+ 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.3PK30B
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf exonerate-2.4.0
+ /usr/bin/gzip -dc /builddir/build/SOURCES/exonerate-2.4.0.tar.gz
+ /usr/bin/tar -xof -
+ 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.H4HNs0
+ 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.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'
+ 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'
+ '[' 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:2554): WARNING **: 19:54:29.372: Compiled with assertion checking - will run slowly
** Message: 19:54:29.416: Starting building bootstrapping components
** Message: 19:54:29.436: Processing model [est2genome]
** Message: 19:54:29.485: Bootstrapper processing model [est2genome]
** Message: 19:54:29.486: Process optimal [optimal:est2genome]
** (process:2554): WARNING **: 19:54:29.490: Creating codegen directory [/builddir/build/BUILD/exonerate-2.4.0/codegen]
** (process:2554): WARNING **: 19:54:29.494: Creating codegen directory [/builddir/build/BUILD/exonerate-2.4.0/codegen]
** (process:2554): WARNING **: 19:54:29.496: Creating codegen directory [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu]
** (process:2554): WARNING **: 19:54:29.500: Creating codegen directory [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu]
** Message: 19:54:29.555: 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: 19:54:58.145: 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: 19:55:38.272: 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: 19:56:15.854: 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: 19:57:43.377: 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: 19:59:34.159: 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: 19:59:34.163: 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: 19:59:34.358: Adding function [optimal_58_est2genome_32_find_32_score]
** Message: 19:59:34.360: 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: 19:59:34.362: 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: 19:59:34.611: Adding function [optimal_58_est2genome_32_find_32_path]
** Message: 19:59:34.615: 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: 19:59:34.618: 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: 19:59:34.922: Adding function [optimal_58_est2genome_32_find_32_region]
** Message: 19:59:34.926: 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: 19:59:34.928: 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: 19:59:35.355: Adding function [optimal_58_est2genome_32_find_32_checkpoint]
** Message: 19:59:35.358: 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: 19:59:35.359: 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: 19:59:35.887: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation]
** Message: 19:59:36.154: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]]
** Message: 19:59:36.248: 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: 20:00:17.142: 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: 20:01:14.126: 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: 20:01:14.129: 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: 20:01:14.764: 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: 20:01:14.767: 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: 20:01:14.770: 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: 20:01:15.464: 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: 20:01:15.467: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]]
** Message: 20:01:15.527: 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: 20:01:41.419: 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: 20:02:16.806: 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: 20:02:16.810: 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: 20:02:17.614: 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: 20:02:17.616: 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: 20:02:17.618: 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: 20:02:18.454: 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: 20:02:18.457: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]]
** Message: 20:02:18.562: 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: 20:03:01.091: 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: 20:04:00.524: 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: 20:04:00.528: 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: 20:04:01.406: 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: 20:04:01.408: 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: 20:04:01.409: 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: 20:04:02.434: 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: 20:04:02.436: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]]
** Message: 20:04:02.494: 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: 20:04:29.786: 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: 20:05:05.058: 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: 20:05:05.060: 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: 20:05:06.111: 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: 20:05:06.115: 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: 20:05:06.117: 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: 20:05:07.233: 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: 20:05:07.235: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]]
** Message: 20:05:07.359: 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: 20:06:22.190: 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: 20:08:10.415: 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: 20:08:10.418: 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: 20:08:11.471: 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: 20:08:11.474: 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: 20:08:11.475: 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: 20:08:12.645: 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: 20:08:12.647: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]]
** Message: 20:08:12.701: 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: 20:08:36.545: 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: 20:09:07.091: 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: 20:09:07.094: 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: 20:09:08.250: 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: 20:09:08.252: 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: 20:09:08.254: 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: 20:09:09.508: 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: 20:09:09.511: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]]
** Message: 20:09:09.642: 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: 20:10:33.274: 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: 20:10:33.276: 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: 20:10:34.608: 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: 20:10:34.610: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]]
** Message: 20:10:34.692: 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: 20:11:17.143: 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: 20:12:24.307: 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: 20:12:24.311: 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: 20:12:25.999: 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: 20:12:26.003: 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: 20:12:26.004: 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: 20:12:27.849: 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: 