697: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:51:44.699: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:51:50.826: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 05:51:50.829: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 05:51:50.938: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 05:53:06.824: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 05:55:11.556: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 05:55:11.564: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 05:55:18.082: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 05:55:18.085: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 05:55:18.086: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 05:55:24.565: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 05:55:24.567: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] ** Message: 05:55:24.934: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 06:02:40.563: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 06:02:40.566: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 06:02:47.100: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 06:02:47.103: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] ** Message: 06:02:47.372: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c ** Message: 06:05:20.447: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c ** Message: 06:09:19.881: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] ** Message: 06:09:19.890: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o ** Message: 06:09:26.810: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] ** Message: 06:09:26.812: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] ** Message: 06:09:26.813: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o ** Message: 06:09:34.021: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] ** Message: 06:09:34.092: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c: In function 'Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary': /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c:30:25: warning: unused variable 'shadow' [-Wunused-variable] register C4_Shadow *shadow; ^~~~~~ /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c:29:34: warning: unused variable 'span_data' [-Wunused-variable] register Scheduler_SpanData *span_data; ^~~~~~~~~ /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c:28:24: warning: unused variable 'span_seed' [-Wunused-variable] Scheduler_SpanSeed span_seed; ^~~~~~~~~ ** Message: 06:09:51.966: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.c ** Message: 06:10:11.413: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] ** Message: 06:10:11.417: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o ** Message: 06:10:18.538: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] ** Message: 06:10:18.541: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] ** Message: 06:10:18.543: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o ** Message: 06:10:25.671: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] ** Message: 06:10:25.689: Processing model [cdna2genome] ** Message: 06:10:25.731: Bootstrapper processing model [cdna2genome] ** Message: 06:10:25.733: Process optimal [optimal:cdna2genome] ** Message: 06:10:25.995: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.c ** Message: 06:15:07.122: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.c ** Message: 06:23:41.973: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.c ** Message: 06:31:20.135: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.c: In function 'optimal_58_cdna2genome_32_find_32_checkpoint': /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.c:35:29: warning: variable 'transition' set but not used [-Wunused-but-set-variable] register C4_Transition *transition; ^~~~~~~~~~ ** Message: 07:01:49.543: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.c ** Message: 07:48:38.878: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] ** Message: 07:48:38.882: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o ** Message: 07:48:46.298: Adding function [optimal_58_cdna2genome_32_find_32_score] ** Message: 07:48:46.302: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] ** Message: 07:48:46.305: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o ** Message: 07:48:54.647: Adding function [optimal_58_cdna2genome_32_find_32_path] ** Message: 07:48:54.650: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] ** Message: 07:48:54.653: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o ** Message: 07:49:02.425: Adding function [optimal_58_cdna2genome_32_find_32_region] ** Message: 07:49:02.429: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] ** Message: 07:49:02.431: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o ** Message: 07:49:11.255: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] ** Message: 07:49:11.261: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] ** Message: 07:49:11.262: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o ** Message: 07:49:20.862: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] ** Message: 07:49:20.942: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c: In function 'Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary': /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c:30:25: warning: unused variable 'shadow' [-Wunused-variable] register C4_Shadow *shadow; ^~~~~~ /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c:29:34: warning: unused variable 'span_data' [-Wunused-variable] register Scheduler_SpanData *span_data; ^~~~~~~~~ /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c:28:24: warning: unused variable 'span_seed' [-Wunused-variable] Scheduler_SpanSeed span_seed; ^~~~~~~~~ ** Message: 07:49:52.031: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c ** Message: 07:50:26.630: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 07:50:26.633: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 07:50:36.921: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] ** Message: 07:50:36.923: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] ** Message: 07:50:36.925: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o ** Message: 07:50:47.356: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] ** Message: 07:50:47.373: Processing model [coding2genome] ** Message: 07:50:47.401: Bootstrapper processing model [coding2genome] ** Message: 07:50:47.402: Process optimal [optimal:coding2genome] ** Message: 07:50:47.550: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.c ** Message: 07:52:31.586: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.c ** Message: 07:55:12.794: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.c ** Message: 07:57:28.985: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.c: In function 'optimal_58_coding2genome_32_find_32_checkpoint': /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.c:35:29: warning: variable 'transition' set but not used [-Wunused-but-set-variable] register C4_Transition *transition; ^~~~~~~~~~ ** Message: 08:05:30.735: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.c ** Message: 08:17:01.677: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] ** Message: 08:17:01.680: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o ** Message: 08:17:10.774: Adding function [optimal_58_coding2genome_32_find_32_score] ** Message: 08:17:10.778: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] ** Message: 08:17:10.781: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o ** Message: 08:17:20.537: Adding function [optimal_58_coding2genome_32_find_32_path] ** Message: 08:17:20.539: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] ** Message: 08:17:20.542: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o ** Message: 08:17:29.983: Adding function [optimal_58_coding2genome_32_find_32_region] ** Message: 08:17:29.987: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] ** Message: 08:17:29.988: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o ** Message: 08:17:39.833: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] ** Message: 08:17:39.837: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] ** Message: 08:17:39.839: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o ** Message: 08:17:50.458: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] ** Message: 08:17:50.503: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c: In function 'Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary': /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c:30:25: warning: unused variable 'shadow' [-Wunused-variable] register C4_Shadow *shadow; ^~~~~~ /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c:29:34: warning: unused variable 'span_data' [-Wunused-variable] register Scheduler_SpanData *span_data; ^~~~~~~~~ /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c:28:24: warning: unused variable 'span_seed' [-Wunused-variable] Scheduler_SpanSeed span_seed; ^~~~~~~~~ ** Message: 08:18:08.506: Compiling codegen: gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/model -I/builddir/build/BUILD/exonerate-2.4.0/src/comparison -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/bsdp -I/builddir/build/BUILD/exonerate-2.4.0/src/sdp -o /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o -c /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.c ** Message: 08:18:27.945: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] ** Message: 08:18:27.948: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o ** Message: 08:18:37.998: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] ** Message: 08:18:38.001: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] ** Message: 08:18:38.002: Adding object file [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o ** Message: 08:18:48.504: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] ** Message: 08:18:48.519: Compiling with: [gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/builddir/build/BUILD/exonerate-2.4.0/src/c4 -I/builddir/build/BUILD/exonerate-2.4.0/src/sequence -I/builddir/build/BUILD/exonerate-2.4.0/src/general -I/builddir/build/BUILD/exonerate-2.4.0/src/struct -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -o c4_model_lookup.o -c c4_model_lookup.c] ** Message: 08:18:55.534: Adding: [c4_model_lookup.o] ** Message: 08:18:55.538: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o ** Message: 08:19:06.118: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a ** Message: 08:19:18.917: Done ** Message: 08:19:18.922: Finished building bootstrapping components gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I. \ -DUSE_COMPILED_MODELS \ -c ../../src/c4/viterbi.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I. \ -DUSE_COMPILED_MODELS \ -c ../../src/sdp/scheduler.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o exonerate exonerate.o viterbi.o scheduler.o c4_model_archive.a ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/seeder.o ../../src/comparison/comparison.o ../../src/database/fastapipe.o ../../src/database/fastadb.o ../../src/struct/dejavu.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/sparsecache.o ../../src/hub/gam.o ../../src/hub/bsam.o ../../src/hub/analysis.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/lookahead.o ../../src/sdp/straceback.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/socket.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c ipcress.c ipcress.c: In function 'Ipcress_prepare_PCR': ipcress.c:264:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(primer_a); ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ipcress.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ ipcress.c:265:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] g_strup(primer_b); ^~~~~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ipcress.c:16: /usr/include/glib-2.0/glib/gstrfuncs.h:210:23: note: declared here gchar* g_strup (gchar *string); ^~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o ipcress ipcress.o ../../src/comparison/pcr.o ../../src/comparison/wordhood.o ../../src/database/fastadb.o ../../src/sequence/alphabet.o ../../src/sequence/sequence.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/fsm.o ../../src/struct/slist.o ../../src/struct/matrix.o ../../src/struct/recyclebin.o ../../src/struct/sparsecache.o ../../src/general/lineparse.o ../../src/general/argument.o ../../src/general/compoundfile.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"riscv64-redhat-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/builddir/build/BUILD/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c exonerate-server.c exonerate-server.c: In function 'Exonerate_Server_get_seq': exonerate-server.c:269:32: warning: variable 'ds' set but not used [-Wunused-but-set-variable] register Dataset_Sequence *ds; ^~ exonerate-server.c: In function 'Exonerate_Server_process': exonerate-server.c:655:24: warning: comparison of constant '10' with boolean expression is always false [-Wbool-compare] if(!msg[msg_len-1] == '\n') ^~ exonerate-server.c:655:24: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] exonerate-server.c:655:8: note: add parentheses around left hand side expression to silence this warning if(!msg[msg_len-1] == '\n') ^~~~~~~~~~~~~~~ ( ) exonerate-server.c:669:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'guint64 {aka long unsigned int}' [-Wformat=] (*reply) = g_strdup_printf("dbinfo: %s %s" ^~~~~~~~~~~~~~~ exonerate-server.c:676:19: server->dataset->header->number_of_seqs, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ exonerate-server.c:669:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'guint64 {aka long unsigned int}' [-Wformat=] exonerate-server.c:669:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 6 has type 'guint64 {aka long unsigned int}' [-Wformat=] gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o exonerate-server exonerate-server.o ../../src/general/socket.o ../../src/general/argument.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/database/dataset.o ../../src/database/index.o ../../src/database/fastadb.o ../../src/struct/bitarray.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/struct/splaytree.o ../../src/struct/noitree.