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view clustalomega/clustal-omega-1.0.2/configure.ac @ 1:bc707542e5de
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| author | clustalomega |
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| date | Thu, 21 Jul 2011 13:35:08 -0400 |
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# configure.ac for Clustal Omega # # RCS $Id: configure.ac 256 2011-06-23 13:57:28Z fabian $ # release # #AC_INIT([Clustal Omega], [0.1.1], [clustalw@ucd.ie]) #PACKAGE_CODENAME="OppidumLeonis" #r238 #AC_INIT([Clustal Omega], [0.2.0], [clustalw@ucd.ie]) #PACKAGE_CODENAME="IbiMeVidebunt" #r250 #AC_INIT([Clustal Omega], [1.0.1], [clustalw@ucd.ie]) #PACKAGE_CODENAME="DeshilHollesEamus" #r255 AC_INIT([Clustal Omega], [1.0.2], [clustalw@ucd.ie]) PACKAGE_CODENAME="DeshilHollesEamus" # The AC_INIT macro can take any source file as an argument. It just # checks that the file is there, which should, in turn, mean that the # source directory is there. AC_INIT generates the following m4 # macros, output variables and preprocessor symbols: AC_SUBST(PACKAGE_NAME) AC_SUBST(PACKAGE_TARNAME) AC_SUBST(PACKAGE_VERSION) AC_SUBST(PACKAGE_STRING) AC_SUBST(PACKAGE_BUGREPORT) AC_SUBST(PACKAGE_CODENAME) AC_MSG_NOTICE([ Welcome to $PACKAGE_NAME - version $PACKAGE_VERSION ($PACKAGE_CODENAME) +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 ]) # # Created with http://www.glassgiant.com/ascii/ and Wikipedia's Omega # Replaced all dollars with S's. # # # ,MMMMMMMMMD: MMMMM # NMMMMMMMMMMMMMM+ SMMMM # DMMMMMMMMMMMMMMMMMM, +MMMM # MMMMMMMMM8ZSO8MMMMMMMM +MMMM # MMMMM7 SMMMM +MMMM # MMMO MM? +MMMM # ?MMI NMIIMMMM # MMM MMMMMMM # MM # MN # MD # MM # MM? ,~+ISON # =MMI MMSOMMMM # MMMZ MMS +MMMM # MMMM8: :NMMM +MMMM # MMMMMMMMMDOODMMMMMMMMM +MMMM # MMMMMMMMMMMMMMMMMMMM +MMMM # OMMMMMMMMMMMMMMZ SMMMM # MMMMMMMMMM+ MMMMM # # AC_MSG_NOTICE([Configuring for your system...]) AC_PREREQ(2.6) # 2.60 needed for AC_USE_SYSTEM_EXTENSIONS # consider 2.64 which allows to define a URL as well # The AM_INIT_AUTOMAKE line adds several standard checks. # This macro is always needed for automake # Obsolete: It takes the program name and version number as arguments. AM_INIT_AUTOMAKE # config header: provides a way for people to customise the # configuration for their platform, via #defines. config.h.in can be # generated automatically with the autoheader tool. However, you need # a stamp-h file in your project to ensure that automake regenerates # config.h from config.h.in. Type 'touch stamp-h' to add this file to # your project. # AM_CONFIG_HEADER(src/config.h) # the following allows to install a copy config.h for libclustalo in a # namespace like way, i.e. no name clash with your own config.h AX_PREFIX_CONFIG_H(src/clustal-omega-config.h) # This macro was introduced in Autoconf 2.60. If possible, enable # extensions