D: [iurt_root_command] chroot
warning: Found bdb_ro Packages database while attempting sqlite backend: using bdb_ro backend.
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.mga9.src.rpm
Building target platforms: aarch64
Building for target aarch64
Executing(%prep): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.CIySED
+ 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 -f
+ /usr/bin/cat /home/iurt/rpmbuild/SOURCES/wise2.4.1-replace-isnumber.patch
+ /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch -f
+ /usr/bin/cat /home/iurt/rpmbuild/SOURCES/wise2.4.1-fix-makefile.patch
+ /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch -f
+ /usr/bin/cat /home/iurt/rpmbuild/SOURCES/wise2.4.1-clean-makefile.patch
+ /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch -f
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.n3EjLS
+ 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  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  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  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  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  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  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 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 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 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;
      |            ^~~~~~
prior.c:10:1: note: include '<string.h>' or provide a declaration of 'strcmp'
    9 | #include "funcs.h"
  +++ |+#include <string.h>
   10 | #include "squid.h"
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
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(cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-c -O3  `pkg-config --cflags glib-2.0 --libs glib-2.0`" libdyna.a )
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cc -c -O3  -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0  -I../base/ basematrix.c
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cc -c -O3  -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0  -I../base/ codonmapper.c
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cc -c -O3  -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -lglib-2.0  -I../base/ searchstatinterface.c
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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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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:5:1: note: include '<stdlib.h>' or provide a declaration of 'free'
    4 | #include"gapstat.h"
  +++ |+#include <stdlib.h>
    5 | 
mott_api.c:64:3: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch]
   64 |   free(freq0);
      |   ^~~~
mott_api.c:64:3: note: include '<stdlib.h>' or provide a declaration of 'free'
mott_api.c: In function 'SW_PValueMott':
mott_api.c:104:7: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch]
  104 |       free(freqA);
      |       ^~~~
mott_api.c:104:7: note: include '<stdlib.h>' 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' [-Wbuiltin-declaration-mismatch]
  144 |     free(h+hmin);
      |     ^~~~
mott_api.c:144:5: note: include '<stdlib.h>' or provide a declaration of 'free'
mott_api.c:155:5: warning: incompatible implicit declaration of built-in function 'free' [-Wbuiltin-declaration-mismatch]
  155 |     free(h+hmin);
      |     ^~~~
mott_api.c:155:5: note: include '<stdlib.h>' 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: note: include '<stdlib.h>' or provide a declaration of 'calloc'
mott_api.c:179:16: warning: incompatible implicit declaration of built-in function 'calloc' [-Wbuiltin-declaration-mismatch]
mott_api.c:179:16: note: include '<stdlib.h>' 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:5:1: note: include '<ctype.h>' or provide a declaration of 'toupper'
    4 | #include"gapstat.h"
  +++ |+#include <ctype.h>
    5 | 
mott_api.c: In function 'RobinsonResidueFrequencies2':
mott_api.c:230:27: warning: incompatible implicit declaration of built-in function 'calloc' [-Wbuiltin-declaration-mismatch]
  230 |   double *freq = (double*)calloc(256, sizeof(double));
      |                           ^~~~~~
mott_api.c:230:27: note: include '<stdlib.h>' 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/ 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'
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'
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 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 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_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 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 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 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 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 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_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 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 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:568:82: 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 -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'
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'
(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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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/ 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'
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/ 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/ 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/ 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 -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/ 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/ 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/ type.c
cc -pthread -c -g  -DUNIX  -I../base/ -I../base/ module.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/ 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/ friend.c
cc -pthread -c -g  -DUNIX  -I../base/ -I../base/ dynadb.c
cc -pthread -c -g  -DUNIX  -I../base/ -I../base/ wisec.c
cc -pthread -c -g  -DUNIX  -I../base/ -I../base/ variable.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/ ftext.c
cc -pthread -c -g  -DUNIX  -I../base/ -I../base/ labelmaster.c
cc -pthread -c -g  -DUNIX  -I../base/ -I../base/ dyna2.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/ display.c
cc -pthread -c -g  -DUNIX  -I../base/ -I../base/ docugen.c
cc -pthread -c -g  -DUNIX  -I../base/ -I../base/ exprtree.c
cc -pthread -c -g  -DUNIX  -I../base/ -I../base/ api.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/ dpimpl.c
cc -pthread -c -g  -DUNIX  -I../base/ -I../base/ telegraph.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/ probal.c
cc -pthread -c -g  -DUNIX  -I../base/ -I../base/ dbthread.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:1033:17: 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  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  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  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  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  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  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
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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
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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
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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
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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
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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);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~
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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
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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
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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
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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
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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
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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
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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
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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);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~
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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
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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
