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Clustal Omega Log File
Raw
Log File.txt
Al-Hammad@AL-HAMMAD-PC ~
$ tar xfz argtable2-13.tar.gz
Al-Hammad@AL-HAMMAD-PC ~
$ tar xfz clustal-omega-1.2.0.tar.gz
Al-Hammad@AL-HAMMAD-PC ~
$ cd argtable2-13; ./configure; make; make install
checking build system type... i686-pc-mingw32
checking host system type... i686-pc-mingw32
checking target system type... i686-pc-mingw32
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... c:/Strawberry/c/x86_64-w64-mingw32/bin/ld.exe
checking if the linker (c:/Strawberry/c/x86_64-w64-mingw32/bin/ld.exe) is GNU ld
... yes
checking for BSD- or MS-compatible name lister (nm)... /c/Strawberry/c/bin/nm
checking the name lister (/c/Strawberry/c/bin/nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 8192
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for c:/Strawberry/c/x86_64-w64-mingw32/bin/ld.exe option to reload obje
ct files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... file_magic ^x86 archive import|
^x86 DLL
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /c/Strawberry/c/bin/nm output from gcc object... ok
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h...
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 for dlfcn.h... no
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -DDLL_EXPORT -DPIC
checking if gcc PIC flag -DDLL_EXPORT -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (c:/Strawberry/c/x86_64-w64-mingw32/bin/ld.exe)
supports shared libraries... yes
checking whether -lc should be explicitly linked in... yes
checking dynamic linker characteristics... Win32 ld.exe
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... yes
checking whether make sets $(MAKE)... (cached) yes
checking for ANSI C header files... (cached) yes
checking libintl.h usability... no
checking libintl.h presence... no
checking for libintl.h... no
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for strftime... yes
checking for working strtod... yes
checking for bzero... no
checking for strchr... yes
checking for strcspn... yes
checking for strrchr... yes
checking for strtol... yes
checking for getopt_long... yes
checking for regcomp... no
checking for strptime... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating example/Makefile
config.status: creating src/Makefile
config.status: creating doc/Makefile
config.status: creating doc/argtable2.3
config.status: creating doc/argtable2.html
config.status: creating tests/Makefile
config.status: creating argtable2.pc
config.status: creating argtable2-uninstalled.pc
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
Making all in src
make[1]: Entering directory `/home/Al-Hammad/argtable2-13/src'
make all-am
make[2]: Entering directory `/home/Al-Hammad/argtable2-13/src'
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -g -O2
-MT argtable2.lo -MD -MP -MF .deps/argtable2.Tpo -c -o argtable2.lo argtable2.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT argtable2.lo -MD -MP -MF .
deps/argtable2.Tpo -c argtable2.c -DDLL_EXPORT -DPIC -o .libs/argtable2.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT argtable2.lo -MD -MP -MF .
deps/argtable2.Tpo -c argtable2.c -o argtable2.o >/dev/null 2>&1
mv -f .deps/argtable2.Tpo .deps/argtable2.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -g -O2
-MT arg_end.lo -MD -MP -MF .deps/arg_end.Tpo -c -o arg_end.lo arg_end.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT arg_end.lo -MD -MP -MF .de
ps/arg_end.Tpo -c arg_end.c -DDLL_EXPORT -DPIC -o .libs/arg_end.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT arg_end.lo -MD -MP -MF .de
ps/arg_end.Tpo -c arg_end.c -o arg_end.o >/dev/null 2>&1
mv -f .deps/arg_end.Tpo .deps/arg_end.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -g -O2
-MT arg_rem.lo -MD -MP -MF .deps/arg_rem.Tpo -c -o arg_rem.lo arg_rem.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT arg_rem.lo -MD -MP -MF .de
ps/arg_rem.Tpo -c arg_rem.c -DDLL_EXPORT -DPIC -o .libs/arg_rem.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT arg_rem.lo -MD -MP -MF .de
ps/arg_rem.Tpo -c arg_rem.c -o arg_rem.o >/dev/null 2>&1
mv -f .deps/arg_rem.Tpo .deps/arg_rem.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -g -O2
-MT arg_lit.lo -MD -MP -MF .deps/arg_lit.Tpo -c -o arg_lit.lo arg_lit.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT arg_lit.lo -MD -MP -MF .de
ps/arg_lit.Tpo -c arg_lit.c -DDLL_EXPORT -DPIC -o .libs/arg_lit.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT arg_lit.lo -MD -MP -MF .de
