Mock Version: 1.1.38
ENTER do(['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/clustal-omega.spec'], False, '/var/lib/mock/fedora-rawhide-x86_64/root/', None, 0, True, False, 1000, 135, None, False, {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'CCACHE_DIR': '/tmp/ccache', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n "<mock-chroot>"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'CCACHE_UMASK': '002'}, logger=<mockbuild.trace_decorator.getLog object at 0x17e6f90>)
Executing command: ['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/clustal-omega.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'CCACHE_DIR': '/tmp/ccache', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n "<mock-chroot>"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'CCACHE_UMASK': '002'}
Building target platforms: x86_64
Building for target x86_64
Wrote: /builddir/build/SRPMS/clustal-omega-1.2.1-2.fc21.src.rpm
Child return code was: 0
LEAVE do --> 

ENTER do(['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps  builddir/build/SPECS/clustal-omega.spec'], False, '/var/lib/mock/fedora-rawhide-x86_64/root/', None, 0, True, False, 1000, 135, None, False, {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'CCACHE_DIR': '/tmp/ccache', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n "<mock-chroot>"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'CCACHE_UMASK': '002'}, logger=<mockbuild.trace_decorator.getLog object at 0x17e6f90>)
Executing command: ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps  builddir/build/SPECS/clustal-omega.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'CCACHE_DIR': '/tmp/ccache', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'echo -n "<mock-chroot>"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'CCACHE_UMASK': '002'}
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.iUHiUl
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf clustal-omega-1.2.1
+ /usr/bin/gzip -dc /builddir/build/SOURCES/clustal-omega-1.2.1.tar.gz
+ /usr/bin/tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd clustal-omega-1.2.1
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ sed -i 's/\r$//' README
+ sed -i s/mktemp/mkstemp/g src/clustal-omega.c
+ sed -i 's/\${AM_CFLAGS} -O3/${AM_CFLAGS}/g' configure
+ sed -i 's/\${AM_CXXFLAGS} -O3/${AM_CXXFLAGS}/g' configure
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.TTX5Jo
+ umask 022
+ cd /builddir/build/BUILD
+ cd clustal-omega-1.2.1
+ export 'CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic' 'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic' 'LDFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic'
+ CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic'
+ CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic'
+ LDFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic'
+ CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic'
+ export LDFLAGS
+ '[' 1 = 1 ']'
++ find . -name config.guess -o -name config.sub
+ for i in '$(find . -name config.guess -o -name config.sub)'
++ basename ./config.sub
+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
+ /usr/bin/rm -f ./config.sub
++ basename ./config.sub
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub
'/usr/lib/rpm/redhat/config.sub' -> './config.sub'
+ for i in '$(find . -name config.guess -o -name config.sub)'
++ basename ./config.guess
+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
+ /usr/bin/rm -f ./config.guess
++ basename ./config.guess
+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess
'/usr/lib/rpm/redhat/config.guess' -> './config.guess'
+ '[' 1 = 1 ']'
+ '[' x '!=' x ']'
+ ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --disable-static
configure:
    Welcome to Clustal Omega - version 1.2.1 (AndreaGiacomo)
                       +NMMMMMMMMMS=
                    MMMMM?      :MMMMM8
                  IMMMMS           MMMMM,
                ~MMMMN              ,MMMMM
               =MMMMM                 MMMMM
              ?MMMMM                  +MMMMM
              MMMMMS                   MMMMM
              MMMMM                    MMMMM:
              MMMMM                    MMMMM+
              MMMMM                    MMMMM~
              MMMMM                    MMMMM
              MMMMMZ                   MMMMM
               MMMMM                  ,MMMMZ
                MMMM8                 MMMM+
                 MMMMS               MMMM,
                   MMMMO           MMMM
            ,N       SMMM        MMM8       +8
            ,M7         M+       M+        :M8
            ,MMMMMMMMMMMMI       MMMMMMMMMMMM8
            ,MMMMMMMMMMMM8       MMMMMMMMMMMM8
            ,MMMMMMMMMMMMN       MMMMMMMMMMMM8
              
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking for x86_64-redhat-linux-gnu-gcc... no
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking build system type... x86_64-redhat-linux-gnu
checking host system type... x86_64-redhat-linux-gnu
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for x86_64-redhat-linux-gnu-objdump... no
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for x86_64-redhat-linux-gnu-ar... no
checking for ar... ar
checking for x86_64-redhat-linux-gnu-strip... no
checking for strip... strip
checking for x86_64-redhat-linux-gnu-ranlib... no
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for a BSD-compatible install... /usr/bin/install -c
checking for x86_64-redhat-linux-gnu-gcc... gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) none
checking how to run the C preprocessor... gcc -E
checking for x86_64-redhat-linux-gnu-g++... no
checking for x86_64-redhat-linux-gnu-c++... no
checking for x86_64-redhat-linux-gnu-gpp... no
checking for x86_64-redhat-linux-gnu-aCC... no
checking for x86_64-redhat-linux-gnu-CC... no
checking for x86_64-redhat-linux-gnu-cxx... no
checking for x86_64-redhat-linux-gnu-cc++... no
checking for x86_64-redhat-linux-gnu-cl.exe... no
checking for x86_64-redhat-linux-gnu-FCC... no
checking for x86_64-redhat-linux-gnu-KCC... no
checking for x86_64-redhat-linux-gnu-RCC... no
checking for x86_64-redhat-linux-gnu-xlC_r... no
checking for x86_64-redhat-linux-gnu-xlC... no
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking how to run the C++ preprocessor... g++ -E
checking for ANSI C header files... (cached) yes
checking assert.h usability... yes
checking assert.h presence... yes
checking for assert.h... yes
checking ctype.h usability... yes
checking ctype.h presence... yes
checking for ctype.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking for memory.h... (cached) yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for inline... inline
checking for log in -lm... yes
checking for log2 in -lm... yes
checking argtable2.h usability... yes
checking argtable2.h presence... yes
checking for argtable2.h... yes
checking for arg_parse in -largtable2... yes
checking for OpenMP flag of C compiler... -fopenmp
checking whether byte ordering is bigendian... no
checking for ntohs... yes
checking for ntohl... yes
checking for ntons... no
checking for ntonl... no
checking size of unsigned short... 2
checking size of unsigned int... 4
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking for stroul... no
checking for strtoull... yes
checking for ftello... yes
checking for fseeko... yes
checking for ftello64... yes
checking for fseeko64... yes
checking for ftell64... no
checking for fseek64... no
checking for off_t... yes
checking size of fpos_t... 16
checking if malloc debugging is wanted... no
checking whether to build with debug information... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating clustalo.pc
config.status: creating Doxyfile
config.status: creating src/clustal/Makefile
config.status: creating src/hhalign/Makefile
config.status: creating src/kmpp/Makefile
config.status: creating src/squid/Makefile
config.status: creating src/config.h
config.status: executing src/clustal-omega-config.h commands
config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines
config.status: executing depfiles commands
config.status: executing libtool commands
+ make V=1 -j8
Making all in src
make[1]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src'
make  all-recursive
make[2]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src'
Making all in hhalign
make[3]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/hhalign'
/bin/sh ../../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src    -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o hhalign.lo hhalign.cpp
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c hhalign.cpp  -fPIC -DPIC -o .libs/hhalign.o
In file included from hhalign.cpp:62:0:
hhutil-C.h: In function 'void ReadDefaultsFile(int&, char**)':
hhutil-C.h:516:53: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     argv_conf[argc_conf]=new(char[strlen(c_first)+1]);
                                                     ^
hhutil-C.h:521:56: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        argv_conf[argc_conf]=new(char[strlen(c_first)+1]);
                                                        ^
In file included from hhalign.cpp:70:0:
hhhmm-C.h: In member function 'HMM& HMM::operator=(HMM&)':
hhhmm-C.h:188:44: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     sname[k]=new(char[strlen(q.sname[k])+1]);
                                            ^