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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
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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);
      |                   ^~~~~~~~~~~~
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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
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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
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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
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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
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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
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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
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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'
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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/ histogram.c
make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/dynlibsrc'
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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'
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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'
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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/ 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/ 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'
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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/ 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/ 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/ 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/ 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/ 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'
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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/ 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=]
  209 |   fprintf(stderr,"START %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
  210 |           use.ru_utime.tv_sec,
  211 |           use.ru_utime.tv_sec/1000,
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=]
  209 |   fprintf(stderr,"START %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  212 |           use.ru_stime.tv_sec,
      |           ~~~~~~~~~~~~~~~~~~~
      |                       |
      |                       __time_t {aka long int}
hsp2hitscan.dy:209:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=]
  209 |   fprintf(stderr,"START %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  213 |           use.ru_stime.tv_sec/1000
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
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=]
  273 |   fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  274 |           use.ru_utime.tv_sec,
  275 |           use.ru_utime.tv_sec/1000,
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=]
  273 |   fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  276 |           use.ru_stime.tv_sec,
      |           ~~~~~~~~~~~~~~~~~~~
      |                       |
      |                       __time_t {aka long int}
hsp2hitscan.dy:273:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=]
  273 |   fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  277 |           use.ru_stime.tv_sec/1000
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
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=]
  286 |   fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  287 |           use.ru_utime.tv_sec,
  288 |           use.ru_utime.tv_sec/1000,
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=]
  286 |   fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  289 |           use.ru_stime.tv_sec,
      |           ~~~~~~~~~~~~~~~~~~~
      |                       |
      |                       __time_t {aka long int}
hsp2hitscan.dy:286:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=]
  286 |   fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  290 |           use.ru_stime.tv_sec/1000
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
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=]
  302 |   fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  303 |           use.ru_utime.tv_sec,
  304 |           use.ru_utime.tv_sec/1000,
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' {aka 'long int'} [-Wformat=]
  302 |   fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  305 |           use.ru_stime.tv_sec,
      |           ~~~~~~~~~~~~~~~~~~~
      |                       |
      |                       __time_t {aka long int}
hsp2hitscan.dy:302:18: warning: format '%d' expects argument of type 'int', but argument 6 has type '__time_t' {aka 'long int'} [-Wformat=]
  302 |   fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  306 |           use.ru_stime.tv_sec/1000
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka 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/ 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/ 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/ functionserver.c
functionserver.dy: In function 'Wise2_main_loop_forking_FunctionServer':
functionserver.dy:129:11: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
  129 |           write(new_socket,buf,9);
      |           ^~~~~~~~~~~~~~~~~~~~~~~
functionserver.dy:141:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result]
  141 |         write(new_socket,buf,6);
      |         ^~~~~~~~~~~~~~~~~~~~~~~
functionserver.dy:183:9: 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'
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'
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'
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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'
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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'
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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 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 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 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_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 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 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_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 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 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 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:351:24: 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 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_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=]
  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: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:568:82: 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=]
  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}
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'
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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/ sw_wrap.c
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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:866,
                 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:270:16: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  270 |         return __fgets_chk_warn (__s, __glibc_objsize (__s), __n, __stream);
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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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);
      |                    ^~~~~~~~~~~~~~~~
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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.
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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/ 
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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
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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
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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
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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
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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/
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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
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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
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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;
      |                ^