ps/arg_lit.Tpo -c arg_lit.c -o arg_lit.o >/dev/null 2>&1
mv -f .deps/arg_lit.Tpo .deps/arg_lit.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -g -O2
-MT arg_int.lo -MD -MP -MF .deps/arg_int.Tpo -c -o arg_int.lo arg_int.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT arg_int.lo -MD -MP -MF .de
ps/arg_int.Tpo -c arg_int.c -DDLL_EXPORT -DPIC -o .libs/arg_int.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT arg_int.lo -MD -MP -MF .de
ps/arg_int.Tpo -c arg_int.c -o arg_int.o >/dev/null 2>&1
mv -f .deps/arg_int.Tpo .deps/arg_int.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -g -O2
-MT arg_dbl.lo -MD -MP -MF .deps/arg_dbl.Tpo -c -o arg_dbl.lo arg_dbl.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT arg_dbl.lo -MD -MP -MF .de
ps/arg_dbl.Tpo -c arg_dbl.c -DDLL_EXPORT -DPIC -o .libs/arg_dbl.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT arg_dbl.lo -MD -MP -MF .de
ps/arg_dbl.Tpo -c arg_dbl.c -o arg_dbl.o >/dev/null 2>&1
mv -f .deps/arg_dbl.Tpo .deps/arg_dbl.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -g -O2
-MT arg_str.lo -MD -MP -MF .deps/arg_str.Tpo -c -o arg_str.lo arg_str.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT arg_str.lo -MD -MP -MF .de
ps/arg_str.Tpo -c arg_str.c -DDLL_EXPORT -DPIC -o .libs/arg_str.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT arg_str.lo -MD -MP -MF .de
ps/arg_str.Tpo -c arg_str.c -o arg_str.o >/dev/null 2>&1
mv -f .deps/arg_str.Tpo .deps/arg_str.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -g -O2
-MT arg_file.lo -MD -MP -MF .deps/arg_file.Tpo -c -o arg_file.lo arg_file.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT arg_file.lo -MD -MP -MF .d
eps/arg_file.Tpo -c arg_file.c -DDLL_EXPORT -DPIC -o .libs/arg_file.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -g -O2 -MT arg_file.lo -MD -MP -MF .d
eps/arg_file.Tpo -c arg_file.c -o arg_file.o >/dev/null 2>&1
mv -f .deps/arg_file.Tpo .deps/arg_file.Plo
/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -version-info 1:8:1 -o li
bargtable2.la -rpath /usr/local/lib argtable2.lo arg_end.lo arg_rem.lo arg_lit.l
o arg_int.lo arg_dbl.lo arg_str.lo arg_file.lo
libtool: link: warning: undefined symbols not allowed in i686-pc-mingw32 shared
libraries
libtool: link: ar cru .libs/libargtable2.a argtable2.o arg_end.o arg_rem.o arg_
lit.o arg_int.o arg_dbl.o arg_str.o arg_file.o
libtool: link: ranlib .libs/libargtable2.a
libtool: link: ( cd ".libs" && rm -f "libargtable2.la" && ln -s "../libargtable2
.la" "libargtable2.la" )
make[2]: Leaving directory `/home/Al-Hammad/argtable2-13/src'
make[1]: Leaving directory `/home/Al-Hammad/argtable2-13/src'
Making all in tests
make[1]: Entering directory `/home/Al-Hammad/argtable2-13/tests'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/Al-Hammad/argtable2-13/tests'
Making all in doc
make[1]: Entering directory `/home/Al-Hammad/argtable2-13/doc'
cp argtable2.3 argtable.3
make[1]: Leaving directory `/home/Al-Hammad/argtable2-13/doc'
make[1]: Entering directory `/home/Al-Hammad/argtable2-13'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/home/Al-Hammad/argtable2-13'
Making install in src
make[1]: Entering directory `/home/Al-Hammad/argtable2-13/src'
make[2]: Entering directory `/home/Al-Hammad/argtable2-13/src'
test -z "/usr/local/lib" || /bin/mkdir -p "/usr/local/lib"
/bin/sh ../libtool --mode=install /bin/install -c 'libargtable2.la' '/usr/lo
cal/lib/libargtable2.la'
libtool: install: /bin/install -c .libs/libargtable2.lai /usr/local/lib/libargta
ble2.la
libtool: install: /bin/install -c .libs/libargtable2.a /usr/local/lib/libargtabl
e2.a
libtool: install: chmod 644 /usr/local/lib/libargtable2.a
libtool: install: ranlib /usr/local/lib/libargtable2.a
----------------------------------------------------------------------
Libraries have been installed in:
/usr/local/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-LLIBDIR' linker flag
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
test -z "/usr/local/include" || /bin/mkdir -p "/usr/local/include"
/bin/install -c -m 644 'argtable2.h' '/usr/local/include/argtable2.h'
make[2]: Leaving directory `/home/Al-Hammad/argtable2-13/src'
make[1]: Leaving directory `/home/Al-Hammad/argtable2-13/src'
Making install in tests
make[1]: Entering directory `/home/Al-Hammad/argtable2-13/tests'
make[2]: Entering directory `/home/Al-Hammad/argtable2-13/tests'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/Al-Hammad/argtable2-13/tests'
make[1]: Leaving directory `/home/Al-Hammad/argtable2-13/tests'
Making install in doc
