Mock Version: 3.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target x86_64 --nodeps /builddir/build/SPECS/mafft.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1684275155.938974/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f42e9e6fad0>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.7x6rfrw0:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.7x6rfrw0:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'abbb6a1a56e84c0ebe545b230ecd0558', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1684275155.938974/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.7x6rfrw0:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target x86_64 --nodeps /builddir/build/SPECS/mafft.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
error: %changelog not in descending chronological order
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1684195200
Wrote: /builddir/build/SRPMS/mafft-7.520-1.20230516221152439026.pr1.fc39.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target x86_64 --nodeps /builddir/build/SPECS/mafft.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1684275155.938974/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f42e9e6fad0>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.7x6rfrw0:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.7x6rfrw0:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '7943032449c5413ebe53bd3332cf69bd', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1684275155.938974/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.7x6rfrw0:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target x86_64 --nodeps /builddir/build/SPECS/mafft.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
error: %changelog not in descending chronological order
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1684195200
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.ca3i7e
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf mafft-v7.520
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/mafft-7.520.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd mafft-v7.520
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.z2OUIQ
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd mafft-v7.520
+ cd core
+ make clean
rm -f *.o *.a *.exe *~ mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  mafft mafft-homologs.rb mafft-sparsecore.rb libdisttbfast.so libdisttbfast.dylib libdisttbfast.dll *.gcda *.gcno 
+ make 'CFLAGS=-fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
cp mafftash_premafft.tmpl mafftash_premafft.pl
cp seekquencer_premafft.tmpl seekquencer_premafft.pl
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c mtxutl.c
mtxutl.c: In function 'FreeFloatHalfMtx':
mtxutl.c:207:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  207 |                 if( mtx[i] ) FreeFloatVec( mtx[i] ); mtx[i] = NULL;
      |                 ^~
mtxutl.c:207:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  207 |                 if( mtx[i] ) FreeFloatVec( mtx[i] ); mtx[i] = NULL;
      |                                                      ^~~
mtxutl.c: In function 'FreeFloatMtx':
mtxutl.c:217:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  217 |                 if( mtx[i] ) FreeFloatVec( mtx[i] ); mtx[i] = NULL;
      |                 ^~
mtxutl.c:217:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  217 |                 if( mtx[i] ) FreeFloatVec( mtx[i] ); mtx[i] = NULL;
      |                                                      ^~~
mtxutl.c: In function 'FreeIntMtx':
mtxutl.c:396:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  396 |                 if( mtx[i] ) free( (char *)mtx[i] ); mtx[i] = NULL;
      |                 ^~
mtxutl.c:396:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  396 |                 if( mtx[i] ) free( (char *)mtx[i] ); mtx[i] = NULL;
      |                                                      ^~~
mtxutl.c: In function 'FreeIntCub':
mtxutl.c:460:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  460 |                 if( cub[i] ) FreeIntMtx( cub[i] ); cub[i] = NULL;
      |                 ^~
mtxutl.c:460:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  460 |                 if( cub[i] ) FreeIntMtx( cub[i] ); cub[i] = NULL;
      |                                                    ^~~
mtxutl.c: In function 'FreeDoubleHalfMtx':
mtxutl.c:515:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  515 |                 if( mtx[i] ) FreeFloatVec( mtx[i] ); mtx[i] = NULL;
      |                 ^~
mtxutl.c:515:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  515 |                 if( mtx[i] ) FreeFloatVec( mtx[i] ); mtx[i] = NULL;
      |                                                      ^~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c io.c
io.c: In function 'putlocalhom_str':
io.c:677:13: warning: variable 'sumoverlap' set but not used [-Wunused-but-set-variable]
  677 |         int sumoverlap;
      |             ^~~~~~~~~~
io.c:676:13: warning: variable 'isumscore' set but not used [-Wunused-but-set-variable]
  676 |         int isumscore;
      |             ^~~~~~~~~
io.c: In function 'Read':
io.c:1155:42: warning: argument 2 of type 'char[500000][256]' with mismatched bound [-Warray-parameter=]
 1155 |         extern void FRead( FILE *x, char y[M][B], int z[M], char **w );
      |                                     ~~~~~^~~~~~~
In file included from mltaln.h:344,
                 from io.c:1:
functions.h:201:35: note: previously declared as 'char[][256]'
  201 | extern void FRead( FILE *fp, char name[][B], int nlen[], char **seq );
      |                              ~~~~~^~~~~~~~~
io.c:1155:55: warning: argument 3 of type 'int[500000]' with mismatched bound [-Warray-parameter=]
 1155 |         extern void FRead( FILE *x, char y[M][B], int z[M], char **w );
      |                                                   ~~~~^~~~
functions.h:201:50: note: previously declared as 'int[]'
  201 | extern void FRead( FILE *fp, char name[][B], int nlen[], char **seq );
      |                                              ~~~~^~~~~~
io.c: In function 'ReadBlastm7_avscore':
io.c:3173:13: warning: variable 'nlocalhom' set but not used [-Wunused-but-set-variable]
 3173 |         int nlocalhom;
      |             ^~~~~~~~~
io.c:3170:35: warning: variable 'tend' set but not used [-Wunused-but-set-variable]
 3170 |         int qstart, qend, tstart, tend;
      |                                   ^~~~
io.c:3170:27: warning: variable 'tstart' set but not used [-Wunused-but-set-variable]
 3170 |         int qstart, qend, tstart, tend;
      |                           ^~~~~~
io.c:3170:21: warning: variable 'qend' set but not used [-Wunused-but-set-variable]
 3170 |         int qstart, qend, tstart, tend;
      |                     ^~~~
io.c:3170:13: warning: variable 'qstart' set but not used [-Wunused-but-set-variable]
 3170 |         int qstart, qend, tstart, tend;
      |             ^~~~~~
io.c: In function 'ReadBlastm7_scoreonly':
io.c:3299:13: warning: variable 'nlocalhom' set but not used [-Wunused-but-set-variable]
 3299 |         int nlocalhom;
      |             ^~~~~~~~~
io.c:3297:35: warning: variable 'tend' set but not used [-Wunused-but-set-variable]
 3297 |         int qstart, qend, tstart, tend;
      |                                   ^~~~
io.c:3297:27: warning: variable 'tstart' set but not used [-Wunused-but-set-variable]
 3297 |         int qstart, qend, tstart, tend;
      |                           ^~~~~~
io.c:3297:21: warning: variable 'qend' set but not used [-Wunused-but-set-variable]
 3297 |         int qstart, qend, tstart, tend;
      |                     ^~~~
io.c:3297:13: warning: variable 'qstart' set but not used [-Wunused-but-set-variable]
 3297 |         int qstart, qend, tstart, tend;
      |             ^~~~~~
io.c:3295:13: warning: variable 'overlapaa' set but not used [-Wunused-but-set-variable]
 3295 |         int overlapaa;
      |             ^~~~~~~~~
io.c: In function 'ReadBlastm7':
io.c:3414:35: warning: variable 'tend' set but not used [-Wunused-but-set-variable]
 3414 |         int qstart, qend, tstart, tend;
      |                                   ^~~~
io.c:3414:21: warning: variable 'qend' set but not used [-Wunused-but-set-variable]
 3414 |         int qstart, qend, tstart, tend;
      |                     ^~~~
io.c: In function 'codon2id':
io.c:6427:28: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
 6427 |         if( id0 < 0 || id1 < 0 | id2 < 0 ) return( -1 );
      |                        ~~~~^~~
io.c:6422:28: warning: unused variable 'id' [-Wunused-variable]
 6422 |         int id0, id1, id2, id;
      |                            ^~
io.c: In function 'PreRead':
io.c:1120:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1120 |         fgets( b, B-1, fp ); *locnjob = atoi( b );
      |         ^~~~~~~~~~~~~~~~~~~
io.c:1125:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1125 |                 fgets( b, B-1, fp );
      |                 ^~~~~~~~~~~~~~~~~~~
io.c:1129:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1129 |                         fgets( b, B-1, fp ); nleni = atoi( b );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'FRead':
io.c:1165:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1165 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c:1255:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1255 |                 fgets( b, B-1, fp ); nlen[i] = atoi( b );      /* seq i no nagasa */
      |                 ^~~~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_doublehalf_part_pointer':
io.c:2708:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2708 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c:2710:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2710 |     fgets( b, B, fp ); nseq0 = atoi( b );  // 2020/Oct/23
      |     ^~~~~~~~~~~~~~~~~
io.c:2716:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2716 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_doublehalf_pointer':
io.c:2746:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2746 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c:2747:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2747 |     fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 )
      |     ^~~~~~~~~~~~~~~~~
io.c:2752:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2752 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_doublehalf':
io.c:2780:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2780 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c:2781:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2781 |     fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
      |     ^~~~~~~~~~~~~~~~~
io.c:2782:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2782 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_double':
io.c:2810:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2810 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c:2811:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2811 |     fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
      |     ^~~~~~~~~~~~~~~~~
io.c:2812:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2812 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_int':
io.c:2840:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2840 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c:2841:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2841 |     fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
      |     ^~~~~~~~~~~~~~~~~
io.c:2842:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2842 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_pointer':
io.c:2871:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2871 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c:2872:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2872 |     fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
      |     ^~~~~~~~~~~~~~~~~
io.c:2873:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2873 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2':
io.c:2901:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2901 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c:2902:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2902 |     fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
      |     ^~~~~~~~~~~~~~~~~
io.c:2903:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2903 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta_sub':
io.c:3103:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3103 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c:3118:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3118 |             fgets( b, B-1, fp );
      |             ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadSsearch':
io.c:3137:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3137 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadBlastm7_avscore':
io.c:3265:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3265 |                 fgets( b, B-1, fp );
      |                 ^~~~~~~~~~~~~~~~~~~
io.c:3272:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3272 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c:3273:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3273 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadBlastm7_scoreonly':
io.c:3388:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3388 |                 fgets( b, B-1, fp );
      |                 ^~~~~~~~~~~~~~~~~~~
io.c:3395:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3395 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c:3396:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3396 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadBlastm7':
io.c:3506:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3506 |                 fgets( b, B-1, fp );
      |                 ^~~~~~~~~~~~~~~~~~~
io.c:3513:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3513 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c:3514:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3514 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34noalign':
io.c:3538:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3538 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10_nuc':
io.c:3575:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3575 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c:3601:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3601 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10':
io.c:3714:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3714 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c:3738:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3738 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10_scoreonly_nucbk':
io.c:3841:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3841 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10_scoreonly_nuc':
io.c:3891:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3891 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10_scoreonly':
io.c:3952:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3952 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34':
io.c:4008:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4008 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c:4034:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4034 |                 fgets( b, B-1, fp ); // initn:
      |                 ^~~~~~~~~~~~~~~~~~~
io.c:4037:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4037 |                 fgets( b, B-1, fp ); // Smith-Waterman score
      |                 ^~~~~~~~~~~~~~~~~~~
io.c:4049:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4049 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta3':
io.c:4071:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4071 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta':
io.c:4096:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4096 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadOpt':
io.c:4133:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4133 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadOpt2':
io.c:4154:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4154 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'readOtherOptions':
io.c:4250:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4250 |                 fgets( b, B-1, fp );
      |                 ^~~~~~~~~~~~~~~~~~~
io.c: In function 'loadaamtx':
io.c:5509:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5509 |                 fgets( inorder, 999, mf );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~
io.c:5541:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5541 |                 fgets( line, 999, mf );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c:5564:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5564 |                 fgets( line, 999, mf );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'readsubalignmentstable':
io.c:5720:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5720 |                         fgets( line, linelen-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
io.c:5741:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5741 |                         fgets( line, linelen-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'readmccaskill':
io.c:5795:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5795 |         fgets( gett, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~
io.c:5805:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5805 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'readpairfoldalign':
io.c:5864:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5864 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c:5877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5877 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c:5884:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5884 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c:5898:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5898 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c:5904:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5904 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'readexternalanchors':
io.c:6342:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 6342 |                 fgets( buf, 9999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c mltaln9.c
mltaln9.c: In function 'score_calc5':
mltaln9.c:482:12: warning: variable 'c' set but not used [-Wunused-but-set-variable]
  482 |     double c;
      |            ^
mltaln9.c: In function 'setnearest_double_fullmtx':
mltaln9.c:1447:18: warning: variable 'effptpt' set but not used [-Wunused-but-set-variable]
 1447 |         double **effptpt;
      |                  ^~~~~~~
mltaln9.c: In function 'loadtree':
mltaln9.c:2494:46: warning: variable 'maxijm' set but not used [-Wunused-but-set-variable]
 2494 |         int i, j, k, miniim, maxiim, minijm, maxijm;
      |                                              ^~~~~~
mltaln9.c:2494:38: warning: variable 'minijm' set but not used [-Wunused-but-set-variable]
 2494 |         int i, j, k, miniim, maxiim, minijm, maxijm;
      |                                      ^~~~~~
mltaln9.c:2494:30: warning: variable 'maxiim' set but not used [-Wunused-but-set-variable]
 2494 |         int i, j, k, miniim, maxiim, minijm, maxijm;
      |                              ^~~~~~
mltaln9.c:2494:22: warning: variable 'miniim' set but not used [-Wunused-but-set-variable]
 2494 |         int i, j, k, miniim, maxiim, minijm, maxijm;
      |                      ^~~~~~
mltaln9.c: In function 'msaresetnearestthread':
mltaln9.c:3630:17: warning: variable 'acptinit' set but not used [-Wunused-but-set-variable]
 3630 |         Bchain *acptinit;
      |                 ^~~~~~~~
mltaln9.c: In function 'kmerresetnearestthread':
mltaln9.c:3721:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3721 |                                 if( pointt ) free( singlettable1 ); singlettable1 = NULL;// kmer
      |                                 ^~
mltaln9.c:3721:69: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3721 |                                 if( pointt ) free( singlettable1 ); singlettable1 = NULL;// kmer
      |                                                                     ^~~~~~~~~~~~~
mltaln9.c:3686:17: warning: variable 'acptinit' set but not used [-Wunused-but-set-variable]
 3686 |         Bchain *acptinit;
      |                 ^~~~~~~~
mltaln9.c: In function 'compacttree_memsaveselectable':
mltaln9.c:5941:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5941 |                 if( partmtx[im] ) free( partmtx[im] ); partmtx[im] = NULL;
      |                 ^~
mltaln9.c:5941:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5941 |                 if( partmtx[im] ) free( partmtx[im] ); partmtx[im] = NULL;
      |                                                        ^~~~~~~
mltaln9.c:5942:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5942 |                 if( partmtx[jm] ) free( partmtx[jm] ); partmtx[jm] = NULL;
      |                 ^~
mltaln9.c:5942:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5942 |                 if( partmtx[jm] ) free( partmtx[jm] ); partmtx[jm] = NULL;
      |                                                        ^~~~~~~
mltaln9.c:6108:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 6108 |                 if( partmtx[im] ) free( partmtx[im] ); partmtx[im] = NULL;
      |                 ^~
mltaln9.c:6108:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 6108 |                 if( partmtx[im] ) free( partmtx[im] ); partmtx[im] = NULL;
      |                                                        ^~~~~~~
mltaln9.c:5513:18: warning: variable 'clusterfuncpt' set but not used [-Wunused-but-set-variable]
 5513 |         double (*clusterfuncpt[1])(double,double);
      |                  ^~~~~~~~~~~~~
mltaln9.c: In function 'DSPscore':
mltaln9.c:11228:12: warning: variable 'c' set but not used [-Wunused-but-set-variable]
11228 |     double c;
      |            ^
mltaln9.c: In function 'searchAnchors':
mltaln9.c:11291:13: warning: unused variable 'alloclen' [-Wunused-variable]
11291 |         int alloclen = 0;
      |             ^~~~~~~~
mltaln9.c: In function 'new_OpeningGapCount':
mltaln9.c:12599:41: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12599 |                                 if( !gb *  gc ) *fpt += feff;
      |                                     ~~~~^~~~~
mltaln9.c: In function 'new_OpeningGapCount_zure':
mltaln9.c:12653:41: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12653 |                                 if( !gb *  gc ) *fpt += feff;
      |                                     ~~~~^~~~~
mltaln9.c:12660:33: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12660 |                         if( !gb *  gc ) *fpt += feff;
      |                             ~~~~^~~~~
mltaln9.c: In function 'new_FinalGapCount_zure':
mltaln9.c:12716:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12716 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c:12724:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12724 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c: In function 'new_FinalGapCount':
mltaln9.c:12780:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12780 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c:12788:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12788 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c: In function 'st_OpeningGapAdd':
mltaln9.c:12822:33: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12822 |                         if( !gb *  gc ) *fpt += feff;
      |                             ~~~~^~~~~
mltaln9.c: In function 'st_OpeningGapCount':
mltaln9.c:12860:41: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12860 |                                 if( !gb *  gc ) *fpt += feff;
      |                                     ~~~~^~~~~
mltaln9.c: In function 'st_FinalGapCount_zure':
mltaln9.c:12891:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12891 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c:12900:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12900 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c: In function 'st_FinalGapAdd':
mltaln9.c:12935:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12935 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c:12945:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12945 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c: In function 'st_FinalGapCount':
mltaln9.c:12974:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12974 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c:12983:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12983 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c: In function 'getGapPattern':
mltaln9.c:13011:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
13011 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c: In function 'addonetip2fixedpos':
mltaln9.c:13954:13: warning: variable 'seqlengthcondition' set but not used [-Wunused-but-set-variable]
