D: [iurt_root_command] chroot warning: %make is deprecated, use %make_build instead warning: %make is deprecated, use %make_build instead warning: %make is deprecated, use %make_build instead warning: %make is deprecated, use %make_build instead warning: %make is deprecated, use %make_build instead Installing /home/iurt/rpmbuild/SRPMS/wise2-2.4.1-9.mga8.src.rpm Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.oIqBxn + umask 022 + cd /home/iurt/rpmbuild/BUILD + '[' 1 -eq 1 ']' + '[' 1 -eq 1 ']' + '[' 1 -eq 1 ']' + cd /home/iurt/rpmbuild/BUILD + rm -rf wise2.4.1 + /usr/bin/gzip -dc /home/iurt/rpmbuild/SOURCES/wise2.4.1.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd wise2.4.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/bin/cat /home/iurt/rpmbuild/SOURCES/fix_getline.patch + /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch + /usr/bin/cat /home/iurt/rpmbuild/SOURCES/wise2.4.1-replace-isnumber.patch + /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch + /usr/bin/cat /home/iurt/rpmbuild/SOURCES/wise2.4.1-fix-makefile.patch + /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch + /usr/bin/cat /home/iurt/rpmbuild/SOURCES/wise2.4.1-clean-makefile.patch + /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.HQumap + umask 022 + cd /home/iurt/rpmbuild/BUILD + cd wise2.4.1 + '[' 1 -eq 1 ']' + '[' 1 -eq 1 ']' + cd src + /usr/bin/make -O -j8 all (cd base ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0 --libs glib-2.0`" libwisebase.a ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wisetime.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wisememman.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wiseoverlay.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wiserandom.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wisefile.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wisestreaminterface.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wiseconfig.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 linesubs.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wiseerror.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 commandline.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wisestring.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: creating libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' (cd HMMer2 ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0 --libs glib-2.0`" libhmmer.a ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c emulation.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c emit.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c debug.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c misc.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c mathsupport.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c alphabet.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c masks.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c plan9.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c tophits.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c prior.c prior.c: In function 'P7ReadPrior': prior.c:102:12: warning: implicit declaration of function 'strcmp' [-Wimplicit-function-declaration] 102 | if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; | ^~~~~~ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c modelmakers.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c aligneval.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c trace.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c histogram.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c getopt.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c dayhoff.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c cluster.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c plan7.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c file.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c hmmio.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c iupac.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c alignio.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c revcomp.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c sqerror.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c msf.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c sre_ctype.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c core_algorithms.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c interleaved.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c stack.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c translate.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c selex.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c sre_string.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c types.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c sre_math.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c weight.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c sqio.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c gnuregex.c gnuregex.c: In function 're_match_2': gnuregex.c:3752:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ gnuregex.c:3752:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2482 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4064:13: note: in expansion of macro 'POP_FAILURE_POINT' 4064 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2485 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4064:13: note: in expansion of macro 'POP_FAILURE_POINT' 4064 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2482 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4278:11: note: in expansion of macro 'POP_FAILURE_POINT' 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2485 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4278:11: note: in expansion of macro 'POP_FAILURE_POINT' 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o a - alphabet.o a - core_algorithms.o a - debug.o a - emit.o a - emulation.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - prior.o a - tophits.o a - trace.o a - aligneval.o a - alignio.o a - cluster.o a - dayhoff.o a - file.o a - getopt.o a - gnuregex.o a - interleaved.o a - iupac.o a - msf.o a - revcomp.o a - selex.o a - sqerror.o a - sqio.o a - sre_ctype.o a - sre_math.o a - sre_string.o a - stack.o a - translate.o a - types.o a - weight.o if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi chmod 644 libhmmer.a make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/HMMer2' (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0 --libs glib-2.0`" libdyna.a ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ basematrix.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ shattermatrix.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ dnamatrix.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ probability.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ packaln.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ alnconvert.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ alnrange.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ dprunimpl.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ complexevalset.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ dbsearchimpl.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ dpenvelope.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ complexsequence.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ complexconsensi.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ sequencestream.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ seqalign.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ matrixdebug.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hspstream.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ codonmatrix.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ codon.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hitlist.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ aln.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ sequence.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ compmat.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hsp.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ genericindexresult.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ seqlookup.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ codonmapper.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ arrayseqlookup.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ sequencedb.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ searchstatinterface.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ linkedlist_lookpos.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ searchstatlookup.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ singlenumberspace.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hscore.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ protein.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ proteindb.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ pairbaseseq.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ randomdb.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ cdna.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ genomicdb.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ dna.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ embl.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ genomic.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ cdnadb.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ randommodel.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ pairbase.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ histogram.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ translation.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ dynlibcross.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ btcanvas.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ asciibtcanvas.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ gene.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ transcript.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ genomicregion.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o ar: creating libdyna.a if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0 --libs glib-2.0`" libdyna_glib.a ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hspscaninterface.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ shadowseq.