make[1]: Entering directory `/home/Al-Hammad/argtable2-13/doc'
make[2]: Entering directory `/home/Al-Hammad/argtable2-13/doc'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/usr/local/share/doc/argtable2" || /bin/mkdir -p "/usr/local/share/doc/
argtable2"
/bin/install -c -m 644 'argtable2-advanced.html' '/usr/local/share/doc/argtable
2/argtable2-advanced.html'
/bin/install -c -m 644 'argtable2-advanced.pdf' '/usr/local/share/doc/argtable2
/argtable2-advanced.pdf'
/bin/install -c -m 644 'argtable2-advanced.ps' '/usr/local/share/doc/argtable2/
argtable2-advanced.ps'
/bin/install -c -m 644 'argtable2-intro.html' '/usr/local/share/doc/argtable2/a
rgtable2-intro.html'
/bin/install -c -m 644 'argtable2-intro.pdf' '/usr/local/share/doc/argtable2/ar
gtable2-intro.pdf'
/bin/install -c -m 644 'argtable2-intro.ps' '/usr/local/share/doc/argtable2/arg
table2-intro.ps'
/bin/install -c -m 644 'argtable2.html' '/usr/local/share/doc/argtable2/argtabl
e2.html'
/bin/install -c -m 644 'argtable2.pdf' '/usr/local/share/doc/argtable2/argtable
2.pdf'
/bin/install -c -m 644 'argtable2.ps' '/usr/local/share/doc/argtable2/argtable2
.ps'
/bin/install -c -m 644 'argxxx.gif' '/usr/local/share/doc/argtable2/argxxx.gif'
/bin/install -c -m 644 'arg_int.gif' '/usr/local/share/doc/argtable2/arg_int.gi
f'
test -z "/usr/local/share/man/man3" || /bin/mkdir -p "/usr/local/share/man/man3"
/bin/install -c -m 644 'argtable2.3' '/usr/local/share/man/man3/argtable2.3'
/bin/install -c -m 644 'argtable.3' '/usr/local/share/man/man3/argtable.3'
make[2]: Leaving directory `/home/Al-Hammad/argtable2-13/doc'
make[1]: Leaving directory `/home/Al-Hammad/argtable2-13/doc'
make[1]: Entering directory `/home/Al-Hammad/argtable2-13'
make[2]: Entering directory `/home/Al-Hammad/argtable2-13'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/usr/local/share/doc/argtable2/example" || /bin/mkdir -p "/usr/local/sh
are/doc/argtable2/example"
/bin/install -c -m 644 'example/Makefile' '/usr/local/share/doc/argtable2/examp
le/Makefile'
/bin/install -c -m 644 'example/README.txt' '/usr/local/share/doc/argtable2/exa
mple/README.txt'
/bin/install -c -m 644 'example/argcustom.c' '/usr/local/share/doc/argtable2/ex
ample/argcustom.c'
/bin/install -c -m 644 'example/argxxx.c' '/usr/local/share/doc/argtable2/examp
le/argxxx.c'
/bin/install -c -m 644 'example/argxxx.h' '/usr/local/share/doc/argtable2/examp
le/argxxx.h'
/bin/install -c -m 644 'example/callbacks.c' '/usr/local/share/doc/argtable2/ex
ample/callbacks.c'
/bin/install -c -m 644 'example/echo.c' '/usr/local/share/doc/argtable2/example
/echo.c'
/bin/install -c -m 644 'example/hasoptvalue.c' '/usr/local/share/doc/argtable2/
example/hasoptvalue.c'
/bin/install -c -m 644 'example/ls.c' '/usr/local/share/doc/argtable2/example/l
s.c'
/bin/install -c -m 644 'example/multisyntax.c' '/usr/local/share/doc/argtable2/
example/multisyntax.c'
/bin/install -c -m 644 'example/mv.c' '/usr/local/share/doc/argtable2/example/m
v.c'
/bin/install -c -m 644 'example/myprog.c' '/usr/local/share/doc/argtable2/examp
le/myprog.c'
/bin/install -c -m 644 'example/myprog_C89.c' '/usr/local/share/doc/argtable2/e
xample/myprog_C89.c'
/bin/install -c -m 644 'example/rm.c' '/usr/local/share/doc/argtable2/example/r
m.c'
/bin/install -c -m 644 'example/uname.c' '/usr/local/share/doc/argtable2/exampl
e/uname.c'
test -z "/usr/local/lib/pkgconfig" || /bin/mkdir -p "/usr/local/lib/pkgconfig"
/bin/install -c -m 644 'argtable2.pc' '/usr/local/lib/pkgconfig/argtable2.pc'
make[2]: Leaving directory `/home/Al-Hammad/argtable2-13'
make[1]: Leaving directory `/home/Al-Hammad/argtable2-13'
Al-Hammad@AL-HAMMAD-PC ~/argtable2-13
$ cd ~/clustal-omega-1.2.0
Al-Hammad@AL-HAMMAD-PC ~/clustal-omega-1.2.0
$ ./ configure CFLAGS='-I/usr/local/include -DSRE_STRICT_ANSI' LDFLAGS='-L/usr/
local/lib'
sh: ./: is a directory
Al-Hammad@AL-HAMMAD-PC ~/clustal-omega-1.2.0
$ ./configure CFLAGS='-I/usr/local/include -DSRE_STRICT_ANSI' LDFLAGS='-L/usr/l
ocal/lib'
configure:
Welcome to Clustal Omega - version 1.2.0 (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... /bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking for C compiler default output file name... a.exe
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... .exe
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... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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... i686-pc-mingw32
checking host system type... i686-pc-mingw32
checking whether make sets $(MAKE)... (cached) yes