to C or Posix on hosts that normally disable the # extensions. AC_USE_SYSTEM_EXTENSIONS # for cross compilation # AC_CANONICAL_HOST ## AC_CANONICAL_BUILD ## AC_CANONICAL_TARGET # Set the @SET_MAKE@ variable=make if $(MAKE) not set AC_PROG_MAKE_SET # AC_PROG_RANLIB will allow you to build code in sub-directories into # temporary libraries, which make will then link in with the rest of # the code. # Rendered obsolte by LT_INIT: AC_PROG_RANLIB #AC_PROG_LIBTOOL LT_INIT # AC_PROG_INSTALL will generate an install target so that users may # just type 'make install' to install the software. AC_PROG_INSTALL # check for C++ preprocessor and compiler and the library compiler # (might change the compiler flags) # # Determine a C compiler to use. If using the GNU C compiler, set # shell variable GCC to `yes'. If output variable CFLAGS was not # already set, set it to `-g -O2' for the GNU C compiler (`-O2' on # systems where GCC does not accept `-g'), or `-g' for other # compilers. AC_PROG_CC # Set output variable CPP to a command that runs the C preprocessor. AC_PROG_CPP # # Determine a C++ compiler to use. If output variable CXXFLAGS was not # already set, set it to `-g -O2' for the GNU C++ compiler (`-O2' on # systems where G++ does not accept `-g'), or `-g' for other # compilers. AC_PROG_CXX # Set CXXCPP to a command that runs the C++ preprocessor AC_PROG_CXXCPP # # reset compiler flags to initial flags #CXXFLAGS=$OLD_CXXFLAGS # safety check: AC_CONFIG_SRCDIR([src/clustal.h]) # Let source files know in which context they are being used AC_DEFINE([CLUSTALO], [1], [Let all files know they are being used inside Clustal Omega]) AC_DEFINE_UNQUOTED(PACKAGE_CODENAME, "$PACKAGE_CODENAME", [The package code name]) # Get svn revision #AC_PATH_PROG(svnversioncommand, svnversion) #if test "X$svnversioncommand" = "X" || test `$svnversioncommand -n '.'` = "exported"; then #AC_DEFINE_UNQUOTED(SVN_VERSION, ["`cat saved_svn_version.txt`"], [repository svn version]) #else #AC_DEFINE_UNQUOTED(SVN_VERSION, ["`svnversion -n`"], [repository svn version]) #`svnversion -n > saved_svn_version.txt` #fi # AW: we might need this in the future # case "$host_os" in linux*) # AC_DEFINE(LINUX,1,[This is a Linux system]) AC_DEFINE_UNQUOTED(LINUX,1,[This is a LINUX system]) # AM_CONDITIONAL(HAVE_GNU_LD, true) # AM_CONDITIONAL(SOMEBSD, false) # XTRA_CPPLIBS=-lstdc++ # LIBEXT=.so ;; freebsd*) AC_DEFINE_UNQUOTED(SOMEBSD,1,[This is a BSD system]) # AC_CHECK_LIB(c_r, pthread_create) # AM_CONDITIONAL(HAVE_GNU_LD, true) # AM_CONDITIONAL(SOMEBSD, true) # XTRA_CPPLIBS=-lstdc++ # LIBEXT=.so ;; openbsd*) AC_DEFINE_UNQUOTED(SOMEBSD,1,[This is a BSD system]) # AC_CHECK_LIB(c_r, pthread_create) # AM_CONDITIONAL(HAVE_GNU_LD, true) # AM_CONDITIONAL(SOMEBSD, true) # XTRA_CPPLIBS=-lstdc++ # LIBEXT=.so ;; netbsd*) AC_DEFINE_UNQUOTED(SOMEBSD,1,[This is a BSD