13954 |         int seqlengthcondition;
      |             ^~~~~~~~~~~~~~~~~~
mltaln9.c: In function 'makeskiptable':
mltaln9.c:15247:29: warning: variable 'gaplen' set but not used [-Wunused-but-set-variable]
15247 |         int i, j, posinseq, gaplen;
      |                             ^~~~~~
mltaln9.c: In function 'readlocalhomfromfile_autofid':
mltaln9.c:15740:17: warning: variable 'k2' set but not used [-Wunused-but-set-variable]
15740 |         int k1, k2;
      |                 ^~
mltaln9.c:15740:13: warning: variable 'k1' set but not used [-Wunused-but-set-variable]
15740 |         int k1, k2;
      |             ^~
mltaln9.c: In function 'check_guidetreefile':
mltaln9.c:2850:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2850 |         fgets( string, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c: In function 'readlocalhomtable2_single_bin_noseek':
mltaln9.c:15688:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
15688 |         fread( &size, sizeof( int ), 1, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:15689:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
15689 |         fread( &opt, sizeof( double ), 1, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:15692:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
15692 |         fread( m, size*sizeof( int ), 3, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:15728:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
15728 |         fread( &c, sizeof( char ), 1, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c: At top level:
mltaln9.c:1852:12: warning: 'compfuncpair' defined but not used [-Wunused-function]
 1852 | static int compfuncpair( const void *p, const void *q )
      |            ^~~~~~~~~~~~
mltaln9.c: In function 'calcnearestthread':
mltaln9.c:4557:35: warning: 'distfunc' may be used uninitialized [-Wmaybe-uninitialized]
 4557 |                         tmpdist = distfunc( bseq[pos], bseq[i], selfscore[pos], selfscore[i], alloclen );
      |                                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:4500:18: note: 'distfunc' was declared here
 4500 |         double (*distfunc)( char *, char *, double, double, int );
      |                  ^~~~~~~~
mltaln9.c:4566:32: warning: 'neighbor' may be used uninitialized [-Wmaybe-uninitialized]
 4566 |                 neighbors[pos] = neighbor;
      |                 ~~~~~~~~~~~~~~~^~~~~~~~~~
mltaln9.c:4499:13: note: 'neighbor' was declared here
 4499 |         int neighbor, i;
      |             ^~~~~~~~
mltaln9.c: In function 'createchain':
mltaln9.c:2161:75: warning: 'tree' may be used uninitialized [-Wmaybe-uninitialized]
 2161 |                 posinit += sprintf( instanttree+posinit, "%s:%7.5f,", tree[im], len[0][0] );
      |                                                                           ^
mltaln9.c:2063:16: note: 'tree' was declared here
 2063 |         char **tree;
      |                ^~~~
mltaln9.c:2161:28: warning: 'instanttree' may be used uninitialized [-Wmaybe-uninitialized]
 2161 |                 posinit += sprintf( instanttree+posinit, "%s:%7.5f,", tree[im], len[0][0] );
      |                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:2064:15: note: 'instanttree' was declared here
 2064 |         char *instanttree;
      |               ^~~~~~~~~~~
mltaln9.c:2161:25: warning: 'posinit' may be used uninitialized [-Wmaybe-uninitialized]
 2161 |                 posinit += sprintf( instanttree+posinit, "%s:%7.5f,", tree[im], len[0][0] );
      |                         ^~
mltaln9.c:2065:13: note: 'posinit' was declared here
 2065 |         int posinit;
      |             ^~~~~~~
mltaln9.c:2281:17: warning: 'nametmp' may be used uninitialized [-Wmaybe-uninitialized]
 2281 |                 free( nametmp );
      |                 ^~~~~~~~~~~~~~~
mltaln9.c:2067:15: note: 'nametmp' was declared here
 2067 |         char *nametmp, *nameptr, *tmpptr;
      |               ^~~~~~~
mltaln9.c:2113:31: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 2113 |                 instanttree = calloc( treelen, sizeof( char ) );
      |                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from mltaln.h:13,
                 from mltaln9.c:1:
/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
mltaln9.c:2124:17: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 2124 |         order = calloc( nseq, sizeof( int ) );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
mltaln9.c: In function 'loadtree':
mltaln9.c:2751:86: warning: 'tree' may be used uninitialized [-Wmaybe-uninitialized]
 2751 |                         treetmp = realloc( treetmp, strlen( tree[im] ) + strlen( tree[jm] ) + 100 ); // 22 de juubunn (:%7,:%7) %7 ha minus kamo
      |                                                                                      ^
mltaln9.c:2505:16: note: 'tree' was declared here
 2505 |         char **tree;
      |                ^~~~
mltaln9.c:2822:17: warning: 'nametmp' may be used uninitialized [-Wmaybe-uninitialized]
 2822 |                 free( nametmp );
      |                 ^~~~~~~~~~~~~~~
mltaln9.c:2507:15: note: 'nametmp' was declared here
 2507 |         char *nametmp, *nameptr, *tmpptr;
      |               ^~~~~~~
In file included from /usr/include/stdio.h:964,
                 from mltaln.h:12:
In function 'fgets',
    inlined from 'check_guidetreefile' at mltaln9.c:2850:2:
/usr/include/bits/stdio2.h:215:12: warning: call to '*__fgets_chk' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  215 |     return __fgets_chk_warn (__s, sz, __n, __stream);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'includemember',
    inlined from 'recalcpairs_para4' at mltaln9.c:5020:9,
    inlined from 'compacttreedpdist' at mltaln9.c:5469:2:
mltaln9.c:15069:31: warning: 'addmem' may be used uninitialized [-Wmaybe-uninitialized]
15069 |                 for( j=0; cand[j]>-1; j++ )
      |                           ~~~~^~~
mltaln9.c: In function 'compacttreedpdist':
mltaln9.c:4913:39: note: 'addmem' was declared here
 4913 |         int **memhist, *mem0, *mem1, *addmem;
      |                                       ^~~~~~
mltaln9.c: In function 'compacttree_memsaveselectable':
mltaln9.c:5964:86: warning: 'tree' may be used uninitialized [-Wmaybe-uninitialized]
 5964 |                         treetmp = realloc( treetmp, strlen( tree[im] ) + strlen( tree[jm] ) + 100 ); // 22 de juubunn (:%7,:%7) %7 ha minus kamo
      |                                                                                      ^
mltaln9.c:5509:16: note: 'tree' was declared here
 5509 |         char **tree; //static?
      |                ^~~~
mltaln9.c:6116:17: warning: 'nametmp' may be used uninitialized [-Wmaybe-uninitialized]
 6116 |                 free( nametmp );
      |                 ^~~~~~~~~~~~~~~
mltaln9.c:5511:15: note: 'nametmp' was declared here
 5511 |         char *nametmp, *nameptr, *tmpptr; //static?
      |               ^~~~~~~
mltaln9.c: In function 'fixed_musclesupg_double_realloc_nobk_halfmtx_treeout_memsave':
mltaln9.c:6531:28: warning: 'density' may be used uninitialized [-Wmaybe-uninitialized]
 6531 |         if( treeout == 2 ) free( density );
      |                            ^~~~~~~~~~~~~~~
mltaln9.c:6156:17: note: 'density' was declared here
 6156 |         double *density;
      |                 ^~~~~~~
mltaln9.c:6494:28: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 6494 |                 int *mem = calloc( sizeof( int ), nseq );
      |                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
mltaln9.c: In function 'fixed_supg_double_treeout_constrained':
mltaln9.c:7515:42: warning: 'testtopol' may be used uninitialized [-Wmaybe-uninitialized]
 7515 |                                 *intpt++ = im;
      |                                 ~~~~~~~~~^~~~
mltaln9.c:7283:14: note: 'testtopol' was declared here
 7283 |         int *testtopol, **inconsistent;
      |              ^~~~~~~~~
mltaln9.c:7438:67: warning: 'inconsistent' may be used uninitialized [-Wmaybe-uninitialized]
 7438 |                 for( i=0; i<ninconsistentpairs; i++ ) inconsistent[inconsistentpairlist[i][0]][inconsistentpairlist[i][1]] = 0;
      |                                                                   ^
mltaln9.c:7283:27: note: 'inconsistent' was declared here
 7283 |         int *testtopol, **inconsistent;
      |                           ^~~~~~~~~~~~
mltaln9.c:7551:60: warning: 'warned' may be used uninitialized [-Wmaybe-uninitialized]
 7551 |                                                 if( !warned[i] )
      |                                                            ^
mltaln9.c:7287:14: note: 'warned' was declared here
 7287 |         int *warned;
      |              ^~~~~~
mltaln9.c:7562:80: warning: 'inconsistentpairlist' may be used uninitialized [-Wmaybe-uninitialized]
 7562 |                                                         inconsistentpairlist = realloc( inconsistentpairlist, (ninconsistentpairs+1)*sizeof( int * ) );
      |                                                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:7284:15: note: 'inconsistentpairlist' was declared here
 7284 |         int **inconsistentpairlist;
      |               ^~~~~~~~~~~~~~~~~~~~
mltaln9.c: In function 'addonetip2fixedpos':
mltaln9.c:14257:55: warning: 'addedlen' may be used uninitialized [-Wmaybe-uninitialized]
14257 |                         lenc[posinnew][0] = len[i][0] - addedlen; // 2014/6/10
      |                                             ~~~~~~~~~~^~~~~~~~~~
mltaln9.c:13939:49: note: 'addedlen' was declared here
13939 |         double minscore, minscoreo, eff0, eff1, addedlen, tmpmin;
      |                                                 ^~~~~~~~
mltaln9.c:14440:15: warning: 'neighbor' may be used uninitialized [-Wmaybe-uninitialized]
14440 |         return( neighbor );
      |               ^
mltaln9.c:13946:13: note: 'neighbor' was declared here
13946 |         int neighbor;
      |             ^~~~~~~~
mltaln9.c: In function 'addonetip':
mltaln9.c:14759:55: warning: 'addedlen' may be used uninitialized [-Wmaybe-uninitialized]
14759 |                         lenc[posinnew][0] = len[i][0] - addedlen; // 2014/6/10
      |                                             ~~~~~~~~~~^~~~~~~~~~
mltaln9.c:14448:49: note: 'addedlen' was declared here
14448 |         double minscore, minscoreo, eff0, eff1, addedlen, tmpmin;
      |                                                 ^~~~~~~~
mltaln9.c:14942:15: warning: 'neighbor' may be used uninitialized [-Wmaybe-uninitialized]
14942 |         return( neighbor );
      |               ^
mltaln9.c:14455:13: note: 'neighbor' was declared here
14455 |         int neighbor;
      |             ^~~~~~~~
mltaln9.c: In function 'fillimp_file':
mltaln9.c:16019:20: warning: 'handle' may be used uninitialized [-Wmaybe-uninitialized]
16019 |         pthread_t *handle;
      |                    ^~~~~~
mltaln9.c:16194:61: warning: 'localimpmtx' may be used uninitialized [-Wmaybe-uninitialized]
16194 |                                 targ[i].impmtx = localimpmtx[i];
      |                                                  ~~~~~~~~~~~^~~
mltaln9.c:16021:19: note: 'localimpmtx' was declared here
16021 |         double ***localimpmtx;
      |                   ^~~~~~~~~~~
mltaln9.c:16023:29: warning: 'localndone' may be used uninitialized [-Wmaybe-uninitialized]
16023 |         unsigned long long *localndone;
      |                             ^~~~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c tddis.c
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c constants.c
In file included from constants.c:6:
JTT.c:9:56: warning: argument 3 of type 'unsigned char[26]' with mismatched bound [-Warray-parameter=]
    9 | void JTTmtx( double **rsr, double *freq, unsigned char locamino[26], char locgrp[26], int isTM )
      |                                          ~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from mltaln.h:344,
                 from constants.c:1:
functions.h:181:63: note: previously declared as 'unsigned char[128]'
  181 | extern void JTTmtx( double **rsr, double *freq, unsigned char locamino[0x80], char locgrp[0x80], int isTM );
      |                                                 ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
JTT.c:9:75: warning: argument 4 of type 'char[26]' with mismatched bound [-Warray-parameter=]
    9 | void JTTmtx( double **rsr, double *freq, unsigned char locamino[26], char locgrp[26], int isTM )
      |                                                                      ~~~~~^~~~~~~~~~
functions.h:181:84: note: previously declared as 'char[128]'
  181 | extern void JTTmtx( double **rsr, double *freq, unsigned char locamino[0x80], char locgrp[0x80], int isTM );
      |                                                                               ~~~~~^~~~~~~~~~~~
In file included from constants.c:7:
blosum.c: In function 'extendedmtx':
blosum.c:429:30: warning: operation on '*(*(matrix + (sizetype)((long unsigned int)i * 8)) + (sizetype)((long unsigned int)i * 8))' may be undefined [-Wsequence-point]
  429 |                 matrix[i][i] = matrix[i][i] = (double)1.0;
      |                 ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
constants.c: In function 'constants':
constants.c:713:39: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  713 |                 if( userdefined ) if( i=checkscoremtx( n_distmp, nseq, seq ) )
      |                                       ^
constants.c: In function 'freeconstants':
constants.c:1542:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1542 |         if( n_disLN ) FreeDoubleMtx( n_disLN ); n_disLN = NULL;
      |         ^~
constants.c:1542:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1542 |         if( n_disLN ) FreeDoubleMtx( n_disLN ); n_disLN = NULL;
      |                                                 ^~~~~~~
constants.c:1543:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1543 |         if( n_dis ) FreeIntMtx( n_dis ); n_dis = NULL;
      |         ^~
constants.c:1543:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1543 |         if( n_dis ) FreeIntMtx( n_dis ); n_dis = NULL;
      |                                          ^~~~~
constants.c:1544:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1544 |         if( n_disFFT ) FreeIntMtx( n_disFFT ); n_disFFT = NULL;
      |         ^~
constants.c:1544:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1544 |         if( n_disFFT ) FreeIntMtx( n_disFFT ); n_disFFT = NULL;
      |                                                ^~~~~~~~
constants.c:1545:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1545 |         if( n_dis_consweight_multi ) FreeDoubleMtx( n_dis_consweight_multi ); n_dis_consweight_multi = NULL;
      |         ^~
constants.c:1545:79: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1545 |         if( n_dis_consweight_multi ) FreeDoubleMtx( n_dis_consweight_multi ); n_dis_consweight_multi = NULL;
      |                                                                               ^~~~~~~~~~~~~~~~~~~~~~
constants.c:1546:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1546 |         if( amino_dis ) FreeIntMtx( amino_dis ); amino_dis = NULL;
      |         ^~
constants.c:1546:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1546 |         if( amino_dis ) FreeIntMtx( amino_dis ); amino_dis = NULL;
      |                                                  ^~~~~~~~~
constants.c:1547:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1547 |         if( amino_dis_consweight_multi ) FreeDoubleMtx( amino_dis_consweight_multi ); amino_dis_consweight_multi = NULL;
      |         ^~
constants.c:1547:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1547 |         if( amino_dis_consweight_multi ) FreeDoubleMtx( amino_dis_consweight_multi ); amino_dis_consweight_multi = NULL;
      |                                                                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~
blosum.c: In function 'overridematrix':
blosum.c:372:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  372 |                 fgets( buf, 499, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c nj.c
nj.c: In function 'nj':
nj.c:168:43: warning: 'r' may be used uninitialized [-Wmaybe-uninitialized]
  168 |     len2 = ( mtx[MIN(i,im)][MAX(i,im)] - r[im] + r[i] ) / 2;
      |                                          ~^~~~
nj.c:85:12: note: 'r' declared here
   85 |     double r[M];
      |            ^
nj.c:168:43: warning: 'r' may be used uninitialized [-Wmaybe-uninitialized]
  168 |     len2 = ( mtx[MIN(i,im)][MAX(i,im)] - r[im] + r[i] ) / 2;
      |                                          ~^~~~
nj.c:85:12: note: 'r' declared here
   85 |     double r[M];
      |            ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c partSalignmm.c  
partSalignmm.c: In function 'Atracking':
partSalignmm.c:542:59: warning: variable 'lastk' set but not used [-Wunused-but-set-variable]
  542 |         int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, lastk, limk;
      |                                                           ^~~~~
partSalignmm.c: In function 'partA__align_variousdist':
partSalignmm.c:1859:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1859 |                         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |                         ^~
partSalignmm.c:1859:80: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1859 |                         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |                                                                                ^~~~~~~~~
partSalignmm.c:1860:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1860 |                         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |                         ^~
partSalignmm.c:1860:80: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1860 |                         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |                                                                                ^~~~~~~~~
partSalignmm.c:1861:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1861 |                         if( nmask ) free( nmask ); nmask = NULL;
      |                         ^~
partSalignmm.c:1861:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1861 |                         if( nmask ) free( nmask ); nmask = NULL;
      |                                                    ^~~~~
partSalignmm.c:2114:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2114 |         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |         ^~
partSalignmm.c:2114:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2114 |         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |                                                                ^~~~~~~~~
partSalignmm.c:2115:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2115 |         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |         ^~
partSalignmm.c:2115:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2115 |         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |                                                                ^~~~~~~~~
partSalignmm.c:2116:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2116 |         if( nmask ) free( nmask ); nmask = NULL;
      |         ^~
partSalignmm.c:2116:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2116 |         if( nmask ) free( nmask ); nmask = NULL;
      |                                    ^~~~~
partSalignmm.c: In function 'partA__align':
partSalignmm.c:1268:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 1268 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
partSalignmm.c:743:17: note: 'wmrecordspt' was declared here
  743 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
partSalignmm.c:1268:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
 1268 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
partSalignmm.c:743:31: note: 'wmrecords1pt' was declared here
  743 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
partSalignmm.c:1248:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 1248 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
partSalignmm.c:743:46: note: 'prevwmrecordspt' was declared here
  743 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
partSalignmm.c:1271:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
 1271 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
partSalignmm.c:744:14: note: 'warpipt' was declared here
  744 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
partSalignmm.c:1272:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
 1272 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
partSalignmm.c:744:24: note: 'warpjpt' was declared here
  744 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
partSalignmm.c: In function 'partA__align_variousdist':
partSalignmm.c:2012:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 2012 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
partSalignmm.c:1439:17: note: 'wmrecordspt' was declared here
 1439 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
partSalignmm.c:2012:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
 2012 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
partSalignmm.c:1439:31: note: 'wmrecords1pt' was declared here
 1439 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
partSalignmm.c:1992:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 1992 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
partSalignmm.c:1439:46: note: 'prevwmrecordspt' was declared here
 1439 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
partSalignmm.c:2015:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
 2015 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
partSalignmm.c:1440:14: note: 'warpipt' was declared here
 1440 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
partSalignmm.c:2016:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
 2016 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
partSalignmm.c:1440:24: note: 'warpjpt' was declared here
 1440 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Lalignmm.c 
Lalignmm.c: In function 'MSalign2m2m_rec':
Lalignmm.c:393:15: warning: variable 'gaps' set but not used [-Wunused-but-set-variable]
  393 |         char *gaps;
      |               ^~~~
Lalignmm.c: In function 'Lalignmm_hmout':
Lalignmm.c:2180:21: warning: variable 'nglen2' set but not used [-Wunused-but-set-variable]
 2180 |         int nglen1, nglen2;
      |                     ^~~~~~
Lalignmm.c:2180:13: warning: variable 'nglen1' set but not used [-Wunused-but-set-variable]
 2180 |         int nglen1, nglen2;
      |             ^~~~~~
Lalignmm.c: In function 'Lalign2m2m_hmout':
Lalignmm.c:2381:21: warning: variable 'nglen2' set but not used [-Wunused-but-set-variable]
 2381 |         int nglen1, nglen2;
      |                     ^~~~~~
Lalignmm.c:2381:13: warning: variable 'nglen1' set but not used [-Wunused-but-set-variable]
 2381 |         int nglen1, nglen2;
      |             ^~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c rna.c 
rna.c: In function 'rnaalifoldcall':
rna.c:225:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  225 |         system( cmd );
      |         ^~~~~~~~~~~~~
rna.c:245:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  245 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
rna.c:285:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  285 |         system( cmd );
      |         ^~~~~~~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Salignmm.c 
Salignmm.c: In function 'A__align_variousdist':
Salignmm.c:2811:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2811 |                         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |                         ^~
Salignmm.c:2811:80: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2811 |                         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |                                                                                ^~~~~~~~~
Salignmm.c:2812:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2812 |                         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |                         ^~
Salignmm.c:2812:80: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2812 |                         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |                                                                                ^~~~~~~~~
Salignmm.c:2813:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2813 |                         if( nmask ) free( nmask ); nmask = NULL;
      |                         ^~
Salignmm.c:2813:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2813 |                         if( nmask ) free( nmask ); nmask = NULL;
      |                                                    ^~~~~
Salignmm.c:3099:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3099 |         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |         ^~