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ subseqhash.c subseqhash.dy: In function 'Wise2_is_populated_subseqhash_ghash': subseqhash.dy:111:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 111 | if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { | ^ subseqhash.dy: In function 'Wise2_lookup_subseqhash_ghash': subseqhash.dy:128:85: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 128 | return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number)); | ^ subseqhash.dy: In function 'Wise2_add_seq_subseqhash_ghash': subseqhash.dy:160:54: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 160 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^ subseqhash.dy:161:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 161 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^ subseqhash.dy: In function 'Wise2_add_direct_number_subseqhash_ghash': subseqhash.dy:188:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 188 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^ subseqhash.dy:189:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 189 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ proteinstreamedindex.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ intallocator.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hspscanruntime.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ shadowseqindex.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hsphandler.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ proteinindexcons.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hsplookupscan.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ dnaindexcons.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hsp2hitscan.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hspthreadeddb.c hspthreadeddb.dy: In function 'Wise2_threadeddb_scan_worker': hspthreadeddb.dy:154:77: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ^ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hsplookupthreaded.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ staticseq.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hsptwohitscan.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' (cd external ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0 --libs glib-2.0`" all ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/external' (cd mott; make CC="cc" CFLAGS="-c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 " all) make[2]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/external/mott' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../../dynlibsrc -I../../base wise2_mott_bridge.c make[2]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/external/mott' make[2]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/external/mott' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c -o mott_api.o mott_api.c mott_api.c: In function 'InitPvaluesMott': mott_api.c:64:3: warning: implicit declaration of function 'free' [-Wimplicit-function-declaration] 64 | free(freq0); | ^~~~ mott_api.c:64:3: warning: incompatible implicit declaration of built-in function 'free' mott_api.c:5:1: note: include '' or provide a declaration of 'free' 4 | #include"gapstat.h" +++ |+#include 5 | mott_api.c: In function 'SW_PValueMott': mott_api.c:104:7: warning: incompatible implicit declaration of built-in function 'free' 104 | free(freqA); | ^~~~ mott_api.c:104:7: note: include '' or provide a declaration of 'free' mott_api.c: In function 'KarlinAltschulStatistics2': mott_api.c:144:5: warning: incompatible implicit declaration of built-in function 'free' 144 | free(h+hmin); | ^~~~ mott_api.c:144:5: note: include '' or provide a declaration of 'free' mott_api.c:155:5: warning: incompatible implicit declaration of built-in function 'free' 155 | free(h+hmin); | ^~~~ mott_api.c:155:5: note: include '' or provide a declaration of 'free' mott_api.c: In function 'GetHistogram': mott_api.c:179:16: warning: implicit declaration of function 'calloc' [-Wimplicit-function-declaration] 179 | h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; | ^~~~~~ mott_api.c:179:16: warning: incompatible implicit declaration of built-in function 'calloc' mott_api.c:179:16: note: include '' or provide a declaration of 'calloc' mott_api.c: In function 'PseudoResidueFrequencies2': mott_api.c:207:12: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] 207 | freq[toupper(seq[n])]++; | ^~~~~~~ mott_api.c: In function 'RobinsonResidueFrequencies2': mott_api.c:230:27: warning: incompatible implicit declaration of built-in function 'calloc' 230 | double *freq = (double*)calloc(256, sizeof(double)); | ^~~~~~ mott_api.c:230:27: note: include '' or provide a declaration of 'calloc' make[2]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/external/mott' make[2]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/external/mott' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -c -o gaplib.o gaplib.c make[2]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/external/mott' make[2]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/external/mott' ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi make[2]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/external/mott' make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/external' (cd socket ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0 --libs glib-2.0`" libwisesocket.a ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ directsocketwrite.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ anonobj.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ transferinterface.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ functionclient.c functionclient.dy: In function 'Wise2_new_FunctionProxyCoordinator': functionclient.dy:193:24: warning: passing argument 2 of 'connect' from incompatible pointer type [-Wincompatible-pointer-types] 193 | connect(out->socket, &server, sizeof(server)); | ^~~~~~~ | | | struct sockaddr_in * In file included from functionclient.c:7: /usr/include/sys/socket.h:126:52: note: expected 'const struct sockaddr *' but argument is of type 'struct sockaddr_in *' 126 | extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t __len); | ^ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ functionserver.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' (cd dnaindex ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0 --libs glib-2.0`" all ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models dnamapping.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_count.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy: In function 'Wise2_add_direct_number_CompressedProteinIndex': compressed_protein_index.dy:223:10: warning: returning 'void *' from a function with return type 'boolean' {aka 'int'} makes integer from pointer without a cast [-Wint-conversion] 223 | return NULL; | ^~~~ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c kmer_assembly_untangler.dy: In function 'Wise2_show_KmerAssemblyPath': kmer_assembly_untangler.dy:52:65: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 52 | fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base); | ^ kmer_assembly_untangler.dy: In function 'Wise2_old_attempt_forward_untangle_KmerAssembly': kmer_assembly_untangler.dy:568:75: warning: passing argument 4 of 'Wise2_lift_backward_tangled_tail' from incompatible pointer type [-Wincompatible-pointer-types] 568 | lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); | ^~~~~~~~~~~~~~~~~ | | | long int * In file included from kmer_assembly_untangler.c:4: kmer_assembly_untangler.h:174:116: note: expected 'int *' but argument is of type 'long int *' 174 | void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); | ~~~~~~^~~~~~~~~~~ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models assembly.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' (cd network ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0 --libs glib-2.0`" all ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' cc -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` -lpthread make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' (cd models ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0 --libs glib-2.0`" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ dnal.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ psw.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ seqaligndisplay.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ sw_wrap.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ pswdb.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ dbac.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ dbadisplay.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ geneparser21.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ geneparameter.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ proteinsw.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ dnaalign.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ slimdba.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ pba.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genestats.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ geneoutput.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ dba.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ abc.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genewisehsp.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ splicesitemodeler.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ geneutil.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ bigdba.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genefrequency.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ threestatemodel.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ gwlite.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genewise6.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genestretch6.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ geneloop6.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genewise4.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genephase6.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' dyc -l -D -n Wise2_ -a _api.h -b _api.t -latex -perl -pthreads -dbtrace 5 -nocwarn phasemodel.dy make[1]: dyc: No such file or directory make[1]: *** [makefile:379: phasemodel.c] Error 127 make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: *** Waiting for unfinished jobs.... make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ estwrap.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ gwrap.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ matchsum.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ gwlitemodel.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genewisemodel.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ geneloop21.