20:12:27.852: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]]
** Message: 20:12:28.001: 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: 20:13:51.706: 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_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: 20:15:57.256: 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: 20:15:57.259: 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: 20:15:59.258: 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: 20:15:59.261: 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: 20:15:59.263: 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: 20:16:01.430: 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: 20:16:01.434: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]]
** Message: 20:16:01.494: 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: 20:16:31.182: 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: 20:17:09.115: 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: 20:17:09.118: 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: 20:17:11.223: 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: 20:17:11.230: 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: 20:17:11.231: 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: 20:17:13.423: 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: 20:17:13.435: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]]
** Message: 20:17:13.570: 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: 20:18:42.823: 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: 20:18:42.826: 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: 20:18:45.079: 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: 20:18:45.082: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]]
** Message: 20:18:45.174: 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: 20:19:26.440: 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: 20:20:21.462: 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: 20:20:21.464: 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: 20:20:23.455: 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: 20:20:23.458: 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: 20:20:23.459: 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: 20:20:25.454: 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: 20:20:25.493: 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: 20:20:39.150: 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: 20:20:56.150: 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: 20:20:56.152: 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: 20:20:58.519: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary]
** Message: 20:20:58.522: 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: 20:20:58.523: 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: 20:21:00.869: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary]
** Message: 20:21:00.878: Processing model [protein2genome]
** Message: 20:21:00.902: Bootstrapper processing model [protein2genome:local]
** Message: 20:21:00.903: Process optimal [optimal:protein2genome:local]
** Message: 20:21:00.971: 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: 20:21:37.804: 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: 20:22:30.419: 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: 20:23:16.073: 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: 20:25:25.306: 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: 20:28:14.624: 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: 20:28:14.627: 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: 20:28:16.743: Adding function [optimal_58_protein2genome_58_local_32_find_32_score]
** Message: 20:28:16.747: 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: 20:28:16.748: 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: 20:28:18.911: Adding function [optimal_58_protein2genome_58_local_32_find_32_path]
** Message: 20:28:18.914: Adding: [/builddir/build/BUILD/exonerate-2.4.0/codegen/riscv64_45_redhat_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o]
** Message: 20:28:18.916: 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: 20:28:21.235: Adding function [optimal_58_protein2genome_58_local_32_find_32_region]
** Message: 20:28:21.238: 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: 20:28:21.240: 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: 20:28:23.687: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint]
** Message: 20:28:23.693: 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: 20:28:23.695: 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: 20:28:26.286: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation]
** Message: 20:28:27.152: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]]
** Message: 20:28:27.330: 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: 20:30:26.810: 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: 20:33:29.806: 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: 20:33:29.810: 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: 20:33:32.366: 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: 20:33:32.369: 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: 20:33:32.370: 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: 20:33:35.286: 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: 20:33:35.289: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]]
** Message: 20:33:35.384: 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: 20:34:35.583: 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: 20:36:05.859: 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: 20:36:05.861: 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: 20:36:08.670: 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: 20:36:08.672: 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: 20:36:08.673: 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: 20:36:11.745: 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: 20:36:11.747: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]]
** Message: 20:36:12.018: 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: 20:40:57.737: 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: 20:49:38.668: 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: 20:49:38.705: 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: 20:49:42.797: 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: 20:49:42.800: 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: 20:49:42.803: 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: 20:49:47.049: 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: 20:49:47.052: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]]
** Message: 20:49:47.172: 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: 20:51:02.606: 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: 20:52:58.209: 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: 20:52:58.214: 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: 20:53:02.646: 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: 20:53:02.651: 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: 20:53:02.653: 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: 20:53:07.400: 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: 20:53:07.404: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]]
** Message: 20:53:07.767: 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: 21:00:16.826: 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: 21:00:16.842: 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: 21:00:22.131: 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: 