source: trunk/configure.ac @ 2981

Last change on this file since 2981 was 2981, checked in by Peter, 10 years ago

Skip yat_pc_test.sh when -without-samtools. fixes #748
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Line 
1## Process this file with autoconf to produce a configure script.
2##
3## $Id: configure.ac 2981 2013-02-04 11:24:51Z peter $
4
5# Copyright (C) 2003 Daniel Dalevi, Jari Häkkinen
6# Copyright (C) 2004 Jari Häkkinen
7# Copyright (C) 2005, 2006 Jari Häkkinen, Peter Johansson
8# Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
9# Copyright (C) 2009 Jari Häkkinen, Peter Johansson
10# Copyright (C) 2010, 2011 Peter Johansson
11# Copyright (C) 2012 Jari Häkkinen, