# -*- Autoconf -*- # Configure template for the EMBOSS package. # Process this file with autoconf to produce a configure script. AC_PREREQ([2.64]) AC_INIT([EMBOSS], [6.6.0], [emboss-bug@emboss.open-bio.org], [EMBOSS], [http://emboss.open-bio.org/]) AC_REVISION([$Revision: 1.162 $]) AC_CONFIG_SRCDIR([ajax/acd/ajacd.c]) AC_CONFIG_HEADERS([ajax/core/config.h]) AC_CONFIG_MACRO_DIR([m4]) # Make sure CFLAGS is defined to stop AC_PROG_CC adding -g. CFLAGS="${CFLAGS} " # Checks for programs. AC_PROG_AWK AC_PROG_CC([icc gcc cc]) AC_PROG_CXX([icpc g++]) AC_PROG_CPP AC_PROG_INSTALL AC_PROG_LN_S AC_PROG_MAKE_SET AC_PROG_MKDIR_P AM_INIT_AUTOMAKE # Use libtool to make a shared library. 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AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wstrict-prototypes"]) # Warn if a global function is defined without a previous prototype # declaration. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wmissing-prototypes"]) # Warn for obsolescent usages, according to the C Standard, # in a declaration. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wold-style-definition"]) # Warn if a global function is defined without a previous declaration. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wmissing-declarations"]) # When compiling C, give string constants the type const char[length] # so that copying the address of one into a non-const char * pointer # will get a warning. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wwrite-strings"]) # Warn whenever a local variable or type declaration shadows another # variable, parameter, type, or class member (in C++), or whenever a # built-in function is shadowed. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wshadow"]) # Warn when a declaration is found after a statement in a block. 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AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wredundant-decls"]) # Warn if the loop cannot be optimized because the compiler could not # assume anything on the bounds of the loop indices. # -Wunsafe-loop-optimizations objects to loops with increments more # than 1 because if the end is at INT_MAX it could run forever ... # rarely # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wunsafe-loop-optimizations"]) # Warn for implicit conversions that may alter a value. # -Wconversion is brain-damaged - complains about char arguments # every time # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wconversion"]) # Warn about certain constructs that behave differently in traditional # and ISO C. # -Wtraditional gives #elif and #error msgs # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wtraditional"]) # Warn if floating point values are used in equality comparisons. # -Wfloat-equal will not allow tests for values still 0.0 # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wfloat-equal"]) # This option is only active when -ftree-vrp is active # (default for -O2 and above). 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AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wall"]) # This option tells the compiler to display a shorter form of # diagnostic output. # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wbrief"]) # This option warns if cast is used to override pointer type # qualifier AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wcast-qual"]) # This option tells the compiler to perform compile-time code # checking for certain code. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wcheck"]) # This option determines whether a warning is issued when /* # appears in the middle of a /* */ comment. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wcomment"]) # Set maximum number of template instantiation contexts shown in # diagnostic. # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wcontext-limit=n"]) # This option enables warnings for implicit conversions that may # alter a value. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wconversion"]) # This option determines whether warnings are issued for deprecated # features. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wdeprecated"]) # This option enables warnings based on certain C++ programming # guidelines. # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Weffc++"]) # This option changes all warnings to errors. # Alternate: -diag-error warn # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Werror"]) # This option changes all warnings and remarks to errors. # Alternate: -diag-error warn, remark # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Werror-all"]) # This option determines whether warnings are issued about extra # tokens at the end of preprocessor directives. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wextra-tokens"]) # This option determines whether argument checking is enabled for # calls to printf, scanf, and so forth. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wformat"]) # This option determines whether the compiler issues a warning when # the use of format functions may cause security problems. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wformat-security"]) # This option enables diagnostics about what is inlined and what is # not inlined. # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Winline"]) # This option determines whether a warning is issued if the return # type of main is not expected. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wmain"]) # This option determines whether warnings are issued for global # functions and variables without prior declaration. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wmissing-declarations"]) # Determines whether warnings are issued for missing prototypes. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wmissing-prototypes"]) # This option enables warnings if a multicharacter constant # ('ABC') is used. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wmultichar"]) # Issue a warning when a class appears to be polymorphic, # yet it declares a non-virtual one. # This option is supported in C++ only. # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wnon-virtual-dtor"]) # This option warns about operations that could result in # integer overflow. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Woverflow"]) # This option tells the compiler to display diagnostics for 64-bit # porting. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wp64"]) # Determines whether warnings are issued for questionable pointer # arithmetic. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wpointer-arith"]) # his option determines whether a warning is issued about the # use of #pragma once. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wpragma-once"]) # Issue a warning when the order of member initializers does not # match the order in which they must be executed. # This option is supported with C++ only. # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wreorder"]) # This option determines whether warnings are issued when a function # uses the default int return type or when a return statement is # used in a void function. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wreturn-type"]) # This option determines whether a warning is issued when a variable # declaration hides a previous declaration. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wshadow"]) # This option warns for code that might violate the optimizer's # strict aliasing rules. Warnings are issued only when using # -fstrict-aliasing or -ansi-alias. # AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wstrict-aliasing"]) # This option determines whether warnings are issued for functions # declared or defined without specified argument types. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wstrict-prototypes"]) # This option determines whether warnings are issued if any trigraphs # are encountered that might change the meaning of the program. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wtrigraphs"]) # This option determines whether a warning is issued if a variable # is used before being initialized. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wuninitialized"]) # This option determines whether a warning is issued if an unknown # #pragma directive is used. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wunknown-pragmas"]) # This option determines whether a warning is issued if a declared # function is not used. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wunused-function"]) # This option determines whether a warning is issued if a local or # non-constant static variable is unused after being declared. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wunused-variable"]) # This option issues a diagnostic message if const char* is # converted to (non-const) char *. AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wwrite-strings"]) # Disable warning #981 operands are evaluated in unspecified order # http://software.intel.com/en-us/articles/cdiag981/ AS_VAR_APPEND([DEVWARN_CFLAGS], [" -diag-disable 981"]) ]) ]) AC_SUBST([DEVWARN_CFLAGS]) # Compiler extra developer warning settings: --enable-devextrawarnings, # appends DEVWARN_CFLAGS # Will only have an effect if --enable-devwarnings also given AC_ARG_ENABLE([devextrawarnings], [AS_HELP_STRING([--enable-devextrawarnings], [add extra warnings to devwarnings])]) AS_IF([test "x${enable_devwarnings}" = "xyes" && test "x${enable_devextrawarnings}" = "xyes"], [ AS_CASE([${CC}], [gcc], [ # flags used by Ubuntu 8.10 to check open has 2/3 arguments etc. AC_DEFINE([_FORTIFY_SOURCE], [2], [Set to 2 for open args]) # compiler flags CPPFLAGS="-fstack-protector ${CPPFLAGS}" # warnings used by Ubuntu 8.10 # -Wall already includes: # -Wformat AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wformat-security -Wl,-z,relro"]) # -Wpadded means moving char to end of structs - but also flags # end of struct so need to add padding at end AS_VAR_APPEND([DEVWARN_CFLAGS], [" -Wpadded"]) ]) ]) # Compile deprecated functions still used in the book text for 6.2.0 AC_ARG_ENABLE([buildbookdeprecated], [AS_HELP_STRING([--enable-buildbookdeprecated], [build deprecated functions used in books for 6.2.0])]) # Compile all deprecated functions AC_ARG_ENABLE([buildalldeprecated], [AS_HELP_STRING([--enable-buildalldeprecated], [build all deprecated functions])]) AS_IF([test "x${enable_buildbookdeprecated}" = "xyes" || test "x${enable_buildalldeprecated}" = "xyes"], [ AC_DEFINE([AJ_COMPILE_DEPRECATED_BOOK], [1], [Define to 1 to compile deprecated functions used in book texts for 6.2.0]) ]) AS_IF([test "x${enable_buildalldeprecated}" = "xyes"], [ AC_DEFINE([AJ_COMPILE_DEPRECATED], [1], [Define to 1 to compile all deprecated functions]) ]) # Add extensions to Solaris for some reentrant functions AS_CASE([${host_os}], [solaris*], [AS_VAR_APPEND([CFLAGS], [" -D__EXTENSIONS__"])]) # Test whether --with-sgiabi given for IRIX (n32m3 n32m4 64m3 64m4) AS_CASE([${host_os}], [irix*], [ AS_CASE([${CC}], [gcc], [], [cc], [CHECK_SGI]) ]) dnl PCRE library definitions - see the MAJOR and MINOR values dnl to see which version's configure.in these lines come from dnl Provide the current PCRE version information. Do not use numbers dnl with leading zeros for the minor version, as they end up in a C dnl macro, and may be treated as octal constants. Stick to single dnl digits for minor numbers less than 10. There are unlikely to be dnl that many releases anyway. PCRE_MAJOR="7" PCRE_MINOR="9" PCRE_DATE="11-Apr-2009" PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" dnl Default values for miscellaneous macros POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" dnl Provide versioning information for libtool shared libraries that dnl are built by default on Unix systems. PCRE_LIB_VERSION="0:1:0" PCRE_POSIXLIB_VERSION="0:0:0" dnl