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# -*- Autoconf -*-
# Process this file with autoconf to produce a configure script.
AC_PREREQ(2.59)
AC_INIT([Stacks], [2.68])
AC_CONFIG_AUX_DIR([config])
AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])
AC_CONFIG_SRCDIR([src/ustacks.cc])
#AC_CONFIG_SRCDIR([htslib/hts.c])
AC_CONFIG_HEADERS([config.h])
m4_pattern_allow([AC_OPENMP])
# Checks for programs.
AC_PROG_CXX
AM_PROG_CC_C_O
AX_CXX_COMPILE_STDCXX(11,, [mandatory])
# Checks for ar-based static libs.
AC_PROG_RANLIB
m4_ifdef([AM_PROG_AR], [AM_PROG_AR])
# Checks for libraries.
AC_CHECK_LIB([gomp], [omp_set_num_threads],, [AC_MSG_WARN([Unable to locate OpenMP library, you should probably specify '--disable-openmp'.])])
AC_CHECK_LIB([z], [gzread],, [AC_MSG_ERROR([Zlib not found, reading gzipped files will not be possible.])])
# Checks for header files.
AC_HEADER_DIRENT
AC_HEADER_STDC
AC_CHECK_HEADERS([float.h limits.h stdlib.h string.h])
AC_CHECK_HEADERS([unistd.h])
# Check for OpenMP parallel execution support
AC_OPENMP
# Checks for typedefs, structures, and compiler characteristics.
AC_HEADER_STDBOOL
AC_C_CONST
AC_TYPE_SIZE_T
# Checks for library functions.
AC_FUNC_CLOSEDIR_VOID
AC_FUNC_MALLOC
AC_FUNC_REALLOC
AC_CHECK_FUNCS([floor memset pow sqrt])
AC_CHECK_FUNCS([clock_gettime])
# `clock_gettime()`, declared in unistd.h, may be in librt (e.g. for glibc).
if test $ac_cv_func_clock_gettime = no; then
AC_CHECK_LIB(rt, clock_gettime,
[LIBS="-lrt $LIBS"
AC_DEFINE(HAVE_CLOCK_GETTIME, 1, [Define to 1 if you have the `clock_gettime' function.])
])
fi
#
# Test if regular expressions are functional. Early regex implementations have nonfunctional stubs,
# so the check for C++11 succeeds, but the compiled code will throw an exception.
#
AC_LANG(C++)
AC_DEFUN([AC_REGEX_FUNC], [
AC_CACHE_CHECK([for functional regular expressions], [stacks_cv_header_regex_func],
[
stacks_cv_header_regex_func=no
AC_RUN_IFELSE([AC_LANG_SOURCE([[
#include <regex>
int main() {
const std::regex regex(".*");
const std::string string = "This should match!";
const auto result = std::regex_search(string, regex);
return result ? 0 : 1;
}
]])],
[stacks_cv_header_regex_func=yes],
[AC_MSG_ERROR([Regular expressions are not functional, you need g++ 4.9.0 or greater.])],
[AC_MSG_WARN([Requires g++ 4.9.0 or greater.])]
)])
if test "$stacks_cv_header_regex_func" = yes; then
AC_DEFINE([REGEX_FUNCTIONAL], [1], [Regular expressions are defined and implemented])
fi
])
AC_REGEX_FUNC
# For test harness
AC_PROG_AWK
AC_CONFIG_FILES([Makefile])
AC_OUTPUT
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