system]) # AC_CHECK_LIB(c_r, pthread_create) # AM_CONDITIONAL(HAVE_GNU_LD, true) # AM_CONDITIONAL(SOMEBSD, true) # XTRA_CPPLIBS=-lstdc++ # LIBEXT=.so ;; *solaris*) AC_DEFINE_UNQUOTED(SOLARIS,1,[This is a Solaris system]) # AC_CHECK_LIB(resolv, res_init) # XTRA_CPPLIBS=-lstdc++ # AM_CONDITIONAL(HAVE_GNU_LD, false) # AM_CONDITIONAL(SOMEBSD, false) # CFLAGS="-D_POSIX_PTHREAD_SEMANTICS $CFLAGS" # LIBEXT=.so ;; darwin*) AC_DEFINE_UNQUOTED(DARWIN,1,[This is a Darwin system]) # AM_CONDITIONAL(HAVE_GNU_LD, false) # AM_CONDITIONAL(SOMEBSD, false) # CFLAGS="-fno-common $CFLAGS" # LIBEXT=.so ;; cygwin*) AC_DEFINE_UNQUOTED(CYGWIN,1,[This is a CYGWIN system]) # LDFLAGS="$LDFLAGS -no-undefined" # AM_CONDITIONAL(SOMEBSD, false) # AM_CONDITIONAL(HAVE_GNU_LD, false) # LIBEXT=.dll ;; mingw*) AC_DEFINE_UNQUOTED(MINGW,1,[This is a MinGW system]) # AC_DEFINE_UNQUOTED(WINDOWS,1,[This is a Windows system]) # AC_CHECK_LIB(intl, gettext) # AC_CHECK_LIB(ws2_32, _head_libws2_32_a,,[AC_MSG_ERROR([libextractor requires Winsock2])]) # AC_CHECK_LIB(plibc, plibc_init,,[AC_MSG_ERROR([libextractor requires PlibC])]) # LDFLAGS="$LDFLAGS -no-undefined -Wl,--export-all-symbols" # LIBSOLD=$LIBS # AM_CONDITIONAL(HAVE_GNU_LD, true) # AM_CONDITIONAL(SOMEBSD, false) # LIBEXT=.dll ;; *) # AC_MSG_RESULT(Unrecognised OS $host_os) AC_DEFINE_UNQUOTED(OTHEROS,1,[Some strange OS]) # AC_MSG_RESULT(otheros) # AM_CONDITIONAL(HAVE_GNU_LD, false) # AM_CONDITIONAL(SOMEBSD, false) # LIBEXT=.so ;; esac # Checks for standard header files. # obsolescent according to http://www.gnu.org/software/hello/manual/autoconf/Particular-Headers.html AC_HEADER_STDC # Guess the next one is obsolete as well then? AC_CHECK_HEADERS(assert.h ctype.h float.h limits.h math.h memory.h stdarg.h stdio.h stdlib.h string.h time.h unistd.h) # awk '/^#include *</ {print $2}' $(find src/ -name \*.[ch] -or -name \*.cpp) | grep -v argtable2.h | sort -u | tr -d '<>' # Checks for typedefs, structures, and compiler characteristics. AC_C_CONST AC_TYPE_SIZE_T AC_C_INLINE # Checks for library functions. # AC_CHECK_FUNCS(strdup strstr strchr erand48) # AW is there an automatic way to extract library functions used in the program? # explicit libm check AC_CHECK_LIB(m, log,, AC_MSG_ERROR([Could not find libm])) AC_CHECK_LIB(m, log2, AC_DEFINE(HAVE_LOG2, 1, [Has log2()])) # --- argtable header and library check # # AC_CHECK_HEADERS([argtable2.h], [], AC_MSG_ERROR([Could not find argtable2.h. Try $ ./configure CFLAGS='-Iyour-argtable2-include-path])) AC_CHECK_LIB(argtable2, arg_parse, [], AC_MSG_ERROR([Could not find libargtable2. Try $ ./configure LDFLAGS="-Lyour-argtable2-lib-path'])) # enable python if requested (--with-python) # #AC_ARG_WITH([python], # [AS_HELP_STRING([--with-python], # [Enable Python Interface])], # [with_python=$withval], # [with_python=no]) #if test "$with_python" = "yes"; then # AC_MSG_CHECKING([for python-config to get compiler flags]) # AC_CHECK_PROG(python_config, 'python-config', yes) # if test "${python_config}" != "yes"; then # AC_MSG_ERROR("Could not run python-config.") # fi # PYTHON_CFLAGS=`python-config --cflags` # PYTHON_LDFLAGS=`python-config --ldflags` # AC_DEFINE([PYTHON_ENABLED], [1], [define for python usage]) #fi #AC_SUBST(PYTHON_CFLAGS) #AC_SUBST(PYTHON_LDFLAGS) # --- SSE support # "One instruction to do the same operation on 4 packed elements simultaneously." # # http://www.codeproject.com/KB/recipes/sseintro.aspx?msg=568491 # http://www.drdobbs.com/go-parallel/blog/archives/2010/03/getting_amazing.html # http://software.intel.com/file/1000 # # AC_MSG_CHECKING(for SSE in current arch/CFLAGS) # AC_LINK_IFELSE([ # AC_LANG_PROGRAM([[ # #include <xmmintrin.h> # __m128 testfunc(float *a, float *b) { # return _mm_add_ps(_mm_loadu_ps(a), _mm_loadu_ps(b)); # } # ]])], # [has_sse=yes], [has_sse=no] # ) # AC_MSG_RESULT($has_sse) # # AC_ARG_ENABLE([sse], # [AS_HELP_STRING([--enable-sse], # [Enable SSE support])], # [has_sse="$enableval"], # [has_sse=no]) # # if test x"$has_sse" = x"yes"; then # AC_DEFINE([USE_SSE], , [Enable SSE support]) # CFLAGS="${CFLAGS} -msse" # fi # --- openmp # AC_CONFIG_MACRO_DIR([m4]) m4_include([m4/ax_openmp.m4]) AC_ARG_WITH([openmp], AS_HELP_STRING([--without-openmp], [Do not use OpenMP])) AS_IF([test "x$with_openmp" = "xno"], [], [AX_OPENMP( AC_DEFINE([HAVE_OPENMP],[1],[Defined if OpenMP should and can be used]) )] ) AC_SUBST(OPENMP_CFLAGS) # according to http://beagle-lib.googlecode.com/svn-history/r824/trunk/configure.ac: # "OpenMP checker only defines for C when compiling both C and C++" OPENMP_CXXFLAGS=$OPENMP_CFLAGS AC_SUBST(OPENMP_CXXFLAGS) # version 2: enable openmp only if explicitely asked for it #AC_ARG_ENABLE(openmp, AS_HELP_STRING([--enable-openmp], [Multi-threaded parallel version using OpenMP])) #if test -n "${enable_openmp}" -a x"${enable_openmp}" != x"no"; then # m4_include([m4/ax_openmp.m4]) # AX_OPENMP(AC_DEFINE(HAVE_OPENMP, 1, [enable OpenMP support]), # AC_MSG_ERROR([Compiler does not seem to support OpenMP])) # AC_SUBST(OPENMP_CFLAGS) # AC_SUBST(OPENMP_CXXFLAGS) #fi # --- squid # # # Extra checks for squid; see their configure, config.log, squidconf.h # etc. For example, I'm not sure about USE_HOST_BYTESWAP_FUNCTIONS, # SIZEOF_UNSIGNED_LONG, HAVE_STRTOUL and HAVE_STRTOULL # # Might not just have to set compiler flags but create use squidconf.h.in # # The following hopefully takes about byte ordering (big-endian...). # My hope is that it will set WORDS_BIGENDIAN and # USE_HOST_BYTESWAP_FUNCTIONS (as used by squid) if necessary: # AC_C_BIGENDIAN(AC_MSG_WARN([$PACKAGE_NAME hasn't been tested on Big-Endian machines...expecting trouble!])) AC_CHECK_FUNCS([ntohs ntohl ntons ntonl]) # AC_CHECK_SIZEOF(unsigned short) AC_CHECK_SIZEOF(unsigned