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... c:/Strawberry/c/x86_64-w64-mingw32/bin/ld.exe
checking if the linker (c:/Strawberry/c/x86_64-w64-mingw32/bin/ld.exe) is GNU ld
... yes
checking for BSD- or MS-compatible name lister (nm)... /c/Strawberry/c/bin/nm
checking the name lister (/c/Strawberry/c/bin/nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 8192
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for c:/Strawberry/c/x86_64-w64-mingw32/bin/ld.exe option to reload obje
ct files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... file_magic ^x86 archive import|
^x86 DLL
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /c/Strawberry/c/bin/nm output from gcc object... ok
checking for dlfcn.h... no
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -DDLL_EXPORT -DPIC
checking if gcc PIC flag -DDLL_EXPORT -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (c:/Strawberry/c/x86_64-w64-mingw32/bin/ld.exe)
supports shared libraries... yes
checking whether -lc should be explicitly linked in... yes
checking dynamic linker characteristics... Win32 ld.exe
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... yes
checking for a BSD-compatible install... /bin/install -c
checking for gcc... (cached) 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) gcc3
checking how to run the C preprocessor... gcc -E
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++... gcc3
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... c:/Strawberry/c/x86_64-w64-mingw32/bin/ld.exe
checking if the linker (c:/Strawberry/c/x86_64-w64-mingw32/bin/ld.exe) is GNU ld
... yes
checking whether the g++ linker (c:/Strawberry/c/x86_64-w64-mingw32/bin/ld.exe)
supports shared libraries... yes
checking for g++ option to produce PIC... -DDLL_EXPORT -DPIC
checking if g++ PIC flag -DDLL_EXPORT -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (c:/Strawberry/c/x86_64-w64-mingw32/bin/ld.exe)
supports shared libraries... yes
checking dynamic linker characteristics... Win32 ld.exe
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... no
configure: WARNING: argtable2.h: accepted by the compiler, rejected by the prepr
ocessor!
configure: WARNING: argtable2.h: proceeding with the compiler's result
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... no
checking for ntohl... no
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... 4
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... 8
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 sr
c/config.h defines
config.status: executing depfiles commands
config.status: executing libtool commands
Al-Hammad@AL-HAMMAD-PC ~/clustal-omega-1.2.0
$make; make install
Making all in src
make[1]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/src'
make all-recursive
make[2]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/src'
Making all in hhalign
make[3]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/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 -O3 -g -O2 -MT hhalign.lo -MD -MP -MF .deps/hhalign.Tpo -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 -O3 -g -O2 -MT hhalign.lo -MD -MP -MF .deps/hhalign.Tpo -c hhalign.cpp -DDLL_EXPORT -DPIC -o .libs/hhalign.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -MT hhalign.lo -MD -MP -MF .deps/hhalign.Tpo -c hhalign.cpp -o hhalign.o >/dev/null 2>&1
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/bin/sh ../../libtool --tag=CXX --mode=link g++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -L/usr/local/lib -o libhhalign.la hhalign.lo -largtable2 -lm
*** Warning: This system can not link to static lib archive /usr/local/lib/libargtable2.la.
*** I have the capability to make that library automatically link in when
*** you link to this library. But I can only do this if you have a
*** shared version of the library, which you do not appear to have.
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 `/home/Al-Hammad/clustal-omega-1.2.0/src/hhalign'
Making all in squid
make[3]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/src/squid'
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT a2m.lo -MD -MP -MF .deps/a2m.Tpo -c -o a2m.lo a2m.c
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/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -DCLUSTALO -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT hsregex.lo -MD -MP -MF .deps/hsregex.Tpo -c -o hsregex.lo hsregex.c
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*** Warning: This system can not link to static lib archive /usr/local/lib/libargtable2.la.