Salignmm.c:3099:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3099 |         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |                                                                ^~~~~~~~~
Salignmm.c:3100:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3100 |         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |         ^~
Salignmm.c:3100:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3100 |         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |                                                                ^~~~~~~~~
Salignmm.c:3101:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3101 |         if( nmask ) free( nmask ); nmask = NULL;
      |         ^~
Salignmm.c:3101:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3101 |         if( nmask ) free( nmask ); nmask = NULL;
      |                                    ^~~~~
Salignmm.c: In function 'Atracking':
Salignmm.c:1083:15: warning: 'wm' may be used uninitialized [-Wmaybe-uninitialized]
 1083 |         return( wm );
      |               ^
Salignmm.c:860:16: note: 'wm' was declared here
  860 |         double wm;
      |                ^~
Salignmm.c: In function 'A__align':
Salignmm.c:1987:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 1987 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
Salignmm.c:1165:17: note: 'wmrecordspt' was declared here
 1165 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
Salignmm.c:1987:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
 1987 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
Salignmm.c:1165:31: note: 'wmrecords1pt' was declared here
 1165 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
Salignmm.c:1960:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 1960 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] ) ) > wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
Salignmm.c:1165:46: note: 'prevwmrecordspt' was declared here
 1165 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
Salignmm.c:1990:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
 1990 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Salignmm.c:1166:14: note: 'warpipt' was declared here
 1166 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
Salignmm.c:1991:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
 1991 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Salignmm.c:1166:24: note: 'warpjpt' was declared here
 1166 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
Salignmm.c: In function 'A__align_variousdist':
Salignmm.c:2990:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 2990 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
Salignmm.c:2293:17: note: 'wmrecordspt' was declared here
 2293 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
Salignmm.c:2990:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
 2990 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
Salignmm.c:2293:31: note: 'wmrecords1pt' was declared here
 2293 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
Salignmm.c:2968:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 2968 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] ) ) > wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
Salignmm.c:2293:46: note: 'prevwmrecordspt' was declared here
 2293 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
Salignmm.c:2993:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
 2993 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Salignmm.c:2294:14: note: 'warpipt' was declared here
 2294 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
Salignmm.c:2994:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
 2994 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Salignmm.c:2294:24: note: 'warpjpt' was declared here
 2294 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Dalignmm.c 
Dalignmm.c: In function 'calcpfac_gapex_noidatend':
Dalignmm.c:1576:29: warning: variable 'pfac2' set but not used [-Wunused-but-set-variable]
 1576 |         double pfac, pfac1, pfac2, pfac10;
      |                             ^~~~~
Dalignmm.c: In function 'D__align':
Dalignmm.c:2640:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2640 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                         ^~
Dalignmm.c:2640:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2640 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2641:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2641 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                         ^~
Dalignmm.c:2641:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2641 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2642:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2642 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                         ^~
Dalignmm.c:2642:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2642 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2643:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2643 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                         ^~
Dalignmm.c:2643:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2643 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2645:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2645 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                         ^~
Dalignmm.c:2645:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2645 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2646:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2646 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                         ^~
Dalignmm.c:2646:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2646 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2647:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2647 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                         ^~
Dalignmm.c:2647:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2647 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2648:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2648 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                         ^~
Dalignmm.c:2648:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2648 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2649:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2649 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                         ^~
Dalignmm.c:2649:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2649 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2650:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2650 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                         ^~
Dalignmm.c:2650:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2650 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2651:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2651 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                         ^~
Dalignmm.c:2651:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2651 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2652:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2652 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                         ^~
Dalignmm.c:2652:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2652 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2653:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2653 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                         ^~
Dalignmm.c:2653:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2653 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c:2654:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2654 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                         ^~
Dalignmm.c:2654:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2654 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c:2778:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2778 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                         ^~
Dalignmm.c:2778:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2778 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2779:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2779 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                         ^~
Dalignmm.c:2779:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2779 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2780:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2780 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                         ^~
Dalignmm.c:2780:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2780 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2781:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2781 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                         ^~
Dalignmm.c:2781:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2781 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2783:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2783 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                         ^~
Dalignmm.c:2783:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2783 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2784:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2784 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                         ^~
Dalignmm.c:2784:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2784 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2785:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2785 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                         ^~
Dalignmm.c:2785:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2785 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2786:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2786 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                         ^~
Dalignmm.c:2786:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2786 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2787:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2787 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                         ^~
Dalignmm.c:2787:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2787 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2788:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2788 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                         ^~
Dalignmm.c:2788:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2788 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2789:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2789 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                         ^~
Dalignmm.c:2789:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2789 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2790:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2790 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                         ^~
Dalignmm.c:2790:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2790 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2791:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2791 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                         ^~
Dalignmm.c:2791:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2791 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c:2792:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2792 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                         ^~
Dalignmm.c:2792:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2792 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c: In function 'D__align_variousdist':
Dalignmm.c:4478:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4478 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                         ^~
Dalignmm.c:4478:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4478 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4479:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4479 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                         ^~
Dalignmm.c:4479:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4479 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4480:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4480 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                         ^~
Dalignmm.c:4480:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4480 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4481:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4481 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                         ^~
Dalignmm.c:4481:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4481 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4483:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4483 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                         ^~
Dalignmm.c:4483:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4483 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4484:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4484 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                         ^~
Dalignmm.c:4484:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4484 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4485:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4485 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                         ^~
Dalignmm.c:4485:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4485 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4486:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4486 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                         ^~
Dalignmm.c:4486:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4486 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4487:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4487 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                         ^~
Dalignmm.c:4487:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4487 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4488:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4488 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                         ^~
Dalignmm.c:4488:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4488 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4489:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4489 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                         ^~
Dalignmm.c:4489:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4489 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4490:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4490 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                         ^~
Dalignmm.c:4490:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4490 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4491:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4491 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                         ^~
Dalignmm.c:4491:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4491 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c:4492:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4492 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                         ^~
Dalignmm.c:4492:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4492 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c:4648:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4648 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                         ^~
Dalignmm.c:4648:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4648 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4649:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4649 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                         ^~
Dalignmm.c:4649:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4649 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4650:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4650 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                         ^~
Dalignmm.c:4650:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4650 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4651:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4651 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                         ^~
Dalignmm.c:4651:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4651 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4653:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4653 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                         ^~
Dalignmm.c:4653:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4653 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4654:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4654 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                         ^~
Dalignmm.c:4654:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4654 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4655:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4655 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                         ^~
Dalignmm.c:4655:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4655 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4656:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4656 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                         ^~
Dalignmm.c:4656:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4656 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4657:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4657 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                         ^~
Dalignmm.c:4657:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4657 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4658:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4658 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                         ^~
Dalignmm.c:4658:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4658 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4659:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4659 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                         ^~
Dalignmm.c:4659:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4659 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4660:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4660 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                         ^~
Dalignmm.c:4660:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4660 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4661:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4661 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                         ^~
Dalignmm.c:4661:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4661 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c:4662:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4662 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                         ^~
Dalignmm.c:4662:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4662 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c:5225:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5225 |                         if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL;
      |                         ^~
Dalignmm.c:5225:66: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5225 |                         if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL;
      |                                                                  ^~~~~~~~~
Dalignmm.c:5226:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5226 |                         if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL;
      |                         ^~
Dalignmm.c:5226:66: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5226 |                         if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL;
      |                                                                  ^~~~~~~~~
Dalignmm.c:5227:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5227 |                         if( nmask ) free( nmask ); nmask = NULL;
      |                         ^~
Dalignmm.c:5227:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5227 |                         if( nmask ) free( nmask ); nmask = NULL;
      |                                                    ^~~~~
Dalignmm.c:6121:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 6121 |         if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL;
      |         ^~
Dalignmm.c:6121:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 6121 |         if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL;
      |                                                  ^~~~~~~~~
Dalignmm.c:6122:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 6122 |         if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL;
      |         ^~
Dalignmm.c:6122:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 6122 |         if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL;
      |                                                  ^~~~~~~~~
Dalignmm.c:6123:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 6123 |         if( nmask ) free( nmask ); nmask = NULL;
      |         ^~
Dalignmm.c:6123:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 6123 |         if( nmask ) free( nmask ); nmask = NULL;
      |                                    ^~~~~
Dalignmm.c: In function 'D__align':
Dalignmm.c:3956:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 3956 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
Dalignmm.c:2593:17: note: 'wmrecordspt' was declared here
 2593 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
Dalignmm.c:3956:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
 3956 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
Dalignmm.c:2593:31: note: 'wmrecords1pt' was declared here
 2593 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
Dalignmm.c:3931:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 3931 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
Dalignmm.c:2593:46: note: 'prevwmrecordspt' was declared here
 2593 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
Dalignmm.c:3959:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
 3959 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Dalignmm.c:2594:14: note: 'warpipt' was declared here
 2594 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
Dalignmm.c:3960:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
 3960 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Dalignmm.c:2594:24: note: 'warpjpt' was declared here
 2594 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
Dalignmm.c: In function 'D__align_variousdist':
Dalignmm.c:5889:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 5889 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
Dalignmm.c:4429:17: note: 'wmrecordspt' was declared here
 4429 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
Dalignmm.c:5889:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
 5889 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
Dalignmm.c:4429:31: note: 'wmrecords1pt' was declared here
 4429 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
Dalignmm.c:5864:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 5864 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
Dalignmm.c:4429:46: note: 'prevwmrecordspt' was declared here
 4429 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
Dalignmm.c:5892:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
 5892 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Dalignmm.c:4430:14: note: 'warpipt' was declared here
 4430 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
Dalignmm.c:5893:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
 5893 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Dalignmm.c:4430:24: note: 'warpjpt' was declared here
 4430 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Falign.c
Falign.c: In function 'Fgetlag':
Falign.c:204:26: warning: variable 'nlen4' set but not used [-Wunused-but-set-variable]
  204 |         int nlen, nlen2, nlen4;
      |                          ^~~~~
Falign.c: In function 'Falign':
Falign.c:933:29: warning: unused variable 'p' [-Wunused-variable]
  933 |                         int p;
      |                             ^
Falign.c:776:26: warning: variable 'nlen4' set but not used [-Wunused-but-set-variable]
  776 |         int nlen, nlen2, nlen4;
      |                          ^~~~~
Falign.c: In function 'Falign_givenanchors':
Falign.c:1919:26: warning: variable 'nlen4' set but not used [-Wunused-but-set-variable]
 1919 |         int nlen, nlen2, nlen4;
      |                          ^~~~~
Falign.c: In function 'Falign_udpari_long':
Falign.c:2594:26: warning: variable 'nlen4' set but not used [-Wunused-but-set-variable]
 2594 |         int nlen, nlen2, nlen4;
      |                          ^~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Falign_localhom.c
Falign_localhom.c: In function 'Falign_localhom':
Falign_localhom.c:176:26: warning: variable 'nlen4' set but not used [-Wunused-but-set-variable]
  176 |         int nlen, nlen2, nlen4;
      |                          ^~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Galign11.c 
Galign11.c: In function 'G__align11psg':
Galign11.c:332:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  332 |                         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                         ^~
Galign11.c:332:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  332 |                         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                                                    ^~~~~
Galign11.c:333:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  333 |                         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                         ^~
Galign11.c:333:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  333 |                         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                                                    ^~~~~
Galign11.c:334:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  334 |                         if( w1 ) FreeFloatVec( w1 ); w1 = NULL;
      |                         ^~
Galign11.c:334:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  334 |                         if( w1 ) FreeFloatVec( w1 ); w1 = NULL;
      |                                                      ^~
Galign11.c:335:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  335 |                         if( w2 ) FreeFloatVec( w2 ); w2 = NULL;
      |                         ^~
Galign11.c:335:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  335 |                         if( w2 ) FreeFloatVec( w2 ); w2 = NULL;
      |                                                      ^~
Galign11.c:336:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  336 |                         if( match ) FreeFloatVec( match ); match = NULL;
      |                         ^~
Galign11.c:336:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  336 |                         if( match ) FreeFloatVec( match ); match = NULL;
      |                                                            ^~~~~
Galign11.c:337:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  337 |                         if( initverticalw ) FreeFloatVec( initverticalw ); initverticalw = NULL;
      |                         ^~
Galign11.c:337:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  337 |                         if( initverticalw ) FreeFloatVec( initverticalw ); initverticalw = NULL;
      |                                                                            ^~~~~~~~~~~~~
Galign11.c:338:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  338 |                         if( lastverticalw ) FreeFloatVec( lastverticalw ); lastverticalw = NULL;
      |                         ^~
Galign11.c:338:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  338 |                         if( lastverticalw ) FreeFloatVec( lastverticalw ); lastverticalw = NULL;
      |                                                                            ^~~~~~~~~~~~~
Galign11.c:340:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  340 |                         if( m ) FreeFloatVec( m ); m = NULL;
      |                         ^~
Galign11.c:340:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  340 |                         if( m ) FreeFloatVec( m ); m = NULL;
      |                                                    ^
Galign11.c:341:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  341 |                         if( mp ) FreeIntVec( mp ); mp = NULL;
      |                         ^~
Galign11.c:341:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  341 |                         if( mp ) FreeIntVec( mp ); mp = NULL;
      |                                                    ^~
Galign11.c:343:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  343 |                         if( mseq ) FreeCharMtx( mseq ); mseq = NULL;
      |                         ^~
Galign11.c:343:57: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  343 |                         if( mseq ) FreeCharMtx( mseq ); mseq = NULL;
      |                                                         ^~~~
Galign11.c:347:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  347 |                         if( doublework ) FreeFloatMtx( doublework ); doublework = NULL;
      |                         ^~
Galign11.c:347:70: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  347 |                         if( doublework ) FreeFloatMtx( doublework ); doublework = NULL;
      |                                                                      ^~~~~~~~~~
Galign11.c:348:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  348 |                         if( intwork ) FreeIntMtx( intwork ); intwork = NULL;
      |                         ^~
Galign11.c:348:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  348 |                         if( intwork ) FreeIntMtx( intwork ); intwork = NULL;
      |                                                              ^~~~~~~
Galign11.c:350:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  350 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
Galign11.c:350:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  350 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Galign11.c:352:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  352 |                         if( codonseq1 ) FreeIntMtx( codonseq1 ); codonseq1 = NULL;
      |                         ^~
Galign11.c:352:66: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  352 |                         if( codonseq1 ) FreeIntMtx( codonseq1 ); codonseq1 = NULL;
      |                                                                  ^~~~~~~~~
Galign11.c:353:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  353 |                         if( codonseq2 ) FreeIntMtx( codonseq2 ); codonseq2 = NULL;
      |                         ^~
Galign11.c:353:66: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  353 |                         if( codonseq2 ) FreeIntMtx( codonseq2 ); codonseq2 = NULL;
      |                                                                  ^~~~~~~~~
Galign11.c: In function 'G__align11':
Galign11.c:977:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  977 |                         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                         ^~
Galign11.c:977:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  977 |                         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                                                    ^~~~~
Galign11.c:978:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  978 |                         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                         ^~
Galign11.c:978:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  978 |                         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                                                    ^~~~~
Galign11.c:979:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  979 |                         if( w1 ) FreeFloatVec( w1 ); w1 = NULL;
      |                         ^~
Galign11.c:979:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  979 |                         if( w1 ) FreeFloatVec( w1 ); w1 = NULL;
      |                                                      ^~
Galign11.c:980:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  980 |                         if( w2 ) FreeFloatVec( w2 ); w2 = NULL;
      |                         ^~
Galign11.c:980:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  980 |                         if( w2 ) FreeFloatVec( w2 ); w2 = NULL;
      |                                                      ^~
Galign11.c:981:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  981 |                         if( match ) FreeFloatVec( match ); match = NULL;
      |                         ^~
Galign11.c:981:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  981 |                         if( match ) FreeFloatVec( match ); match = NULL;
      |                                                            ^~~~~
Galign11.c:982:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  982 |                         if( initverticalw ) FreeFloatVec( initverticalw ); initverticalw = NULL;
      |                         ^~
Galign11.c:982:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  982 |                         if( initverticalw ) FreeFloatVec( initverticalw ); initverticalw = NULL;
      |                                                                            ^~~~~~~~~~~~~
Galign11.c:983:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  983 |                         if( lastverticalw ) FreeFloatVec( lastverticalw ); lastverticalw = NULL;
      |                         ^~
Galign11.c:983:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  983 |                         if( lastverticalw ) FreeFloatVec( lastverticalw ); lastverticalw = NULL;
      |                                                                            ^~~~~~~~~~~~~
Galign11.c:985:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  985 |                         if( m ) FreeFloatVec( m ); m = NULL;
      |                         ^~
Galign11.c:985:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  985 |                         if( m ) FreeFloatVec( m ); m = NULL;
      |                                                    ^
Galign11.c:986:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  986 |                         if( mp ) FreeIntVec( mp ); mp = NULL;
      |                         ^~
Galign11.c:986:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  986 |                         if( mp ) FreeIntVec( mp ); mp = NULL;
      |                                                    ^~
Galign11.c:988:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  988 |                         if( mseq ) FreeCharMtx( mseq ); mseq = NULL;
      |                         ^~
Galign11.c:988:57: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  988 |                         if( mseq ) FreeCharMtx( mseq ); mseq = NULL;
      |                                                         ^~~~
Galign11.c:992:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  992 |                         if( doublework ) FreeFloatMtx( doublework ); doublework = NULL;
      |                         ^~
Galign11.c:992:70: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  992 |                         if( doublework ) FreeFloatMtx( doublework ); doublework = NULL;
      |                                                                      ^~~~~~~~~~
Galign11.c:993:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  993 |                         if( intwork ) FreeIntMtx( intwork ); intwork = NULL;
      |                         ^~
Galign11.c:993:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  993 |                         if( intwork ) FreeIntMtx( intwork ); intwork = NULL;
      |                                                              ^~~~~~~
Galign11.c:995:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  995 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
Galign11.c:995:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  995 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Galign11.c: In function 'Atracking':
Galign11.c:261:15: warning: 'wm' may be used uninitialized [-Wmaybe-uninitialized]
  261 |         return( wm );
      |               ^
Galign11.c:107:16: note: 'wm' was declared here
  107 |         double wm, g;
      |                ^~
Galign11.c: In function 'G__align11psg':
Galign11.c:815:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
  815 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
Galign11.c:323:17: note: 'wmrecordspt' was declared here
  323 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
Galign11.c:815:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
  815 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
Galign11.c:323:31: note: 'wmrecords1pt' was declared here
  323 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
Galign11.c:787:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
  787 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_tmp )> wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
Galign11.c:323:46: note: 'prevwmrecordspt' was declared here
  323 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
Galign11.c:822:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
  822 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Galign11.c:324:14: note: 'warpipt' was declared here
  324 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
Galign11.c:823:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
  823 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Galign11.c:324:24: note: 'warpjpt' was declared here
  324 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
Galign11.c: In function 'G__align11':
Galign11.c:1376:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 1376 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
Galign11.c:967:17: note: 'wmrecordspt' was declared here
  967 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
Galign11.c:1376:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
 1376 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
Galign11.c:967:31: note: 'wmrecords1pt' was declared here
  967 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
Galign11.c:1348:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 1348 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_tmp )> wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
Galign11.c:967:46: note: 'prevwmrecordspt' was declared here
  967 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
Galign11.c:1383:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
 1383 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Galign11.c:968:14: note: 'warpipt' was declared here
  968 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
Galign11.c:1384:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
 1384 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Galign11.c:968:24: note: 'warpjpt' was declared here
  968 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Lalign11.c 
Lalign11.c: In function 'L__align11':
Lalign11.c:285:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  285 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
Lalign11.c:285:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  285 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Lalign11.c:340:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  340 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
Lalign11.c:340:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  340 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Lalign11.c: In function 'L__align11_noalign':
Lalign11.c:807:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  807 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
Lalign11.c:807:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  807 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Lalign11.c:845:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  845 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
Lalign11.c:845:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  845 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Lalign11.c: In function 'L__align11':
Lalign11.c:629:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
  629 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
Lalign11.c:262:17: note: 'wmrecordspt' was declared here
  262 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
Lalign11.c:629:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
  629 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
Lalign11.c:262:31: note: 'wmrecords1pt' was declared here
  262 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
Lalign11.c:601:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
  601 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_tmp )> wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
Lalign11.c:262:46: note: 'prevwmrecordspt' was declared here
  262 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
Lalign11.c:636:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
  636 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Lalign11.c:263:14: note: 'warpipt' was declared here
  263 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
Lalign11.c:637:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
  637 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Lalign11.c:263:24: note: 'warpjpt' was declared here
  263 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c genalign11.c 
genalign11.c: In function 'genL__align11':
genalign11.c:190:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  190 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
genalign11.c:190:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  190 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
genalign11.c:234:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  234 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
genalign11.c:234:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  234 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c MSalignmm.c 
MSalignmm.c: In function 'MSalignmm_rec':
MSalignmm.c:1911:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 1911 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                 ^~~
MSalignmm.c:1911:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1911 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                                                            ^~~~
MSalignmm.c:1922:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 1922 |                 for( i=0,j=len; i<l; i++,j++ ) mgt1[j] = '-'; mgt1[j] = 0;
      |                 ^~~
MSalignmm.c:1922:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1922 |                 for( i=0,j=len; i<l; i++,j++ ) mgt1[j] = '-'; mgt1[j] = 0;
      |                                                               ^~~~
MSalignmm.c:1923:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 1923 |                 for( i=0,j=len; i<l; i++,j++ ) mgt2[j] = 'o'; mgt2[j] = 0;
      |                 ^~~
MSalignmm.c:1923:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1923 |                 for( i=0,j=len; i<l; i++,j++ ) mgt2[j] = 'o'; mgt2[j] = 0;
      |                                                               ^~~~
MSalignmm.c:1934:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 1934 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                 ^~~
MSalignmm.c:1934:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1934 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                                                            ^~~~
MSalignmm.c:1945:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 1945 |                 for( i=0,j=len; i<l; i++,j++ ) mgt1[j] = 'o'; mgt1[j] = 0;
      |                 ^~~
MSalignmm.c:1945:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1945 |                 for( i=0,j=len; i<l; i++,j++ ) mgt1[j] = 'o'; mgt1[j] = 0;
      |                                                               ^~~~
MSalignmm.c:1946:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 1946 |                 for( i=0,j=len; i<l; i++,j++ ) mgt2[j] = '-'; mgt2[j] = 0;
      |                 ^~~
MSalignmm.c:1946:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1946 |                 for( i=0,j=len; i<l; i++,j++ ) mgt2[j] = '-'; mgt2[j] = 0;
      |                                                               ^~~~
MSalignmm.c:1000:13: warning: variable 'lasti' set but not used [-Wunused-but-set-variable]
 1000 |         int lasti, lastj, imid;
      |             ^~~~~
MSalignmm.c: In function 'MSalignmm_rec_variousdist':
MSalignmm.c:3803:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 3803 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                 ^~~
MSalignmm.c:3803:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 3803 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                                                            ^~~~
MSalignmm.c:3824:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 3824 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                 ^~~
MSalignmm.c:3824:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 3824 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                                                            ^~~~
MSalignmm.c:2889:13: warning: variable 'lasti' set but not used [-Wunused-but-set-variable]
 2889 |         int lasti, lastj, imid;
      |             ^~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c fftFunctions.c
fftFunctions.c: In function 'keika':
fftFunctions.c:10:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   10 |         if( current == 0 )
      |         ^~
fftFunctions.c:13:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
   13 |                 fprintf( stderr, "\b\b\b\b\b\b\b\b" );
      |                 ^~~~~~~
fftFunctions.c: In function 'alignableReagion':
fftFunctions.c:209:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  209 |                 if( stra ) FreeDoubleVec( stra ); stra = NULL;
      |                 ^~
fftFunctions.c:209:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  209 |                 if( stra ) FreeDoubleVec( stra ); stra = NULL;
      |                                                   ^~~~
fftFunctions.c:210:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  210 |                 if( prf1 ) FreeDoubleVec( prf1 ); prf1 = NULL;
      |                 ^~
fftFunctions.c:210:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  210 |                 if( prf1 ) FreeDoubleVec( prf1 ); prf1 = NULL;
      |                                                   ^~~~
fftFunctions.c:211:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  211 |                 if( prf2 ) FreeDoubleVec( prf2 ); prf2 = NULL;
      |                 ^~
fftFunctions.c:211:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  211 |                 if( prf2 ) FreeDoubleVec( prf2 ); prf2 = NULL;
      |                                                   ^~~~
fftFunctions.c:212:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  212 |                 if( hat1 ) FreeIntVec( hat1 ); hat1 = NULL;
      |                 ^~
fftFunctions.c:212:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  212 |                 if( hat1 ) FreeIntVec( hat1 ); hat1 = NULL;
      |                                                ^~~~
fftFunctions.c:213:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  213 |                 if( hat2 ) FreeIntVec( hat2 ); hat2 = NULL;
      |                 ^~
fftFunctions.c:213:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  213 |                 if( hat2 ) FreeIntVec( hat2 ); hat2 = NULL;
      |                                                ^~~~
fftFunctions.c: In function 'blockAlign2':
fftFunctions.c:404:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  404 |                         if( result1 ) free( result1 ); result1 = NULL;
      |                         ^~
fftFunctions.c:404:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  404 |                         if( result1 ) free( result1 ); result1 = NULL;
      |                                                        ^~~~~~~
fftFunctions.c:405:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  405 |                         if( result2 ) free( result2 ); result2 = NULL;
      |                         ^~
fftFunctions.c:405:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  405 |                         if( result2 ) free( result2 ); result2 = NULL;
      |                                                        ^~~~~~~
fftFunctions.c:406:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  406 |                         if( ocut1 ) free( ocut1 ); ocut1 = NULL;
      |                         ^~
fftFunctions.c:406:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  406 |                         if( ocut1 ) free( ocut1 ); ocut1 = NULL;
      |                                                    ^~~~~
fftFunctions.c:407:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  407 |                         if( ocut2 ) free( ocut2 ); ocut2 = NULL;
      |                         ^~
fftFunctions.c:407:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  407 |                         if( ocut2 ) free( ocut2 ); ocut2 = NULL;
      |                                                    ^~~~~
fftFunctions.c:408:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  408 |                         if( track ) FreeIntMtx( track ); track = NULL;
      |                         ^~
fftFunctions.c:408:58: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  408 |                         if( track ) FreeIntMtx( track ); track = NULL;
      |                                                          ^~~~~
fftFunctions.c:409:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  409 |                         if( crossscore ) FreeDoubleMtx( crossscore ); crossscore = NULL;
      |                         ^~
fftFunctions.c:409:71: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  409 |                         if( crossscore ) FreeDoubleMtx( crossscore ); crossscore = NULL;
      |                                                                       ^~~~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c fft.c 
fft.c: In function 'fft':
fft.c:55:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   55 |                         if (bitrev) free(bitrev); bitrev = NULL;
      |                         ^~
fft.c:55:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
   55 |                         if (bitrev) free(bitrev); bitrev = NULL;
      |                                                   ^~~~~~
fft.c:56:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   56 |                         if (sintbl) free(sintbl); sintbl = NULL;
      |                         ^~
fft.c:56:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
   56 |                         if (sintbl) free(sintbl); sintbl = NULL;
      |                                                   ^~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c tditeration.c
tditeration.c: In function 'Writeoptions':
tditeration.c:208:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  208 |     if( weight && !utree )
      |     ^~
tditeration.c:211:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  211 |         if( treemethod == 'n' )
      |         ^~
tditeration.c: In function 'athread':
tditeration.c:1032:56: warning: variable 'totalwm' set but not used [-Wunused-but-set-variable]
 1032 |                                                 double totalwm;
      |                                                        ^~~~~~~
tditeration.c: In function 'TreeDependentIteration':
tditeration.c:2142:56: warning: variable 'totalwm' set but not used [-Wunused-but-set-variable]
 2142 |                                                 double totalwm;
      |                                                        ^~~~~~~
tditeration.c: In function 'athread':
tditeration.c:694:33: warning: 'rnapairboth' may be used uninitialized [-Wmaybe-uninitialized]
  694 |                                 freelocalarrays
      |                                 ^~~~~~~~~~~~~~~
  695 |                                 (
      |                                 ~
  696 |                                         tscorehistory,
      |                                         ~~~~~~~~~~~~~~
  697 |                                         grouprna1, grouprna2,
      |                                         ~~~~~~~~~~~~~~~~~~~~~
  698 |                                         rnapairboth,
      |                                         ~~~~~~~~~~~~
  699 |                                         indication1, indication2,
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~
  700 |                                         distarr,
      |                                         ~~~~~~~~
  701 |                                         effarr, effarrforlocalhom, effarr1, effarr2,
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  702 |                                         mseq1, mseq2,
      |                                         ~~~~~~~~~~~~~
  703 |                                         localcopy,
      |                                         ~~~~~~~~~~
  704 |                                         gapmap1, gapmap2,
      |                                         ~~~~~~~~~~~~~~~~~
  705 |                                         effarr1_kozo, effarr2_kozo, effarr_kozo,
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  706 |                                         memlist, pairbuf,
      |                                         ~~~~~~~~~~~~~~~~~
  707 |                                         localhomshrink,
      |                                         ~~~~~~~~~~~~~~~
  708 |                                         swaplist,
      |                                         ~~~~~~~~~
  709 |                                         smalldistmtx,
      |                                         ~~~~~~~~~~~~~
  710 |                                         scoringmatrices,
      |                                         ~~~~~~~~~~~~~~~~
  711 |                                         eff1s, eff2s,
      |                                         ~~~~~~~~~~~~~
  712 |                                         whichmtx
      |                                         ~~~~~~~~
  713 |                                 );
      |                                 ~
tditeration.c:383:18: note: 'rnapairboth' was declared here
  383 |         RNApair *rnapairboth;
      |                  ^~~~~~~~~~~
tditeration.c:878:49: warning: 'localhomshrink' may be used uninitialized [-Wmaybe-uninitialized]
  878 |                                                 msshrinklocalhom_fast_half( memlist[0], memlist[1], localhomtable, localhomshrink );
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tditeration.c:384:21: note: 'localhomshrink' was declared here
  384 |         LocalHom ***localhomshrink;
      |                     ^~~~~~~~~~~~~~
tditeration.c: In function 'TreeDependentIteration':
tditeration.c:1493:44: warning: 'candidates' may be used uninitialized [-Wmaybe-uninitialized]
 1493 |                         targ[i].candidates = candidates;
      |                         ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
tditeration.c:1452:25: note: 'candidates' was declared here
 1452 |                 char ***candidates;
      |                         ^~~~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c dvtditr.c
dvtditr.c: In function 'main':
dvtditr.c:435:13: warning: variable 'returnvalue' set but not used [-Wunused-but-set-variable]
  435 |         int returnvalue;
      |             ^~~~~~~~~~~
dvtditr.c:1020:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1020 |                                 system( "cp infile.tree GuideTree" ); // tekitou
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dvtditr.c:984:43: warning: 'insubtable' may be used uninitialized [-Wmaybe-uninitialized]
  984 |                                 insubtable[subtable[i][j]] = 1;
      |                                           ^
dvtditr.c:451:14: note: 'insubtable' was declared here
  451 |         int *insubtable;
      |              ^~~~~~~~~~
dvtditr.c:1076:17: warning: 'preservegaps' may be used uninitialized [-Wmaybe-uninitialized]
 1076 |                 free( preservegaps );
      |                 ^~~~~~~~~~~~~~~~~~~~
dvtditr.c:452:14: note: 'preservegaps' was declared here
  452 |         int *preservegaps;
      |              ^~~~~~~~~~~~
dvtditr.c:1069:25: warning: 'subalnpt' may be used uninitialized [-Wmaybe-uninitialized]
 1069 |                         commongappick( j, subalnpt[i] );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dvtditr.c:453:17: note: 'subalnpt' was declared here
  453 |         char ***subalnpt;
      |                 ^~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c defs.c
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c SAalignmm.c -o SAalignmm.o
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c treeOperation.c
treeOperation.c: In function 'distFromABranch_rec':
treeOperation.c:492:24: warning: variable 'dir_pa' set but not used [-Wunused-but-set-variable]
  492 |         int dir_ch[3], dir_pa;
      |                        ^~~~~~
treeOperation.c: In function 'weightFromABranch_rec':
treeOperation.c:575:24: warning: variable 'dir_pa' set but not used [-Wunused-but-set-variable]
  575 |         int dir_ch[3], dir_pa;
      |                        ^~~~~~
treeOperation.c: In function 'assignstrweight_rec':
treeOperation.c:645:24: warning: variable 'dir_pa' set but not used [-Wunused-but-set-variable]
  645 |         int dir_ch[3], dir_pa;
      |                        ^~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c addfunctions.c
addfunctions.c: In function 'profilealignment2':
addfunctions.c:38:16: warning: variable 'newlen' set but not used [-Wunused-but-set-variable]
   38 |         int i, newlen;
      |                ^~~~~~
addfunctions.c: In function 'restoregaponlysites':
addfunctions.c:1913:16: warning: unused variable 'j' [-Wunused-variable]
 1913 |         int i, j, p;
      |                ^
gcc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o MSalignmm.o fftFunctions.o fft.o tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o   -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
In function 'generatesubalignmentstable',
    inlined from 'main' at dvtditr.c:815:7:
mltaln9.c:15290:23: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
15290 |         distfromtip = calloc( nseq, sizeof( double ) );
      |                       ^
/usr/include/stdlib.h: In function 'main':
/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c dndfast7.c
dndfast7.c: In function 'main':
dndfast7.c:326:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  326 |         system( com );
      |         ^~~~~~~~~~~~~
gcc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -c -o dndblast.o dndblast.c
dndblast.c: In function 'main':
dndblast.c:201:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  201 |                         system( com );
      |                         ^~~~~~~~~~~~~
dndblast.c:382:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  382 |         system( com );
      |         ^~~~~~~~~~~~~
gcc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c sextet5.c
gcc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c mafft-distance.c
gcc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c MSalign11.c 
MSalign11.c: In function 'backdp':
MSalign11.c:133:13: warning: variable 'mpi' set but not used [-Wunused-but-set-variable]
  133 |         int mpi;
      |             ^~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c suboptalign11.c 
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c pairlocalalignmain.c
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c pairlocalalign.c
pairlocalalign.c: In function 'calllast_once':
pairlocalalign.c:1056:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1056 |                 system( command );
      |                 ^~~~~~~~~~~~~~~~~
pairlocalalign.c:1092:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1092 |                 system( command );
      |                 ^~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'readlastresx':
pairlocalalign.c:608:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  608 |                 fgets( gett, 9999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'calllast_fast':
pairlocalalign.c:981:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  981 |                 system( command );
      |                 ^~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'lastcallthread':
pairlocalalign.c:872:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  872 |                                 system( command );
      |                                 ^~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'readlastresx_singleq':
pairlocalalign.c:374:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  374 |                 fgets( gett, 9999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'readhat4':
pairlocalalign.c:1532:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1532 |         fgets( oneline, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1544:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1544 |                 fgets( oneline, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'recalllara':
pairlocalalign.c:1245:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1245 |         fgets( com, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'callmxscarna_giving_bpp':
pairlocalalign.c:1408:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1408 |         system( com );
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1410:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1410 |         system( com );
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1430:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1430 |         system( com ); // for cygwin, wakaran
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1451:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1451 |         system( com ); // for cygwin, wakaran
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1465:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1465 |         system( com ); // for cygwin, wakaran
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1485:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1485 |         fgets( com, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1487:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1487 |         fgets( com, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'calldafs_giving_bpp':
pairlocalalign.c:1291:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1291 |         system( com );
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1293:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1293 |         system( com );
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1313:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1313 |         system( com ); // for cygwin, wakaran
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1334:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1334 |         system( com ); // for cygwin, wakaran
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1344:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1344 |         system( com ); // for cygwin, wakaran
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1364:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1364 |         fgets( com, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1366:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1366 |         fgets( com, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1368:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1368 |         fgets( com, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'pairalign_node':
pairlocalalign.c:3467:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 3467 |         system( "rm -rf hat3dir" ); // toriaezu
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:3468:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 3468 |         system( "mkdir hat3dir" ); // toriaezu
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:3473:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 3473 |                 system( fn );
      |                 ^~~~~~~~~~~~
pairlocalalign.c: In function 'putlocalhom_last.constprop.0.isra.0':
pairlocalalign.c:219:50: warning: 'localhompt0' may be used uninitialized [-Wmaybe-uninitialized]
  219 |                         for( tmppt2=localhompt0; tmppt2; tmppt2=tmppt2->next )
      |                                                  ^~~~~~
pairlocalalign.c:140:19: note: 'localhompt0' was declared here
  140 |         LocalHom *localhompt0;
      |                   ^~~~~~~~~~~
pairlocalalign.c: In function 'athread':
pairlocalalign.c:2237:66: warning: 'dumseq1' may be used uninitialized [-Wmaybe-uninitialized]
 2237 |                                                         pscore = genL__align11( n_dis_consweight_multi, dumseq1, dumseq2, alloclen, &dum1, &dum2 ); // uwagaki
      |                                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1955:58: note: 'dumseq1' was declared here
 1955 |         char **mseq1, **mseq2, **distseq1, **distseq2, **dumseq1, **dumseq2;
      |                                                          ^~~~~~~
pairlocalalign.c:2237:66: warning: 'dumseq2' may be used uninitialized [-Wmaybe-uninitialized]
 2237 |                                                         pscore = genL__align11( n_dis_consweight_multi, dumseq1, dumseq2, alloclen, &dum1, &dum2 ); // uwagaki
      |                                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1955:69: note: 'dumseq2' was declared here
 1955 |         char **mseq1, **mseq2, **distseq1, **distseq2, **dumseq1, **dumseq2;
      |                                                                     ^~~~~~~
pairlocalalign.c: In function 'pairlocalalign':
pairlocalalign.c:3212:17: warning: 'infp' may be used uninitialized [-Wmaybe-uninitialized]
 3212 |                 fclose( infp );
      |                 ^~~~~~~~~~~~~~
pairlocalalign.c:3100:15: note: 'infp' was declared here
 3100 |         FILE *infp;
      |               ^~~~
In function 'pairalign',
    inlined from 'pairlocalalign' at pairlocalalign.c:3257:2:
pairlocalalign.c:2776:82: warning: 'dumseq1' may be used uninitialized [-Wmaybe-uninitialized]
 2776 |                                                                         pscore = genL__align11( n_dis_consweight_multi, dumseq1, dumseq2, alloclen, &dum1, &dum2 ); // uwagaki
      |                                                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'pairlocalalign':
pairlocalalign.c:2405:16: note: 'dumseq1' was declared here
 2405 |         char **dumseq1, **dumseq2;
      |                ^~~~~~~
In function 'pairalign',
    inlined from 'pairlocalalign' at pairlocalalign.c:3257:2:
pairlocalalign.c:2776:82: warning: 'dumseq2' may be used uninitialized [-Wmaybe-uninitialized]
 2776 |                                                                         pscore = genL__align11( n_dis_consweight_multi, dumseq1, dumseq2, alloclen, &dum1, &dum2 ); // uwagaki
      |                                                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'pairlocalalign':
pairlocalalign.c:2405:27: note: 'dumseq2' was declared here
 2405 |         char **dumseq1, **dumseq2;
      |                           ^~~~~~~
gcc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairlocalalignmain.o pairlocalalign.o defs.o fft.o fftFunctions.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
In function 'Atracking',
    inlined from 'A__align.constprop' at Salignmm.c:2067:9:
Salignmm.c:959:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  959 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking',
    inlined from 'A__align.constprop' at Salignmm.c:2067:9:
Salignmm.c:961:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  961 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c multi2hat3s.c
multi2hat3s.c: In function 'pairalign':
multi2hat3s.c:143:15: warning: variable 'aseq' set but not used [-Wunused-but-set-variable]
  143 |         char *aseq;
      |               ^~~~
multi2hat3s.c:142:24: warning: variable 'effarr2' set but not used [-Wunused-but-set-variable]
  142 |         static double *effarr2 = NULL;
      |                        ^~~~~~~
gcc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o defs.o fft.o fftFunctions.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c pairash.c
pairash.c: In function 'pairalign':
pairash.c:1027:20: warning: variable 'clus2' set but not used [-Wunused-but-set-variable]
 1027 |         int clus1, clus2;
      |                    ^~~~~
pairash.c:1027:13: warning: variable 'clus1' set but not used [-Wunused-but-set-variable]
 1027 |         int clus1, clus2;
      |             ^~~~~
pairash.c: In function 'prepareash':
pairash.c:639:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  639 |                 fgets( line, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:681:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  681 |                 fgets( line, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'callrash':
pairash.c:485:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  485 |                 system( com );
      |                 ^~~~~~~~~~~~~
pairash.c: In function 'readrash':
pairash.c:277:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  277 |                 fgets( line, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:284:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  284 |                         fgets( line, 999, fp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:289:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  289 |                         fgets( line, 999, fp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:294:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  294 |                         fgets( line, 999, fp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'preparetmalign':
pairash.c:530:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  530 |                 fgets( line, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:576:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  576 |                 fgets( line, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:587:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  587 |                         system( command );
      |                         ^~~~~~~~~~~~~~~~~
pairash.c: In function 'checkcbeta':
pairash.c:321:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  321 |                 fgets( linec, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'calltmalign':
pairash.c:347:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  347 |                 system( com );
      |                 ^~~~~~~~~~~~~
pairash.c:356:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  356 |                         fgets( com, 100, fp );
      |                         ^~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'readtmalign':
pairash.c:228:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  228 |                 fgets( line, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:232:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  232 |         fgets( line, nlenmax*2, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairash.c:235:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  235 |         fgets( line, nlenmax*2, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairash.c:238:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  238 |         fgets( line, nlenmax*2, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'callrash.isra.0':
pairash.c:428:43: warning: '.' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=]
  428 |                 sprintf( cachefile, "%s/%s.%s.rash", cachedir, fname1, fname2 );
      |                                           ^
In file included from /usr/include/stdio.h:964,
                 from mltaln.h:12,
                 from pairash.c:1:
In function 'sprintf',
    inlined from 'callrash.isra.0' at pairash.c:428:3:
/usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output 8 or more bytes (assuming 10007) into a destination of size 10000
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
pairash.c: In function 'callrash.isra.0':
pairash.c:484:36: warning: '%s' directive writing up to 9999 bytes into a region of size 9996 [-Wformat-overflow=]
  484 |                 sprintf( com, "cat %s > %s.rashout", cachefile, pairid );
      |                                    ^~                ~~~~~~~~~
In function 'sprintf',
    inlined from 'callrash.isra.0' at pairash.c:484:3:
/usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 16 and 11014 bytes into a destination of size 10000
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
pairash.c: In function 'calltmalign.isra.0':
pairash.c:346:41: warning: '%s' directive writing up to 9999 bytes into a region of size 9991 [-Wformat-overflow=]
  346 |                 sprintf( com, "mkdir -p %s", cachedir );
      |                                         ^~   ~~~~~~~~
In function 'sprintf',
    inlined from 'calltmalign.isra.0' at pairash.c:346:3:
/usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 10 and 10009 bytes into a destination of size 10000
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
pairash.c: In function 'calltmalign.isra.0':
pairash.c:349:45: warning: '-' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=]
  349 |                 sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 );
      |                                             ^
In function 'sprintf',
    inlined from 'calltmalign.isra.0' at pairash.c:349:3:
/usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output 3 or more bytes (assuming 10002) into a destination of size 10000
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
pairash.c: In function 'preparetmalign.constprop.0':
pairash.c:586:50: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=]
  586 |                         sprintf( command, "cp %s %s.pdb", sline, fname );
      |                                                  ^~              ~~~~~
In function 'sprintf',
    inlined from 'preparetmalign.constprop.0' at pairash.c:586:4:
/usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output 9 or more bytes (assuming 1008) into a destination of size 1000
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
pairash.c: In function 'preparetmalign.constprop.0':
pairash.c:588:65: warning: '%s' directive writing up to 999 bytes into a region of size 983 [-Wformat-overflow=]
  588 |                         sprintf( command, "perl \"%s/clean.pl\" %s.pdb", whereispairalign, fname );
      |                                                                 ^~                         ~~~~~
In function 'sprintf',
    inlined from 'preparetmalign.constprop.0' at pairash.c:588:4:
/usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output 22 or more bytes (assuming 1021) into a destination of size 1000
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
In function 'pairalign',
    inlined from 'main' at pairash.c:1425:2:
pairash.c:1092:17: warning: 'checkseq' may be used uninitialized [-Wmaybe-uninitialized]
 1092 |                 strcpy( checkseq[i], seq[i] );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'main':
pairash.c:1041:16: note: 'checkseq' was declared here
 1041 |         char **checkseq;
      |                ^~~~~~~~
gcc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairash.o defs.o fft.o fftFunctions.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c addsingle.c
addsingle.c: In function 'addsinglethread':
addsingle.c:2038:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2038 |                 if( mergeoralign ) free( mergeoralign );  mergeoralign = NULL;
      |                 ^~
addsingle.c:2038:59: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2038 |                 if( mergeoralign ) free( mergeoralign );  mergeoralign = NULL;
      |                                                           ^~~~~~~~~~~~
addsingle.c:2039:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2039 |                 if( nogaplenjusttodecideaddhereornot ) free( nogaplenjusttodecideaddhereornot ); nogaplenjusttodecideaddhereornot = NULL;
      |                 ^~
addsingle.c:2039:98: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2039 |                 if( nogaplenjusttodecideaddhereornot ) free( nogaplenjusttodecideaddhereornot ); nogaplenjusttodecideaddhereornot = NULL;
      |                                                                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
addsingle.c:2040:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2040 |                 if( alnleninnode ) free( alnleninnode ); alnleninnode = NULL;
      |                 ^~
addsingle.c:2040:58: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2040 |                 if( alnleninnode ) free( alnleninnode ); alnleninnode = NULL;
      |                                                          ^~~~~~~~~~~~
addsingle.c:2041:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2041 |                 if( tmpseq ) free( tmpseq ); tmpseq = NULL;
      |                 ^~
addsingle.c:2041:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2041 |                 if( tmpseq ) free( tmpseq ); tmpseq = NULL;
      |                                              ^~~~~~
addsingle.c:2042:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2042 |                 if( bseq ) FreeCharMtx( bseq ); bseq = NULL;
      |                 ^~
addsingle.c:2042:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2042 |                 if( bseq ) FreeCharMtx( bseq ); bseq = NULL;
      |                                                 ^~~~
addsingle.c:2043:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2043 |                 if( namec ) free( namec ); namec = NULL;
      |                 ^~
addsingle.c:2043:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2043 |                 if( namec ) free( namec ); namec = NULL;
      |                                            ^~~~~
addsingle.c:2044:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2044 |                 if( nlenc ) free( nlenc  ); nlenc = NULL;
      |                 ^~
addsingle.c:2044:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2044 |                 if( nlenc ) free( nlenc  ); nlenc = NULL;
      |                                             ^~~~~
addsingle.c:2045:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2045 |                 if( depc ) free( depc ); depc = NULL;
      |                 ^~
addsingle.c:2045:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2045 |                 if( depc ) free( depc ); depc = NULL;
      |                                          ^~~~
addsingle.c:2046:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2046 |                 if( topolc ) FreeIntCub( topolc ); topolc = NULL;
      |                 ^~
addsingle.c:2046:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2046 |                 if( topolc ) FreeIntCub( topolc ); topolc = NULL;
      |                                                    ^~~~~~
addsingle.c:2047:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2047 |                 if( lenc ) FreeFloatMtx( lenc ); lenc = NULL;
      |                 ^~
addsingle.c:2047:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2047 |                 if( lenc ) FreeFloatMtx( lenc ); lenc = NULL;
      |                                                  ^~~~
addsingle.c:2048:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2048 |                 if( effc ) FreeDoubleVec( effc ); effc = NULL;
      |                 ^~
addsingle.c:2048:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2048 |                 if( effc ) FreeDoubleVec( effc ); effc = NULL;
      |                                                   ^~~~
addsingle.c:2049:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2049 |                 if( memlist0 ) free( memlist0 ); memlist0 = NULL;
      |                 ^~
addsingle.c:2049:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2049 |                 if( memlist0 ) free( memlist0 ); memlist0 = NULL;
      |                                                  ^~~~~~~~
addsingle.c:2050:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2050 |                 if( memlist1 ) free( memlist1 ); memlist1 = NULL;
      |                 ^~
addsingle.c:2050:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2050 |                 if( memlist1 ) free( memlist1 ); memlist1 = NULL;
      |                                                  ^~~~~~~~
addsingle.c:2051:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2051 |                 if( addmem ) free( addmem ); addmem = NULL;
      |                 ^~
addsingle.c:2051:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2051 |                 if( addmem ) free( addmem ); addmem = NULL;
      |                                              ^~~~~~
addsingle.c:2052:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2052 |                 if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                 ^~
addsingle.c:2052:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2052 |                 if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                                            ^~~~~
addsingle.c:2053:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2053 |                 if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                 ^~
addsingle.c:2053:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2053 |                 if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                                            ^~~~~
addsingle.c:1635:24: warning: variable 'pscore' set but not used [-Wunused-but-set-variable]
 1635 |                 double pscore;
      |                        ^~~~~~
addsingle.c:1634:26: warning: unused variable 'difflist' [-Wunused-variable]
 1634 |                 GapPos **difflist = targ->difflist;
      |                          ^~~~~~~~
addsingle.c: In function 'main':
addsingle.c:3835:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3835 |         if( addbk ) FreeCharMtx( addbk ); addbk = NULL;
      |         ^~
addsingle.c:3835:43: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3835 |         if( addbk ) FreeCharMtx( addbk ); addbk = NULL;
      |                                           ^~~~~
addsingle.c:3848:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3848 |         if( originalgaps ) free( originalgaps ); originalgaps = NULL;
      |         ^~
addsingle.c:3848:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3848 |         if( originalgaps ) free( originalgaps ); originalgaps = NULL;
      |                                                  ^~~~~~~~~~~~
addsingle.c:2974:25: warning: variable 'len_kozo' set but not used [-Wunused-but-set-variable]
 2974 |         static double **len_kozo;
      |                         ^~~~~~~~
addsingle.c:2972:23: warning: variable 'topol_kozo' set but not used [-Wunused-but-set-variable]
 2972 |         static int ***topol_kozo;
      |                       ^~~~~~~~~~
addsingle.c:2969:24: warning: variable 'eff_kozo' set but not used [-Wunused-but-set-variable]
 2969 |         static double *eff_kozo, *eff_kozo_mapped = NULL;
      |                        ^~~~~~~~
addsingle.c:2968:35: warning: variable 'iscore_kozo' set but not used [-Wunused-but-set-variable]
 2968 |         static double **iscore, **iscore_kozo;
      |                                   ^~~~~~~~~~~
addsingle.c:3532:33: warning: 'addtree' may be used uninitialized [-Wmaybe-uninitialized]
 3532 |                 targ[0].addtree = addtree;
      |                 ~~~~~~~~~~~~~~~~^~~~~~~~~
addsingle.c:3005:18: note: 'addtree' was declared here
 3005 |         Addtree *addtree;
      |                  ^~~~~~~
gcc -o addsingle mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o addsingle.o defs.o fft.o fftFunctions.o addfunctions.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:959:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  959 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:961:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  961 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking_localhom',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2062:3:
Salignmm.c:469:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  469 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking_localhom',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2062:3:
Salignmm.c:471:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  471 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
gcc -o maffttext2hex maffttext2hex.c  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
maffttext2hex.c: In function 'main':
maffttext2hex.c:55:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
   55 |                         fgets( (char *)buf, 999, fp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -o hex2maffttext hex2maffttext.c  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c splittbfast.c
splittbfast.c: In function 'callfasta':
splittbfast.c:317:20: warning: variable 'ninbk' set but not used [-Wunused-but-set-variable]
  317 |         static int ninbk = 0;
      |                    ^~~~~
splittbfast.c:316:24: warning: variable 'scoresbk' set but not used [-Wunused-but-set-variable]
  316 |         static Scores *scoresbk = NULL;
      |                        ^~~~~~~~
splittbfast.c: In function 'pairalign':
splittbfast.c:953:24: warning: variable 'tscore' set but not used [-Wunused-but-set-variable]
  953 |         double pscore, tscore;
      |                        ^~~~~~
splittbfast.c:953:16: warning: variable 'pscore' set but not used [-Wunused-but-set-variable]
  953 |         double pscore, tscore;
      |                ^~~~~~
splittbfast.c: In function 'splitseq_mq':
splittbfast.c:1491:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 1491 |         for( i=0; i<nin; i++ ) pickkouho[i] = i+1; nkouho = nin-1; // zenbu
      |         ^~~
splittbfast.c:1491:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1491 |         for( i=0; i<nin; i++ ) pickkouho[i] = i+1; nkouho = nin-1; // zenbu
      |                                                    ^~~~~~
splittbfast.c: In function 'main':
splittbfast.c:2696:13: warning: variable 'completed' set but not used [-Wunused-but-set-variable]
 2696 |         int completed;
      |             ^~~~~~~~~
splittbfast.c:3236:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 3236 |                 system( com );
      |                 ^~~~~~~~~~~~~
gcc -o splittbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o  Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o splittbfast.o defs.o fft.o fftFunctions.o   -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:959:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  959 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:961:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  961 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c disttbfast.c
disttbfast.c: In function 'checkanchors_strongestfirst_considerseparation':
disttbfast.c:1512:51: warning: operation on '(a + (sizetype)((long unsigned int)p * 28))->startj' may be undefined [-Wsequence-point]
 1512 |                         a[p].starti = a[p].startj = a[p].startj = a[p].endj = -1;
      |                                       ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
disttbfast.c:1552:59: warning: operation on '(a + (sizetype)((long unsigned int)q * 28))->startj' may be undefined [-Wsequence-point]
 1552 |                                 a[q].starti = a[q].startj = a[q].startj = a[q].endj = -1;
      |                                               ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
disttbfast.c: In function 'checkanchors_strongestfirst':
disttbfast.c:1613:59: warning: operation on '(a + (sizetype)((long unsigned int)q * 28))->startj' may be undefined [-Wsequence-point]
 1613 |                                 a[q].starti = a[q].startj = a[q].startj = a[q].endj = -1;
      |                                               ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
disttbfast.c: In function 'dooneiteration':
disttbfast.c:2650:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2650 |         if( effarr1 ) free( effarr1 ); effarr1 = NULL;
      |         ^~
disttbfast.c:2650:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2650 |         if( effarr1 ) free( effarr1 ); effarr1 = NULL;
      |                                        ^~~~~~~
disttbfast.c:2651:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2651 |         if( effarr2 ) free( effarr2 ); effarr2 = NULL;
      |         ^~
disttbfast.c:2651:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2651 |         if( effarr2 ) free( effarr2 ); effarr2 = NULL;
      |                                        ^~~~~~~
disttbfast.c:2652:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2652 |         if( indication1 ) free( indication1 ); indication1 = NULL;
      |         ^~
disttbfast.c:2652:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2652 |         if( indication1 ) free( indication1 ); indication1 = NULL;
      |                                                ^~~~~~~~~~~
disttbfast.c:2653:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2653 |         if( indication2 ) free( indication2 ); indication2 = NULL;
      |         ^~
disttbfast.c:2653:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2653 |         if( indication2 ) free( indication2 ); indication2 = NULL;
      |                                                ^~~~~~~~~~~
disttbfast.c:2654:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2654 |         if( fftlog ) free( fftlog ); fftlog = NULL;
      |         ^~
disttbfast.c:2654:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2654 |         if( fftlog ) free( fftlog ); fftlog = NULL;
      |                                      ^~~~~~
disttbfast.c:2655:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2655 |         if( alreadyaligned ) free( alreadyaligned ); alreadyaligned = NULL;
      |         ^~
disttbfast.c:2655:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2655 |         if( alreadyaligned ) free( alreadyaligned ); alreadyaligned = NULL;
      |                                                      ^~~~~~~~~~~~~~
disttbfast.c:2658:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2658 |                 if( dynamicmtx ) FreeDoubleMtx( dynamicmtx ); dynamicmtx = NULL;
      |                 ^~
disttbfast.c:2658:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2658 |                 if( dynamicmtx ) FreeDoubleMtx( dynamicmtx ); dynamicmtx = NULL;
      |                                                               ^~~~~~~~~~
disttbfast.c:2660:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2660 |         if( localmem ) free( localmem ); localmem = NULL;
      |         ^~
disttbfast.c:2660:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2660 |         if( localmem ) free( localmem ); localmem = NULL;
      |                                          ^~~~~~~~
disttbfast.c:2662:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2662 |         if( skiptable1 ) FreeIntMtx( skiptable1 ); skiptable1 = NULL;
      |         ^~
disttbfast.c:2662:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2662 |         if( skiptable1 ) FreeIntMtx( skiptable1 ); skiptable1 = NULL;
      |                                                    ^~~~~~~~~~
disttbfast.c:2663:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2663 |         if( skiptable2 ) FreeIntMtx( skiptable2 ); skiptable2 = NULL;
      |         ^~
disttbfast.c:2663:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2663 |         if( skiptable2 ) FreeIntMtx( skiptable2 ); skiptable2 = NULL;
      |                                                    ^~~~~~~~~~
disttbfast.c:2350:16: warning: variable 'pscore' set but not used [-Wunused-but-set-variable]
 2350 |         double pscore;
      |                ^~~~~~
disttbfast.c: In function 'treebase':
disttbfast.c:3229:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3229 |         if( effarr1 ) free( effarr1 ); effarr1 = NULL;
      |         ^~
disttbfast.c:3229:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3229 |         if( effarr1 ) free( effarr1 ); effarr1 = NULL;
      |                                        ^~~~~~~
disttbfast.c:3230:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3230 |         if( effarr2 ) free( effarr2 ); effarr2 = NULL;
      |         ^~
disttbfast.c:3230:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3230 |         if( effarr2 ) free( effarr2 ); effarr2 = NULL;
      |                                        ^~~~~~~
disttbfast.c:3231:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3231 |         if( indication1 ) free( indication1 ); indication1 = NULL;
      |         ^~
disttbfast.c:3231:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3231 |         if( indication1 ) free( indication1 ); indication1 = NULL;
      |                                                ^~~~~~~~~~~
disttbfast.c:3232:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3232 |         if( indication2 ) free( indication2 ); indication2 = NULL;
      |         ^~
disttbfast.c:3232:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3232 |         if( indication2 ) free( indication2 ); indication2 = NULL;
      |                                                ^~~~~~~~~~~
disttbfast.c:3233:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3233 |         if( fftlog ) free( fftlog ); fftlog = NULL;
      |         ^~
disttbfast.c:3233:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3233 |         if( fftlog ) free( fftlog ); fftlog = NULL;
      |                                      ^~~~~~
disttbfast.c:3234:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3234 |         if( gaplen ) free( gaplen ); gaplen = NULL;
      |         ^~
disttbfast.c:3234:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3234 |         if( gaplen ) free( gaplen ); gaplen = NULL;
      |                                      ^~~~~~
disttbfast.c:3235:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3235 |         if( gapmap ) free( gapmap ); gapmap = NULL;
      |         ^~
disttbfast.c:3235:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3235 |         if( gapmap ) free( gapmap ); gapmap = NULL;
      |                                      ^~~~~~
disttbfast.c:3236:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3236 |         if( alreadyaligned ) free( alreadyaligned ); alreadyaligned = NULL;
      |         ^~
disttbfast.c:3236:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3236 |         if( alreadyaligned ) free( alreadyaligned ); alreadyaligned = NULL;
      |                                                      ^~~~~~~~~~~~~~
disttbfast.c:3239:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3239 |                 if( dynamicmtx ) FreeDoubleMtx( dynamicmtx ); dynamicmtx = NULL;
      |                 ^~
disttbfast.c:3239:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3239 |                 if( dynamicmtx ) FreeDoubleMtx( dynamicmtx ); dynamicmtx = NULL;
      |                                                               ^~~~~~~~~~
disttbfast.c:3241:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3241 |         if( localmem ) free( localmem ); localmem = NULL;
      |         ^~
disttbfast.c:3241:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3241 |         if( localmem ) free( localmem ); localmem = NULL;
      |                                          ^~~~~~~~
disttbfast.c:3243:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3243 |         if( skiptable1 ) FreeIntMtx( skiptable1 ); skiptable1 = NULL;
      |         ^~
disttbfast.c:3243:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3243 |         if( skiptable1 ) FreeIntMtx( skiptable1 ); skiptable1 = NULL;
      |                                                    ^~~~~~~~~~
disttbfast.c:3244:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3244 |         if( skiptable2 ) FreeIntMtx( skiptable2 ); skiptable2 = NULL;
      |         ^~
disttbfast.c:3244:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3244 |         if( skiptable2 ) FreeIntMtx( skiptable2 ); skiptable2 = NULL;
      |                                                    ^~~~~~~~~~
disttbfast.c:2671:30: warning: variable 'len2nocommongap' set but not used [-Wunused-but-set-variable]
 2671 |         int len1nocommongap, len2nocommongap;
      |                              ^~~~~~~~~~~~~~~
disttbfast.c: In function 'disttbfast':
disttbfast.c:4151:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4151 |                                 if( mindistfrom ) free( mindistfrom ); mindistfrom = NULL;
      |                                 ^~
disttbfast.c:4151:72: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4151 |                                 if( mindistfrom ) free( mindistfrom ); mindistfrom = NULL;
      |                                                                        ^~~~~~~~~~~
disttbfast.c:4153:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4153 |                                 if( selfscore ) free( selfscore ); selfscore = NULL;
      |                                 ^~
disttbfast.c:4153:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4153 |                                 if( selfscore ) free( selfscore ); selfscore = NULL;
      |                                                                    ^~~~~~~~~
disttbfast.c:4154:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4154 |                                 if( bseq ) FreeCharMtx( bseq ); bseq = NULL; // nikaime dake
      |                                 ^~
disttbfast.c:4154:65: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4154 |                                 if( bseq ) FreeCharMtx( bseq ); bseq = NULL; // nikaime dake
      |                                                                 ^~~~
disttbfast.c:4155:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4155 |                                 if( skiptable) FreeIntMtx( skiptable ); skiptable = NULL; // nikaime dake
      |                                 ^~
disttbfast.c:4155:73: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4155 |                                 if( skiptable) FreeIntMtx( skiptable ); skiptable = NULL; // nikaime dake
      |                                                                         ^~~~~~~~~
disttbfast.c:4156:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4156 |                                 if( pointt ) FreeIntMtx( pointt ); pointt = NULL; // ikkaime dake.
      |                                 ^~
disttbfast.c:4156:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4156 |                                 if( pointt ) FreeIntMtx( pointt ); pointt = NULL; // ikkaime dake.