int) AC_CHECK_SIZEOF(unsigned long) AC_CHECK_SIZEOF(unsigned long long) # AC_CHECK_FUNCS([stroul strtoull]) AC_CHECK_FUNCS([ftello fseeko]) AC_CHECK_FUNCS([ftello64 fseeko64]) AC_CHECK_FUNCS([ftell64 fseek64]) # AC_TYPE_OFF_T AC_CHECK_SIZEOF(fpos_t) # # struct stat64 and stat64 test: # version 1: #AC_CHECK_TYPE(struct stat64, # [AC_CHECK_FUNC([stat64], # AC_DEFINE([HAVE_STAT64], [1], [Define if you have the stat64 function]))]) # version 2: #AC_MSG_CHECKING(for struct stat64) #AC_CACHE_VAL(sc_cv_type_stat64, #[AC_TRY_COMPILE([#include <sys/stat.h>],[struct stat64 s;], #[sc_cv_type_stat64=yes], #[sc_cv_type_stat64=no])]) #if test $sc_cv_type_stat64 = yes; then # AC_MSG_RESULT($sc_cv_type_stat64) # AC_CHECK_FUNC([stat64], AC_DEFINE([HAVE_STAT64], [1], [Define if you have the stat64 function])) # #AC_DEFINE(HAVE_STAT64, [1], [Define if you have the stat64 function]) #fi # # # Above fails on myosin because storage size of struct 64 is unknown: # ssi.c:480: error: storage size of ‘s1’ isn’t known # # On my MacBook OS X 10.6 I get: # ssi.c:481: warning: ‘stat64’ is deprecated (declared at /usr/include/sys/stat.h:465) # # So forget about it: we won't use stat64 or define HAVE_STAT64 and # consequently do no tests here # # Add support for the Dmalloc package. If the user runs configure with # --with-dmalloc, then define WITH_DMALLOC and add -ldmalloc to LIBS. AM_WITH_DMALLOC # Check if svnversion is installed #AC_PATH_PROG([SVNVERSION_BIN], [svnversionFIXME], [no]) ## checking if we build in a subversion WC #wc_found="no"; #if test "$SVNVERSION_BIN" != "no"; then # SVNVERSION=`$SVNVERSION_BIN -n $srcdir` # if test $SVNVERSION != "exported"; # then # AC_MSG_NOTICE($SVNVERSION); # fi #fi # --- debugging # # # AC_MSG_CHECKING([whether to build with debug information]) AC_ARG_ENABLE([debug], [AS_HELP_STRING([--enable-debug], [Enable debugging (default=no)])], [debugit="$enableval"], [debugit=no]) AC_MSG_RESULT([$debugit]) if test x"$debugit" = x"yes"; then # User variables CFLAGS/CXXFLAGS are used last during compilation and # can therefore overwrite system settings. # # if debugging was requested, add debugging info at the end of # C[XX]FLAGS, which makes sure previous optimisation flags are # overwritten (normally C[XX]FLAGS should not be modified as they # are user variables): # switch off assert etc # AC_DEFINE([DEBUG],[],[Debug Mode]) CFLAGS="${CFLAGS} -g -ansi -Wall -O0" CXXFLAGS="${CXXFLAGS} -g -ansi -Wall -O0" else # switch off assert etc AC_DEFINE([NDEBUG],[],[No-debug Mode]) # if no debugging is requested, we make optimisation explicit AM_CXXFLAGS="${AM_CXXFLAGS} -O3" AM_CFLAGS="${AM_CFLAGS} -O3" fi AC_SUBST([AM_CXXFLAGS]) AC_SUBST([AM_CFLAGS]) AC_SUBST([AM_LDFLAGS]) AC_CONFIG_FILES(Makefile src/Makefile clustalo.pc Doxyfile src/clustal/Makefile src/hhalign/Makefile src/kmpp/Makefile src/squid/Makefile) AC_OUTPUT