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genewise21.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make: *** [makefile:95: realall] Error 2 + : + cd ../src/dyc/ + /usr/bin/make -O -j8 newdyc make: *** No rule to make target 'newdyc'. Stop. + : + export PATH=/usr/local/bin:/usr/bin:/usr/local/games:/usr/games:/usr/local/sbin:/usr/sbin:/home/iurt/.local/bin:/home/iurt/bin:/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dyc + PATH=/usr/local/bin:/usr/bin:/usr/local/games:/usr/games:/usr/local/sbin:/usr/sbin:/home/iurt/.local/bin:/home/iurt/bin:/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dyc + /usr/bin/make -O -j8 linux cc -pthread -c -g -DUNIX -I../base/ -I../base/ module.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ type.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dyc.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dynfile.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ method.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ friend.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dynadb.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ inputfile.c inputfile.c:8:8: warning: type defaults to 'int' in declaration of 'linecount' [-Wimplicit-int] 8 | static linecount = 0; | ^~~~~~~~~ cc -pthread -c -g -DUNIX -I../base/ -I../base/ wisec.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ modulefunc.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dynafunc.c dynafunc.dy: In function 'write_GenericMatrix_func': dynafunc.dy:2355:3: warning: implicit declaration of function 'write_shatter_functions'; did you mean 'write_dc_functions'? [-Wimplicit-function-declaration] 2355 | write_shatter_functions(dfp,gm,dpi); | ^~~~~~~~~~~~~~~~~~~~~~~ | write_dc_functions cc -pthread -c -g -DUNIX -I../base/ -I../base/ dyna2.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ ftext.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ labelmaster.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ display.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ api.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ objectinfo.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ funcinfo.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ variable.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ docugen.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dpimpl.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ exprtree.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ compugen.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ input.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dynashadow.c dynashadow.dy: In function 'optimised_shadow_GenericMatrix': dynashadow.dy:2180:31: warning: passing argument 2 of 'write_main_shadow_block' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 2180 | write_main_shadow_block(dfp,gm,"DC_OPT_SHADOW_MATRIX","mat","DC_OPT_SHADOW_SPECIAL","DC_OPT_SHADOW_MATRIX_SP","DC_OPT_SHADOW_SPECIAL_SP",7,TRUE,TRUE,0,TRUE); | ^~ In file included from dynashadow.c:4: dynashadow.h:163:60: note: expected 'GenericMatrix *' but argument is of type 'const GenericMatrix *' 163 | void write_main_shadow_block(DYNFILE * dfp,GenericMatrix * gm,char * matrixtag,char * pointer_tag,char * specialtag,char * shadow_main_tag,char * shadow_special_tag,int shadow_length,boolean shadow_on_special,boolean use_special,int debug,int use_shadow_pointer); | ~~~~~~~~~~~~~~~~^~ dynashadow.dy:2187:36: warning: passing argument 2 of 'write_special_shadow_block' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 2187 | write_special_shadow_block(dfp,gm,"DC_OPT_SHADOW_MATRIX","mat","DC_OPT_SHADOW_SPECIAL","DC_OPT_SHADOW_MATRIX_SP","DC_OPT_SHADOW_SPECIAL_SP",7,TRUE,0); | ^~ In file included from dynashadow.c:4: dynashadow.h:189:63: note: expected 'GenericMatrix *' but argument is of type 'const GenericMatrix *' 189 | void write_special_shadow_block(DYNFILE * dfp,GenericMatrix * gm,char * matrix,char * pointer_tag,char * special,char * shadow_main_tag,char * shadow_special_tag,int shadow_length,boolean shadow_on_special,int debug); | ~~~~~~~~~~~~~~~~^~ cc -pthread -c -g -DUNIX -I../base/ -I../base/ dbthread.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ probal.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ telegraph.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dynadebug.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dyshatter.c flex calc.l cc -DLINUX -c -I../base/ y.tab.c cc -DLINUX -c -I../base/ lex.yy.c lex.yy.c: In function 'yy_get_next_buffer': calc.l:8:33: warning: implicit declaration of function 'my_yyinput'; did you mean 'yyunput'? [-Wimplicit-function-declaration] 8 | #define YY_INPUT(b, r, ms) (r = my_yyinput(b, ms)) | ^~~~~~~~~~ lex.yy.c:1033:3: note: in expansion of macro 'YY_INPUT' 1033 | /* Read in more data. */ | ^~~~~~~~ cc -o dyc dyc.o dyna2.o dynfile.o wisec.o dynafunc.o module.o type.o method.o dynadb.o friend.o inputfile.o variable.o modulefunc.o api.o display.o dynashadow.o labelmaster.o ftext.o funcinfo.o objectinfo.o exprtree.o compugen.o docugen.o input.o dpimpl.o dbthread.o probal.o telegraph.o dynadebug.o dyshatter.o y.tab.o lex.yy.o -lwisebase -g -lm -L../base/ -lpthread + cd ../../src + export WISECONFIGDIR=/home/iurt/rpmbuild/BUILD/wise2.4.1/src/../wisecfg + WISECONFIGDIR=/home/iurt/rpmbuild/BUILD/wise2.4.1/src/../wisecfg + /usr/bin/make -O -j8 init cd base ; /usr/bin/make init make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' dyc -n Wise2_ -a _api.h -b _api.t -l -D *.dy Warning Error You have not documented scan_and_replace Warning Error You have not documented scan_and_replace_line Warning Error You have not documented push_scan_and_replace_pair Warning Error You have not documented pop_scan_and_replace_pair Warning Error You have not documented flush_scan_and_replace Warning Error You have not documented read_plain_scan_and_replace Warning Error You have not documented read_scan_and_replace_file Warning Error You have 7 undocumented functions make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cd dynlibsrc; /usr/bin/make init make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' dyc -l -D -F -n Wise2_ -a _api.h -b _api.t -latex -perl *.dy Warning Error arrayseqlookup.dy:15: For element long - got no good default. Returning 0 Warning Error arrayseqlookup.dy:21: For element SeqLookupResultStruct - got no good default. Returning 0 Warning Error codon.dy:52: For element aa - got no good default. Returning 0 Warning Error hscore.dy:19: For element BytePosition - got no good default. Returning 0 Warning Error hscore.dy:51: For element DataScore - got no good default. Returning 0 Warning Error hscore.dy:52: For element DataEntry - got no good default. Returning 0 Warning Error hscore.dy:53: For element DataEntry - got no good default. Returning 0 Warning Error hscore.dy:74: For element long - got no good default. Returning 0 Warning Error hspscaninterface.dy:33: For element void - got no good default. Returning 0 Warning Error linkedlist_lookpos.dy:16: For element SeqLookupResultStruct - got no good default. Returning 0 Warning Error matrixdebug.dy:24: For element void - got no good default. Returning 0 Warning Error matrixdebug.dy:30: For element void - got no good default. Returning 0 Warning Error matrixdebug.dy:54: For element void - got no good default. Returning 0 Warning Error pthreadpool.dy:16: For element void - got no good default. Returning 0 Warning Error pthreadpool.dy:26: For element pthread_t - got no good default. Returning 0 Warning Error searchstatinterface.dy:15: For element void - got no good default. Returning 0 Warning Error seqlookup.dy:46: For element void - got no good default. Returning 0 Warning Error seqlookup.dy:67: For element void - got no good default. Returning 0 Warning Error seqlookup.dy:92: For element void - got no good default. Returning 0 Warning Error subseqlookup.dy:13: For element SeqLookupPos - got no good default. Returning 0 make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cd models ; /usr/bin/make init make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' dyc -l -D -n Wise2_ -a _api.h -b _api.t -latex -perl -pthreads -dbtrace 5 -nocwarn *.dy Warning Error You have not documented weighted_coding_AlignGeneColumn Warning Error You have not documented window_AlignGeneModel Warning Error You have not documented create_NonCodingSimpleModel Warning Error You have not documented simple_non_coding_AlignGeneColumn Warning Error You have not documented weighted_non_coding_AlignGeneColumn Warning Error You have not documented weighted_simple_non_coding_AlignGeneColumn Warning Error You have not documented simple_coding_AlignGeneColumn Warning Error You have not documented fill_reverse_AlignGeneColumn Warning Error You have not documented fill_forward_AlignGeneColumn Warning Error You have not documented new_empty_AlignGeneColumnStore Warning Error You have not documented free_AlignGeneCodon Warning Error You have not documented new_AlignGeneModel Warning Error You have not documented show_AlignGeneModel Warning Error You have not documented create_AlignGeneModel Warning Error You have not documented prob_SpliceSiteProb Warning Error You have not documented non_coding_probability_AlignGeneModel Warning Error You have not documented coding_probability_AlignGeneModel Warning Error You have not documented new_AlignGeneModelParam_from_argv Warning Error You have not documented show_help_AlignGeneModelParam Warning Error You have not documented std_AlignGeneModelParam Warning Error You have not documented AlignGeneModelScore_from_AlignGeneModel Warning Error You have not documented free_Probability Warning Error You have not documented free_Score Warning Error You have 23 undocumented functions Warning Error In preparing matrix AlignWise Type [AlignGeneModelFrame*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix AlignWise Type [AlignGeneModelScore*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error No database types - must have dbtypes for pthreads support Warning Error In preparing matrix BigDnaMatchBlock Type [DnaMatrix*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix BigDnaMatchBlock Type [DnaMatrix*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix BigDnaMatchBlock Type [DnaMatrix*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix BigDnaMatchBlock Type [DnaMatrix*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix BigDnaMatchBlock Type [DnaMatrix*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error Asking for threads, but the types in this matrix BigDnaMatchBlock are not thread safe Warning Error In preparing matrix CdnaWise10 Type [GeneParser4Score *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix CdnaWise10 Type [CodonMatrixScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix CdnaWise10 Type [RandomCodonScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix CloneWise Type [MappedCloneSet *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix CloneWise Type [MappedCloneSet *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix CloneWise Type [MappedCloneMatch*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error No database types - must have dbtypes for pthreads support Warning Error In preparing matrix DnaMatchBlock Type [DnaMatrix*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix DnaMatchBlock Type [DnaMatrix*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix DnaMatchBlock Type [DnaMatrix*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix DnaMatchBlock Type [DnaMatrix*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error Asking for threads, but the types in this matrix DnaMatchBlock are not thread safe Warning Error In preparing matrix DnaAlign Type [DnaStartEnd *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error Asking for threads, but the types in this matrix DnaAlign are not thread safe Warning Error You have not documented DnaHmmScore_from_DnaHmmProb Warning Error You have not documented make_consensus_DnaHmmProb Warning Error You have not documented DnaHmmScoreUnit_from_DnaHmmProbUnit Warning Error You have not documented new_DnaHmmProb_from_SeqAlign_ungapped Warning Error You have not documented new_DnaHmmProbUnit_from_ColumnCount_ungapped Warning Error You have not documented set_N_DnaHmmProb Warning Error You have not documented fold_RandomModelDNA_DnaHmmProb Warning Error You have 7 undocumented functions Warning Error You have not documented show_help_DnaMatchPara Warning Error You have not documented new_DnaMatchPara_from_argv Warning Error You have not documented HitList_from_Sequence_SequenceSet_DNA Warning Error You have 3 undocumented functions Warning Error You have not documented new_TransFactor_from_DnaProfile Warning Error You have not documented bits_entropy_DnaProfile Warning Error You have not documented merged_SeqAlign Warning Error You have not documented DnaProfileScore_from_DnaProfile Warning Error You have not documented fold_RandomModel_DnaProfile Warning Error You have not documented naive_DnaProfile_from_Sequence Warning Error You have not documented naive_DnaProfile_from_SeqAlign Warning Error You have not documented show_DnaProfile Warning Error You have 8 undocumented functions Warning Error In preparing matrix DnaProfileMat Type [DnaProfileScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix DnaProfileMat Type [DnaProfileScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix DnaProfileMat Type [DnaProfileMatchScore*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix DnaProfileMat Cannot automatically find length string for element type [DnaProfileScore *] (perhaps it is not a logical type). You should have a field:len in this line if it is not a logical type. Assuming [len] anyway Warning Error In preparing matrix DnaProfileMat Cannot automatically find length string for element type [DnaProfileScore *] (perhaps it is not a logical type). You should have a field:len in this line if it is not a logical type. Assuming [len] anyway Warning Error No database types - must have dbtypes for pthreads support Warning Error You have not documented new_ALLR_DnaProfileMatchScore Warning Error You have not documented new_DnaProfileMatchScore Warning Error You have 2 undocumented functions Warning Error You have not documented TransFactorSet_from_DnaProfileSet Warning Error You have not documented balanced_4_Sequence_fasta_stream Warning Error You have not documented simple_cascade_Sequence_fasta_stream Warning Error You have not documented new_leaf_DnaProfileNode Warning Error You have not documented populate_DnaProfileNode_from_root Warning Error You have not documented join_two_DnaProfileNode Warning Error You have not documented new_DnaProfileEnginePara_from_argv Warning Error You have not documented show_help_DnaProfileEnginePara Warning Error You have not documented filter_DnaProfileSet Warning Error You have not documented DnaProfileSet_from_leaf_leaf Warning Error You have not documented DnaProfileSet_from_node_node Warning Error You have not documented DnaProfileSet_from_leaf_node Warning Error You have not documented DnaProfileMatchPair_from_DnaProfile Warning Error You have not documented sort_DnaProfileMatchPairSet_by_score Warning Error You have not documented compare_DnaProfileMatchPair Warning Error You have not documented show_DnaProfileSet Warning Error You have 16 undocumented functions Warning Error In preparing matrix EditDistance Type [EditString*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix EditDistance Type [EditString*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix EditDistance Cannot automatically find length string for element type [EditString*] (perhaps it is not a logical type). You should have a field:len in this line if it is not a logical type. Assuming [len] anyway Warning Error In preparing matrix EditDistance Cannot automatically find length string for element type [EditString*] (perhaps it is not a logical type). You should have a field:len in this line if it is not a logical type. Assuming [len] anyway Warning Error No database types - must have dbtypes for pthreads support Warning Error You have not documented new_EditString Warning Error You have 1 undocumented functions Warning Error You have not documented indicate_intron_used Warning Error You have not documented read_est_evidence Warning Error You have not documented new_est_GenomeEvidenceUnit Warning Error You have not documented est_utr5_start Warning Error You have not documented est_utr3_end Warning Error You have not documented est_start_pot Warning Error You have not documented est_stop_pot Warning Error You have not documented est_cds_frameshift Warning Error You have not documented est_cds_3SS Warning Error You have not documented est_cds_5SS Warning Error You have not documented est_intron_pot Warning Error You have not documented est_cds_pot Warning Error You have not documented est_3ss Warning Error You have not documented est_5ss Warning Error You have not documented est_utr_pot Warning Error You have 15 undocumented functions Warning Error estfrag3.dy:26: In reading matrix definition for EstFrag3 No need for globaldefaultscore lines anymore Warning Error estfrag3.dy:183: In reading matrix definition for EstFrag3 In Reading state START No need for defscore lines anymore Warning Error In preparing matrix EstFrag3 Multiple definitions for CDNA_HMM - taking the last one Warning Error In preparing matrix EstFrag3 Type [cDNAParserScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix EstFrag3 Multiple definitions for CDNA_HMM - taking the last one Warning Error Asking for threads, but the types in this matrix EstFrag3 are not thread safe Warning Error In preparing matrix EstLoop3 Type [cDNAParserScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix EstQuick3 Type [cDNAParserScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix EstSlim3 Type [cDNAParserScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix EstSlimLoop3 Type [cDNAParserScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error estwise3.dy:22: In reading matrix definition for EstWise3 No need for globaldefaultscore lines anymore Warning Error estwise3.dy:176: In reading matrix definition for EstWise3 In Reading state START No need for defscore lines anymore Warning Error In preparing matrix EstWise3 Type [cDNAParserScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix FiveStateProtein Type [FiveStateScore*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix FiveStateProtein Cannot automatically find length string for element type [FiveStateScore*] (perhaps it is not a logical type). You should have a field:len in this line if it is not a logical type. Assuming [len] anyway Warning Error No database types - must have dbtypes for pthreads support Warning Error You have not documented dump_FiveStateModel Warning Error You have not documented dump_FiveStateScore Warning Error You have not documented read_FiveStateFrameSet_file Warning Error You have not documented read_FiveStateFrameSet Warning Error You have not documented blank_FiveStateUnit Warning Error You have not documented FiveStateModel_from_FiveStateFrameSet Warning Error You have not documented fold_RandomModel_into_FiveStateModel Warning Error You have not documented FiveStateModel_from_flat_ThreeStateModel Warning Error You have not documented FiveStateScore_from_FiveStateModel Warning Error You have not documented FiveStateScoreUnit_from_FiveStateUnit Warning Error You have 10 undocumented functions Warning Error You have not documented match_central_line_std Warning Error You have not documented protdna_btc_display Warning Error You have not documented write_alignment_separator Warning Error You have not documented write_name_start_stuff Warning Error You have not documented write_intron_desc Warning Error You have not documented write_3intron_match Warning Error You have not documented write_5intron_match Warning Error You have not documented write_codon_match Warning Error You have 8 undocumented functions Warning Error You have not documented read_line_GeneSingleCons Warning Error You have not documented untouched_GeneFrequency21 Warning Error You have 2 undocumented functions Warning Error geneloop21.dy:27: In reading matrix definition for GeneLoop21 No need for globaldefaultscore lines anymore Warning Error geneloop21.dy:406: In reading matrix definition for GeneLoop21 In Reading state START No need for defscore lines anymore Warning Error In preparing matrix GeneLoop21 Type [GeneParser21Score *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix GeneLoop21 Type [RandomCodonScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix GeneLoop21 Type [RandomModelDNAScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error geneloop6.dy:18: In reading matrix definition for GeneLoop6 No need for globaldefaultscore lines anymore Warning Error geneloop6.dy:197: In reading matrix definition for GeneLoop6 In Reading state START No need for defscore lines anymore Warning Error In preparing matrix GeneLoop6 