hhhmm-C.h:193:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     seq[k]=new(char[strlen(q.seq[k])+1]); 
                                        ^
hhhmm-C.h: In member function 'int HMM::Read(FILE*, char*)':
hhhmm-C.h:329:48: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
         char *cur_seq = new(char[par.maxColCnt]); //Sequence currently read in
                                                ^
hhhmm-C.h:360:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       seq[k-1]=new(char[strlen(cur_seq)+1]); 
                                           ^
hhhmm-C.h:367:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0'
                                           ^
hhhmm-C.h:463:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
      seq[k]=new(char[strlen(cur_seq)+1]); 
                                        ^
In file included from hhalign.cpp:70:0:
hhhmm-C.h: In member function 'int HMM::ReadHMMer(FILE*, char*)':
hhhmm-C.h:735:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
                                                  ^
hhhmm-C.h:756:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]);
                                                  ^
hhhmm-C.h:777:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]);
                                                  ^
hhhmm-C.h:859:46: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
    seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
                                              ^
hhhmm-C.h:1035:46: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       sname[k+1]=new(char[strlen(longname)+1]);
                                              ^
hhhmm-C.h:1037:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       seq[k]=new(char[L+2]); 
                           ^
hhhmm-C.h:1040:29: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       seq[k+1]=new(char[L+2]); 
                             ^
hhhmm-C.h:1058:44: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       sname[k]=new(char[strlen(longname)+1]);
                                            ^
hhhmm-C.h:1062:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       seq[k]=new(char[L+2]); 
                           ^
hhhmm-C.h: In member function 'int HMM::ReadHMMer3(FILE*, char*)':
hhhmm-C.h:1237:68: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
                          seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
                                                                    ^
hhhmm-C.h:1258:68: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
                          seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]);
                                                                    ^
hhhmm-C.h:1279:68: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
                          seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]);
                                                                    ^
hhhmm-C.h:1349:60: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
                  seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
                                                            ^
hhhmm-C.h:1529:49: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
          sname[k+1]=new(char[strlen(longname)+1]);
                                                 ^
hhhmm-C.h:1531:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
          seq[k]=new(char[L+2]);
                              ^
hhhmm-C.h:1534:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
          seq[k+1]=new(char[L+2]);
                                ^
hhhmm-C.h:1552:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
          sname[k]=new(char[strlen(longname)+1]);
                                               ^
hhhmm-C.h:1554:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
          seq[k]=new(char[L+2]);
                              ^
hhhmm-C.h:1140:12: warning: variable 'dAlphaInv' set but not used [-Wunused-but-set-variable]
     double dAlphaInv = 1.00 / (double)(iAlpha); /* weight of AA */
            ^
In file included from hhalign.cpp:70:0:
hhhmm-C.h: In member function 'void HMM::InsertCalibration(char*)':
hhhmm-C.h:2109:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   char** lines = new(char*[3*L+100000]);
                                       ^
hhhmm-C.h:2138:44: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       lines[nline]=new(char[strlen(line)+1]); 
                                            ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h: In constructor 'Alignment::Alignment(int, int)':
hhalignment-C.h:80:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   sname = new(char*[maxseq+2]); /* MR1 */
                              ^
hhalignment-C.h:81:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   seq = new(char*[maxseq+2]); /* MR1 */
                            ^
hhalignment-C.h:82:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   l = new(int[maxres]);
                      ^
hhalignment-C.h:83:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   X = new(char*[maxseq+2]);  /* MR1 */
                          ^
hhalignment-C.h:84:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   I = new(short unsigned int*[maxseq+2]); /* MR1 */
                                        ^
hhalignment-C.h:85:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   keep = new(char[maxseq+2]); /* MR1 */
                            ^
hhalignment-C.h:86:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   display = new(char[maxseq+2]); /* MR1 */
                               ^
hhalignment-C.h:87:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   wg = new(float[maxseq+2]); /* MR1 */
                           ^
hhalignment-C.h:88:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   nseqs = new(int[maxres+2]); /* MR1 */
                            ^
hhalignment-C.h: In member function 'void Alignment::Read(FILE*, char*, char*)':
hhalignment-C.h:141:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   char *cur_seq=new(char[par.maxColCnt]);
                                        ^
hhalignment-C.h:183:61: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
                           seq[k]=new(char[strlen(cur_seq)+2]);
                                                             ^
hhalignment-C.h:185:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
                           X[k]=new(char[strlen(cur_seq)+2]);
                                                           ^
hhalignment-C.h:187:73: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
                           I[k]=new(short unsigned int[strlen(cur_seq)+2]);
                                                                         ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h:236:58: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
                   sname[k] = new(char[strlen(cur_name)+1]);
                                                          ^
hhalignment-C.h:245:32: warning: variable 'ptr2' set but not used [-Wunused-but-set-variable]
                   char *ptr1, *ptr2;
                                ^
hhalignment-C.h:351:45: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
           seq[k]=new(char[strlen(cur_seq)+2]);
                                             ^
hhalignment-C.h:353:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
           X[k]=new(char[strlen(cur_seq)+2]);
                                           ^
hhalignment-C.h:355:57: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
           I[k]=new(short unsigned int[strlen(cur_seq)+2]);
                                                         ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h: In member function 'void Alignment::Compress(const char*)':
hhalignment-C.h:423:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     h = new(/*short*/ unsigned int[N_in+2]); /* short -> overflow, FS, r235 -> r236 */
                                  ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h:555:52: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             percent_gaps = new(float[par.maxColCnt]);
                                                    ^
hhalignment-C.h:561:49: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             if (nres==NULL) nres=new(int[N_in]);
                                                 ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h:783:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             match_state = new(char[par.maxColCnt]);
                                                  ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h: In member function 'int Alignment::FilterForDisplay(int, int, int, float, int)':
hhalignment-C.h:945:35: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     char *dummy = new(char[N_in+1]);
                                   ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int)':
hhalignment-C.h:1008:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid
                              ^
hhalignment-C.h:1009:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0;
                                ^
hhalignment-C.h:1010:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering /* MR1, used to be called idmax*/
                           ^
hhalignment-C.h:1011:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL]
                               ^