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/program' Making all in util make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/util' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastaclean.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastaclean fastaclean.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastaclip.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastaclip fastaclip.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastachecksum.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastachecksum fastachecksum.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastacomposition.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastacomposition fastacomposition.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastadiff.c fastadiff.c: In function 'fasta_diff': fastadiff.c:70:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] comp = g_strcasecmp; ^~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/general/argument.h:26, from fastadiff.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastadiff fastadiff.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastaexplode.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastaexplode fastaexplode.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastafetch.c fastafetch.c: In function 'get_query_list': fastafetch.c:121:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(query, "stdin")){ ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/general/argument.h:26, from fastafetch.c:21: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastafetch fastafetch.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastahardmask.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastahardmask fastahardmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastaindex.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastaindex fastaindex.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastalength.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastalength fastalength.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastanrdb.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastanrdb fastanrdb.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastaoverlap.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastaoverlap fastaoverlap.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastareformat.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastareformat fastareformat.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastaremove.c fastaremove.c: In function 'Argument_main': fastaremove.c:73:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(remove_path, "stdin")){ ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/general/argument.h:26, from fastaremove.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastaremove fastaremove.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastarevcomp.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastarevcomp fastarevcomp.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastasoftmask.c fastasoftmask.c: In function 'fasta_softmask': fastasoftmask.c:67:36: warning: self-comparison always evaluates to false [-Wtautological-compare] if(fdbs_unmasked->seq->len != fdbs_unmasked->seq->len) ^~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastasoftmask fastasoftmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastasort.c fastasort.c: In function 'SortKey_Mask_create': fastasort.c:130:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] if(!g_strcasecmp(sort_key, "id")) ^~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ fastasort.c:132:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] else if(!g_strcasecmp(sort_key, "len")) ^~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ fastasort.c:134:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] else if(!g_strcasecmp(sort_key, "seq")) ^~~~ In file included from /usr/include/glib-2.0/glib.h:79:0, from ../../src/general/argument.h:26, from fastasort.c:20: /usr/include/glib-2.0/glib/gstrfuncs.h:201:23: note: declared here gint g_strcasecmp (const gchar *s1, ^~~~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastasort fastasort.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastasplit.c fastasplit.c: In function 'Argument_main': fastasplit.c:92:13: warning: 'g_basename' is deprecated: Use 'g_path_get_basename' instead [-Wdeprecated-declarations] output_dir, G_DIR_SEPARATOR, g_basename(query_path)); ^~~~~~~~~~ In file included from /usr/include/glib-2.0/glib.h:48:0, from ../../src/general/argument.h:26, from fastasplit.c:20: /usr/include/glib-2.0/glib/gfileutils.h:163:14: note: declared here const gchar *g_basename (const gchar *file_name); ^~~~~~~~~~ gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastasplit fastasplit.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastasubseq.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastasubseq fastasubseq.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastatranslate.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastatranslate fastatranslate.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastavalidcds.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastavalidcds fastavalidcds.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fasta2esd.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fasta2esd fasta2esd.o ../../src/database/dataset.o ../../src/struct/bitarray.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c fastaannotatecdna.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o fastaannotatecdna fastaannotatecdna.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c esd2esi.c gcc -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 -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -o esd2esi esd2esi.o ../../src/database/dataset.o ../../src/database/index.o ../../src/general/threadref.o ../../src/struct/bitarray.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/struct/noitree.o ../../src/struct/splaytree.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/util' make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src' make[1]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src' Making all in test make[1]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test' Making all in data make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/data' Making all in cdna make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/data/cdna' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/data/cdna' Making all in protein make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/data/protein' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/data/protein' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/data' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/data' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/data' Making all in exonerate make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/exonerate' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/exonerate' Making all in ipcress make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/ipcress' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/ipcress' Making