1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145
|
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
|