hhalignment-C.h:1012:36: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid)
                                    ^
hhalignment-C.h:1013:24: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i
                        ^
hhalignment-C.h:1042:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             first=new(int[N_in]);// first non-gap position in sequence k
                                ^
hhalignment-C.h:1043:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             last =new(int[N_in]);// last  non-gap position in sequence k
                                ^
hhalignment-C.h:1056:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             nres=new(int[N_in]);
                               ^
hhalignment-C.h:1070:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences
                                ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h: In member function 'int Alignment::HomologyFilter(int, float, float)':
hhalignment-C.h:1313:33: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     char* coreseq=new(char[N_in]); // coreseq[k]=1 if sequence belongs to core of alignment (i.e. it is very similar to query)
                                 ^
hhalignment-C.h: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM&)':
hhalignment-C.h:1364:36: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore
                                    ^
hhalignment-C.h:1373:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             first=new(int[N_in]);// first non-gap position in sequence k
                                ^
hhalignment-C.h:1374:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             last =new(int[N_in]);// last non-gap position in sequence k
                                ^
hhalignment-C.h:1387:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             nres=new(int[N_in]);
                               ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h:1428:19: warning: variable 'score_M' set but not used [-Wunused-but-set-variable]
             float score_M=0.0;
                   ^
hhalignment-C.h:1429:19: warning: variable 'score_prev' set but not used [-Wunused-but-set-variable]
             float score_prev=0.0;
                   ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h: In member function 'void Alignment::FrequenciesAndTransitions(HMM&, char*)':
hhalignment-C.h:1669:49: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
                     q.seq[q.ncons]=new(char[L+2]);
                                                 ^
hhalignment-C.h:1676:64: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
                     q.sname[q.nfirst]=new(char[strlen(name)+11]);
                                                                ^
hhalignment-C.h:1680:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
                     q.seq[q.nfirst]=new(char[L+2]);
                                                  ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h:1738:61: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
                     q.sname[nn]=new(char[strlen(sname[k])+1]);
                                                             ^
hhalignment-C.h:1741:57: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
                     q.seq[nn]=new(char[strlen(seq[k])+1]);
                                                         ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h: In member function 'void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM&, char*)':
hhalignment-C.h:1828:41: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
                                         ^
hhalignment-C.h:1835:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   wi = new(float[N_in+2]);
                         ^
hhalignment-C.h:1844:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   n = new(int*[L+2]);
                    ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h: In member function 'void Alignment::Transitions_from_I_state(HMM&, char*)':
hhalignment-C.h:2054:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
                                           ^
hhalignment-C.h:2062:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     wi = new(float[N_in+2]);
                           ^
hhalignment-C.h:2073:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     n = new(int*[L+2]);
                      ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h: In member function 'void Alignment::Transitions_from_D_state(HMM&, char*)':
hhalignment-C.h:2256:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     float *Neff = new(float[par.maxResLen]); // diversity of subalignment i 
                                           ^
hhalignment-C.h:2265:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     wi = new(float[N_in+2]); /* FIXME: FS */
                           ^
hhalignment-C.h:2275:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     n = new(int*[L+2]);
                      ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h: In member function 'void Alignment::MergeMasterSlave(Hit&, char*)':
hhalignment-C.h:2546:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
  int* imatch=new(int[hit.j2+1]);
                               ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h:2678:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
  char* new_seq=new(char[2*maxcol]);
                                  ^
hhalignment-C.h:2691:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
  seq[N_in]=new(char[h]);
                       ^
hhalignment-C.h:2694:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
  X[N_in]=new(char[h]);
                     ^
hhalignment-C.h:2696:35: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
  I[N_in]=new(short unsigned int[h]);
                                   ^
hhalignment-C.h:2698:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
  sname[N_in]=new(char[strlen(Tali.sname[k])+1]);
                                               ^
hhalignment-C.h: In member function 'void Alignment::AddSequence(char*, int*)':
hhalignment-C.h:2729:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
  X[N_in]=new(char[L+2]);
                       ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h: In member function 'void Alignment::GetPositionSpecificWeights(float**)':
hhalignment-C.h:2779:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
  n = new(int*[L+2]);
                   ^
In file included from hhalign.cpp:71:0:
hhalignment-C.h: In member function 'void Alignment::Transfer(char**, int)':
hhalignment-C.h:2896:51: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
         I[k] = new(short unsigned int[iLen+2+GOOD_MEASURE]);
                                                   ^
hhalignment-C.h:2897:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
         X[k] = new(char[iLen+2+GOOD_MEASURE]);
                                     ^
hhalignment-C.h:2898:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
         seq[k] = new(char[iLen+2+GOOD_MEASURE]);
                                       ^
In file included from hhalign.cpp:72:0:
hhhit-C.h: In member function 'void Hit::AllocateBacktraceMatrix(int, int)':
hhhit-C.h:179:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   bMM=new(char*[Nq]);
                    ^
hhhit-C.h:180:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   bMI=new(char*[Nq]);
                    ^
hhhit-C.h:181:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   bIM=new(char*[Nq]);
                    ^
hhhit-C.h:182:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   bDG=new(char*[Nq]);
                    ^
hhhit-C.h:183:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   bGD=new(char*[Nq]);
                    ^
hhhit-C.h:184:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   cell_off=new(char*[Nq]);
                         ^
hhhit-C.h:187:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       bMM[i]=new(char[Nt]);
                          ^
hhhit-C.h:188:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       bMI[i]=new(char[Nt]);
                          ^
hhhit-C.h:189:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       bIM[i]=new(char[Nt]);
                          ^
hhhit-C.h:190:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       bGD[i]=new(char[Nt]);
                          ^
hhhit-C.h:191:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       bDG[i]=new(char[Nt]);
                          ^
hhhit-C.h:192:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       cell_off[i]=new(char[Nt]);
                               ^
hhhit-C.h: In member function 'void Hit::AllocateForwardMatrix(int, int)':
hhhit-C.h:239:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   F_MM=new(double*[Nq]);
                       ^
hhhit-C.h:240:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   F_MI=new(double*[Nq]);
                       ^
hhhit-C.h:241:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   F_DG=new(double*[Nq]);
                       ^
hhhit-C.h:242:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   F_IM=new(double*[Nq]);
                       ^
hhhit-C.h:243:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   F_GD=new(double*[Nq]);
                       ^
hhhit-C.h:244:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   scale=new(double[Nq+1]); // need Nq+3?