Type [GeneParser4Score *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error You have not documented show_GeneOutput Warning Error You have not documented id_map_func Warning Error You have not documented new_GeneOutputPara_from_argv Warning Error You have not documented show_help_GeneOutputPara Warning Error You have 4 undocumented functions Warning Error You have not documented GeneWiseCodonModel_from_GeneFrequencies Warning Error You have not documented GeneParameter21_from_GeneFrequency21 Warning Error You have 2 undocumented functions Warning Error You have not documented fudged_mixed_RandomModelDNA_from_GeneParser21 Warning Error You have not documented add_flat_error_probabilities_GeneParser21 Warning Error You have not documented add_error_probabilities_GeneParser21 Warning Error You have not documented GeneParser21_from_GeneFrequency21_cds Warning Error You have not documented RandomModelDNA_from_central_GeneParser21 Warning Error You have not documented show_GeneParser21 Warning Error You have not documented std_GeneParser21 Warning Error You have not documented removed_probability_from_cds Warning Error You have not documented GeneParser21_fold_in_RandomModelDNA Warning Error You have not documented GeneParser21Score_from_GeneParser21 Warning Error You have 10 undocumented functions Warning Error You have not documented std_GeneParser4 Warning Error You have not documented GeneParser4Score_from_GeneParser21Score Warning Error You have not documented GeneParser4Score_from_GeneParser4 Warning Error You have 3 undocumented functions Warning Error genephase6.dy:19: In reading matrix definition for GenePhase6 No need for globaldefaultscore lines anymore Warning Error genephase6.dy:197: In reading matrix definition for GenePhase6 In Reading state START No need for defscore lines anymore Warning Error In preparing matrix GenePhase6 Type [GenePhaseScore*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix GenePhase6 Type [GeneParser4Score *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix GenePhase6 Type [GeneralGeneModelScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error No database types - must have dbtypes for pthreads support Warning Error You have not documented AlnBlock_from_phased_protein_wrap Warning Error You have 1 undocumented functions Warning Error genestats.dy:45: For element Bits - got no good default. Returning 0 Warning Error genestats.dy:46: For element Bits - got no good default. Returning 0 Warning Error genestats.dy:47: For element Bits - got no good default. Returning 0 Warning Error In preparing matrix GeneStretch6 Type [GeneParser4Score *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix GeneStretch6 Type [GeneralGeneModelScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error You have not documented exon_type_AlnColumn_genomewise Warning Error You have not documented show_utr_exon_genomewise Warning Error You have 2 undocumented functions Warning Error In preparing matrix GeneWise21 Type [GeneParser21Score *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix GeneWise21 Type [RandomCodonScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix GeneWise21 Type [RandomModelDNAScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error genewise4.dy:158: In reading matrix definition for GeneWise4 In Reading state START No need for defscore lines anymore Warning Error In preparing matrix GeneWise4 Type [GeneParser4Score *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix GeneWise6 Type [GeneParser4Score *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error You have not documented new_GeneWiseRunPara_from_argv Warning Error You have not documented show_help_GeneWiseRunPara Warning Error You have not documented DPEnvelope_from_protein_gen Warning Error You have not documented consistent_GeneWiseHSP Warning Error You have not documented compare_GeneWiseHSP_start Warning Error You have not documented add_GeneWiseHSPmanager_HSPset Warning Error You have 6 undocumented functions Warning Error In preparing matrix GenomeWise9 Type [GenomeEvidenceSet*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix GenomeWise9 Type [RandomCodonScore *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix GenomeWise9 Cannot automatically find length string for element type [GenomeEvidenceSet*] (perhaps it is not a logical type). You should have a field:len in this line if it is not a logical type. Assuming [len] anyway Warning Error No database types - must have dbtypes for pthreads support Warning Error In preparing matrix GeneLiteModel Type [GeneParser4Score *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error You have not documented GwLiteSegmentScore_from_GwLiteSegment Warning Error You have 1 undocumented functions Warning Error You have not documented HitList_from_LinearHSPmanager_heuristic_threaded Warning Error You have not documented worker_thread_LM2HitList Warning Error You have not documented HitList_from_LinearHSPmanager_heuristic_threaded Warning Error You have not documented HitList_from_LinearHSPmanager_heuristic Warning Error You have not documented HitPair_from_HSPset_heuristic Warning Error You have not documented build_HSP2AlnHelper Warning Error You have not documented show_help_HSPset2HitPairPara Warning Error You have not documented new_HSPset2HitPairPara_from_argv Warning Error You have 8 undocumented functions Warning Error Asking for threads, but the types in this matrix LargeBlockAligner are not thread safe Warning Error You have not documented HitList_from_LocalCisHitSet Warning Error You have not documented expand_to_subhits_LocalCisHitSet Warning Error You have not documented show_help_LocalCisHitSetPara Warning Error You have not documented new_LocalCisHitSetPara_from_argv Warning Error You have not documented show_pretty_LocalCisHitSet Warning Error You have not documented show_summary_LocalCisHitSet Warning Error You have not documented greedy_weed_LocalCisHitSet Warning Error You have not documented sort_LocalCisHitSet_by_score Warning Error You have not documented sort_LocalCisHitSet_by_start Warning Error You have not documented compare_LocalCisHit_score Warning Error You have not documented compare_LocalCisHit_start Warning Error You have not documented is_query_overlap_LocalCisHit Warning Error You have not documented is_target_overlap_LocalCisHit Warning Error You have not documented is_consumed_HSP Warning Error You have not documented make_LocalCisHitSet Warning Error You have not documented make_LocalCisHit Warning Error You have not documented make_motif_LocalCisHit Warning Error You have 17 undocumented functions Warning Error You have not documented standard_LocalCisHitScore Warning Error You have not documented standard_LocalCisHitProb Warning Error You have not documented LocalCisHitScore_from_LocalCisHitProb Warning Error You have 3 undocumented functions Warning Error In preparing matrix LocalCloneWise Type [MappedCloneSet *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix LocalCloneWise Type [MappedCloneSet *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix LocalCloneWise Type [MappedCloneMatch*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error No database types - must have dbtypes for pthreads support Warning Error In preparing matrix LocalDnaMatchBlock Type [LocalCisHitScore*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error Asking for threads, but the types in this matrix LocalDnaMatchBlock are not thread safe Warning Error You have not documented new_MappedCloneMatch Warning Error You have not documented MappedCloneSet_skip Warning Error You have not documented MappedCloneSet_match Warning Error You have not documented old_MappedCloneSet_match Warning Error You have 4 undocumented functions Warning Error You have not documented MotifMatrixScore_from_MotifMatrixPara Warning Error You have not documented new_MotifMatrixPara_from_argv Warning Error You have not documented show_help_MotifMatrixPara Warning Error You have not documented new_MotifConsMatrix Warning Error You have 4 undocumented functions Warning Error In preparing matrix LocalMotifMatrix Type [MotifConsMatrix*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix LocalMotifMatrix Type [MotifMatrixScore*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error Asking for threads, but the types in this matrix LocalMotifMatrix are not thread safe Warning Error You have not documented process_HSP Warning Error You have not documented query_to_reverse_target Warning Error You have 2 undocumented functions Warning Error You have not documented read_ProteinIntronList Warning Error You have not documented read_ProteinIntronList_from_filename Warning Error You have not documented new_PhasedProteinPara_from_argv Warning Error You have not documented show_help_PhasedProteinPara Warning Error You have not documented write_fasta_PhasedProtein Warning Error You have not documented read_fasta_PhasedProtein_file Warning Error You have not documented read_fasta_PhasedProtein Warning Error You have not documented GenePhaseModel_from_ThreeStateModel Warning Error You have not documented GenePhaseScore_from_GenePhaseModel Warning Error You have 9 undocumented functions Warning Error In preparing matrix PseudoWise7 Type [GeneParser4Score *] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error You have not documented new_DnaSequenceHitList Warning Error You have not documented show_SegmentHitList Warning Error You have not documented show_SegmentHit Warning Error You have not documented sort_SegmentHitList_by_qstart Warning Error You have not documented compare_SegmentHit_by_qstart Warning Error You have not documented read_msptmp_DnaSequenceHitList Warning Error You have not documented verify_SegmentHit Warning Error You have not documented SegmentHit_from_msptmp_line Warning Error You have not documented SegmentHit_from_MSPcrunch_line Warning Error You have 9 undocumented functions Warning Error In preparing matrix SlimDnaMatchBlock Type [DnaMatrix*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error Asking for threads, but the types in this matrix SlimDnaMatchBlock are not thread safe Warning Error You have not documented SpliceSiteModeler_ComplexSequence_eval_func Warning Error You have not documented ComplexSequenceEval_from_SpliceSiteModel Warning Error You have not documented SpliceSiteModel_score Warning Error You have not documented std_5SS_SpliceSiteModel Warning Error You have not documented std_3SS_SpliceSiteModel Warning