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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
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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
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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
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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
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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
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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
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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<leni;i++)  {
      |                        ^
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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/ transfactor.c
transfactor.dy: In function 'Wise2_read_ben_IUPAC_TransFactorSet':
transfactor.dy:680:21: warning: '%s' directive writing up to 511 bytes into a region of size between 495 and 504 [-Wformat-overflow=]
  680 |     sprintf(sbuffer,"motif_%d_%s",motif_no,buffer);
      |                     ^~~~~~~~~~~~~          ~~~~~~
In file included from /usr/include/stdio.h:866,
                 from ../base/wisebase.h:6,
                 from pwmdna.h:6,
                 from transfactor.h:6,
                 from transfactor.c:4:
/usr/include/bits/stdio2.h:38:10: note: '__builtin___sprintf_chk' output between 9 and 529 bytes into a destination of size 512
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   40 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
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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/ pairwiseshortdna.c
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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/ motifmatrixdp.c
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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/  -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c 
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cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
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cc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o   -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
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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` hsp2aln_sw.c
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cc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
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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/ localdba.c
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cc -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../network/net_hspscan.o ../network/client_multihspscan.o  -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  -lm -lpthread 
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cc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
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cc -g -o promoterwise promoterwise.o localdba.o  localcishit.o localcispara.o dbadisplay.o  motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o  pairwiseshortdna.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm `pkg-config --libs glib-2.0` -lpthread
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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/ genewise21.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'
ar ru libmodel.a geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o 
ar: creating libmodel.a
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 -g -o estwise estwise.o  geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o  -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase  -lm
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 -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o  -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  -lm
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 -g -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o   -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase  -lm
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 -g -o genewisedb genewisedb.o  geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o   -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase  -lm 
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/ genomewise9.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 -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
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/ pseudowise7.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 -g -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o  -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase  -lm
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/ sywise20.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 -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o  standardout.o geneutil.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src/models'
/usr/bin/make bin
make[1]: Entering directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src'
mkdir bin
cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin
make[1]: Leaving directory '/home/iurt/rpmbuild/BUILD/wise2.4.1/src'
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.tGcI3G
+ umask 022
+ cd /home/iurt/rpmbuild/BUILD
+ '[' 1 -eq 1 ']'
+ '[' /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64 '!=' / ']'
+ rm -rf /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64
++ dirname /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64
+ mkdir -p /home/iurt/rpmbuild/BUILDROOT
+ mkdir /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64
+ cd wise2.4.1
+ '[' 1 -eq 1 ']'
+ install -d -m 755 /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/bin
+ install -m 755 src/models/pswdb src/models/psw src/models/genewisedb src/models/estwisedb src/models/estwise src/models/genewise src/models/dba src/models/dnal src/models/genomewise /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/bin
+ install -d -m 755 /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/share/wise
+ install -m 644 wisecfg/BLOSUM30.bla wisecfg/BLOSUM45.bla wisecfg/BLOSUM62.bla wisecfg/BLOSUM80.bla wisecfg/aa.rnd wisecfg/cb.tmf wisecfg/codon.martian wisecfg/codon.table wisecfg/gene.stat wisecfg/gon120.bla wisecfg/gon160.bla wisecfg/gon200.bla wisecfg/gon250.bla wisecfg/gon350.bla wisecfg/human.gf wisecfg/human.gp wisecfg/human.stats wisecfg/idenity.bla wisecfg/methods wisecfg/pb.gf wisecfg/pombe.gf wisecfg/tm.pri wisecfg/wag55 wisecfg/wag65 wisecfg/wag75 wisecfg/wag85 wisecfg/wise.2 wisecfg/wise.per wisecfg/worm.gf /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/share/wise
+ install -d -m 755 /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/etc/profile.d
+ echo 'export WISECONFIGDIR=/usr/share/wise'
+ echo 'setenv WISECONFIGDIR /usr/share/wise'
+ /usr/bin/find-debuginfo -j8 --strict-build-id -m -i --build-id-seed 2.4.1-9.mga9 --unique-debug-suffix -2.4.1-9.mga9.aarch64 --unique-debug-src-base wise2-2.4.1-9.mga9.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /home/iurt/rpmbuild/BUILD/wise2.4.1

extracting debug info from /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/bin/dba
extracting debug info from /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/bin/dnal
extracting debug info from /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/bin/estwise
extracting debug info from /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/bin/genewisedb
extracting debug info from /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/bin/estwisedb
extracting debug info from /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/bin/genewise
extracting debug info from /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/bin/genomewise
extracting debug info from /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/bin/psw
extracting debug info from /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/bin/pswdb
dwz: ./usr/bin/dba-2.4.1-9.mga9.aarch64.debug: Unknown debugging section .debug_line_str
dwz: ./usr/bin/dnal-2.4.1-9.mga9.aarch64.debug: Unknown debugging section .debug_line_str
dwz: ./usr/bin/estwise-2.4.1-9.mga9.aarch64.debug: Unknown debugging section .debug_line_str
dwz: ./usr/bin/estwisedb-2.4.1-9.mga9.aarch64.debug: Unknown debugging section .debug_line_str
dwz: ./usr/bin/genewise-2.4.1-9.mga9.aarch64.debug: Unknown debugging section .debug_line_str
dwz: ./usr/bin/genewisedb-2.4.1-9.mga9.aarch64.debug: Unknown debugging section .debug_line_str
dwz: ./usr/bin/genomewise-2.4.1-9.mga9.aarch64.debug: Unknown debugging section .debug_line_str
dwz: ./usr/bin/psw-2.4.1-9.mga9.aarch64.debug: Unknown debugging section .debug_line_str
dwz: ./usr/bin/pswdb-2.4.1-9.mga9.aarch64.debug: Unknown debugging section .debug_line_str
dwz: Too few files for multifile optimization
original debug info size: 21540kB, size after compression: 21540kB
/usr/bin/sepdebugcrcfix: Updated 0 CRC32s, 9 CRC32s did match.