                         ^
hhhit-C.h:247:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       F_MM[i] = new(double[Nt]);
                               ^
hhhit-C.h:248:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       F_MI[i] = new(double[Nt]);
                               ^
hhhit-C.h:249:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       F_DG[i] = new(double[Nt]);
                               ^
hhhit-C.h:250:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       F_IM[i] = new(double[Nt]);
                               ^
hhhit-C.h:251:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       F_GD[i] = new(double[Nt]);
                               ^
hhhit-C.h: In member function 'void Hit::AllocateBackwardMatrix(int, int)':
hhhit-C.h:296:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   B_MM=new(double*[Nq]);
                       ^
hhhit-C.h:303:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       B_MM[i] = new(double[Nt]);
                               ^
In file included from hhalign.cpp:72:0:
hhhit-C.h: In member function 'void Hit::Viterbi(HMM&, HMM&, float**)':
hhhit-C.h:376:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     float *sMM = new(float[par.maxResLen]);   // sMM[i][j] = score of best alignment up to indices (i,j) ending in (Match,Match) 
                                          ^
hhhit-C.h:377:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     float *sGD = new(float[par.maxResLen]);   // sGD[i][j] = score of best alignment up to indices (i,j) ending in (Gap,Delete) 
                                          ^
hhhit-C.h:378:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     float *sDG = new(float[par.maxResLen]);   // sDG[i][j] = score of best alignment up to indices (i,j) ending in (Delete,Gap)
                                          ^
hhhit-C.h:379:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     float *sIM = new(float[par.maxResLen]);   // sIM[i][j] = score of best alignment up to indices (i,j) ending in (Ins,Match)
                                          ^
hhhit-C.h:380:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     float *sMI = new(float[par.maxResLen]);   // sMI[i][j] = score of best alignment up to indices (i,j) ending in (Match,Ins) 
                                          ^
In file included from hhalign.cpp:72:0:
hhhit-C.h: In member function 'void Hit::Backtrace(HMM&, HMM&)':
hhhit-C.h:1126:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
                                        ^
hhhit-C.h:1127:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   S    = new( float[nsteps+1]);
                           ^
hhhit-C.h:1128:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   S_ss = new( float[nsteps+1]);
                              ^
hhhit-C.h: In member function 'void Hit::StochasticBacktrace(HMM&, HMM&, char)':
hhhit-C.h:1228:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   double* scale_cum = new(double[q.L+2]);
                                        ^
hhhit-C.h:1247:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       double* sumF=new(double[q.L+t.L]);
                                       ^
In file included from hhalign.cpp:72:0:
hhhit-C.h:1371:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
                                        ^
hhhit-C.h:1372:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   S    = new( float[nsteps+1]);
                           ^
hhhit-C.h:1373:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   S_ss = new( float[nsteps+1]);
                              ^
In file included from hhalign.cpp:72:0:
hhhit-C.h: In member function 'void Hit::BacktraceMAC(HMM&, HMM&)':
hhhit-C.h:1475:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
                                        ^
hhhit-C.h:1476:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   S    = new( float[nsteps+1]);
                           ^
hhhit-C.h:1477:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   S_ss = new( float[nsteps+1]);
                              ^
hhhit-C.h:1478:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   P_posterior = new( float[nsteps+1]);
                                     ^
In file included from hhalign.cpp:72:0:
hhhit-C.h: In member function 'void Hit::InitializeBacktrace(HMM&, HMM&)':
hhhit-C.h:1683:54: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             longname=new(char[strlen(t.longname)+1])();
                                                      ^
hhhit-C.h:1684:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             name    =new(char[strlen(t.name)+1])();
                                               ^
hhhit-C.h:1685:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             file    =new(char[strlen(t.file)+1])();
                                               ^
hhhit-C.h:1696:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             sname=new(char*[t.n_display])();   // Call Compare only once with irep=1
                                           ^
hhhit-C.h:1697:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
             seq  =new(char*[t.n_display])();   // Call Compare only once with irep=1
                                          ^
In file included from hhalign.cpp:72:0:
hhhit-C.h:1730:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     this->i = new( int[i2+j2+2])();
                                  ^
hhhit-C.h:1731:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     this->j = new( int[i2+j2+2])();
                                  ^
hhhit-C.h:1732:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
     states  = new( char[i2+j2+2])();
                                  ^
In file included from hhalign.cpp:73:0:
hhhalfalignment-C.h: In constructor 'HalfAlignment::HalfAlignment(int)':
hhhalfalignment-C.h:66:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   h = new(int[maxseqdis]);   //h[k] = next position of sequence k to be written
                         ^
hhhalfalignment-C.h:67:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   s = new(char*[maxseqdis]);  //s[k][h] = character in column h, sequence k of output alignment
                           ^
hhhalfalignment-C.h:68:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   l = new(int*[maxseqdis]);   //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k
                          ^
hhhalfalignment-C.h:69:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   m = new(int*[maxseqdis]);   //counts positions:        m[k][i] = position of match state i in string seq[k]  
                          ^
In file included from hhalign.cpp:74:0:
hhfullalignment-C.h: In member function 'void FullAlignment::PrintHHR(FILE*, Hit&)':
hhfullalignment-C.h:359:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   lq = new(short unsigned int[qa->n+2]);
                                       ^
hhfullalignment-C.h:360:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   lt = new(short unsigned int[ta->n+2]);
                                       ^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring()':
hhhitlist-C.h:1285:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Z = new(float*[N]);
                    ^
hhhitlist-C.h:1288:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       Z[k] = new(float[N]);
                          ^
hhhitlist-C.h:1293:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   C = new(float*[N]);
                    ^
hhhitlist-C.h:1296:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       C[k] = new(float[N]);
                          ^
hhhitlist-C.h:1303:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Zq = new(float[N]);
                    ^
hhhitlist-C.h:1304:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Ztq = new(float[N]);
                     ^
hhhitlist-C.h:1305:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Zrq = new(float[N]);
                     ^
hhhitlist-C.h:1306:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   fold = new(char*[N]);
                      ^
hhhitlist-C.h:1307:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   fam = new(char*[N]);
                     ^
hhhitlist-C.h:1308:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Prob = new(float[N]);
                      ^
hhhitlist-C.h:1309:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   ll = new(int[N]);
                  ^
hhhitlist-C.h:1310:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   w = new(float[N]);
                   ^
hhhitlist-C.h:1373:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       double** Csub = new(double*[M]);
                                     ^
hhhitlist-C.h:1374:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       double** Cinv = new(double*[M]);
                                     ^
hhhitlist-C.h:1377:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
    Csub[m] = new(double[M]);
                           ^
hhhitlist-C.h:1378:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
    Cinv[m] = new(double[M]);
                           ^
hhhitlist-C.h:1453:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
    double** Csub = new(double*[M]);
                                  ^
hhhitlist-C.h:1456:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        Csub[m] = new(double[M]);
                               ^
hhhitlist-C.h:1470:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        double** Cinv = new(double*[M]);
                                      ^
hhhitlist-C.h:1471:51: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        for (m=0; m<M; m++) Cinv[m] = new(double[M]);
                                                   ^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h:1256:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