Error You have not documented new_SpliceSiteModel Warning Error You have 6 undocumented functions Warning Error You have not documented show_help_StandardOutputOptions Warning Error You have not documented new_StandardOutputOptions_from_argv Warning Error You have not documented show_StandardOutputOptions Warning Error You have 3 undocumented functions Warning Error You have not documented SyExonScore_flat_model Warning Error You have not documented SyExonModel_flat_model Warning Error You have not documented SyExonScore_from_SyExonModel Warning Error You have not documented SyExonScoreUnit_from_SyExon Warning Error You have not documented dump_SyExonScore Warning Error You have 5 undocumented functions Warning Error sywise20.dy:250: In reading matrix definition for SyWise20 In Reading state START No need for defscore lines anymore Warning Error In preparing matrix SyWise20 Type [SyExonScore*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix SyWise20 Type [ComplexSequence*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix SyWise20 Type [PairBaseCodonModelScore*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix SyWise20 Type [PairBaseModelScore*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix SyWise20 Type [PairBaseCodonModelScore*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix SyWise20 Type [PairBaseCodonModelScore*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix SyWise20 Cannot automatically find length string for element type [SyExonScore*] (perhaps it is not a logical type). You should have a field:len in this line if it is not a logical type. Assuming [len] anyway Warning Error No database types - must have dbtypes for pthreads support Warning Error threestatedb.dy:29: For element long - got no good default. Returning 0 Warning Error In preparing matrix ThreeStateProtein Type [ThreeStateScore*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix ThreeStateProtein Cannot automatically find length string for element type [ThreeStateScore*] (perhaps it is not a logical type). You should have a field:len in this line if it is not a logical type. Assuming [len] anyway Warning Error No database types - must have dbtypes for pthreads support Warning Error In preparing matrix ThreeStateLoop Type [ThreeStateScore*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix ThreeStateLoop Cannot automatically find length string for element type [ThreeStateScore*] (perhaps it is not a logical type). You should have a field:len in this line if it is not a logical type. Assuming [len] anyway Warning Error No database types - must have dbtypes for pthreads support Warning Error You have not documented show_context_match_TransFactorMatchSetCompara Warning Error You have not documented circular_permuted_TransFactorSet Warning Error You have not documented show_TransFactorMatchSet Warning Error You have not documented show_help_TransFactorMatchPara Warning Error You have not documented show_help_TransFactorComparaPara Warning Error You have not documented new_TransFactorComparaPara_from_argv Warning Error You have not documented calculate_TransFactorMatchSetCompara Warning Error You have not documented show_help_TransFactorBuildPara Warning Error You have not documented new_TransFactorBuildPara_from_argv Warning Error You have not documented new_TransFactorMatchPara_from_argv Warning Error You have not documented build_TransFactorSet Warning Error You have not documented build_pwm_TransFactor Warning Error You have not documented calculate_TransFactorMatchSet Warning Error You have not documented min_prob_TransFactor Warning Error You have not documented max_prob_TransFactor Warning Error You have not documented write_TransFactorSet Warning Error You have not documented write_TransFactor Warning Error You have not documented read_TransFactorSet_file Warning Error You have not documented read_ben_IUPAC_TransFactorSet_file Warning Error You have not documented read_ben_IUPAC_TransFactorSet Warning Error You have not documented read_laurence_TransFactorSet_file Warning Error You have not documented read_laurence_TransFactorSet Warning Error You have not documented read_TransFactorSet Warning Error You have not documented read_TransFactor Warning Error You have not documented compare_start_TransFactorMatch Warning Error You have not documented sort_by_start_TransFactorMatchSet Warning Error You have 26 undocumented functions Warning Error You have not documented show_help_TransFactorRegionPara Warning Error You have not documented new_TransFactorRegionPara_from_argv Warning Error You have not documented show_TransFactorRegionSet Warning Error You have not documented new_TransFactorRegionSet Warning Error You have not documented new_dp_TransFactorRegionSet Warning Error You have not documented new_window_TransFactorRegionSet Warning Error You have 6 undocumented functions Warning Error In preparing matrix TransRegionMatrix Type [TransRegionModel*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix TransRegionMatrix Type [SequenceBaseCoverage*] is not recognised as a logical Dynamite type. Assumming it is a real C type Warning Error In preparing matrix TransRegionMatrix Cannot automatically find length string for element type [TransRegionModel*] (perhaps it is not a logical type). You should have a field:len in this line if it is not a logical type. Assuming [len] anyway Warning Error In preparing matrix TransRegionMatrix Cannot automatically find length string for element type [SequenceBaseCoverage*] (perhaps it is not a logical type). You should have a field:len in this line if it is not a logical type. Assuming [len] anyway Warning Error No database types - must have dbtypes for pthreads support Warning Error You have not documented new_SequenceBaseCoverage Warning Error You have not documented new_logodds_TransRegionModel Warning Error You have 2 undocumented functions make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cd dyc ; /usr/bin/make init make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dyc' dyc -l *.dy Warning Error You have 22 undocumented functions Warning Error You have 1 undocumented functions Warning Error You have 21 undocumented functions Warning Error You have 4 undocumented functions Warning Error You have 25 undocumented functions Warning Error You have 7 undocumented functions Warning Error You have 23 undocumented functions Warning Error You have 22 undocumented functions Warning Error You have 32 undocumented functions Warning Error You have 3 undocumented functions Warning Error You have 20 undocumented functions Warning Error You have 2 undocumented functions Warning Error You have 18 undocumented functions Warning Error You have 4 undocumented functions Warning Error You have 4 undocumented functions Warning Error You have 13 undocumented functions Warning Error You have 3 undocumented functions Warning Error You have 12 undocumented functions Warning Error You have 5 undocumented functions Warning Error You have 2 undocumented functions Warning Error You have 4 undocumented functions Warning Error You have 33 undocumented functions make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dyc' cd socket ; /usr/bin/make init make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' dyc -l -n Wise2_ -a _api.h -b _api.t -latex -perl *.dy Warning Error anonobj.dy:13: For element void - got no good default. Returning 0 Warning Error You have 5 undocumented functions Warning Error You have 3 undocumented functions Warning Error You have 4 undocumented functions Warning Error You have 8 undocumented functions Warning Error You have 4 undocumented functions Warning Error transferinterface.dy:11: For element void - got no good default. Returning 0 Warning Error transferinterface.dy:14: For element void - got no good default. Returning 0 Warning Error You have 4 undocumented functions make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' cd dnaindex ; /usr/bin/make init make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' dyc -l -n Wise2_ -pthreads -dbtrace 5 -nocwarn *.dy Warning Error assembly.dy:51: For element long - got no good default. Returning 0 Warning Error assembly.dy:52: For element long - got no good default. Returning 0 Warning Error You have 9 undocumented functions Warning Error You have 5 undocumented functions Warning Error You have 3 undocumented functions Warning Error You have 2 undocumented functions Warning Error assembly_stream_interface.dy:11: For element void - got no good default. Returning 0 Warning Error You have 19 undocumented functions Warning Error You have 16 undocumented functions Warning Error You have 6 undocumented functions Warning Error You have 3 undocumented functions Warning Error You have 22 undocumented functions Warning Error You have 15 undocumented functions Warning Error You have 6 undocumented functions Warning Error You have 10 undocumented functions Warning Error kmer_assembly_untangler.dy:24: For element long - got no good default. Returning 0 Warning Error You have 14 undocumented functions Warning Error kmer_count.dy:15: For element KmerCount - got no good default. Returning 0 Warning Error You have 2 undocumented functions Warning Error You have 5 undocumented functions Warning Error You have 8 undocumented functions Warning Error You have 7 undocumented functions Warning Error You have 1 undocumented functions Warning Error You have 2 undocumented functions Warning Error singleseqspace.dy:13: For element long - got no good default. Returning 0 Warning Error singleseqspace.dy:14: For element long - got no good default. Returning 0 Warning Error singleseqspace.dy:19: For element long - got no good default. Returning 0 Warning Error You have 4 undocumented functions make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cd network; /usr/bin/make init make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' dyc -l -n Wise2_ -a _api.h -b _api.t -latex -perl *.dy Warning Error You have 5 undocumented functions Warning Error You have 12 undocumented functions make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' ++ pkg-config --libs glib-2.0 --cflags glib-2.0 + /usr/bin/make -O -j8 'CFLAGS=-c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 ' all (cd base ; /usr/bin/make CC="cc" CFLAGS="-c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 " libwisebase.a ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wisetime.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wiserandom.