21:00:22.134: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]]
** Message: 21:00:22.393: 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: 21:02:55.129: 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: 21:07:01.124: 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: 21:07:01.135: 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: 21:07:06.450: 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: 21:07:06.459: 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: 21:07:06.463: 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: 21:07:12.004: 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: 21:07:12.014: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]]
** Message: 21:07:12.155: 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: 21:08:34.625: 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: 21:10:39.328: 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: 21:10:39.356: 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: 21:10:44.943: 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: 21:10:44.946: 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: 21:10:44.948: 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: 21:10:50.615: 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: 21:10:50.620: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]]
** Message: 21:10:51.036: 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: 21:18:39.677: 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: 21:18:39.682: 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: 21:18:45.974: 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: 21:18:45.977: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]]
** Message: 21:18:46.215: 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: 21:21:32.916: 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: 21:25:54.113: 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: 21:25:54.116: 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: 21:26:00.979: 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: 21:26:00.982: 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: 21:26:00.984: 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: 21:26:07.888: 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: 21:26:07.891: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]]
** Message: 21:26:08.056: 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: 21:27:32.479: 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: 21:29:35.887: 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: 21:29:35.890: 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: 21:29:42.563: 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: 21:29:42.583: 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: 21:29:42.585: 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: 21:29:49.072: 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: 21:29:49.075: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]]
** Message: 21:29:49.506: 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/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: 21:37:29.426: 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: 21:37:29.430: 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: 21:37:36.635: 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: 21:37:36.639: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]]
** Message: 21:37:36.888: 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: 21:40:06.142: 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: 21:44:13.119: 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: 21:44:13.123: 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: 21:44:20.866: 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: 21:44:20.868: 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: 21:44:20.870: 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: 21:44:28.286: 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: 21:44:28.343: 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: 21:44:45.066: 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: 21:45:04.041: 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: 21:45:04.045: 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: 21:45:11.683: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary]
** Message: 21:45:11.691: 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: 21:45:11.692: 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: 21:45:19.039: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary]
** Message: 21:45:19.054: Processing model [cdna2genome]
** Message: 21:45:19.100: Bootstrapper processing model [cdna2genome]
** Message: 21:45:19.102: Process optimal [optimal:cdna2genome]
** Message: 21:45:19.375: 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: 21:49:52.491: 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: 21:57:51.199: 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: 22:04:55.740: 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: 22:35:59.396: 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: 23:21:04.071: 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: 23:21:04.075: 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: 23:21:11.807: Adding function [optimal_58_cdna2genome_32_find_32_score]
** Message: 23:21:11.810: 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: 23:21:11.812: 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: 23:21:19.873: Adding function [optimal_58_cdna2genome_32_find_32_path]
** Message: 23:21:19.877: 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: 23:21:19.879: 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: 23:21:28.023: Adding function [optimal_58_cdna2genome_32_find_32_region]
** Message: 23:21:28.026: 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: 23:21:28.028: 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: 23:21:36.884: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint]
** Message: 23:21:36.888: 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: 23:21:36.891: 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: 23:21:48.063: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation]
** Message: 23:21:48.120: 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: 23:22:19.952: 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: 23:22:54.396: 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: 23:22:54.399: 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: 23:23:04.322: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary]
** Message: 23:23:04.326: 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: 23:23:04.327: 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: 23:23:14.204: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary]
** Message: 23:23:14.222: Processing model [coding2genome]
** Message: 23:23:14.251: Bootstrapper processing model [coding2genome]
** Message: 23:23:14.252: Process optimal [optimal:coding2genome]
** Message: 23:23:14.410: 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: 23:24:58.182: 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: 23:27:37.719: 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: 23:29:59.074: 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: 23:37:54.966: 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/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: 23:49:39.553: 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: 23:49:39.557: 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: 23:49:49.761: Adding function [optimal_58_coding2genome_32_find_32_score]
** Message: 23:49:49.764: 