   size_t unused; /* disable fread gcc warning */
          ^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring2()':
hhhitlist-C.h:1650:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Z = new(float*[N]);
                    ^
hhhitlist-C.h:1653:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       Z[k] = new(float[N]);
                          ^
hhhitlist-C.h:1658:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   C = new(float*[N]);
                    ^
hhhitlist-C.h:1661:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       C[k] = new(float[N]);
                          ^
hhhitlist-C.h:1668:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Zq = new(float[N]);
                    ^
hhhitlist-C.h:1669:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Ztq = new(float[N]);
                     ^
hhhitlist-C.h:1670:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Zrq = new(float[N]);
                     ^
hhhitlist-C.h:1671:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   fold = new(char*[N]);
                      ^
hhhitlist-C.h:1672:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   fam = new(char*[N]);
                     ^
hhhitlist-C.h:1673:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Prob = new(float[N]);
                      ^
hhhitlist-C.h:1674:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   ll = new(int[N]);
                  ^
hhhitlist-C.h:1675:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   w = new(float[N]);
                   ^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h:1739:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       double** Csub = new(double*[M]);
                                     ^
hhhitlist-C.h:1740:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       double** Cinv = new(double*[M]);
                                     ^
hhhitlist-C.h:1743:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
    Csub[m] = new(double[M]);
                           ^
hhhitlist-C.h:1744:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
    Cinv[m] = new(double[M]);
                           ^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h:1821:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
    double** Csub = new(double*[M]);
                                  ^
hhhitlist-C.h:1824:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        Csub[m] = new(double[M]);
                               ^
hhhitlist-C.h:1838:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        double** Cinv = new(double*[M]);
                                      ^
hhhitlist-C.h:1839:51: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        for (m=0; m<M; m++) Cinv[m] = new(double[M]);
                                                   ^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h:1621:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
   size_t unused; /* disable fread gcc warning */
          ^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring3()':
hhhitlist-C.h:2020:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Z = new(float*[N]);
                    ^
hhhitlist-C.h:2023:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       Z[k] = new(float[N]);
                          ^
hhhitlist-C.h:2028:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   C = new(float*[N]);
                    ^
hhhitlist-C.h:2031:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       C[k] = new(float[N]);
                          ^
hhhitlist-C.h:2038:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Zq = new(float[N]);
                    ^
hhhitlist-C.h:2039:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Ztq = new(float[N]);
                     ^
hhhitlist-C.h:2040:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Zrq = new(float[N]);
                     ^
hhhitlist-C.h:2041:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   fold = new(char*[N]);
                      ^
hhhitlist-C.h:2042:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   fam = new(char*[N]);
                     ^
hhhitlist-C.h:2043:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Prob = new(float[N]);
                      ^
hhhitlist-C.h:2044:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   ll = new(int[N]);
                  ^
hhhitlist-C.h:2045:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   w = new(float[N]);
                   ^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h:2114:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
    double** Csub = new(double*[M]);
                                  ^
hhhitlist-C.h:2115:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
    double** Cinv = new(double*[M]);
                                  ^
hhhitlist-C.h:2118:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        Csub[m] = new(double[M]);
                               ^
hhhitlist-C.h:2119:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        Cinv[m] = new(double[M]);
                               ^
hhhitlist-C.h:2186:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
    double** Csub = new(double*[M]);
                                  ^
hhhitlist-C.h:2189:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        Csub[m] = new(double[M]);
                               ^
hhhitlist-C.h:2203:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        double** Cinv = new(double*[M]);
                                      ^
hhhitlist-C.h:2204:51: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        for (m=0; m<M; m++) Cinv[m] = new(double[M]);
                                                   ^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h:1991:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
   size_t unused; /* disable fread gcc warning */
          ^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring4()':
hhhitlist-C.h:2385:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Z = new(float*[N]);
                    ^
hhhitlist-C.h:2388:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       Z[k] = new(float[N]);
                          ^
hhhitlist-C.h:2393:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   C = new(float*[N]);
                    ^
hhhitlist-C.h:2396:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       C[k] = new(float[N]);
                          ^
hhhitlist-C.h:2403:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Zq = new(float[N]);
                    ^
hhhitlist-C.h:2404:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Ztq = new(float[N]);
                     ^
hhhitlist-C.h:2405:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Zrq = new(float[N]);
                     ^
hhhitlist-C.h:2406:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   fold = new(char*[N]);
                      ^
hhhitlist-C.h:2407:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   fam = new(char*[N]);
                     ^
hhhitlist-C.h:2408:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   Prob = new(float[N]);
                      ^
hhhitlist-C.h:2409:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   ll = new(int[N]);
                  ^
hhhitlist-C.h:2410:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   w = new(float[N]);
                   ^
hhhitlist-C.h:2472:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
       double** Csub = new(double*[M]);
                                     ^
hhhitlist-C.h:2475:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
    Csub[m] = new(double[M]);
                           ^
hhhitlist-C.h:2538:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
    double** Csub = new(double*[M]);
                                  ^
hhhitlist-C.h:2541:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
        Csub[m] = new(double[M]);
                               ^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h:2356:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
   size_t unused; /* disable fread gcc warning */
          ^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h: In member function 'void HitList::InvertMatrix(double**, double**, int)':
hhhitlist-C.h:2840:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   double** V = new(double*[N]);
                              ^
hhhitlist-C.h:2841:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   double* s  = new(double[N]);
                            ^
hhhitlist-C.h:2842:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   for (k=0; k<N; k++) V[k] = new(double[N]);
                                           ^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h: In member function 'void HitList::SVD(double**, int, double*, double**)':
hhhitlist-C.h:2925:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
   rv1=new(double[n]);
                    ^
hhalign.cpp: In function 'int hhalign(char**, int, double*, char**, int, double*, double*, hmm_light*, char*, char*, char*, char*, hhalign_para, hhalign_scores*, int, int, char*, char*)':
hhalign.cpp:714:9: warning: variable 'Nali' set but not used [-Wunused-but-set-variable]
     int Nali;                    /* number of normally backtraced alignments 
         ^
/bin/sh ../../libtool --tag=CXX   --mode=link g++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -o libhhalign.la  hhalign.lo  -largtable2 -lm 
libtool: link: ar cru .libs/libhhalign.a .libs/hhalign.o 
libtool: link: ranlib .libs/libhhalign.a
libtool: link: ( cd ".libs" && rm -f "libhhalign.la" && ln -s "../libhhalign.la" "libhhalign.la" )
make[3]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/hhalign'
Making all in squid
make[3]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/squid'