Define where the EMBOSS package is located AC_SUBST([AJAX_FIXED_ROOT]) AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" AC_SUBST([EMBOSS_TOP]) EMBOSS_TOP=`pwd` AC_SUBST([AJAX_SYSTEM]) AJAX_SYSTEM="\\\"`uname`\\\"" dnl FIXME: This does no longer seem required with Autoconf 2.67? dnl Intel MacOSX 10.6 puts X11 in a non-standard place dnl AS_IF([test "x${with_x}" != "xno"], dnl [ dnl AS_CASE([${host_os}], dnl [darwin*], dnl [ dnl OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` dnl AS_IF([test ${OSXX} '>' '10.4'], dnl [AS_VAR_APPEND([CFLAGS], [" -I/usr/X11/include -L/usr/X11/lib"])]) dnl ]) dnl ]) # Checks for header files. AC_PATH_XTRA AC_HEADER_DIRENT AC_HEADER_STDC AC_CHECK_HEADERS([unistd.h TargetConfig.h]) # Checks for typedefs, structures, and compiler characteristics. AC_C_BIGENDIAN AC_C_CONST AC_C_INLINE AC_TYPE_PID_T AC_TYPE_SIZE_T AC_STRUCT_TM # Checks for library functions. AC_FUNC_GETPGRP AC_FUNC_STRFTIME AC_FUNC_FORK AC_FUNC_VPRINTF AC_CHECK_FUNCS([memmove]) AS_IF([test "x${with_x}" != "xno"], [LF_EMBOSS_PATH_XLIB]) # Library checks. AC_CHECK_LIB([c], [socket], [LIBS="${LIBS}"], [LIBS="${LIBS} -lsocket"]) AC_CHECK_LIB([m], [main]) # GD for FreeBSD requires libiconv AS_CASE([${host_os}], [freebsd*], [ AS_IF([test "x${with_pngdriver}" != "xno"], [AC_CHECK_LIB([iconv], [main], [LIBS="${LIBS}"], [LIBS="-liconv ${LIBS}"])]) ]) AM_CONDITIONAL([AMPNG], [false]) AM_CONDITIONAL([AMPDF], [false]) CHECK_GENERAL CHECK_IDXDBS CHECK_JAVA CHECK_HPDF CHECK_AXIS2C CHECK_PNGDRIVER AX_LIB_MYSQL AX_LIB_POSTGRESQL dnl "Export" these variables for PCRE AC_SUBST([HAVE_MEMMOVE]) AC_SUBST([HAVE_STRERROR]) AC_SUBST([PCRE_MAJOR]) AC_SUBST([PCRE_MINOR]) AC_SUBST([PCRE_DATE]) AC_SUBST([PCRE_VERSION]) AC_SUBST([PCRE_LIB_VERSION]) AC_SUBST([PCRE_POSIXLIB_VERSION]) AC_SUBST([POSIX_MALLOC_THRESHOLD]) # Enable debugging: --enable-debug, sets CFLAGS AC_ARG_ENABLE([debug], [AS_HELP_STRING([--enable-debug], [debug (-g option on compiler)])]) AS_IF([test "x${enable_debug}" = "xyes"], [AS_VAR_APPEND([CFLAGS], [" -g"])]) # Turn off irritating linker warnings in IRIX AS_CASE([${host_os}], [irix*], [ CFLAGS="-Wl,-LD_MSG:off=85:off=84:off=16:off=134 ${CFLAGS}" ]) # Enable the large file interface: --enable-large, appends CPPFLAGS AC_ARG_ENABLE([large], [AS_HELP_STRING([--enable-large], [over 2Gb file support @<:@default=yes@:>@])]) AC_MSG_CHECKING([for large file support]) AS_IF([test "x${enable_large}" = "xno"], [ AC_MSG_RESULT([no]) ], [ AS_CASE([${host_os}], [linux*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_LinuxLF"]) AS_VAR_APPEND([CPPFLAGS], [" -D_LARGEFILE_SOURCE"]) AS_VAR_APPEND([CPPFLAGS], [" -D_LARGEFILE64_SOURCE"]) AS_VAR_APPEND([CPPFLAGS], [" -D_FILE_OFFSET_BITS=64"]) ], [freebsd*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_FreeBSDLF"]) ], [solaris*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_SolarisLF"]) AS_VAR_APPEND([CPPFLAGS], [" -D_LARGEFILE_SOURCE"]) AS_VAR_APPEND([CPPFLAGS], [" -D_FILE_OFFSET_BITS=64"]) ], [osf*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_OSF1LF"]) ], [irix*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_IRIXLF"]) AS_VAR_APPEND([CPPFLAGS], [" -D_LARGEFILE64_SOURCE"]) ], [aix*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_AIXLF"]) AS_VAR_APPEND([CPPFLAGS], [" -D_LARGE_FILES"]) ], [hpux*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_HPUXLF"]) AS_VAR_APPEND([CPPFLAGS], [" -D_LARGEFILE_SOURCE"]) AS_VAR_APPEND([CPPFLAGS], [" -D_FILE_OFFSET_BITS=64"]) ], [darwin*], [ AS_VAR_APPEND([CPPFLAGS], [" -DAJ_MACOSXLF"]) ]) AC_MSG_RESULT([yes]) ]) # Enable libraries provided by the system rather than EMBOSS: # --enable-systemlibs, sets ESYSTEMLIBS AC_ARG_ENABLE([systemlibs], [AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])]) AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) # Enable the purify tool: --enable-purify, sets CC and LIBTOOL