*** I have the capability to make that library automatically link in when
*** you link to this library. But I can only do this if you have a
*** shared version of the library, which you do not appear to have.
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Making all in kmpp
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*** Warning: This system can not link to static lib archive /usr/local/lib/libargtable2.la.
*** I have the capability to make that library automatically link in when
*** you link to this library. But I can only do this if you have a
*** shared version of the library, which you do not appear to have.
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/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT muscle_upgma.lo -MD -MP -MF .deps/muscle_upgma.Tpo -c -o muscle_upgma.lo muscle_upgma.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT muscle_upgma.lo -MD -MP -MF .deps/muscle_upgma.Tpo -c muscle_upgma.c -DDLL_EXPORT -DPIC -o .libs/muscle_upgma.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT muscle_upgma.lo -MD -MP -MF .deps/muscle_upgma.Tpo -c muscle_upgma.c -o muscle_upgma.o >/dev/null 2>&1
mv -f .deps/muscle_upgma.Tpo .deps/muscle_upgma.Plo
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT muscle_tree.lo -MD -MP -MF .deps/muscle_tree.Tpo -c -o muscle_tree.lo muscle_tree.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT muscle_tree.lo -MD -MP -MF .deps/muscle_tree.Tpo -c muscle_tree.c -DDLL_EXPORT -DPIC -o .libs/muscle_tree.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT muscle_tree.lo -MD -MP -MF .deps/muscle_tree.Tpo -c muscle_tree.c -o muscle_tree.o >/dev/null 2>&1
mv -f .deps/muscle_tree.Tpo .deps/muscle_tree.Plo
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT mbed.lo -MD -MP -MF .deps/mbed.Tpo -c -o mbed.lo mbed.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT mbed.lo -MD -MP -MF .deps/mbed.Tpo -c mbed.c -DDLL_EXPORT -DPIC -o .libs/mbed.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT mbed.lo -MD -MP -MF .deps/mbed.Tpo -c mbed.c -o mbed.o >/dev/null 2>&1
mv -f .deps/mbed.Tpo .deps/mbed.Plo
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT pair_dist.lo -MD -MP -MF .deps/pair_dist.Tpo -c -o pair_dist.lo pair_dist.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT pair_dist.lo -MD -MP -MF .deps/pair_dist.Tpo -c pair_dist.c -DDLL_EXPORT -DPIC -o .libs/pair_dist.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT pair_dist.lo -MD -MP -MF .deps/pair_dist.Tpo -c pair_dist.c -o pair_dist.o >/dev/null 2>&1
mv -f .deps/pair_dist.Tpo .deps/pair_dist.Plo
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT progress.lo -MD -MP -MF .deps/progress.Tpo -c -o progress.lo progress.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT progress.lo -MD -MP -MF .deps/progress.Tpo -c progress.c -DDLL_EXPORT -DPIC -o .libs/progress.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT progress.lo -MD -MP -MF .deps/progress.Tpo -c progress.c -o progress.o >/dev/null 2>&1
mv -f .deps/progress.Tpo .deps/progress.Plo
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT seq.lo -MD -MP -MF .deps/seq.Tpo -c -o seq.lo seq.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT seq.lo -MD -MP -MF .deps/seq.Tpo -c seq.c -DDLL_EXPORT -DPIC -o .libs/seq.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT seq.lo -MD -MP -MF .deps/seq.Tpo -c seq.c -o seq.o >/dev/null 2>&1
mv -f .deps/seq.Tpo .deps/seq.Plo
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT symmatrix.lo -MD -MP -MF .deps/symmatrix.Tpo -c -o symmatrix.lo symmatrix.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT symmatrix.lo -MD -MP -MF .deps/symmatrix.Tpo -c symmatrix.c -DDLL_EXPORT -DPIC -o .libs/symmatrix.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT symmatrix.lo -MD -MP -MF .deps/symmatrix.Tpo -c symmatrix.c -o symmatrix.o >/dev/null 2>&1
mv -f .deps/symmatrix.Tpo .deps/symmatrix.Plo
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT tree.lo -MD -MP -MF .deps/tree.Tpo -c -o tree.lo tree.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT tree.lo -MD -MP -MF .deps/tree.Tpo -c tree.c -DDLL_EXPORT -DPIC -o .libs/tree.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT tree.lo -MD -MP -MF .deps/tree.Tpo -c tree.c -o tree.o >/dev/null 2>&1
mv -f .deps/tree.Tpo .deps/tree.Plo
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT util.lo -MD -MP -MF .deps/util.Tpo -c -o util.lo util.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT util.lo -MD -MP -MF .deps/util.Tpo -c util.c -DDLL_EXPORT -DPIC -o .libs/util.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT util.lo -MD -MP -MF .deps/util.Tpo -c util.c -o util.o >/dev/null 2>&1
mv -f .deps/util.Tpo .deps/util.Plo
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT weights.lo -MD -MP -MF .deps/weights.Tpo -c -o weights.lo weights.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT weights.lo -MD -MP -MF .deps/weights.Tpo -c weights.c -DDLL_EXPORT -DPIC -o .libs/weights.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -MT weights.lo -MD -MP -MF .deps/weights.Tpo -c weights.c -o weights.o >/dev/null 2>&1
mv -f .deps/weights.Tpo .deps/weights.Plo
/bin/sh ../../libtool --tag=CC --mode=link gcc -fopenmp -O3 -I/usr/local/include -DSRE_STRICT_ANSI -L/usr/local/lib -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
*** Warning: This system can not link to static lib archive /usr/local/lib/libargtable2.la.
*** I have the capability to make that library automatically link in when
*** you link to this library. But I can only do this if you have a
*** shared version of the library, which you do not appear to have.
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 `/home/Al-Hammad/clustal-omega-1.2.0/src/clustal'
make[3]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/src'
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -O3 -fopenmp -I/usr/local/include -DSRE_STRICT_ANSI -MT clustal-omega.lo -MD -MP -MF .deps/clustal-omega.Tpo -c -o clustal-omega.lo clustal-omega.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -O3 -fopenmp -I/usr/local/include -DSRE_STRICT_ANSI -MT clustal-omega.lo -MD -MP -MF .deps/clustal-omega.Tpo -c clustal-omega.c -DDLL_EXPORT -DPIC -o .libs/clustal-omega.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -O3 -fopenmp -I/usr/local/include -DSRE_STRICT_ANSI -MT clustal-omega.lo -MD -MP -MF .deps/clustal-omega.Tpo -c clustal-omega.c -o clustal-omega.o >/dev/null 2>&1
mv -f .deps/clustal-omega.Tpo .deps/clustal-omega.Plo
/bin/sh ../libtool --tag=CC --mode=link gcc -O3 -fopenmp -I/usr/local/include -DSRE_STRICT_ANSI -static -L/usr/local/lib -o libclustalo.la -rpath /usr/local/lib 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 "/home/Al-Hammad/clustal-omega-1.2.0/src/clustal/.libs/libclustal.a")
libtool: link: (cd .libs/libclustalo.lax/libhhalign.a && ar x "/home/Al-Hammad/clustal-omega-1.2.0/src/hhalign/.libs/libhhalign.a")
libtool: link: (cd .libs/libclustalo.lax/libsquid.a && ar x "/home/Al-Hammad/clustal-omega-1.2.0/src/squid/.libs/libsquid.a")
libtool: link: (cd .libs/libclustalo.lax/libkmpp.a && ar x "/home/Al-Hammad/clustal-omega-1.2.0/src/kmpp/.libs/libkmpp.a")
libtool: link: ar cru .libs/libclustalo.a clustal-omega.o .libs/libclustalo.lax/libclustal.a/hhalign_wrapper.o .libs/libclustalo.lax/libclustal.a/ktuple_pair.o .libs/libclustalo.lax/libclustal.a/list.o .libs/libclustalo.lax/libclustal.a/log.o .libs/libclustalo.lax/libclustal.a/mbed.o .libs/libclustalo.lax/libclustal.a/muscle_tree.o .libs/libclustalo.lax/libclustal.a/muscle_upgma.o .libs/libclustalo.lax/libclustal.a/pair_dist.o .libs/libclustalo.lax/libclustal.a/progress.o .libs/libclustalo.lax/libclustal.a/seq.o .libs/libclustalo.lax/libclustal.a/symmatrix.o .libs/libclustalo.lax/libclustal.a/tree.o .libs/libclustalo.lax/libclustal.a/util.o .libs/libclustalo.lax/libclustal.a/weights.o .libs/libclustalo.lax/libhhalign.a/hhalign.o .libs/libclustalo.lax/libsquid.a/a2m.o .libs/libclustalo.lax/libsquid.a/aligneval.o .libs/libclustalo.lax/libsquid.a/alignio.o .libs/libclustalo.lax/libsquid.a/clustal.o .libs/libclustalo.lax/libsquid.a/cluster.o .libs/libclustalo.lax/libsquid.a/dayhoff.o .libs/libclustalo.lax/libsquid.a/eps.o .libs/libclustalo.lax/libsquid.a/file.o .libs/libclustalo.lax/libsquid.a/getopt.o .libs/libclustalo.lax/libsquid.a/gki.o .libs/libclustalo.lax/libsquid.a/gsi.o .libs/libclustalo.lax/libsquid.a/gsi64.o .libs/libclustalo.lax/libsquid.a/hsregex.o .libs/libclustalo.lax/libsquid.a/iupac.o .libs/libclustalo.lax/libsquid.a/msa.o .libs/libclustalo.lax/libsquid.a/msf.o .libs/libclustalo.lax/libsquid.a/phylip.o .libs/libclustalo.lax/libsquid.a/revcomp.o .libs/libclustalo.lax/libsquid.a/rk.o .libs/libclustalo.lax/libsquid.a/selex.o .libs/libclustalo.lax/libsquid.a/seqencode.o .libs/libclustalo.lax/libsquid.a/shuffle.o .libs/libclustalo.lax/libsquid.a/sqerror.o .libs/libclustalo.lax/libsquid.a/sqio.o .libs/libclustalo.lax/libsquid.a/squidcore.o .libs/libclustalo.lax/libsquid.a/sre_ctype.o .libs/libclustalo.lax/libsquid.a/sre_math.o .libs/libclustalo.lax/libsquid.a/sre_random.o .libs/libclustalo.lax/libsquid.a/sre_string.o .libs/libclustalo.lax/libsquid.a/ssi.o .libs/libclustalo.lax/libsquid.a/stack.o .libs/libclustalo.lax/libsquid.a/stockholm.o .libs/libclustalo.lax/libsquid.a/stopwatch.o .libs/libclustalo.lax/libsquid.a/translate.o .libs/libclustalo.lax/libsquid.a/types.o .libs/libclustalo.lax/libsquid.a/vectorops.o .libs/libclustalo.lax/libsquid.a/weight.o .libs/libclustalo.lax/libkmpp.a/KMeans.o .libs/libclustalo.lax/libkmpp.a/KmTree.o .libs/libclustalo.lax/libkmpp.a/KmUtils.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" )
g++ -DHAVE_CONFIG_H -I. -O3 -fopenmp -g -O2 -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cpp
mv -f .deps/main.Tpo .deps/main.Po
gcc -DHAVE_CONFIG_H -I. -O3 -fopenmp -I/usr/local/include -DSRE_STRICT_ANSI -MT mymain.o -MD -MP -MF .deps/mymain.Tpo -c -o mymain.o mymain.c
mv -f .deps/mymain.Tpo .deps/mymain.Po
/bin/sh ../libtool --tag=CXX --mode=link g++ -O3 -fopenmp -g -O2 -L/usr/local/lib -o clustalo.exe main.o mymain.o libclustalo.la -largtable2 -lm
libtool: link: g++ -O3 -fopenmp -g -O2 -o .libs/clustalo.exe main.o mymain.o -L/usr/local/lib ./.libs/libclustalo.a /usr/local/lib/libargtable2.a
make[3]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0/src'
make[2]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0/src'
make[1]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0/src'
make[1]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0'
Making install in src
make[1]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/src'
Making install in hhalign
make[2]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/src/hhalign'
make[3]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/src/hhalign'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/usr/local/include/clustalo/hhalign" || /bin/mkdir -p "/usr/local/include/clustalo/hhalign"
/bin/install -c -m 644 'general.h' '/usr/local/include/clustalo/hhalign/general.h'
/bin/install -c -m 644 'hhfunc.h' '/usr/local/include/clustalo/hhalign/hhfunc.h'
make[3]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0/src/hhalign'
make[2]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0/src/hhalign'
Making install in squid
make[2]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/src/squid'
make[3]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/src/squid'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/usr/local/include/clustalo/squid" || /bin/mkdir -p "/usr/local/include/clustalo/squid"
/bin/install -c -m 644 'gki.h' '/usr/local/include/clustalo/squid/gki.h'
/bin/install -c -m 644 'gsi64.h' '/usr/local/include/clustalo/squid/gsi64.h'
/bin/install -c -m 644 'msa.h' '/usr/local/include/clustalo/squid/msa.h'
/bin/install -c -m 644 'rk.h' '/usr/local/include/clustalo/squid/rk.h'
/bin/install -c -m 644 'squid.h' '/usr/local/include/clustalo/squid/squid.h'
/bin/install -c -m 644 'stopwatch.h' '/usr/local/include/clustalo/squid/stopwatch.h'
/bin/install -c -m 644 'sqfuncs.h' '/usr/local/include/clustalo/squid/sqfuncs.h'
/bin/install -c -m 644 'sre_random.h' '/usr/local/include/clustalo/squid/sre_random.h'
/bin/install -c -m 644 'ssi.h' '/usr/local/include/clustalo/squid/ssi.h'
/bin/install -c -m 644 'stockholm.h' '/usr/local/include/clustalo/squid/stockholm.h'
/bin/install -c -m 644 'vectorops.h' '/usr/local/include/clustalo/squid/vectorops.h'
/bin/install -c -m 644 'version.h' '/usr/local/include/clustalo/squid/version.h'
make[3]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0/src/squid'
make[2]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0/src/squid'
Making install in kmpp
make[2]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/src/kmpp'
make[3]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/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 `/home/Al-Hammad/clustal-omega-1.2.0/src/kmpp'
