# -*- Autoconf -*- # Configure template for the EMBOSS package. # Process this file with autoconf to produce a configure script. AC_PREREQ([2.59]) AC_INIT([EMBOSS], [6.4.0], [emboss-bug@emboss.open-bio.org], [EMBOSS], [http://emboss.sourceforge.net/]) AC_REVISION([$Revision: 1.152 $]) AC_CONFIG_SRCDIR([ajax/acd/ajacd.c]) AC_CONFIG_HEADERS([ajax/core/config.h]) AC_CONFIG_MACRO_DIR([m4]) # Make sure CFLAGS is defined to stop LT_INIT adding -g CFLAGS="$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. LT_INIT dnl Check if 64 bit pointer support is required on 32 bit machines dnl Disabled by default use_64bit_ptrs=no AC_ARG_ENABLE([64], AS_HELP_STRING([--enable-64], [64 bit pointers on 32 bit machines])) AS_IF([test "x$enable_64" = "xyes"], [AC_MSG_CHECKING([for 64bit compilation support]) use_64bit_ptrs=yes case $host_os in aix*) CPPFLAGS="-DAJ_AIX64 $CPPFLAGS" case $CC in gcc) ;; *) CC="$CC -q64" ;; esac NM="nm -B -X 64" AR="ar -X 64" ;; hpux*) case $CC in gcc) ;; *) CC="$CC +DD64" ;; esac AC_DEFINE([HPUX64PTRS],[1],[Set to 1 if HPUX 64bit ptrs on 32 bit m/c]) ;; *) ;; esac AC_MSG_RESULT([done]) ]) dnl End of checks for 64 bit pointers on 32 bit machines dnl Compiler optimisations dnl The Solaris 64bit ptr check has to be done here owing to param order AC_ARG_WITH([optimisation], AS_HELP_STRING([--without-optimisation], [Disable compiler optimisation])) AS_IF([test "x$with_optimisation" != "xno"], [case $CC in gcc) dnl Intel MacOSX requires reduced optimisation for PCRE code dnl other OSs just use -O2 case $host_os in darwin*) if test "$host_cpu" = "i386"; then CFLAGS="$CFLAGS -O1" else CFLAGS="$CFLAGS -O2" fi ;; *) CFLAGS="$CFLAGS -O2" ;; esac ;; *) case $host_os in aix*) CFLAGS="$CFLAGS -O3 -qstrict -qarch=auto -qtune=auto" ;; irix*) LD="/usr/bin/ld -IPA" CFLAGS="$CFLAGS -O3" ;; hpux*) CFLAGS="$CFLAGS -fast" ;; osf*) CFLAGS="$CFLAGS -fast -U_FASTMATH" ;; solaris*) CFLAGS="$CFLAGS -O" dnl test for 64 bit ptr here (see Solaris 64bit above) if test "${enable_64}" = "yes" ; then CFLAGS="$CFLAGS -xtarget=ultra -xarch=v9" fi ;; linux*) dnl Default optimisation for non-gcc compilers under Linux CFLAGS="$CFLAGS -O2" ;; freebsd*) CFLAGS="$CFLAGS -O2" ;; esac esac ]) dnl end of compiler tests # Compiler warning settings: --enable-warnings, WARN_CFLAGS have_warnings=no AC_ARG_ENABLE([warnings], [AS_HELP_STRING([--enable-warnings], [warnings])]) AS_IF([test "${enable_warnings}" = "yes"], [have_warnings=yes AS_CASE($CC, [gcc], [WARN_CFLAGS="-Wall -fno-strict-aliasing"]) ]) AC_SUBST([WARN_CFLAGS]) # Compiler developer warning settings: --enable-devwarnings, DEVWARN_CFLAGS have_devwarnings=no AC_ARG_ENABLE([devwarnings], [AS_HELP_STRING([--enable-devwarnings], [strict warnings for developers])]) AS_IF([test "${enable_devwarnings}" = "yes"], [have_devwarnings=yes AS_CASE($CC, [gcc], [ # -Wextra: more warnings beyond what -Wall provides # -Wclobbered -Wempty-body -Wignored-qualifiers # -Wmissing-field-initializers -Wmissing-parameter-type (C only) # -Wold-style-declaration (C only) -Woverride-init -Wsign-compare # -Wtype-limits -Wuninitialized -Wunused-parameter (only with # -Wunused or -Wall) DEVWARN_CFLAGS="-Wextra" # prototype warnings. prototypes required for all functions DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wstrict-prototypes" DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wmissing-prototypes" DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wold-style-definition" DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wmissing-declarations" DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wwrite-strings" # catches things like index as a variable name DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wshadow" DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wdeclaration-after-statement" DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wundef" DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wpointer-arith" DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wcast-qual" DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wcast-align" # casts of function results that can lose data e.g. double to int DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wbad-function-cast" # comparing signed and unsigned values DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wsign-compare" DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wmissing-field-initializers" DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wmissing-noreturn" DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wnested-externs" # useful messages DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wredundant-decls" # -Wunsafe-loop-optimizations objects to loops with increments more # than 1 because if the end is at INT_MAX it could run forever ... # rarely # DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wunsafe-loop-optimizations" # -Wconversion is brain-damaged - complains about char arguments # every time # DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wconversion" # -Wtraditional gives #elif and #error msgs # DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wtraditional" # -Wwrite-strings upsets struct initialisation # DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wwrite-strings" # -Wfloat-equal will not allow tests for values still 0.0 # DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wfloat-equal" # -Warray-bounds gives false positives in gcc 4.6.0 # Disable rather than use a non-portable pragma # DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wno-array-bounds" ], [icc], [ # Diagnostic options for the Intel(R) C++ compiler version 11.1. # http://software.intel.com/en-us/articles/intel-c-compiler-professional-edition-for-linux-documentation/ # This option specifies the level of diagnostic messages to be # generated by the compiler. 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DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wcomment" # Set maximum number of template instantiation contexts shown in # diagnostic. # DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wcontext-limit=n" # This option enables warnings for implicit conversions that may # alter a value. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wconversion" # This option determines whether warnings are issued for deprecated # features. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wdeprecated" # This option enables warnings based on certain C++ programming # guidelines. # DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Weffc++" # This option changes all warnings to errors. # Alternate: -diag-error warn # DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Werror" # This option changes all warnings and remarks to errors. # Alternate: -diag-error warn, remark # DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Werror-all" # This option determines whether warnings are issued about extra # tokens at the end of preprocessor directives. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wextra-tokens" # This option determines whether argument checking is enabled for # calls to printf, scanf, and so forth. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wformat" # This option determines whether the compiler issues a warning when # the use of format functions may cause security problems. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wformat-security" # This option enables diagnostics about what is inlined and what is # not inlined. # DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Winline" # This option determines whether a warning is issued if the return # type of main is not expected. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wmain" # This option determines whether warnings are issued for global # functions and variables without prior declaration. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wmissing-declarations" # Determines whether warnings are issued for missing prototypes. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wmissing-prototypes" # This option enables warnings if a multicharacter constant # ('ABC') is used. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wmultichar" # ssue a warning when a class appears to be polymorphic, # yet it declares a non-virtual one. # This option is supported in C++ only. # DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wnon-virtual-dtor" # This option warns about operations that could result in # integer overflow. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Woverflow" # This option tells the compiler to display diagnostics for 64-bit # porting. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wp64" # Determines whether warnings are issued for questionable pointer # arithmetic. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wpointer-arith" # his option determines whether a warning is issued about the # use of #pragma once. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wpragma-once" # Issue a warning when the order of member initializers does not # match the order in which they must be executed. # This option is supported with C++ only. # DEVWARN_CFLAGS="$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. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wreturn-type" # This option determines whether a warning is issued when a variable # declaration hides a previous declaration. DEVWARN_CFLAGS="$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. # DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wstrict-aliasing" # This option determines whether warnings are issued for functions # declared or defined without specified argument types. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wstrict-prototypes" # This option determines whether warnings are issued if any trigraphs # are encountered that might change the meaning of the program. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wtrigraphs" # This option determines whether a warning is issued if a variable # is used before being initialized. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wuninitialized" # This option determines whether a warning is issued if an unknown # #pragma directive is used. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wunknown-pragmas" # This option determines whether a warning is issued if a declared # function is not used. DEVWARN_CFLAGS="$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. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wunused-variable" # This option issues a diagnostic message if const char* is # converted to (non-const) char *. DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wwrite-strings" # Disable warning #981 operands are evaluated in unspecified order # http://software.intel.com/en-us/articles/cdiag981/ DEVWARN_CFLAGS="$DEVWARN_CFLAGS -diag-disable 981" ]) ]) AC_SUBST([DEVWARN_CFLAGS]) # Compiler extra developer warning settings: --enable-devextrawarnings # Will only have an effect if --enable-devwarnings also given AC_ARG_ENABLE([devextrawarnings], [AS_HELP_STRING([--enable-devextrawarnings], [add extra warnings to devwarnings])]) if test "${enable_devextrawarnings}" = "yes" ; then if test "$have_devwarnings" = "yes"; then AS_CASE($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 $CPPFLAGS" # warnings used by Ubuntu 8.10 # -Wall already includes: # -Wformat DEVWARN_CFLAGS="$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 DEVWARN_CFLAGS="$DEVWARN_CFLAGS -Wpadded" ]) fi fi dnl Add extensions to Solaris for some reentrant functions case $host_os in solaris*) CFLAGS="$CFLAGS -D__EXTENSIONS__" ;; esac dnl Test whether --with-sgiabi given for IRIX (n32m3 n32m4 64m3 64m4) case $host_os in irix*) case $CC in gcc) ;; cc) CHECK_SGI ;; esac ;; esac dnl PCRE library definitions - see the MAJOR and MINOR values dnl to see which version's configure.in these lines come from dnl Provide the current PCRE version information. Do not use numbers dnl with leading zeros for the minor version, as they end up in a C dnl macro, and may be treated as octal constants. Stick to single dnl digits for minor numbers less than 10. There are unlikely to be dnl that many releases anyway. PCRE_MAJOR=7 PCRE_MINOR=9 PCRE_DATE=11-Apr-2009 PCRE_VERSION=${PCRE_MAJOR}.${PCRE_MINOR} dnl Default values for miscellaneous macros POSIX_MALLOC_THRESHOLD=-DPOSIX_MALLOC_THRESHOLD=10 dnl Provide versioning information for libtool shared libraries that dnl are built by default on Unix systems. PCRE_LIB_VERSION=0:1:0 PCRE_POSIXLIB_VERSION=0:0:0 dnl Define where the EMBOSS package is located AC_SUBST([AJAX_FIXED_ROOT]) AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" AC_SUBST([EMBOSS_TOP]) EMBOSS_TOP=`pwd` AC_SUBST([AJAX_SYSTEM]) AJAX_SYSTEM="\\\"`uname`\\\"" dnl Intel MacOSX 10.6 puts X11 in a non-standard place if test "${with_x}" != "no" ; then case $host_os in darwin*) OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'` if test ${OSXX} '>' '10.4'; then CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib" fi ;; esac fi # 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 dnl Check for library functions AC_FUNC_GETPGRP AC_FUNC_STRFTIME AC_FUNC_FORK AC_FUNC_VPRINTF AC_CHECK_FUNCS([memmove]) if test "${with_x}" != "no" ; then LF_EMBOSS_PATH_XLIB fi dnl Library checks AC_CHECK_LIB(c, socket, LIBS="$LIBS" , LIBS="$LIBS -lsocket") AC_CHECK_LIB(m, main) dnl GD for FreeBSD requires libiconv case $host_os in freebsd*) if test ${with_pngdriver} != "no"; then AC_CHECK_LIB(iconv, main, LIBS="$LIBS", LIBS="-liconv $LIBS") fi ;; esac AM_CONDITIONAL([AMPNG], [false]) AM_CONDITIONAL([AMPDF], [false]) CHECK_GENERAL CHECK_IDXDBS CHECK_JAVA CHECK_JAVAOS CHECK_HPDF CHECK_AXIS2C CHECK_PNGDRIVER CHECK_AUTH CHECK_AMD64 AX_LIB_MYSQL AX_LIB_POSTGRESQL dnl Check for 'ant' for packaging Jemboss and export result AC_CHECK_PROG(javac_in_path,javac,true,false) AC_CHECK_PROG(ant_in_path,ant,true,false) AM_CONDITIONAL([EHAVEANT], [test "$ant_in_path" = "true" && "$javac_in_path" = "true"]) AC_SUBST([EHAVEANT]) dnl "Export" these variables for PCRE AC_SUBST([HAVE_MEMMOVE]) AC_SUBST([HAVE_STRERROR]) AC_SUBST([PCRE_MAJOR]) AC_SUBST([PCRE_MINOR]) AC_SUBST([PCRE_DATE]) AC_SUBST([PCRE_VERSION]) AC_SUBST([PCRE_LIB_VERSION]) AC_SUBST([PCRE_POSIXLIB_VERSION]) AC_SUBST([POSIX_MALLOC_THRESHOLD]) dnl Test if --enable-debug given AC_ARG_ENABLE([debug], [AS_HELP_STRING([--enable-debug], [debug (-g option on compiler)])]) if test "${enable_debug}" = "yes" ; then CFLAGS="$CFLAGS -g" fi dnl Turn off irritating linker warnings in IRIX case $host_os in irix*) CFLAGS="-Wl,-LD_MSG:off=85:off=84:off=16:off=134 $CFLAGS" ;; esac dnl Test if --enable-large is given if test "${enable_large+set}" != set; then enable_large=yes fi AC_ARG_ENABLE([large], [AS_HELP_STRING([--enable-large], [over 2Gb file support (default)])]) if test "${enable_large}" = "yes" ; then AC_MSG_CHECKING([for large file support]) dnl Test for large file support case $host_os in linux*) CPPFLAGS="-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE $CPPFLAGS" CPPFLAGS="-DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 $CPPFLAGS" ;; freebsd*) CPPFLAGS="-DAJ_FreeBSDLF $CPPFLAGS" ;; solaris*) CPPFLAGS="-D_LARGEFILE_SOURCE $CPPFLAGS" CPPFLAGS="-DAJ_SolarisLF -D_FILE_OFFSET_BITS=64 $CPPFLAGS" ;; osf*) CPPFLAGS="-DAJ_OSF1LF $CPPFLAGS" ;; irix*) CPPFLAGS="-DAJ_IRIXLF -D_LARGEFILE64_SOURCE $CPPFLAGS" ;; aix*) CPPFLAGS="-DAJ_AIXLF -D_LARGE_FILES $CPPFLAGS" ;; hpux*) CPPFLAGS="-D_FILE_OFFSET_BITS=64 $CPPFLAGS" CPPFLAGS="-DAJ_HPUXLF -D_LARGEFILE_SOURCE $CPPFLAGS" ;; darwin*) CPPFLAGS="-DAJ_MACOSXLF $CPPFLAGS" ;; esac AC_MSG_RESULT([done]) fi dnl Test if --enable-systemlibs given have_systemlibs=no AC_ARG_ENABLE([systemlibs], [AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles])]) if test "${enable_systemlibs}" = "yes" ; then have_systemlibs=yes fi AM_CONDITIONAL([ESYSTEMLIBS], [test "$have_systemlibs" = "yes"]) AC_SUBST([ESYSTEMLIBS]) dnl Test if purify exists and if --enable-purify given if so dnl set "-g" AC_MSG_CHECKING([for purify]) dnl if(purify -version) < /dev/null > /dev/null 2>&1; then AC_ARG_ENABLE([purify], [AS_HELP_STRING([--enable-purify], [purify])]) if test "${enable_purify}" = "yes" ; then CC="purify --chain-length="20" -best-effort -windows=yes gcc -g" LIBTOOL="$LIBTOOL --tag=CC" AC_MSG_RESULT([yes]) else AC_MSG_RESULT([no]) fi dnl fi dnl Test if --enable-gccprofile given if so dnl set "-pg" if test "${with_gccprofile}" = "yes" ; then CFLAGS="$CFLAGS -pg" LDFLAGS="$LDFLAGS -pg" fi dnl Set extra needed compiler flags if test "$CC" = "cc"; then case "$host" in alpha*-dec-osf*) CFLAGS="$CFLAGS -ieee";; esac fi AM_CONDITIONAL([PURIFY], [test "${enable_purify}" = "yes"]) dnl Set a gcc test flag for use in Makefile.am that can be used in modifiying dnl (dev) warnings in Makefile.am files. AM_CONDITIONAL([ISGCC], [test "$CC" = "gcc"]) dnl Test for cygwin to set AM_LDFLAGS in library & apps Makefile.ams dnl Replaces original version which used 'expr' and so wasn't entirely dnl portable. platform_cygwin='no' AC_MSG_CHECKING([for cygwin]) case "$host" in *-*-mingw*|*-*-cygwin*) platform_cygwin='yes' ;; *) platform_cygwin='no' ;; esac AC_MSG_RESULT([$platform_cygwin]) AM_CONDITIONAL([ISCYGWIN], [test "$platform_cygwin" = "yes"]) AC_SUBST([ISCYGWIN]) 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 case $host_os in aix*) AM_CONDITIONAL([ISAIXIA64], [true]) ;; *) AM_CONDITIONAL([ISAIXIA64], [false]) ;; esac AM_CONDITIONAL([ISSHARED], [test "${enable_shared}" = "yes"]) AC_SUBST([ISAIXIA64]) case $host_os in aix*) if test -d ajax/.libs ; then echo AIX ajax/.libs exists else mkdir ajax/.libs fi case $host_os in aix5*) needajax=no ;; aix4.3.3*) needajax=yes ;; *) needajax=no ;; esac esac AM_CONDITIONAL([NEEDAJAX], [test "$needajax" = "yes"]) AC_SUBST([NEEDAJAX]) dnl HP-UX needs -lsec for shadow passwords case $host_os in hpux*) LDFLAGS="$LDFLAGS -lsec" ;; esac dnl Test if --enable-mprobe is given if test "${enable_mprobe+set}" != set; then enable_mprobe=no fi AC_MSG_CHECKING([for mprobe]) AC_ARG_ENABLE([mprobe], [AS_HELP_STRING([--enable-mprobe], [mprobe memory allocation test])]) if test "${enable_mprobe}" = "yes" ; then CPPFLAGS="-DAJ_MPROBE $CPPFLAGS" AC_MSG_RESULT([yes]) else AC_MSG_RESULT([no]) fi dnl Test if --enable-savestats is given if test "${enable_savestats+set}" != set; then enable_savestats=no fi AC_MSG_CHECKING([for savestats]) AC_ARG_ENABLE([savestats], [AS_HELP_STRING([--enable-savestats], [save statistics and print with debug output])]) if test "${enable_savestats}" = "yes" ; then AC_DEFINE([AJ_SAVESTATS], [1], [Define to 1 to collect AJAX library usage statistics.]) AC_MSG_RESULT([yes]) else AC_MSG_RESULT([no]) fi dnl check and set compilation flags for Jemboss auth server code CHECK_THREADS 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/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