      |                                                                    ^~~~~~
disttbfast.c:4824:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4824 |                         if( skiptable) FreeIntMtx( skiptable ); skiptable = NULL;
      |                         ^~
disttbfast.c:4824:65: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4824 |                         if( skiptable) FreeIntMtx( skiptable ); skiptable = NULL;
      |                                                                 ^~~~~~~~~
disttbfast.c:5106:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5106 |         if( originalgaps ) free( originalgaps ); originalgaps = NULL;
      |         ^~
disttbfast.c:5106:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5106 |         if( originalgaps ) free( originalgaps ); originalgaps = NULL;
      |                                                  ^~~~~~~~~~~~
disttbfast.c:5120:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5120 |         if( nlen ) free( nlen ); nlen = NULL;
      |         ^~
disttbfast.c:5120:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5120 |         if( nlen ) free( nlen ); nlen = NULL;
      |                                  ^~~~
disttbfast.c:5121:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5121 |         if( seq ) FreeCharMtx( seq ); seq = NULL;
      |         ^~
disttbfast.c:5121:39: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5121 |         if( seq ) FreeCharMtx( seq ); seq = NULL;
      |                                       ^~~
disttbfast.c:5122:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5122 |         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |         ^~
disttbfast.c:5122:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5122 |         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                                    ^~~~~
disttbfast.c:5123:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5123 |         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |         ^~
disttbfast.c:5123:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5123 |         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                                    ^~~~~
disttbfast.c:5140:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5140 |         if( topol ) FreeIntCub( topol ); topol = NULL;
      |         ^~
disttbfast.c:5140:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5140 |         if( topol ) FreeIntCub( topol ); topol = NULL;
      |                                          ^~~~~
disttbfast.c:5141:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5141 |         if( len ) FreeFloatMtx( len ); len = NULL;
      |         ^~
disttbfast.c:5141:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5141 |         if( len ) FreeFloatMtx( len ); len = NULL;
      |                                        ^~~
disttbfast.c:5142:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5142 |         if( eff ) free( eff ); eff = NULL;
      |         ^~
disttbfast.c:5142:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5142 |         if( eff ) free( eff ); eff = NULL;
      |                                ^~~
disttbfast.c:5143:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5143 |         if( mergeoralign ) free( mergeoralign ); mergeoralign = NULL;
      |         ^~
disttbfast.c:5143:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5143 |         if( mergeoralign ) free( mergeoralign ); mergeoralign = NULL;
      |                                                  ^~~~~~~~~~~~
disttbfast.c:5144:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5144 |         if( dep ) free( dep ); dep = NULL;
      |         ^~
disttbfast.c:5144:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5144 |         if( dep ) free( dep ); dep = NULL;
      |                                ^~~
disttbfast.c:5145:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5145 |         if( addmem ) free( addmem ); addmem = NULL;
      |         ^~
disttbfast.c:5145:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5145 |         if( addmem ) free( addmem ); addmem = NULL;
      |                                      ^~~~~~
disttbfast.c:5146:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5146 |         if( localmem ) FreeIntMtx( localmem ); localmem = NULL;
      |         ^~
disttbfast.c:5146:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5146 |         if( localmem ) FreeIntMtx( localmem ); localmem = NULL;
      |                                                ^~~~~~~~
disttbfast.c:5147:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5147 |         if( name ) FreeCharMtx( name ); name = NULL;
      |         ^~
disttbfast.c:5147:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5147 |         if( name ) FreeCharMtx( name ); name = NULL;
      |                                         ^~~~
disttbfast.c:5148:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5148 |         if( nogaplen ) free( nogaplen ); nogaplen = NULL;
      |         ^~
disttbfast.c:5148:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5148 |         if( nogaplen ) free( nogaplen ); nogaplen = NULL;
      |                                          ^~~~~~~~
disttbfast.c:5150:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5150 |         if( tmpseq ) free( tmpseq ); tmpseq = NULL;
      |         ^~
disttbfast.c:5150:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5150 |         if( tmpseq ) free( tmpseq ); tmpseq = NULL;
      |                                      ^~~~~~
disttbfast.c:5151:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5151 |         if( grpseq ) free( grpseq ); grpseq = NULL;
      |         ^~
disttbfast.c:5151:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5151 |         if( grpseq ) free( grpseq ); grpseq = NULL;
      |                                      ^~~~~~
disttbfast.c:5152:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5152 |         if( pointt ) FreeIntMtx( pointt ); pointt = NULL;
      |         ^~
disttbfast.c:5152:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5152 |         if( pointt ) FreeIntMtx( pointt ); pointt = NULL;
      |                                            ^~~~~~
disttbfast.c:5153:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5153 |         if( mtx ) FreeFloatHalfMtx( mtx, njob ); mtx = NULL;
      |         ^~
disttbfast.c:5153:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5153 |         if( mtx ) FreeFloatHalfMtx( mtx, njob ); mtx = NULL;
      |                                                  ^~~
disttbfast.c:5154:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5154 |         if( table1 ) free( table1 ); table1 = NULL;
      |         ^~
disttbfast.c:5154:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5154 |         if( table1 ) free( table1 ); table1 = NULL;
      |                                      ^~~~~~
disttbfast.c:5156:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5156 |         if( bseq ) FreeCharMtx( bseq ); bseq = NULL;
      |         ^~
disttbfast.c:5156:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5156 |         if( bseq ) FreeCharMtx( bseq ); bseq = NULL;
      |                                         ^~~~
disttbfast.c:5157:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5157 |         if( selfscore ) free( selfscore ); selfscore = NULL;
      |         ^~
disttbfast.c:5157:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5157 |         if( selfscore ) free( selfscore ); selfscore = NULL;
      |                                            ^~~~~~~~~
disttbfast.c:5158:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5158 |         if( skiptable ) FreeIntMtx( skiptable ); skiptable = NULL;
      |         ^~
disttbfast.c:5158:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5158 |         if( skiptable ) FreeIntMtx( skiptable ); skiptable = NULL;
      |                                                  ^~~~~~~~~
disttbfast.c:5159:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5159 |         if( originalgaps ) free( originalgaps ); originalgaps = NULL;
      |         ^~
disttbfast.c:5159:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5159 |         if( originalgaps ) free( originalgaps ); originalgaps = NULL;
      |                                                  ^~~~~~~~~~~~
disttbfast.c:5168:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5168 |         if( subtable ) FreeIntMtx( subtable ); subtable = NULL;
      |         ^~
disttbfast.c:5168:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5168 |         if( subtable ) FreeIntMtx( subtable ); subtable = NULL;
      |                                                ^~~~~~~~
disttbfast.c:5169:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5169 |         if( insubtable ) free( insubtable ); insubtable = NULL;
      |         ^~
disttbfast.c:5169:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5169 |         if( insubtable ) free( insubtable ); insubtable = NULL;
      |                                              ^~~~~~~~~~
disttbfast.c:5172:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5172 |                 if( subalnpt[i] ) free( subalnpt[i] ); subalnpt[i] = NULL;
      |                 ^~
disttbfast.c:5172:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5172 |                 if( subalnpt[i] ) free( subalnpt[i] ); subalnpt[i] = NULL;
      |                                                        ^~~~~~~~
disttbfast.c:5174:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5174 |         if( subalnpt ) free( subalnpt ); subalnpt = NULL;
      |         ^~
disttbfast.c:5174:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5174 |         if( subalnpt ) free( subalnpt ); subalnpt = NULL;
      |                                          ^~~~~~~~
disttbfast.c:5175:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5175 |         if( preservegaps ) free( preservegaps ); preservegaps = NULL;
      |         ^~
disttbfast.c:5175:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5175 |         if( preservegaps ) free( preservegaps ); preservegaps = NULL;
      |                                                  ^~~~~~~~~~~~
disttbfast.c:5178:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5178 |         if( mindistfrom ) free( mindistfrom ); mindistfrom = NULL;
      |         ^~
disttbfast.c:5178:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5178 |         if( mindistfrom ) free( mindistfrom ); mindistfrom = NULL;
      |                                                ^~~~~~~~~~~
disttbfast.c:5179:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5179 |         if( mindist ) free( mindist ); mindist = NULL;
      |         ^~
disttbfast.c:5179:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5179 |         if( mindist ) free( mindist ); mindist = NULL;
      |                                        ^~~~~~~
disttbfast.c:5185:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5185 |                         if( cpmxhist[i] ) FreeDoubleMtx( cpmxhist[i] ); cpmxhist[i] = NULL;
      |                         ^~
disttbfast.c:5185:73: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5185 |                         if( cpmxhist[i] ) FreeDoubleMtx( cpmxhist[i] ); cpmxhist[i] = NULL;
      |                                                                         ^~~~~~~~
disttbfast.c:5194:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5194 |                         if( memhist[i] ) free( memhist[i] ); memhist[i] = NULL;
      |                         ^~
disttbfast.c:5194:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5194 |                         if( memhist[i] ) free( memhist[i] ); memhist[i] = NULL;
      |                                                              ^~~~~~~
disttbfast.c:3412:13: warning: variable 'posinmem' set but not used [-Wunused-but-set-variable]
 3412 |         int posinmem;
      |             ^~~~~~~~
disttbfast.c:4517:41: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 4517 |                                         system( "cp infile.tree GuideTree" ); // tekitou
      |                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'checkanchors_strongestfirst_considerseparation',
    inlined from 'pickpairanch' at disttbfast.c:1814:3:
disttbfast.c:1495:30: warning: 'nearest' may be used uninitialized [-Wmaybe-uninitialized]
 1495 |                         if( a[nearest].starti < a[p].starti )
      |                              ^
disttbfast.c: In function 'pickpairanch':
disttbfast.c:1480:21: note: 'nearest' was declared here
 1480 |                 int nearest, mindist;
      |                     ^~~~~~~
disttbfast.c: In function 'treebasethread':
disttbfast.c:1933:33: warning: 'dynamicmtx' may be used uninitialized [-Wmaybe-uninitialized]
 1933 |                                 FreeDoubleMtx( dynamicmtx );
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~
disttbfast.c:1865:18: note: 'dynamicmtx' was declared here
 1865 |         double **dynamicmtx;
      |                  ^~~~~~~~~~
gcc -o disttbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
mltaln9.c: In function 'fixed_musclesupg_double_realloc_nobk_halfmtx_treeout_memsave.isra':
mltaln9.c:6494:28: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 6494 |                 int *mem = calloc( sizeof( int ), nseq );
      |                            ^
/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:959:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  959 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:961:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  961 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'fgets',
    inlined from 'check_guidetreefile' at mltaln9.c:2850:2,
    inlined from 'disttbfast.constprop' at disttbfast.c:3623:12:
/usr/include/bits/stdio2.h:215:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  215 |     return __fgets_chk_warn (__s, sz, __n, __stream);
      |            ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c tbfast.c
tbfast.c: In function 'treebasethread':
tbfast.c:815:13: warning: variable 'posinmem' set but not used [-Wunused-but-set-variable]
  815 |         int posinmem;
      |             ^~~~~~~~
tbfast.c:800:16: warning: variable 'pscore' set but not used [-Wunused-but-set-variable]
  800 |         double pscore;
      |                ^~~~~~
tbfast.c: In function 'treebase':
tbfast.c:1252:13: warning: unused variable 'posinmem' [-Wunused-variable]
 1252 |         int posinmem;
      |             ^~~~~~~~
tbfast.c:1227:30: warning: variable 'len2nocommongap' set but not used [-Wunused-but-set-variable]
 1227 |         int len1nocommongap, len2nocommongap;
      |                              ^~~~~~~~~~~~~~~
tbfast.c: In function 'preparepartmtx':
tbfast.c:1869:16: warning: variable 'size' set but not used [-Wunused-but-set-variable]
 1869 |         double size;
      |                ^~~~
tbfast.c: In function 'main':
tbfast.c:2174:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2174 |                         if( expdist ) FreeDoubleMtx( expdist ); expdist = NULL;
      |                         ^~
tbfast.c:2174:65: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2174 |                         if( expdist ) FreeDoubleMtx( expdist ); expdist = NULL;
      |                                                                 ^~~~~~~
tbfast.c:2329:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2329 |                         if( expdist ) FreeDoubleMtx( expdist ); expdist = NULL;
      |                         ^~
tbfast.c:2329:65: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2329 |                         if( expdist ) FreeDoubleMtx( expdist ); expdist = NULL;
      |                                                                 ^~~~~~~
tbfast.c:2890:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2890 |                         if( mindistfrom ) free( mindistfrom ); mindistfrom = NULL;
      |                         ^~
tbfast.c:2890:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2890 |                         if( mindistfrom ) free( mindistfrom ); mindistfrom = NULL;
      |                                                                ^~~~~~~~~~~
tbfast.c:2893:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2893 |                         if( skiptable) FreeIntMtx( skiptable ); skiptable = NULL; // nikaime dake
      |                         ^~
tbfast.c:2893:65: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2893 |                         if( skiptable) FreeIntMtx( skiptable ); skiptable = NULL; // nikaime dake
      |                                                                 ^~~~~~~~~
tbfast.c:3008:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3008 |         if( iscore ) FreeFloatHalfMtx( iscore, njob ); iscore = NULL;
      |         ^~
tbfast.c:3008:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3008 |         if( iscore ) FreeFloatHalfMtx( iscore, njob ); iscore = NULL;
      |                                                        ^~~~~~
tbfast.c:3009:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3009 |         if( iscore_kozo ) FreeFloatHalfMtx( iscore_kozo, nkozo ); iscore = NULL;
      |         ^~
tbfast.c:3009:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3009 |         if( iscore_kozo ) FreeFloatHalfMtx( iscore_kozo, nkozo ); iscore = NULL;
      |                                                                   ^~~~~~
tbfast.c:3010:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3010 |         if( topol_kozo ) FreeIntCub( topol_kozo ); topol_kozo = NULL;
      |         ^~
tbfast.c:3010:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3010 |         if( topol_kozo ) FreeIntCub( topol_kozo ); topol_kozo = NULL;
      |                                                    ^~~~~~~~~~
tbfast.c:3011:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3011 |         if( len_kozo ) FreeFloatMtx( len_kozo ); len_kozo = NULL;
      |         ^~
tbfast.c:3011:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3011 |         if( len_kozo ) FreeFloatMtx( len_kozo ); len_kozo = NULL;
      |                                                  ^~~~~~~~
tbfast.c:3012:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3012 |         if( eff_kozo ) free( eff_kozo ); eff_kozo = NULL;
      |         ^~
tbfast.c:3012:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3012 |         if( eff_kozo ) free( eff_kozo ); eff_kozo = NULL;
      |                                          ^~~~~~~~
tbfast.c:3565:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3565 |         if( constraint && compacttree == 3 && uselh ) free( uselh ); uselh = NULL;
      |         ^~
tbfast.c:3565:70: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3565 |         if( constraint && compacttree == 3 && uselh ) free( uselh ); uselh = NULL;
      |                                                                      ^~~~~
tbfast.c:3602:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3602 |         if( nfilesfornode ) free( nfilesfornode ); nfilesfornode = NULL;
      |         ^~
tbfast.c:3602:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3602 |         if( nfilesfornode ) free( nfilesfornode ); nfilesfornode = NULL;
      |                                                    ^~~~~~~~~~~~~
tbfast.c:3606:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3606 |         if( eff_kozo_mapped ) free( eff_kozo_mapped ); eff_kozo_mapped = NULL;
      |         ^~
tbfast.c:3606:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3606 |         if( eff_kozo_mapped ) free( eff_kozo_mapped ); eff_kozo_mapped = NULL;
      |                                                        ^~~~~~~~~~~~~~~
tbfast.c:3611:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3611 |         if( seq ) FreeCharMtx( seq ); seq = NULL;
      |         ^~
tbfast.c:3611:39: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3611 |         if( seq ) FreeCharMtx( seq ); seq = NULL;
      |                                       ^~~
tbfast.c:3612:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3612 |         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |         ^~
tbfast.c:3612:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3612 |         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                                    ^~~~~
tbfast.c:3613:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3613 |         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |         ^~
tbfast.c:3613:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3613 |         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                                    ^~~~~
tbfast.c:3615:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3615 |         if( name ) FreeCharMtx( name ); name = NULL;
      |         ^~
tbfast.c:3615:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3615 |         if( name ) FreeCharMtx( name ); name = NULL;
      |                                         ^~~~
tbfast.c:3616:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3616 |         if( nlen ) free( nlen ); nlen = NULL;
      |         ^~
tbfast.c:3616:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3616 |         if( nlen ) free( nlen ); nlen = NULL;
      |                                  ^~~~
tbfast.c:3617:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3617 |         if( selfscore ) free( selfscore ); selfscore = NULL;
      |         ^~
tbfast.c:3617:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3617 |         if( selfscore ) free( selfscore ); selfscore = NULL;
      |                                            ^~~~~~~~~
tbfast.c:3618:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3618 |         if( mergeoralign ) free( mergeoralign ); mergeoralign = NULL;
      |         ^~
tbfast.c:3618:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3618 |         if( mergeoralign ) free( mergeoralign ); mergeoralign = NULL;
      |                                                  ^~~~~~~~~~~~
tbfast.c:3629:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3629 |         if( targetmap ) free( targetmap ); targetmap = NULL;
      |         ^~
tbfast.c:3629:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3629 |         if( targetmap ) free( targetmap ); targetmap = NULL;
      |                                            ^~~~~~~~~
tbfast.c:3630:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3630 |         if( targetmapr ) free( targetmapr ); targetmapr = NULL;
      |         ^~
tbfast.c:3630:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3630 |         if( targetmapr ) free( targetmapr ); targetmapr = NULL;
      |                                              ^~~~~~~~~~
tbfast.c:3631:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3631 |         if( uselh ) free( uselh ); uselh = NULL;
      |         ^~
tbfast.c:3631:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3631 |         if( uselh ) free( uselh ); uselh = NULL;
      |                                    ^~~~~
tbfast.c:3633:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3633 |         if( kozoarivec ) free( kozoarivec ); kozoarivec = NULL;
      |         ^~
tbfast.c:3633:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3633 |         if( kozoarivec ) free( kozoarivec ); kozoarivec = NULL;
      |                                              ^~~~~~~~~~
tbfast.c:3634:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3634 |         if( eff_kozo_mapped ) free( eff_kozo_mapped ); eff_kozo_mapped = NULL;
      |         ^~
tbfast.c:3634:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3634 |         if( eff_kozo_mapped ) free( eff_kozo_mapped ); eff_kozo_mapped = NULL;
      |                                                        ^~~~~~~~~~~~~~~
tbfast.c:3635:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3635 |         if( eff_kozo ) free( eff_kozo ); eff_kozo = NULL;
      |         ^~
tbfast.c:3635:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3635 |         if( eff_kozo ) free( eff_kozo ); eff_kozo = NULL;
      |                                          ^~~~~~~~
tbfast.c:3638:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3638 |         if( topol ) FreeIntCub( topol ); topol = NULL;
      |         ^~
tbfast.c:3638:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3638 |         if( topol ) FreeIntCub( topol ); topol = NULL;
      |                                          ^~~~~
tbfast.c:3639:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3639 |         if( topol_kozo ) FreeIntCub( topol_kozo ); topol_kozo = NULL;
      |         ^~
tbfast.c:3639:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3639 |         if( topol_kozo ) FreeIntCub( topol_kozo ); topol_kozo = NULL;
      |                                                    ^~~~~~~~~~
tbfast.c:3640:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3640 |         if( len ) FreeFloatMtx( len ); len = NULL;
      |         ^~
tbfast.c:3640:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3640 |         if( len ) FreeFloatMtx( len ); len = NULL;
      |                                        ^~~
tbfast.c:3641:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3641 |         if( len_kozo ) FreeFloatMtx( len_kozo ); len_kozo = NULL;
      |         ^~
tbfast.c:3641:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3641 |         if( len_kozo ) FreeFloatMtx( len_kozo ); len_kozo = NULL;
      |                                                  ^~~~~~~~
tbfast.c:3642:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3642 |         if( iscore ) FreeFloatHalfMtx( iscore, njob ); iscore = NULL;
      |         ^~
tbfast.c:3642:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3642 |         if( iscore ) FreeFloatHalfMtx( iscore, njob ); iscore = NULL;
      |                                                        ^~~~~~
tbfast.c:3643:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3643 |         if( iscore_kozo && nseed ) FreeFloatHalfMtx( iscore_kozo, nseed ); iscore = NULL; // ? nseed?
      |         ^~
tbfast.c:3643:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3643 |         if( iscore_kozo && nseed ) FreeFloatHalfMtx( iscore_kozo, nseed ); iscore = NULL; // ? nseed?
      |                                                                            ^~~~~~
tbfast.c:3644:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3644 |         if( eff ) free( eff ); eff = NULL;
      |         ^~
tbfast.c:3644:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3644 |         if( eff ) free( eff ); eff = NULL;
      |                                ^~~
tbfast.c:3645:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3645 |         if( dep ) free( dep ); dep = NULL;
      |         ^~
tbfast.c:3645:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3645 |         if( dep ) free( dep ); dep = NULL;
      |                                ^~~
tbfast.c:3646:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3646 |         if( nfilesfornode ) free( nfilesfornode ); nfilesfornode = NULL;
      |         ^~
tbfast.c:3646:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3646 |         if( nfilesfornode ) free( nfilesfornode ); nfilesfornode = NULL;
      |                                                    ^~~~~~~~~~~~~
tbfast.c:3648:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3648 |         if( addmem ) free( addmem ); addmem = NULL;
      |         ^~
tbfast.c:3648:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3648 |         if( addmem ) free( addmem ); addmem = NULL;
      |                                      ^~~~~~
tbfast.c:3649:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3649 |         if( localmem ) FreeIntMtx( localmem ); localmem = NULL;
      |         ^~
tbfast.c:3649:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3649 |         if( localmem ) FreeIntMtx( localmem ); localmem = NULL;
      |                                                ^~~~~~~~
tbfast.c:1916:13: warning: variable 'posinmem' set but not used [-Wunused-but-set-variable]
 1916 |         int posinmem;
      |             ^~~~~~~~
tbfast.c:3254:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 3254 |                                 system( "cp infile.tree GuideTree" ); // tekitou
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tbfast.c:2864:25: warning: 'subtable' may be used uninitialized [-Wmaybe-uninitialized]
 2864 |                         fixed_supg_double_realloc_nobk_halfmtx_treeout_constrained( njob, iscore, topol, len, name, nlen, dep, nsubalignments, subtable, 1 );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tbfast.c:1907:15: note: 'subtable' was declared here
 1907 |         int **subtable;
      |               ^~~~~~~~
tbfast.c:3233:43: warning: 'insubtable' may be used uninitialized [-Wmaybe-uninitialized]
 3233 |                                 insubtable[subtable[i][j]] = 1;
      |                                           ^
tbfast.c:1908:14: note: 'insubtable' was declared here
 1908 |         int *insubtable;
      |              ^~~~~~~~~~
tbfast.c:3309:17: warning: 'preservegaps' may be used uninitialized [-Wmaybe-uninitialized]
 3309 |                 free( preservegaps );
      |                 ^~~~~~~~~~~~~~~~~~~~
tbfast.c:1909:14: note: 'preservegaps' was declared here
 1909 |         int *preservegaps;
      |              ^~~~~~~~~~~~
tbfast.c:3308:17: warning: 'subalnpt' may be used uninitialized [-Wmaybe-uninitialized]
 3308 |                 free( subalnpt );
      |                 ^~~~~~~~~~~~~~~~
tbfast.c:1910:17: note: 'subalnpt' was declared here
 1910 |         char ***subalnpt;
      |                 ^~~~~~~~
tbfast.c:3434:9: warning: 'ntarget' may be used uninitialized [-Wmaybe-uninitialized]
 3434 |         treebase( nlen, bseq, nadd, mergeoralign, mseq1, mseq2, topol, dep, eff, &alloclen, localhomtable, singlerna, eff_kozo_mapped, targetmap, targetmapr, ntarget, uselh, nseed, nfilesfornode );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tbfast.c:1932:13: note: 'ntarget' was declared here
 1932 |         int ntarget;
      |             ^~~~~~~
tbfast.c:2887:25: warning: 'skiptable' may be used uninitialized [-Wmaybe-uninitialized]
 2887 |                         compacttree_memsaveselectable( njob, partmtx, mindistfrom, mindist, NULL, selfscore, seq, skiptable, topol, len, name, NULL, dep, treeout, compacttree, 1 );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tbfast.c:1890:15: note: 'skiptable' was declared here
 1890 |         int **skiptable;
      |               ^~~~~~~~~
gcc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o tbfast.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o   -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
In function 'fgets',
    inlined from 'check_guidetreefile' at mltaln9.c:2850:2:
/usr/include/bits/stdio2.h:215:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  215 |     return __fgets_chk_warn (__s, sz, __n, __stream);
      |            ^
In function 'Atracking',
    inlined from 'A__align.constprop' at Salignmm.c:2067:9:
Salignmm.c:959:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  959 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking',
    inlined from 'A__align.constprop' at Salignmm.c:2067:9:
Salignmm.c:961:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  961 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking_localhom',
    inlined from 'A__align.constprop' at Salignmm.c:2062:3:
Salignmm.c:469:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  469 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking_localhom',
    inlined from 'A__align.constprop' at Salignmm.c:2062:3:
Salignmm.c:471:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  471 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
mltaln9.c: In function 'fixed_musclesupg_double_realloc_nobk_halfmtx_treeout_memsave.constprop':
mltaln9.c:6494:28: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 6494 |                 int *mem = calloc( sizeof( int ), nseq );
      |                            ^
/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c nodepair.c
gcc -o nodepair mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o nodepair.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c mafft-profile.c
mafft-profile.c: In function 'GroupAlign':
mafft-profile.c:190:17: warning: variable 's2' set but not used [-Wunused-but-set-variable]
  190 |         int s1, s2;
      |                 ^~
mafft-profile.c:190:13: warning: variable 's1' set but not used [-Wunused-but-set-variable]
  190 |         int s1, s2;
      |             ^~
mafft-profile.c: In function 'main':
mafft-profile.c:321:23: warning: variable 'bseq' set but not used [-Wunused-but-set-variable]
  321 |         static char **bseq;
      |                       ^~~~
gcc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o SAalignmm.o Galign11.o Lalign11.o genalign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
In function 'Atracking',
    inlined from 'A__align.constprop' at Salignmm.c:2067:9:
Salignmm.c:959:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  959 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking',
    inlined from 'A__align.constprop' at Salignmm.c:2067:9:
Salignmm.c:961:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  961 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c f2cl.c
f2cl.c: In function 'main':
f2cl.c:297:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  297 |                         fgets( gett, B-1, orderfp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c mccaskillwrap.c
mccaskillwrap.c: In function 'main':
mccaskillwrap.c:372:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  372 |                         system( "tr -d '\\r' < _mccaskillinorg > _mccaskillin" ); // for cygwin, wakaran
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mccaskillwrap.c: In function 'athread':
mccaskillwrap.c:115:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  115 |                 system( com );
      |                 ^~~~~~~~~~~~~
mccaskillwrap.c:117:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  117 |                 system( com );
      |                 ^~~~~~~~~~~~~
mccaskillwrap.c:129:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  129 |                 system( com ); // for cygwin, wakaran
      |                 ^~~~~~~~~~~~~
mccaskillwrap.c:155:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  155 |                         system( com );
      |                         ^~~~~~~~~~~~~
mccaskillwrap.c: In function 'readrawmccaskill':
mccaskillwrap.c:46:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
   46 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
gcc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c contrafoldwrap.c
contrafoldwrap.c: In function 'readcontrafold':
contrafoldwrap.c:57:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
   57 |                 fgets( gett, 9999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~
gcc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c countlen.c
gcc -o countlen mtxutl.o io.o countlen.o defs.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c seq2regtable.c
seq2regtable.c: In function 'main':
seq2regtable.c:79:17: warning: 'weboutfp' may be used uninitialized [-Wmaybe-uninitialized]
   79 |                 getnumlen_nogap_outallreg_web( infp, weboutfp, &nlenmin, &isaligned );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seq2regtable.c:48:15: note: 'weboutfp' was declared here
   48 |         FILE *weboutfp;
      |               ^~~~~~~~
gcc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c regtable2seq.c
regtable2seq.c: In function 'readereg':
regtable2seq.c:69:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
   69 |         fgets( gett, 999, regfp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~
regtable2seq.c:97:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
   97 |                 fgets( gett, 999, regfp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~
regtable2seq.c: In function 'readreg':
regtable2seq.c:120:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  120 |                 fgets( gett, 999, regfp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c score.c
gcc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c getlag.c
getlag.c: In function 'treebase':
getlag.c:168:25: warning: variable 'partialeff' set but not used [-Wunused-but-set-variable]
  168 |         static double **partialeff = NULL;
      |                         ^~~~~~~~~~
getlag.c:167:25: warning: variable 'partiallen' set but not used [-Wunused-but-set-variable]
  167 |         static double **partiallen = NULL;
      |                         ^~~~~~~~~~
getlag.c:165:25: warning: variable 'partialmtx' set but not used [-Wunused-but-set-variable]
  165 |         static double **partialmtx = NULL;
      |                         ^~~~~~~~~~
getlag.c:162:16: warning: variable 'pscore' set but not used [-Wunused-but-set-variable]
  162 |         double pscore;
      |                ^~~~~~
getlag.c: In function 'WriteOptions':
getlag.c:282:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
  282 |     else
      |     ^~~~
getlag.c:285:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
  285 |         if( alg == 'a' )
      |         ^~
getlag.c: In function 'main':
getlag.c:335:34: warning: variable 'node1' set but not used [-Wunused-but-set-variable]
  335 |         static double **node0, **node1;
      |                                  ^~~~~
gcc -o getlag mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o Dalignmm.o getlag.o defs.o fft.o fftFunctions.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:959:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  959 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:961:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  961 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c dndpre.c
dndpre.c: In function 'main':
dndpre.c:517:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  517 |         if( skiptable ) FreeIntMtx( skiptable ); skiptable = NULL;
      |         ^~
dndpre.c:517:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  517 |         if( skiptable ) FreeIntMtx( skiptable ); skiptable = NULL;
      |                                                  ^~~~~~~~~
gcc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c setcore.c
setcore.c: In function 'main':
setcore.c:288:34: warning: variable 'node1' set but not used [-Wunused-but-set-variable]
  288 |         static double **node0, **node1;
      |                                  ^~~~~
gcc -o setcore mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o setcore.o defs.o fft.o fftFunctions.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -c -o filter.o filter.c
filter.c: In function 'count_unusual':
filter.c:11:20: warning: unused variable 'len' [-Wunused-variable]
   11 |         int count, len;
      |                    ^~~
filter.c:9:13: warning: unused variable 'i' [-Wunused-variable]
    9 |         int i;
      |             ^
filter.c: In function 'shortenN':
filter.c:26:13: warning: unused variable 'i' [-Wunused-variable]
   26 |         int i;
      |             ^
gcc -o filter mtxutl.o io.o filter.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c replaceu.c
gcc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c restoreu.c
restoreu.c: In function 'main':
restoreu.c:185:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  185 |                         fgets( gett, 999, dlfp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~
restoreu.c:186:29: warning: 'dlfp' may be used uninitialized [-Wmaybe-uninitialized]
  186 |                         if( feof( dlfp ) ) break;
      |                             ^~~~~~~~~~~~
restoreu.c:91:15: note: 'dlfp' was declared here
   91 |         FILE *dlfp;
      |               ^~~~
gcc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c setdirection.c
setdirection.c: In function 'main':
setdirection.c:132:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  132 |                 fgets( line, 99, difp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:964,
                 from mltaln.h:12,
                 from setdirection.c:1:
In function 'fgets',
    inlined from 'main' at setdirection.c:132:3:
/usr/include/bits/stdio2.h:213:12: warning: 'difp' may be used uninitialized [-Wmaybe-uninitialized]
  213 |     return __fgets_alias (__s, __n, __stream);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
setdirection.c: In function 'main':
setdirection.c:66:15: note: 'difp' was declared here
   66 |         FILE *difp;
      |               ^~~~
gcc -o setdirection mtxutl.o io.o setdirection.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c makedirectionlist.c
makedirectionlist.c: In function 'directionthread':
makedirectionlist.c:646:34: warning: 'mseq1' may be used uninitialized [-Wmaybe-uninitialized]
  646 |                         res[j] = L__align11_noalign( n_dis_consweight_multi, mseq1, mseq2 );
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
makedirectionlist.c:600:16: note: 'mseq1' was declared here
  600 |         char **mseq1, **mseq2;
      |                ^~~~~
makedirectionlist.c:646:34: warning: 'mseq2' may be used uninitialized [-Wmaybe-uninitialized]
  646 |                         res[j] = L__align11_noalign( n_dis_consweight_multi, mseq1, mseq2 );
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
makedirectionlist.c:600:25: note: 'mseq2' was declared here
  600 |         char **mseq1, **mseq2;
      |                         ^~~~~
makedirectionlist.c: In function 'main':
makedirectionlist.c:891:33: warning: 'pointt' may be used uninitialized [-Wmaybe-uninitialized]
  891 |                                 makepointtable_nuc( pointt[i], grpseq );
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
makedirectionlist.c:683:16: note: 'pointt' was declared here
  683 |         int  **pointt, **pointt_rev, **spointt;
      |                ^~~~~~
makedirectionlist.c:909:33: warning: 'pointt_rev' may be used uninitialized [-Wmaybe-uninitialized]
  909 |                                 makepointtable_nuc( pointt_rev[i], grpseq );
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
makedirectionlist.c:683:26: note: 'pointt_rev' was declared here
  683 |         int  **pointt, **pointt_rev, **spointt;
      |                          ^~~~~~~~~~
makedirectionlist.c:892:44: warning: 'spointt' may be used uninitialized [-Wmaybe-uninitialized]
  892 |                                 spointt[i] = pointt[i];
      |                                 ~~~~~~~~~~~^~~~~~~~~~~
makedirectionlist.c:683:40: note: 'spointt' was declared here
  683 |         int  **pointt, **pointt_rev, **spointt;
      |                                        ^~~~~~~
gcc -o makedirectionlist mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o  Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread
gcc -o version version.c  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lm  -lpthread 
sed "s:_LIBDIR:/usr/local/libexec/mafft:" mafft.tmpl  > mafft
sed "s:_BINDIR:/usr/local/bin:" mafft-homologs.tmpl  > mafft-homologs.rb
sed "s:_BINDIR:/usr/local/bin:" mafft-sparsecore.tmpl  > mafft-sparsecore.rb
cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts
chmod 755 ../scripts/*
cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  ../binaries
chmod 755 ../binaries/*
done.
+ cd ../extensions
+ make clean
rm -f *.o *.a *.exe *~ mxscarnamod
make clean -C mxscarna_src
make[1]: Entering directory '/builddir/build/BUILD/mafft-v7.520/extensions/mxscarna_src'
rm -f mxscarna  *.o *.h~ *.hpp~ *.cpp~ *.cc~ ./vienna/*.o 
make -C ./probconsRNA clean
make[2]: Entering directory '/builddir/build/BUILD/mafft-v7.520/extensions/mxscarna_src/probconsRNA'
rm -f probcons 
make[2]: Leaving directory '/builddir/build/BUILD/mafft-v7.520/extensions/mxscarna_src/probconsRNA'
make[1]: Leaving directory '/builddir/build/BUILD/mafft-v7.520/extensions/mxscarna_src'
+ make 'CFLAGS=-fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
make CFLAGS1="" -C mxscarna_src
make[1]: Entering directory '/builddir/build/BUILD/mafft-v7.520/extensions/mxscarna_src'
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -c Main.cc -o Main.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -c McCaskill.cpp -o McCaskill.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -c ./vienna/energy_param.cpp -o ./vienna/energy_param.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -c seq2scs.cpp -o seq2scs.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -c Globaldp.cpp -o Globaldp.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -c postProcessings.cpp -o postProcessings.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -c AlifoldMEA.cpp -o AlifoldMEA.o
g++ -L./probconsRNA  -L./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -lm -o mxscarna Main.o McCaskill.o vienna/energy_param.o seq2scs.o Globaldp.o postProcessings.o AlifoldMEA.o
make[1]: Leaving directory '/builddir/build/BUILD/mafft-v7.520/extensions/mxscarna_src'
mv mxscarna_src/mxscarna mxscarnamod
cp mxscarnamod ../binaries
chmod 755 ../binaries/*
done.
+ cd ..
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.FzjY9B
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64
++ dirname /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd mafft-v7.520
+ rm -rf '%{buidroot}'
+ cd core
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64 'INSTALL=/usr/bin/install -p' 'CFLAGS=-fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts
chmod 755 ../scripts/*
cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  ../binaries
chmod 755 ../binaries/*
done.
mkdir -p /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64/usr/local/libexec/mafft
chmod 755 /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64/usr/local/libexec/mafft
mkdir -p /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64/usr/local/bin
chmod 755 /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64/usr/local/bin
chmod 755 mafft mafft-homologs.rb mafft-sparsecore.rb
/usr/bin/install -p mafft mafft-homologs.rb mafft-sparsecore.rb  /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64/usr/local/bin
chmod 755 dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  ||:     # in MinGW, it's ok if this fails
strip dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  ||: # may fail for dash_client on mac.
/usr/bin/install -p dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64/usr/local/libexec/mafft
/usr/bin/install -p mafftash_premafft.pl seekquencer_premafft.pl /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64/usr/local/libexec/mafft
( cd /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64/usr/local/bin; \
rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi mafft-randomcore.rb ; \
ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \
ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \
ln -s mafft einsi; \
ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \
ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \
ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\
rm -f mafft-profile mafft-profile.exe; ln -s /usr/local/libexec/mafft/mafft-profile .; \
rm -f mafft-distance mafft-distance.exe; ln -s /usr/local/libexec/mafft/mafft-distance . )
mkdir -p /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64/usr/local/share/man/man1
chmod 755 /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64/usr/local/share/man/man1
/usr/bin/install -p -m 644 mafft.1 mafft-homologs.1 /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64/usr/local/share/man/man1
+ cd ../extensions
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64 'INSTALL=/usr/bin/install -p' 'CFLAGS=-fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
cp mxscarnamod ../binaries
chmod 755 ../binaries/*
done.
mkdir -p /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64/usr/local/libexec/mafft
chmod 755 /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64/usr/local/libexec/mafft
chmod 755 mxscarnamod
/usr/bin/install -p mxscarnamod /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64/usr/local/libexec/mafft
+ cd ..
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip /usr/bin/strip
+ /usr/lib/rpm/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
mangling shebang in /usr/local/bin/mafft-sparsecore.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/local/bin/mafft-homologs.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/local/bin/mafft from /bin/bash to #!/usr/bin/bash
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2
+ /usr/lib/rpm/redhat/brp-python-hardlink
Processing files: mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64
warning: absolute symlink: /usr/local/bin/mafft-distance -> /usr/local/libexec/mafft/mafft-distance
warning: absolute symlink: /usr/local/bin/mafft-profile -> /usr/local/libexec/mafft/mafft-profile
Provides: mafft = 7.520-1.20230516221152439026.pr1.fc39 mafft(x86-64) = 7.520-1.20230516221152439026.pr1.fc39
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/bash /usr/bin/perl /usr/bin/ruby glibc >= 2.37.9000-9 libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.27)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH)
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64
Wrote: /builddir/build/RPMS/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.V5EdP7
+ umask 022
+ cd /builddir/build/BUILD
+ cd mafft-v7.520
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc39.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.C71hj7
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf mafft-v7.520 mafft-v7.520.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
RPM build warnings:
    absolute symlink: /usr/local/bin/mafft-distance -> /usr/local/libexec/mafft/mafft-distance
    absolute symlink: /usr/local/bin/mafft-profile -> /usr/local/libexec/mafft/mafft-profile
Child return code was: 0