19827 blocks
+ /usr/lib/rpm/check-buildroot
+ '[' -n '' ']'
+ /usr/share/spec-helper/clean_files
+ '[' -n '' ']'
+ /usr/share/spec-helper/compress_files .xz
+ '[' -n '' ']'
+ /usr/share/spec-helper/relink_symlinks
+ '[' -n '' ']'
+ /usr/share/spec-helper/clean_perl
+ '[' -n '' ']'
+ /usr/share/spec-helper/lib_symlinks
+ '[' -n '' ']'
+ /usr/share/spec-helper/gprintify
+ '[' -n '' ']'
+ /usr/share/spec-helper/fix_mo
+ '[' -n '' ']'
+ /usr/share/spec-helper/fix_pamd
+ '[' -n '' ']'
+ /usr/share/spec-helper/remove_info_dir
+ '[' -n '' ']'
+ /usr/share/spec-helper/fix_eol
+ '[' -n '' ']'
+ /usr/share/spec-helper/check_desktop_files
+ '[' -n '' ']'
+ /usr/share/spec-helper/check_elf_files
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python3 1 0
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
*** WARNING: ./usr/src/debug/wise2-2.4.1-9.mga9.aarch64/src/base/wisetime.dy is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/wise2-2.4.1-9.mga9.aarch64/src/base/wiseoverlay.dy is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/wise2-2.4.1-9.mga9.aarch64/src/base/wisememman.dy is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/wise2-2.4.1-9.mga9.aarch64/src/base/wisefile.dy is executable but has no shebang, removing executable bit
Processing files: wise2-2.4.1-9.mga9.aarch64
Executing(%doc): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.GzeYf6
+ umask 022
+ cd /home/iurt/rpmbuild/BUILD
+ cd wise2.4.1
+ DOCDIR=/home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/share/doc/wise2
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/share/doc/wise2
+ cp -pr README /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/share/doc/wise2
+ cp -pr LICENSE /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/share/doc/wise2
+ cp -pr docs /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64/usr/share/doc/wise2
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: config(wise2) = 2.4.1-9.mga9 wise2 = 2.4.1-9.mga9 wise2(aarch-64) = 2.4.1-9.mga9
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libglib-2.0.so.0()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.17)(64bit)
Obsoletes: wise = 2.4.1-3.mga5
Processing files: wise2-debugsource-2.4.1-9.mga9.aarch64
Provides: wise2-debugsource = 2.4.1-9.mga9 wise2-debugsource(aarch-64) = 2.4.1-9.mga9
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: wise2-debuginfo-2.4.1-9.mga9.aarch64
Provides: debuginfo(build-id) = 0fedea868d33fef90cc06e32f442b15672eb0916 debuginfo(build-id) = 38ef0389483c5ef4eb99dd021682706ab6650877 debuginfo(build-id) = 484c4a7ddf4d3cab0b4be0ebdc8c5a6889cf020c debuginfo(build-id) = 6185890dc0ce74ff538d73e8329140b3e0fc33d1 debuginfo(build-id) = c6fd6d0b32c3ed7553318907e090dfbdd217af4b debuginfo(build-id) = c86c7d750cbc215e0b1350ee2a668c724e5a396b debuginfo(build-id) = edaff2dadeda893934cfa4ac501dae769f3274a1 debuginfo(build-id) = eec101731308aac3584f7baa88e04b5021f4b0d9 debuginfo(build-id) = fb46f6cee71b8390aaef64c975d0610444423f92 wise2-debuginfo = 2.4.1-9.mga9 wise2-debuginfo(aarch-64) = 2.4.1-9.mga9
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: wise2-debugsource(aarch-64) = 2.4.1-9.mga9
Checking for unpackaged file(s): /usr/lib/rpm/check-files /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64
Wrote: /home/iurt/rpmbuild/RPMS/aarch64/wise2-2.4.1-9.mga9.aarch64.rpm
Wrote: /home/iurt/rpmbuild/RPMS/aarch64/wise2-debugsource-2.4.1-9.mga9.aarch64.rpm
Wrote: /home/iurt/rpmbuild/RPMS/aarch64/wise2-debuginfo-2.4.1-9.mga9.aarch64.rpm
Executing(%clean): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.yVVrMI
+ umask 022
+ cd /home/iurt/rpmbuild/BUILD
+ cd wise2.4.1
+ /usr/bin/rm -rf /home/iurt/rpmbuild/BUILDROOT/wise2-2.4.1-9.mga9.aarch64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(--clean): /bin/sh -e /home/iurt/rpmbuild/tmp/rpm-tmp.HNPxxu
+ umask 022
+ cd /home/iurt/rpmbuild/BUILD
+ rm -rf wise2.4.1
+ RPM_EC=0
++ jobs -p
+ exit 0
D: [iurt_root_command] Success!