all in util make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/util' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/util' make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test' make[1]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test' make[1]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0' make[1]: Nothing to be done for 'all-am'. make[1]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0' + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Vv0lao + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64 ++ dirname /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64 + cd exonerate-2.4.0 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64 'INSTALL=/usr/bin/install -p' Making install in doc make[1]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/doc' Making install in man make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man' Making install in man1 make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man/man1' make[4]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man/man1' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/make install-man1 make[5]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man/man1' /bin/sh ../../../mkinstalldirs /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/man/man1 mkdir /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr mkdir /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share mkdir /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/man mkdir /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/man/man1 /usr/bin/install -p -m 644 ./exonerate.1 /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/man/man1/exonerate.1 /usr/bin/install -p -m 644 ./ipcress.1 /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/man/man1/ipcress.1 /usr/bin/install -p -m 644 ./exonerate-server.1 /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/man/man1/exonerate-server.1 /usr/bin/install -p -m 644 ./fastautils.1 /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/man/man1/fastautils.1 make[5]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man/man1' make[4]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man/man1' make[3]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man/man1' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man' make[4]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man' make[3]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/doc/man' make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/doc' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/doc' 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/exonerate-2.4.0/doc' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/doc' make[1]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/doc' Making install in src make[1]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src' Making install in struct make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/struct' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/struct' 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/exonerate-2.4.0/src/struct' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/struct' Making install in general make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/general' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/general' 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/exonerate-2.4.0/src/general' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/general' Making install in sequence make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/sequence' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/sequence' 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/exonerate-2.4.0/src/sequence' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/sequence' Making install in comparison make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/comparison' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/comparison' 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/exonerate-2.4.0/src/comparison' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/comparison' Making install in database make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/database' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/database' 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/exonerate-2.4.0/src/database' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/database' Making install in c4 make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/c4' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/c4' 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/exonerate-2.4.0/src/c4' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/c4' Making install in bsdp make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/bsdp' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/bsdp' 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/exonerate-2.4.0/src/bsdp' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/bsdp' Making install in sdp make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/sdp' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/sdp' 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/exonerate-2.4.0/src/sdp' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/sdp' Making install in model make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/model' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/model' 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/exonerate-2.4.0/src/model' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/model' Making install in hub make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/hub' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/hub' 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/exonerate-2.4.0/src/hub' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/hub' Making install in program make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/program' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/program' /bin/sh ../../mkinstalldirs /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin mkdir /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin /usr/bin/install -p exonerate /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/exonerate /usr/bin/install -p ipcress /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/ipcress /usr/bin/install -p exonerate-server /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/exonerate-server make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/program' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/program' Making install in util make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/util' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src/util' /bin/sh ../../mkinstalldirs /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin /usr/bin/install -p fastaclean /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastaclean /usr/bin/install -p fastaclip /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastaclip /usr/bin/install -p fastachecksum /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastachecksum /usr/bin/install -p fastacomposition /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastacomposition /usr/bin/install -p fastadiff /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastadiff /usr/bin/install -p fastaexplode /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastaexplode /usr/bin/install -p fastafetch /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastafetch /usr/bin/install -p fastahardmask /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastahardmask /usr/bin/install -p fastaindex /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastaindex /usr/bin/install -p fastalength /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastalength /usr/bin/install -p fastanrdb /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastanrdb /usr/bin/install -p fastaoverlap /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastaoverlap /usr/bin/install -p fastareformat /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastareformat /usr/bin/install -p fastaremove /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastaremove /usr/bin/install -p fastarevcomp /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastarevcomp /usr/bin/install -p fastasoftmask /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastasoftmask /usr/bin/install -p fastasort /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastasort /usr/bin/install -p fastasplit /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastasplit /usr/bin/install -p fastasubseq /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastasubseq /usr/bin/install -p fastatranslate /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastatranslate /usr/bin/install -p fastavalidcds /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastavalidcds /usr/bin/install -p fasta2esd /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fasta2esd /usr/bin/install -p fastaannotatecdna /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/fastaannotatecdna /usr/bin/install -p esd2esi /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/bin/esd2esi make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/util' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src/util' make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/src' 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/exonerate-2.4.0/src' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src' make[1]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/src' Making install in test make[1]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test' Making install in data make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/data' Making install in cdna make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/data/cdna' make[4]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/data/cdna' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/data/cdna' make[3]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/data/cdna' Making install in protein make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/data/protein' make[4]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/data/protein' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/data/protein' make[3]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/data/protein' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/data' make[4]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/data' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/data' make[3]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/data' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/data' Making install in exonerate make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/exonerate' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/exonerate' 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/exonerate-2.4.0/test/exonerate' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/exonerate' Making install in ipcress make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/ipcress' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/ipcress' 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/exonerate-2.4.0/test/ipcress' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/ipcress' Making install in util make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/util' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test/util' 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/exonerate-2.4.0/test/util' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test/util' make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test' make[3]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0/test' 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/exonerate-2.4.0/test' make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test' make[1]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0/test' make[1]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0' make[2]: Entering directory '/builddir/build/BUILD/exonerate-2.4.0' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0' make[1]: Leaving directory '/builddir/build/BUILD/exonerate-2.4.0' + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig /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 /usr/bin/strip + /usr/lib/rpm/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Processing files: exonerate-2.4.0-1.fc28.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.lo789V + umask 022 + cd /builddir/build/BUILD + cd exonerate-2.4.0 + DOCDIR=/builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/doc/exonerate + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/doc/exonerate + cp -pr README /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/doc/exonerate + cp -pr ChangeLog /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/doc/exonerate + cp -pr AUTHORS /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/doc/exonerate + cp -pr TODO /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/doc/exonerate + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.aKktnY + umask 022 + cd /builddir/build/BUILD + cd exonerate-2.4.0 + LICENSEDIR=/builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/licenses/exonerate + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/licenses/exonerate + cp -pr COPYING /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64/usr/share/licenses/exonerate + exit 0 Provides: exonerate = 2.4.0-1.fc28 exonerate(riscv-64) = 2.4.0-1.fc28 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) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libglib-2.0.so.0()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) rtld(GNU_HASH) Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64 Wrote: /builddir/build/SRPMS/exonerate-2.4.0-1.fc28.src.rpm Wrote: /builddir/build/RPMS/riscv64/exonerate-2.4.0-1.fc28.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.aA1oXi + umask 022 + cd /builddir/build/BUILD + cd exonerate-2.4.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/exonerate-2.4.0-1.fc28.riscv64 + exit 0 + touch /buildok + cleanup + set +e + sync + sleep 5 + sync + poweroff Terminated ++ cleanup ++ set +e ++ sync Terminated +++ cleanup +++ set +e +++ sync +++ sleep 5 +++ sync +++ poweroff