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m4_include([ax_boost_base.m4])
m4_include([ax_boost_thread.m4])
m4_include([ax_boost_system.m4])
m4_include([ax_boost_serialization.m4])
m4_include([ax_bam.m4])
m4_include([ax_check_zlib.m4])
m4_include([ax_check_eigen.m4])
define([svnversion], esyscmd([sh -c "svnversion|tr -d '\n'"]))dnl
AC_INIT([cufflinks], [2.2.1], [cole@cs.umd.edu])
AC_DEFINE(SVN_REVISION, "svnversion", [SVN Revision])
AC_CONFIG_SRCDIR([config.h.in])
AC_CONFIG_HEADERS([config.h])
AC_CONFIG_AUX_DIR([build-aux])
AM_INIT_AUTOMAKE
#AM_PATH_CPPUNIT(1.10.2)
AC_ARG_VAR(PYTHON, [python program])
# Make sure CXXFLAGS is defined so that AC_PROG_CXX doesn't set it.
CXXFLAGS="$CXXFLAGS"
CFLAGS="$CFLAGS"
AC_LANG(C)
# Checks for programs.
AC_PROG_AWK
AC_PROG_CXX
AC_PROG_CC
AC_PROG_MAKE_SET
AC_PROG_RANLIB
AC_PROG_INSTALL
m4_ifdef([AM_PROG_AR], [AM_PROG_AR])
AM_PATH_PYTHON([2.4])
AX_BOOST_BASE([1.47.0])
AX_BAM
AX_BOOST_SYSTEM
AX_BOOST_SERIALIZATION
AX_BOOST_THREAD
AX_CHECK_ZLIB()
AX_EIGEN
# Checks for header files.
AC_CHECK_HEADERS([stdlib.h string.h unistd.h])
# Checks for typedefs, structures, and compiler characteristics.
AC_HEADER_STDBOOL
AC_C_INLINE
AC_TYPE_PID_T
AC_TYPE_SIZE_T
AC_CHECK_TYPES([ptrdiff_t])
# Checks for library functions.
#AC_FUNC_FORK
#AC_CHECK_FUNCS([floor memmove pow regcomp sqrt strchr strcspn strspn strstr])
# check the platform
AC_CANONICAL_HOST
# set CFLAGS and CXXFLAGS
user_CFLAGS=${CFLAGS}
generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024"
ext_CFLAGS=""
debug_CFLAGS=""
#echo "${host_cpu}-${host_os}"
case "${host_cpu}-${host_os}" in
i*86-*linux*)
ext_CFLAGS="-march=i686";;
i*86-darwin*)
CFLAGS="-m64"
AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-arch x86_64"], []);;
esac
AC_ARG_ENABLE(vectorize, [ --enable-vectorize Enable GCC auto-vectorization],
[ext_CFLAGS="${ext_CFLAGS} -ftree-vectorize -msse3 -ffast-math -ftree-vectorizer-verbose=99"], [])
AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2],
[ext_CFLAGS="${ext_CFLAGS} -march=nocona"], [])
AC_ARG_ENABLE([debug],
[AS_HELP_STRING([--enable-debug],
[enable debugging info (default is no)])],
[], [enable_debug=no])
AC_ARG_ENABLE([optim],
[AS_HELP_STRING([--enable-optim@<:@=0|1|2|3@:>@],
[set optimization level (default is 3)])],
[if test "x$enable_optim" = xyes; then enable_optim=3; fi],
[enable_optim=3])
AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"])
AS_IF([test "x$enable_debug" = xyes],
[debug_CFLAGS="-DDEBUG"],
[debug_CFLAGS="-DNDEBUG"])
AC_ARG_ENABLE(profiling, [ --enable-profiling enable profiling with google-perftools],
[ext_LDFLAGS="-lprofiler -ltcmalloc"], [])
CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}"
CXXFLAGS="$CFLAGS"
CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
user_LDFLAGS="$LDFLAGS"
LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}"
# Checks for structures/functions that can be used to determine system memory
AC_CHECK_MEMBERS([struct sysinfo.totalram], [], [], [#include <sys/sysinfo.h>])
AC_CHECK_DECLS([sysctl, CTL_HW, HW_PHYSMEM], [], [], [#include <sys/sysctl.h>])
AM_INIT_AUTOMAKE([-Wall tar-pax foreign])
AC_CONFIG_FILES([Makefile
src/Makefile])
AC_OUTPUT
# dump some configuration confirmations
echo \
"
-- ${PACKAGE_STRING} Configuration Results --
C++ compiler: ${CXX} ${CXXFLAGS} ${LDFLAGS}"
if test x"${GCC}" = x"yes" ; then
gcc_version=`${CC} --version | head -n 1`
echo " GCC version: ${gcc_version}"
else
gcc_version=''
fi
echo \
" Host System type: ${host}
Install prefix: ${prefix}
Install eprefix: ${exec_prefix}
See config.h for further configuration information.
Email <${PACKAGE_BUGREPORT}> with questions and bug reports.
"
if test x"${PYTHON}" = x":" || ! test -x "${PYTHON}"; then
echo "WARNING! python was not found and is required to run some utility scripts"
echo " We recommend installing python and pointing configure to the installed location"
fi
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