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o a2m.lo a2m.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o aligneval.lo aligneval.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o alignio.lo alignio.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o clustal.lo clustal.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o cluster.lo cluster.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o dayhoff.lo dayhoff.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o eps.lo eps.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o file.lo file.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c alignio.c  -fPIC -DPIC -o .libs/alignio.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c dayhoff.c  -fPIC -DPIC -o .libs/dayhoff.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c clustal.c  -fPIC -DPIC -o .libs/clustal.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c cluster.c  -fPIC -DPIC -o .libs/cluster.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c a2m.c  -fPIC -DPIC -o .libs/a2m.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c eps.c  -fPIC -DPIC -o .libs/eps.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c file.c  -fPIC -DPIC -o .libs/file.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c aligneval.c  -fPIC -DPIC -o .libs/aligneval.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o getopt.lo getopt.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c getopt.c  -fPIC -DPIC -o .libs/getopt.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o gki.lo gki.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o gsi.lo gsi.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c gki.c  -fPIC -DPIC -o .libs/gki.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c gsi.c  -fPIC -DPIC -o .libs/gsi.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o gsi64.lo gsi64.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c gsi64.c  -fPIC -DPIC -o .libs/gsi64.o
clustal.c: In function 'WriteClustal':
clustal.c:294:8: warning: field width specifier '*' expects argument of type 'int', but argument 4 has type 'size_t' [-Wformat=]
        fprintf(fp, "%s%*s %s\t%d\n", msa->sqname[idx], namelen+5-utf8len(msa->sqname[idx]), "", buf, piResCnt[idx]);
        ^
clustal.c:299:8: warning: field width specifier '*' expects argument of type 'int', but argument 4 has type 'size_t' [-Wformat=]
        fprintf(fp, "%s%*s %s\n", msa->sqname[idx], namelen+5-utf8len(msa->sqname[idx]), "", buf);
        ^
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o hsregex.lo hsregex.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o iupac.lo iupac.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o msa.lo msa.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c iupac.c  -fPIC -DPIC -o .libs/iupac.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c hsregex.c  -fPIC -DPIC -o .libs/hsregex.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o msf.lo msf.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o phylip.lo phylip.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c msa.c  -fPIC -DPIC -o .libs/msa.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c msf.c  -fPIC -DPIC -o .libs/msf.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c phylip.c  -fPIC -DPIC -o .libs/phylip.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o revcomp.lo revcomp.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c revcomp.c  -fPIC -DPIC -o .libs/revcomp.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o rk.lo rk.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o selex.lo selex.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rk.c  -fPIC -DPIC -o .libs/rk.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o seqencode.lo seqencode.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c selex.c  -fPIC -DPIC -o .libs/selex.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c seqencode.c  -fPIC -DPIC -o .libs/seqencode.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o shuffle.lo shuffle.c
phylip.c: In function 'ReadPhylip':
phylip.c:78:13: warning: variable 'alen' set but not used [-Wunused-but-set-variable]
   int   nseq, alen;
             ^
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o sqerror.lo sqerror.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c shuffle.c  -fPIC -DPIC -o .libs/shuffle.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c sqerror.c  -fPIC -DPIC -o .libs/sqerror.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o sqio.lo sqio.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c sqio.c  -fPIC -DPIC -o .libs/sqio.o
msf.c: In function 'ReadMSF':
msf.c:85:7: warning: variable 'alleged_checksum' set but not used [-Wunused-but-set-variable]
   int     alleged_checksum;
       ^
msf.c:83:7: warning: variable 'alleged_alen' set but not used [-Wunused-but-set-variable]
   int     alleged_alen;
       ^
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o squidcore.lo squidcore.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o sre_ctype.lo sre_ctype.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c squidcore.c  -fPIC -DPIC -o .libs/squidcore.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c sre_ctype.c  -fPIC -DPIC -o .libs/sre_ctype.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o sre_math.lo sre_math.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c sre_math.c  -fPIC -DPIC -o .libs/sre_math.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o sre_random.lo sre_random.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c sre_random.c  -fPIC -DPIC -o .libs/sre_random.o
hsregex.c: In function 'regbranch':
hsregex.c:497:6: warning: 'flags' may be used uninitialized in this function [-Wmaybe-uninitialized]
  int flags;
      ^
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o sre_string.lo sre_string.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o ssi.lo ssi.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c sre_string.c  -fPIC -DPIC -o .libs/sre_string.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c ssi.c  -fPIC -DPIC -o .libs/ssi.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o stack.lo stack.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o stockholm.lo stockholm.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o stopwatch.lo stopwatch.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c stack.c  -fPIC -DPIC -o .libs/stack.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c stockholm.c  -fPIC -DPIC -o .libs/stockholm.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c stopwatch.c  -fPIC -DPIC -o .libs/stopwatch.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o translate.lo translate.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o types.lo types.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c translate.c  -fPIC -DPIC -o .libs/translate.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o vectorops.lo vectorops.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o weight.lo weight.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c types.c  -fPIC -DPIC -o .libs/types.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c vectorops.c  -fPIC -DPIC -o .libs/vectorops.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c weight.c  -fPIC -DPIC -o .libs/weight.o
/bin/sh ../../libtool --tag=CC   --mode=link gcc -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -o libsquid.la  a2m.lo aligneval.lo alignio.lo clustal.lo cluster.lo dayhoff.lo eps.lo file.lo getopt.lo gki.lo gsi.lo gsi64.lo hsregex.lo iupac.lo msa.lo msf.lo phylip.lo revcomp.lo rk.lo selex.lo seqencode.lo shuffle.lo sqerror.lo sqio.lo squidcore.lo sre_ctype.lo sre_math.lo sre_random.lo sre_string.lo ssi.lo stack.lo stockholm.lo stopwatch.lo translate.lo types.lo vectorops.lo weight.lo  -largtable2 -lm 
libtool: link: ar cru .libs/libsquid.a .libs/a2m.o .libs/aligneval.o .libs/alignio.o .libs/clustal.o .libs/cluster.o .libs/dayhoff.o .libs/eps.o .libs/file.o .libs/getopt.o .libs/gki.o .libs/gsi.o .libs/gsi64.o .libs/hsregex.o .libs/iupac.o .libs/msa.o .libs/msf.o .libs/phylip.o .libs/revcomp.o .libs/rk.o .libs/selex.o .libs/seqencode.o .libs/shuffle.o .libs/sqerror.o .libs/sqio.o .libs/squidcore.o .libs/sre_ctype.o .libs/sre_math.o .libs/sre_random.o .libs/sre_string.o .libs/ssi.o .libs/stack.o .libs/stockholm.o .libs/stopwatch.o .libs/translate.o .libs/types.o .libs/vectorops.o .libs/weight.o 
libtool: link: ranlib .libs/libsquid.a
libtool: link: ( cd ".libs" && rm -f "libsquid.la" && ln -s "../libsquid.la" "libsquid.la" )
make[3]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/squid'
Making all in kmpp
make[3]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/kmpp'
/bin/sh ../../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o KMeans.lo KMeans.cpp
/bin/sh ../../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o KmTree.lo KmTree.cpp
/bin/sh ../../libtool --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src    -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o KmUtils.lo KmUtils.cpp
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c KmTree.cpp  -fPIC -DPIC -o .libs/KmTree.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c KMeans.cpp  -fPIC -DPIC -o .libs/KMeans.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c KmUtils.cpp  -fPIC -DPIC -o .libs/KmUtils.o
/bin/sh ../../libtool --tag=CXX   --mode=link g++ -DCLUSTALO   -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -o libkmpp.la  KMeans.lo KmTree.lo KmUtils.lo  -largtable2 -lm 
libtool: link: ar cru .libs/libkmpp.a .libs/KMeans.o .libs/KmTree.o .libs/KmUtils.o 
libtool: link: ranlib .libs/libkmpp.a
libtool: link: ( cd ".libs" && rm -f "libkmpp.la" && ln -s "../libkmpp.la" "libkmpp.la" )
make[3]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/kmpp'
Making all in clustal
make[3]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/clustal'