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wisestreaminterface.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wiseoverlay.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wisememman.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wisefile.c wisefile.dy: In function 'Wise2_myfclose': wisefile.dy:72:18: warning: format '%d' expects argument of type 'int', but argument 3 has type 'FILE *' [-Wformat=] 72 | fprintf(stderr,"Closing %d\n",ofp); | ^~~~~~~~~~~~~~ ~~~ | | | FILE * make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 linesubs.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 commandline.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wiseerror.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 wisestring.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' ar ru libwisebase.a wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/base' (cd HMMer2 ; /usr/bin/make CC="cc" CFLAGS="-c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 " libhmmer.a ) make[1]: 'libhmmer.a' is up to date. (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 " libdyna.a ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ basematrix.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ packaln.c packaln.dy: In function 'Wise2_read_simple_PackAln': packaln.dy:88:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | fgets(buffer,MAXLINE,ifp); | ^~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ shattermatrix.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ probability.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ dnamatrix.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ alnconvert.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ alnrange.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ dprunimpl.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ complexevalset.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ dpenvelope.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ dbsearchimpl.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ matrixdebug.c matrixdebug.dy: In function 'Wise2_user_DebugMatrix': matrixdebug.dy:208:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 208 | fgets(buffer,MAXLINE,in); | ^~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ sequencestream.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ complexconsensi.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ complexsequence.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hspstream.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ seqalign.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ codon.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ aln.c aln.dy: In function 'Wise2_mapped_ascii_AlnBlock': aln.dy:867:19: warning: too many arguments for format [-Wformat-extra-args] 867 | fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); | ^~~~~~~~~~~~ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ sequence.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hitlist.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ codonmatrix.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ genericindexresult.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ codonmapper.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ compmat.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hsp.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ sequencedb.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ seqlookup.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ searchstatlookup.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ arrayseqlookup.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ searchstatinterface.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ linkedlist_lookpos.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hscore.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ singlenumberspace.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ proteindb.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ protein.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ pairbaseseq.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ randomdb.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ genomicdb.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ genomic.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ cdna.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ cdnadb.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ pairbase.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ embl.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ histogram.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ dna.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ randommodel.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ dynlibcross.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ translation.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ btcanvas.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ asciibtcanvas.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ gene.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ transcript.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ genomicregion.c genomicregion.dy: In function 'Wise2_read_EMBL_FT_into_GenomicRegion': genomicregion.dy:756:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 756 | fgets(buffer,maxlen,ifp); | ^~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 " libdyna_glib.a ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hspscaninterface.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ subseqhash.c subseqhash.dy: In function 'Wise2_is_populated_subseqhash_ghash': subseqhash.dy:111:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 111 | if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { | ^ subseqhash.dy: In function 'Wise2_lookup_subseqhash_ghash': subseqhash.dy:128:85: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 128 | return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number)); | ^ subseqhash.dy: In function 'Wise2_add_seq_subseqhash_ghash': subseqhash.dy:160:54: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 160 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^ subseqhash.dy:161:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 161 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^ subseqhash.dy: In function 'Wise2_add_direct_number_subseqhash_ghash': subseqhash.dy:188:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 188 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^ subseqhash.dy:189:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 189 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ proteinstreamedindex.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ shadowseq.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ intallocator.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ shadowseqindex.c shadowseqindex.dy: In function 'Wise2_dump_stats_ShadowSequenceIndex': shadowseqindex.dy:285:15: warning: format '%f' expects argument of type 'double', but argument 4 has type 'long unsigned int' [-Wformat=] 285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long unsigned int make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hspscanruntime.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hsphandler.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ proteinindexcons.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hsplookupscan.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hspthreadeddb.c hspthreadeddb.dy: In function 'Wise2_threadeddb_scan_worker': hspthreadeddb.dy:154:77: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ^ hspthreadeddb.dy:154:18: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Wise2_HSPDatabaseSegment *' [-Wformat=] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ | | | Wise2_HSPDatabaseSegment * make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hsp2hitscan.c hsp2hitscan.dy: In function 'Wise2_one_off_two_hit_HSPscan_query_direct': hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' {aka 'long int'} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' {aka 'long int'} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' {aka 'long int'} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' {aka 'long int'} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 4 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=] hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=] make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ staticseq.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hsplookupthreaded.c hsplookupthreaded.dy: In function 'Wise2_one_off_ordered_HSPscan_scan_query_direct': hsplookupthreaded.dy:263:18: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 263 | fprintf(stderr,"retrieved array with %d elements\n",current_oph); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ | | | long int make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ dnaindexcons.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ hsptwohitscan.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc' (cd external ; /usr/bin/make CC="cc" CFLAGS="-c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 " all ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/external' (cd mott; make CC="cc" CFLAGS="-c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 " all) make[2]: Nothing to be done for 'all'. make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/external' (cd socket ; /usr/bin/make CC="cc" CFLAGS="-c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 " libwisesocket.a ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ directsocketwrite.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ anonobj.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ transferinterface.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ functionclient.c functionclient.dy: In function 'Wise2_new_FunctionProxyCoordinator': functionclient.dy:193:24: warning: passing argument 2 of 'connect' from incompatible pointer type [-Wincompatible-pointer-types] 193 | connect(out->socket, &server, sizeof(server)); | ^~~~~~~ | | | struct sockaddr_in * In file included from functionclient.c:7: /usr/include/sys/socket.h:126:52: note: expected 'const struct sockaddr *' but argument is of type 'struct sockaddr_in *' 126 | extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t __len); | ^ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ functionserver.c functionserver.dy: In function 'Wise2_main_loop_forking_FunctionServer': functionserver.dy:129:4: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 129 | write(new_socket,buf,9); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:141:2: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 141 | write(new_socket,buf,6); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:183:2: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 183 | write(new_socket,buf,5); | ^~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/socket' (cd dnaindex ; /usr/bin/make CC="cc" CFLAGS="-c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 " all ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models dnamapping.