AC_ARG_ENABLE([purify], [AS_HELP_STRING([--enable-purify], [purify])]) AC_MSG_CHECKING([for purify]) AS_IF([test "x${enable_purify}" = "xyes"], [ dnl if(purify -version) < /dev/null > /dev/null 2>&1; then CC="purify --chain-length=20 -best-effort -windows=yes gcc -g" LIBTOOL="${LIBTOOL} --tag=CC" AC_MSG_RESULT([yes]) dnl fi ], [ AC_MSG_RESULT([no]) ]) # Enable GCC profiling: --enable-gccprofile, appends CFLAGS and LDFLAGS if test "x${with_gccprofile}" = "xyes" ; then CFLAGS="${CFLAGS} -pg" LDFLAGS="${LDFLAGS} -pg" fi # Enable GCOV pcoverage analysis: --enable-gcov, appends CFLAGS if test "x${with_gcov}" = "xyes" ; then CFLAGS="${CFLAGS} -fprofile-arcs -ftest-coverage" fi dnl Set extra needed compiler flags if test "x${CC}" = "xcc"; then case "${host}" in alpha*-dec-osf*) CFLAGS="${CFLAGS} -ieee";; esac fi AM_CONDITIONAL([PURIFY], [test "x${enable_purify}" = "xyes"]) dnl Test for cygwin to set AM_LDFLAGS in library & apps Makefile.ams dnl Replaces original version which used 'expr' and so wasn't entirely dnl portable. platform_cygwin="no" AC_MSG_CHECKING([for cygwin]) case "${host}" in *-*-mingw*|*-*-cygwin*) platform_cygwin="yes" ;; *) platform_cygwin="no" ;; esac AC_MSG_RESULT([${platform_cygwin}]) AM_CONDITIONAL([ISCYGWIN], [test "x${platform_cygwin}" = "xyes"]) dnl Tests for AIX dnl If shared needs -Wl,-G in plplot,ajax,nucleus, -lX11 in plplot, dnl and -Wl,brtl -Wl,-bdynamic in emboss dnl We therefore need a static test as well needajax="no" AS_CASE([${host_os}], [aix*], [AM_CONDITIONAL([ISAIXIA64], [true])], [AM_CONDITIONAL([ISAIXIA64], [false])]) AM_CONDITIONAL([ISSHARED], [test "x${enable_shared}" = "xyes"]) AS_CASE([${host_os}], [aix*], [ AS_IF([test -d ajax/.libs], [AS_ECHO(["AIX ajax/.libs exists"])], [mkdir ajax/.libs]) AS_CASE([${host_os}], [aix5*], [needajax="no"], [aix4.3.3*], [needajax="yes"], [needajax="no"]) ]) AM_CONDITIONAL([NEEDAJAX], [test "x${needajax}" = "xyes"]) # HP-UX needs -lsec for shadow passwords AS_CASE([${host_os}], [hpux*], [AS_VAR_APPEND([LDFLAGS], [" -lsec"])]) # GNU mcheck functions: --enable-mcheck, defines HAVE_MCHECK AC_ARG_ENABLE([mcheck], [AS_HELP_STRING([--enable-mcheck], [mcheck and mprobe memory allocation test])]) AS_IF([test "x${enable_mcheck}" = "xyes"], [AC_CHECK_FUNCS([mcheck])]) # Collect AJAX statistics: --enable-savestats, defines AJ_SAVESTATS AC_ARG_ENABLE([savestats], [AS_HELP_STRING([--enable-savestats], [save AJAX statistics and print with debug output])]) AC_MSG_CHECKING([for savestats]) AS_IF([test "x${enable_savestats}" = "xyes"], [ AC_DEFINE([AJ_SAVESTATS], [1], [Define to 1 to collect AJAX library usage statistics.]) AC_MSG_RESULT([yes]) ], [ AC_MSG_RESULT([no]) ]) AC_CONFIG_FILES([Makefile ajax/Makefile ajax/acd/Makefile ajax/ajaxdb/Makefile ajax/core/Makefile ajax/ensembl/Makefile ajax/expat/Makefile ajax/graphics/Makefile ajax/pcre/Makefile ajax/zlib/Makefile doc/Makefile doc/manuals/Makefile doc/programs/Makefile doc/programs/html/Makefile doc/programs/text/Makefile doc/tutorials/Makefile emboss/Makefile emboss/acd/Makefile emboss/data/AAINDEX/Makefile emboss/data/CODONS/Makefile emboss/data/JASPAR_CNE/Makefile emboss/data/JASPAR_CORE/Makefile emboss/data/JASPAR_FAM/Makefile emboss/data/JASPAR_PBM/Makefile emboss/data/JASPAR_PBM_HLH/Makefile emboss/data/JASPAR_PBM_HOMEO/Makefile emboss/data/JASPAR_PHYLOFACTS/Makefile emboss/data/JASPAR_POLII/Makefile emboss/data/JASPAR_SPLICE/Makefile emboss/data/Makefile emboss/data/OBO/Makefile emboss/data/PRINTS/Makefile emboss/data/PROSITE/Makefile emboss/data/REBASE/Makefile emboss/data/TAXONOMY/Makefile emboss/index/Makefile jemboss/Makefile jemboss/runJemboss.sh jemboss/images/Makefile jemboss/lib/Makefile jemboss/lib/axis/Makefile jemboss/resources/Makefile jemboss/utils/Makefile nucleus/Makefile plplot/Makefile plplot/lib/Makefile test/Makefile test/data/Makefile test/embl/Makefile test/genbank/Makefile test/pir/Makefile test/swiss/Makefile test/swnew/Makefile test/testdb/Makefile ]) AC_OUTPUT