make[2]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0/src/kmpp'
Making install in clustal
make[2]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/src/clustal'
make[3]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/src/clustal'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/usr/local/include/clustalo/clustal" || /bin/mkdir -p "/usr/local/include/clustalo/clustal"
/bin/install -c -m 644 'hhalign_wrapper.h' '/usr/local/include/clustalo/clustal/hhalign_wrapper.h'
/bin/install -c -m 644 'ktuple_pair.h' '/usr/local/include/clustalo/clustal/ktuple_pair.h'
/bin/install -c -m 644 'log.h' '/usr/local/include/clustalo/clustal/log.h'
/bin/install -c -m 644 'mbed.h' '/usr/local/include/clustalo/clustal/mbed.h'
/bin/install -c -m 644 'muscle_tree.h' '/usr/local/include/clustalo/clustal/muscle_tree.h'
/bin/install -c -m 644 'pair_dist.h' '/usr/local/include/clustalo/clustal/pair_dist.h'
/bin/install -c -m 644 'progress.h' '/usr/local/include/clustalo/clustal/progress.h'
/bin/install -c -m 644 'seq.h' '/usr/local/include/clustalo/clustal/seq.h'
/bin/install -c -m 644 'symmatrix.h' '/usr/local/include/clustalo/clustal/symmatrix.h'
/bin/install -c -m 644 'tree.h' '/usr/local/include/clustalo/clustal/tree.h'
/bin/install -c -m 644 'util.h' '/usr/local/include/clustalo/clustal/util.h'
/bin/install -c -m 644 'weights.h' '/usr/local/include/clustalo/clustal/weights.h'
make[3]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0/src/clustal'
make[2]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0/src/clustal'
make[2]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/src'
make[3]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0/src'
test -z "/usr/local/lib" || /bin/mkdir -p "/usr/local/lib"
/bin/sh ../libtool --mode=install /bin/install -c 'libclustalo.la' '/usr/local/lib/libclustalo.la'
libtool: install: /bin/install -c .libs/libclustalo.lai /usr/local/lib/libclustalo.la
libtool: install: /bin/install -c .libs/libclustalo.a /usr/local/lib/libclustalo.a
libtool: install: chmod 644 /usr/local/lib/libclustalo.a
libtool: install: ranlib /usr/local/lib/libclustalo.a
----------------------------------------------------------------------
Libraries have been installed in:
/usr/local/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-LLIBDIR' linker flag
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
test -z "/usr/local/bin" || /bin/mkdir -p "/usr/local/bin"
/bin/sh ../libtool --mode=install /bin/install -c 'clustalo.exe' '/usr/local/bin/clustalo.exe'
libtool: install: /bin/install -c .libs/clustalo.exe /usr/local/bin/clustalo.exe
test -z "/usr/local/include/clustalo/" || /bin/mkdir -p "/usr/local/include/clustalo/"
/bin/install -c -m 644 'clustal-omega-config.h' '/usr/local/include/clustalo//clustal-omega-config.h'
/bin/install -c -m 644 'clustal-omega.h' '/usr/local/include/clustalo//clustal-omega.h'
make[3]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0/src'
make[2]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0/src'
make[1]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0/src'
make[1]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0'
make[2]: Entering directory `/home/Al-Hammad/clustal-omega-1.2.0'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/usr/local/share/doc/clustal-omega" || /bin/mkdir -p "/usr/local/share/doc/clustal-omega"
/bin/install -c -m 644 'README' '/usr/local/share/doc/clustal-omega/README'
test -z "/usr/local/lib/pkgconfig" || /bin/mkdir -p "/usr/local/lib/pkgconfig"
/bin/install -c -m 644 'clustalo.pc' '/usr/local/lib/pkgconfig/clustalo.pc'
make[2]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0'
make[1]: Leaving directory `/home/Al-Hammad/clustal-omega-1.2.0'
Al-Hammad@AL-HAMMAD-PC ~/clustal-omega-1.2.0
$
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