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_count.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c kmer_hash.dy: In function 'Wise2_free_KmerHashIndex': kmer_hash.dy:318:19: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 318 | fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer); | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_hash.dy:319:19: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 319 | fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | kmer_t {aka long long int} make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c kmer_assembly.dy: In function 'Wise2_show_KmerAssemblyNode': kmer_assembly.dy:296:15: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 296 | fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy:302:17: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 302 | fprintf(ofp," ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy:309:17: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 309 | fprintf(ofp," ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy: In function 'Wise2_remove_sequence_label_KmerAssemblyLink': kmer_assembly.dy:365:18: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'KmerAssemblyLink *' [-Wformat=] 365 | fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ | | | KmerAssemblyLink * kmer_assembly.dy:367:20: warning: format '%d' expects a matching 'int' argument [-Wformat=] 367 | fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy: In function 'Wise2_add_direct_number_CompressedProteinIndex': compressed_protein_index.dy:223:10: warning: returning 'void *' from a function with return type 'boolean' {aka 'int'} makes integer from pointer without a cast [-Wint-conversion] 223 | return NULL; | ^~~~ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c kmer_assembly_error.dy: In function 'Wise2_mark_tangles_KmerAssembly': kmer_assembly_error.dy:93:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 93 | fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_error.dy:105:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 105 | fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_error.dy: In function 'Wise2_extend_indel_path_KmerAssembly': kmer_assembly_error.dy:351:17: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int *' [-Wformat=] 351 | fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | int * make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c kmer_assembly_untangler.dy: In function 'Wise2_show_KmerAssemblyPath': kmer_assembly_untangler.dy:52:65: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 52 | fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base); | ^ kmer_assembly_untangler.dy: In function 'Wise2_untangle_KmerAssembly': kmer_assembly_untangler.dy:120:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 120 | fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:141:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:141:22: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'kmer_t' {aka 'long long int'} [-Wformat=] kmer_assembly_untangler.dy:157:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 157 | fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:159:22: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 159 | fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy: In function 'Wise2_old_attempt_forward_untangle_KmerAssembly': kmer_assembly_untangler.dy:444:20: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 444 | fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:568:75: warning: passing argument 4 of 'Wise2_lift_backward_tangled_tail' from incompatible pointer type [-Wincompatible-pointer-types] 568 | lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); | ^~~~~~~~~~~~~~~~~ | | | long int * In file included from kmer_assembly_untangler.c:4: kmer_assembly_untangler.h:174:116: note: expected 'int *' but argument is of type 'long int *' 174 | void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); | ~~~~~~^~~~~~~~~~~ kmer_assembly_untangler.dy: In function 'Wise2_lift_forward_tangled_KmerAssemblyPath': kmer_assembly_untangler.dy:746:20: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'kmer_t' {aka 'long long int'} [-Wformat=] 746 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:746:20: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'kmer_t' {aka 'long long int'} [-Wformat=] make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ -I../models assembly.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dnaindex' (cd network ; /usr/bin/make CC="cc" CFLAGS="-c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 " all ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' cc -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` -lpthread make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/network' (cd models ; /usr/bin/make CC="cc" CFLAGS="-c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 " EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ seqaligndisplay.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ sw_wrap.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ dbadisplay.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ geneparser21.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ geneparameter.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ slimdba.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ abc.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ proteinsw.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ dnaalign.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genestats.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ geneoutput.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ pba.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ splicesitemodeler.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genewisehsp.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ geneutil.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ dba.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genefrequency.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ threestatemodel.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ bigdba.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ gwlite.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ geneloop6.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ gwlitemodel.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genewise4.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genestretch6.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genephase6.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ estwrap.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ gwrap.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ cdparser.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ matchsum.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genedisplay.c genedisplay.dy: In function 'Wise2_write_intron_desc': genedisplay.dy:493:20: warning: too many arguments for format [-Wformat-extra-args] 493 | sprintf(buffer," Intron ??? ",in_number); | ^~~~~~~~~~~~~~~~ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genewisemodel.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genewise6.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ phasemodel.c phasemodel.dy: In function 'Wise2_read_fasta_PhasedProtein': phasemodel.dy:241:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fgets(name,10000,ifp); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from ../base/wisebase.h:6, from ../dynlibsrc/probability.h:7, from geneparser21.h:6, from genewisemodel.h:6, from phasemodel.h:6, from phasemodel.c:4: In function 'fgets', inlined from 'Wise2_read_fasta_PhasedProtein' at phasemodel.dy:241:3: /usr/include/bits/stdio2.h:263:9: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 263 | return __fgets_chk_warn (__s, __bos (__s), __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ gwquickdb.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ threestatedb.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ pfamhmmer1db.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ pwmdna.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ estslimloop.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genewisemodeldb.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ standardout.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ geneparser4.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ estslim3.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ seqhit.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ estfrag3.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genomewise.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ estwise3.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ geneloop21.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ estloop3.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ genome_evidence.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ sywise.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ est_evidence.c est_evidence.dy: In function 'Wise2_new_est_GenomeEvidenceUnit': est_evidence.dy:142:16: warning: assignment to 'int (*)(void *)' from incompatible pointer type 'Wise2_EstEvidence * (*)(Wise2_EstEvidence *)' [-Wincompatible-pointer-types] 142 | in->geu_free = free_EstEvidence; | ^ make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ syexonmodel.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ pseudowise.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ estquick3.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ localcispara.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models' cc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -fasynchronous-unwind-tables -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0 -I../base/ -I../dynlibsrc/ motifmatrix.c motifmatrix.c: In function 'Wise2_MotifConsMatrix_alloc_matrix': motifmatrix.c:408:24: warning: assignment to 'char' from 'void *' makes integer from pointer without a cast [-Wint-conversion] 408 | for(i=0;i