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: 23:49:49.766: 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: 23:50:00.443: Adding function [optimal_58_coding2genome_32_find_32_path]
** Message: 23:50:00.447: 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: 23:50:00.449: 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: 23:50:10.956: Adding function [optimal_58_coding2genome_32_find_32_region]
** Message: 23:50:10.960: 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: 23:50:10.962: 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: 23:50:22.250: Adding function [optimal_58_coding2genome_32_find_32_checkpoint]
** Message: 23:50:22.254: 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: 23:50:22.256: 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: 23:50:33.530: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation]
** Message: 23:50:33.583: 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: 23:50:52.688: 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: 23:51:15.429: 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: 23:51:15.432: 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: 23:51:26.707: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary]
** Message: 23:51:26.711: 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: 23:51:26.714: 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: 23:51:37.756: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary]
** Message: 23:51:37.771: 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: 23:51:45.455: Adding: [c4_model_lookup.o]
** Message: 23:51:45.458: Adding object file [c4_model_lookup.o] to archive
ar -Sq c4_model_archive.a c4_model_lookup.o
** Message: 23:51:57.267: Indexing archive [c4_model_archive.a]
ranlib c4_model_archive.a
** Message: 23:52:11.274: Done
** Message: 23:52:11.280: 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.b9wpuB
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64
++ dirname /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64
+ cd exonerate-2.4.0
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/exonerate-2.4.0-4.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-2.4.0-4.fc28.riscv64/usr/share/man/man1
mkdir /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr
mkdir /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share
mkdir /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share/man
mkdir /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share/man/man1
/usr/bin/install -p -m 644 ./exonerate.1 /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share/man/man1/exonerate.1
/usr/bin/install -p -m 644 ./ipcress.1 /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share/man/man1/ipcress.1
/usr/bin/install -p -m 644 ./exonerate-server.1 /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share/man/man1/exonerate-server.1
/usr/bin/install -p -m 644 ./fastautils.1 /builddir/build/BUILDROOT/exonerate-2.4.0-4.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-2.4.0-4.fc28.riscv64/usr/bin
mkdir /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin
/usr/bin/install -p exonerate /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/exonerate
/usr/bin/install -p ipcress /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/ipcress
/usr/bin/install -p exonerate-server /builddir/build/BUILDROOT/exonerate-2.4.0-4.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-2.4.0-4.fc28.riscv64/usr/bin
/usr/bin/install -p fastaclean /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastaclean
/usr/bin/install -p fastaclip /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastaclip
/usr/bin/install -p fastachecksum /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastachecksum
/usr/bin/install -p fastacomposition /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastacomposition
/usr/bin/install -p fastadiff /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastadiff
/usr/bin/install -p fastaexplode /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastaexplode
/usr/bin/install -p fastafetch /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastafetch
/usr/bin/install -p fastahardmask /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastahardmask
/usr/bin/install -p fastaindex /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastaindex
/usr/bin/install -p fastalength /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastalength
/usr/bin/install -p fastanrdb /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastanrdb
/usr/bin/install -p fastaoverlap /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastaoverlap
/usr/bin/install -p fastareformat /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastareformat
/usr/bin/install -p fastaremove /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastaremove
/usr/bin/install -p fastarevcomp /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastarevcomp
/usr/bin/install -p fastasoftmask /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastasoftmask
/usr/bin/install -p fastasort /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastasort
/usr/bin/install -p fastasplit /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastasplit
/usr/bin/install -p fastasubseq /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastasubseq
/usr/bin/install -p fastatranslate /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastatranslate
/usr/bin/install -p fastavalidcds /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastavalidcds
/usr/bin/install -p fasta2esd /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fasta2esd
/usr/bin/install -p fastaannotatecdna /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/bin/fastaannotatecdna
/usr/bin/install -p esd2esi /builddir/build/BUILDROOT/exonerate-2.4.0-4.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-2.4.0-4.fc28.riscv64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Z9H4jF
+ umask 022
+ cd /builddir/build/BUILD
+ cd exonerate-2.4.0
+ DOCDIR=/builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share/doc/exonerate
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share/doc/exonerate
+ cp -pr README /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share/doc/exonerate
+ cp -pr ChangeLog /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share/doc/exonerate
+ cp -pr AUTHORS /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share/doc/exonerate
+ cp -pr TODO /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share/doc/exonerate
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.t2Zwjo
+ umask 022
+ cd /builddir/build/BUILD
+ cd exonerate-2.4.0
+ LICENSEDIR=/builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share/licenses/exonerate
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share/licenses/exonerate
+ cp -pr COPYING /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64/usr/share/licenses/exonerate
+ exit 0
Provides: exonerate = 2.4.0-4.fc28 exonerate(riscv-64) = 2.4.0-4.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-2.4.0-4.fc28.riscv64
Wrote: /builddir/build/SRPMS/exonerate-2.4.0-4.fc28.src.rpm
Wrote: /builddir/build/RPMS/riscv64/exonerate-2.4.0-4.fc28.riscv64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.1SZVxj
+ umask 022
+ cd /builddir/build/BUILD
+ cd exonerate-2.4.0
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/exonerate-2.4.0-4.fc28.riscv64
+ exit 0
+ touch /buildok
+ cleanup
+ set +e
+ sync
+ sleep 5
+ sync
+ poweroff
Terminated
++ cleanup
++ set +e
++ sync
++ sleep 5
Terminated
+++ cleanup
+++ set +e
+++ sync
+++ sleep 5
+++ sync
+++ poweroff