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o hhalign_wrapper.lo hhalign_wrapper.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o ktuple_pair.lo ktuple_pair.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o list.lo list.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o log.lo log.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o muscle_upgma.lo muscle_upgma.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o muscle_tree.lo muscle_tree.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o mbed.lo mbed.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o pair_dist.lo pair_dist.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c ktuple_pair.c  -fPIC -DPIC -o .libs/ktuple_pair.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c hhalign_wrapper.c  -fPIC -DPIC -o .libs/hhalign_wrapper.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c list.c  -fPIC -DPIC -o .libs/list.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c log.c  -fPIC -DPIC -o .libs/log.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c muscle_upgma.c  -fPIC -DPIC -o .libs/muscle_upgma.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c mbed.c  -fPIC -DPIC -o .libs/mbed.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c pair_dist.c  -fPIC -DPIC -o .libs/pair_dist.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c muscle_tree.c  -fPIC -DPIC -o .libs/muscle_tree.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o progress.lo progress.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o seq.lo seq.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c progress.c  -fPIC -DPIC -o .libs/progress.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c seq.c  -fPIC -DPIC -o .libs/seq.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o symmatrix.lo symmatrix.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o tree.lo tree.c
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o util.lo util.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c symmatrix.c  -fPIC -DPIC -o .libs/symmatrix.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c tree.c  -fPIC -DPIC -o .libs/tree.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c util.c  -fPIC -DPIC -o .libs/util.o
/bin/sh ../../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src    -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o weights.lo weights.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c weights.c  -fPIC -DPIC -o .libs/weights.o
mbed.c: In function 'BisectingKmeans':
mbed.c:785:16: warning: variable 'dCost' set but not used [-Wunused-but-set-variable]
         double dCost = -1.0;
                ^
seq.c: In function 'FreeMSeq':
seq.c:746:27: warning: operation on '(*mseq)->filename' may be undefined [-Wsequence-point]
         (*mseq)->filename = CKFREE((*mseq)->filename);
                           ^
hhalign_wrapper.c: In function 'ReAttachLeadingGaps':
hhalign_wrapper.c:259:9: warning: variable 'iSize2' set but not used [-Wunused-but-set-variable]
     int iSize2 = 0; /* #seqs in 2nd profile */
         ^
hhalign_wrapper.c:258:9: warning: variable 'iSize1' set but not used [-Wunused-but-set-variable]
     int iSize1 = 0; /* #seqs in 1st profile */
         ^
hhalign_wrapper.c: In function 'PileUp':
hhalign_wrapper.c:632:9: warning: variable 'iHHret' set but not used [-Wunused-but-set-variable]
     int iHHret = -1; /* return value of hhalign() */
         ^
hhalign_wrapper.c:620:9: warning: variable 'iCountPro' set but not used [-Wunused-but-set-variable]
     int iCountPro = 0; /* count how many sequences are already in profile */
         ^
hhalign_wrapper.c: In function 'HHalignWrapper':
hhalign_wrapper.c:1455:29: warning: operation on '*(ppiLeafList + (sizetype)((long unsigned int)iL * 8ul))' may be undefined [-Wsequence-point]
             ppiLeafList[iL] = CKFREE(ppiLeafList[iL]);
                             ^
hhalign_wrapper.c:1456:29: warning: operation on '*(ppiLeafList + (sizetype)((long unsigned int)iR * 8ul))' may be undefined [-Wsequence-point]
             ppiLeafList[iR] = CKFREE(ppiLeafList[iR]);
                             ^
/bin/sh ../../libtool --tag=CC   --mode=link gcc -fopenmp  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -o libclustal.la  hhalign_wrapper.lo ktuple_pair.lo list.lo log.lo muscle_upgma.lo muscle_tree.lo mbed.lo pair_dist.lo progress.lo seq.lo symmatrix.lo tree.lo util.lo weights.lo  -largtable2 -lm 
libtool: link: ar cru .libs/libclustal.a .libs/hhalign_wrapper.o .libs/ktuple_pair.o .libs/list.o .libs/log.o .libs/muscle_upgma.o .libs/muscle_tree.o .libs/mbed.o .libs/pair_dist.o .libs/progress.o .libs/seq.o .libs/symmatrix.o .libs/tree.o .libs/util.o .libs/weights.o 
libtool: link: ranlib .libs/libclustal.a
libtool: link: ( cd ".libs" && rm -f "libclustal.la" && ln -s "../libclustal.la" "libclustal.la" )
make[3]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/clustal'
make[3]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src'
/bin/sh ../libtool --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.    -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o clustal-omega.lo clustal-omega.c
g++ -DHAVE_CONFIG_H -I.    -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c -o main.o main.cpp
gcc -DHAVE_CONFIG_H -I.    -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -c mymain.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c clustal-omega.c  -fPIC -DPIC -o .libs/clustal-omega.o
clustal-omega.c: In function 'AlnToHHMFile':
clustal-omega.c:392:21: warning: comparison between pointer and integer
     if (NULL == mkstemp(tmp_aln)) {
                     ^
clustal-omega.c: In function 'AlnToHMMFile':
clustal-omega.c:478:21: warning: comparison between pointer and integer
     if (NULL == mkstemp(tmp_aln)) {
                     ^
clustal-omega.c:501:25: warning: comparison between pointer and integer
         if (NULL == mkstemp(tmp_hmm)) {
                         ^
clustal-omega.c: In function 'AlnToHMM':
clustal-omega.c:572:21: warning: comparison between pointer and integer
     if (NULL == mkstemp(pcHMM)) {
                     ^
/bin/sh ../libtool --tag=CC   --mode=link gcc -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -static -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -o libclustalo.la -rpath /usr/lib64 clustal-omega.lo clustal/libclustal.la hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la  -largtable2 -lm 
libtool: link: (cd .libs/libclustalo.lax/libclustal.a && ar x "/builddir/build/BUILD/clustal-omega-1.2.1/src/clustal/.libs/libclustal.a")
libtool: link: (cd .libs/libclustalo.lax/libhhalign.a && ar x "/builddir/build/BUILD/clustal-omega-1.2.1/src/hhalign/.libs/libhhalign.a")
libtool: link: (cd .libs/libclustalo.lax/libsquid.a && ar x "/builddir/build/BUILD/clustal-omega-1.2.1/src/squid/.libs/libsquid.a")
libtool: link: (cd .libs/libclustalo.lax/libkmpp.a && ar x "/builddir/build/BUILD/clustal-omega-1.2.1/src/kmpp/.libs/libkmpp.a")
libtool: link: ar cru .libs/libclustalo.a  .libs/clustal-omega.o  .libs/libclustalo.lax/libclustal.a/ktuple_pair.o .libs/libclustalo.lax/libclustal.a/weights.o .libs/libclustalo.lax/libclustal.a/seq.o .libs/libclustalo.lax/libclustal.a/progress.o .libs/libclustalo.lax/libclustal.a/log.o .libs/libclustalo.lax/libclustal.a/list.o .libs/libclustalo.lax/libclustal.a/hhalign_wrapper.o .libs/libclustalo.lax/libclustal.a/symmatrix.o .libs/libclustalo.lax/libclustal.a/util.o .libs/libclustalo.lax/libclustal.a/muscle_upgma.o .libs/libclustalo.lax/libclustal.a/mbed.o .libs/libclustalo.lax/libclustal.a/tree.o .libs/libclustalo.lax/libclustal.a/muscle_tree.o .libs/libclustalo.lax/libclustal.a/pair_dist.o  .libs/libclustalo.lax/libhhalign.a/hhalign.o  .libs/libclustalo.lax/libsquid.a/msf.o .libs/libclustalo.lax/libsquid.a/gki.o .libs/libclustalo.lax/libsquid.a/msa.o .libs/libclustalo.lax/libsquid.a/sqerror.o .libs/libclustalo.lax/libsquid.a/selex.o .libs/libclustalo.lax/libsquid.a/file.o .libs/libclustalo.lax/libsquid.a/stack.o .libs/libclustalo.lax/libsquid.a/getopt.o .libs/libclustalo.lax/libsquid.a/clustal.o .libs/libclustalo.lax/libsquid.a/sre_random.o .libs/libclustalo.lax/libsquid.a/cluster.o .libs/libclustalo.lax/libsquid.a/seqencode.o .libs/libclustalo.lax/libsquid.a/types.o .libs/libclustalo.lax/libsquid.a/stockholm.o .libs/libclustalo.lax/libsquid.a/revcomp.o .libs/libclustalo.lax/libsquid.a/ssi.o .libs/libclustalo.lax/libsquid.a/sre_string.o .libs/libclustalo.lax/libsquid.a/dayhoff.o .libs/libclustalo.lax/libsquid.a/alignio.o .libs/libclustalo.lax/libsquid.a/squidcore.o .libs/libclustalo.lax/libsquid.a/a2m.o .libs/libclustalo.lax/libsquid.a/eps.o .libs/libclustalo.lax/libsquid.a/gsi.o .libs/libclustalo.lax/libsquid.a/phylip.o .libs/libclustalo.lax/libsquid.a/stopwatch.o .libs/libclustalo.lax/libsquid.a/aligneval.o .libs/libclustalo.lax/libsquid.a/translate.o .libs/libclustalo.lax/libsquid.a/hsregex.o .libs/libclustalo.lax/libsquid.a/weight.o .libs/libclustalo.lax/libsquid.a/gsi64.o .libs/libclustalo.lax/libsquid.a/iupac.o .libs/libclustalo.lax/libsquid.a/rk.o .libs/libclustalo.lax/libsquid.a/sre_ctype.o .libs/libclustalo.lax/libsquid.a/sqio.o .libs/libclustalo.lax/libsquid.a/sre_math.o .libs/libclustalo.lax/libsquid.a/shuffle.o .libs/libclustalo.lax/libsquid.a/vectorops.o  .libs/libclustalo.lax/libkmpp.a/KmUtils.o .libs/libclustalo.lax/libkmpp.a/KmTree.o .libs/libclustalo.lax/libkmpp.a/KMeans.o 
libtool: link: ranlib .libs/libclustalo.a
libtool: link: rm -fr .libs/libclustalo.lax
libtool: link: ( cd ".libs" && rm -f "libclustalo.la" && ln -s "../libclustalo.la" "libclustalo.la" )
/bin/sh ../libtool --tag=CXX   --mode=link g++ -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches  -m64 -mtune=generic -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm 
libtool: link: g++ -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -o clustalo main.o mymain.o  ./.libs/libclustalo.a -largtable2 -lm
make[3]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src'
make[2]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src'
make[1]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src'
make[1]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1'
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.ENzasF
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64
++ dirname /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64
+ cd clustal-omega-1.2.1
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64
Making install in src
make[1]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src'
Making install in hhalign
make[2]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/hhalign'
make[3]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/hhalign'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/usr/include/clustalo/hhalign" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/hhalign"
 /usr/bin/install -c -m 644 'general.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/hhalign/general.h'
 /usr/bin/install -c -m 644 'hhfunc.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/hhalign/hhfunc.h'
make[3]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/hhalign'
make[2]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/hhalign'
Making install in squid
make[2]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/squid'
make[3]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/squid'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/usr/include/clustalo/squid" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/squid"
 /usr/bin/install -c -m 644 'gki.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/squid/gki.h'
 /usr/bin/install -c -m 644 'gsi64.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/squid/gsi64.h'
 /usr/bin/install -c -m 644 'msa.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/squid/msa.h'
 /usr/bin/install -c -m 644 'rk.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/squid/rk.h'
 /usr/bin/install -c -m 644 'squid.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/squid/squid.h'
 /usr/bin/install -c -m 644 'stopwatch.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/squid/stopwatch.h'
 /usr/bin/install -c -m 644 'sqfuncs.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/squid/sqfuncs.h'
 /usr/bin/install -c -m 644 'sre_random.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/squid/sre_random.h'
 /usr/bin/install -c -m 644 'ssi.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/squid/ssi.h'
 /usr/bin/install -c -m 644 'stockholm.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/squid/stockholm.h'
 /usr/bin/install -c -m 644 'vectorops.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/squid/vectorops.h'
 /usr/bin/install -c -m 644 'version.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/squid/version.h'
make[3]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/squid'
make[2]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/squid'
Making install in kmpp
make[2]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/kmpp'
make[3]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/kmpp'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/kmpp'
make[2]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/kmpp'
Making install in clustal
make[2]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/clustal'
make[3]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/clustal'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/usr/include/clustalo/clustal" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/clustal"
 /usr/bin/install -c -m 644 'hhalign_wrapper.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/clustal/hhalign_wrapper.h'
 /usr/bin/install -c -m 644 'ktuple_pair.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/clustal/ktuple_pair.h'
 /usr/bin/install -c -m 644 'log.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/clustal/log.h'
 /usr/bin/install -c -m 644 'mbed.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/clustal/mbed.h'
 /usr/bin/install -c -m 644 'muscle_tree.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/clustal/muscle_tree.h'
 /usr/bin/install -c -m 644 'pair_dist.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/clustal/pair_dist.h'
 /usr/bin/install -c -m 644 'progress.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/clustal/progress.h'
 /usr/bin/install -c -m 644 'seq.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/clustal/seq.h'
 /usr/bin/install -c -m 644 'symmatrix.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/clustal/symmatrix.h'
 /usr/bin/install -c -m 644 'tree.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/clustal/tree.h'
 /usr/bin/install -c -m 644 'util.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/clustal/util.h'
 /usr/bin/install -c -m 644 'weights.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/clustal/weights.h'
make[3]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/clustal'
make[2]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src/clustal'
make[2]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src'
make[3]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1/src'
test -z "/usr/lib64" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/lib64"
 /bin/sh ../libtool   --mode=install /usr/bin/install -c  'libclustalo.la' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/lib64/libclustalo.la'
libtool: install: /usr/bin/install -c .libs/libclustalo.lai /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/lib64/libclustalo.la
libtool: install: /usr/bin/install -c .libs/libclustalo.a /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/lib64/libclustalo.a
libtool: install: chmod 644 /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/lib64/libclustalo.a
libtool: install: ranlib /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/lib64/libclustalo.a
libtool: install: warning: remember to run `libtool --finish /usr/lib64'
test -z "/usr/bin" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/bin"
  /bin/sh ../libtool   --mode=install /usr/bin/install -c 'clustalo' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/bin/clustalo'
libtool: install: /usr/bin/install -c clustalo /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/bin/clustalo
test -z "/usr/include/clustalo/" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo/"
 /usr/bin/install -c -m 644 'clustal-omega-config.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo//clustal-omega-config.h'
 /usr/bin/install -c -m 644 'clustal-omega.h' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/include/clustalo//clustal-omega.h'
make[3]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src'
make[2]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src'
make[1]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1/src'
make[1]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1'
make[2]: Entering directory `/builddir/build/BUILD/clustal-omega-1.2.1'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/usr/share/doc/clustal-omega" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/share/doc/clustal-omega"
 /usr/bin/install -c -m 644 'README' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/share/doc/clustal-omega/README'
test -z "/usr/lib64/pkgconfig" || /usr/bin/mkdir -p "/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/lib64/pkgconfig"
 /usr/bin/install -c -m 644 'clustalo.pc' '/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/lib64/pkgconfig/clustalo.pc'
make[2]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1'
make[1]: Leaving directory `/builddir/build/BUILD/clustal-omega-1.2.1'
+ rm -f /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/lib64/libclustalo.la /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/lib64/libclustalo.a
+ /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 /builddir/build/BUILD/clustal-omega-1.2.1
extracting debug info from /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/bin/clustalo
dwz: Too few files for multifile optimization
/usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
3373 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-java-repack-jars
Processing files: clustal-omega-1.2.1-2.fc21.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.9W5042
+ umask 022
+ cd /builddir/build/BUILD
+ cd clustal-omega-1.2.1
+ DOCDIR=/builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/share/doc/clustal-omega
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/share/doc/clustal-omega
+ cp -pr COPYING /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/share/doc/clustal-omega
+ cp -pr README /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64/usr/share/doc/clustal-omega
+ exit 0
Provides: bundled(squid) = 1.9 clustal-omega = 1.2.1-2.fc21 clustal-omega(x86-64) = 1.2.1-2.fc21
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libargtable2.so.0()(64bit) 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_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(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_3.4.9)(64bit) rtld(GNU_HASH)
Processing files: clustal-omega-devel-1.2.1-2.fc21.x86_64
Provides: clustal-omega-devel = 1.2.1-2.fc21 clustal-omega-devel(x86-64) = 1.2.1-2.fc21 pkgconfig(clustalo) = 1.2.1
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/pkg-config
Processing files: clustal-omega-debuginfo-1.2.1-2.fc21.x86_64
Provides: clustal-omega-debuginfo = 1.2.1-2.fc21 clustal-omega-debuginfo(x86-64) = 1.2.1-2.fc21
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64
Wrote: /builddir/build/RPMS/clustal-omega-1.2.1-2.fc21.x86_64.rpm
Wrote: /builddir/build/RPMS/clustal-omega-devel-1.2.1-2.fc21.x86_64.rpm
Wrote: /builddir/build/RPMS/clustal-omega-debuginfo-1.2.1-2.fc21.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.lOvEjG
+ umask 022
+ cd /builddir/build/BUILD
+ cd clustal-omega-1.2.1
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/clustal-omega-1.2.1-2.fc21.x86_64
+ exit 0
Child return code was: 0
LEAVE do -->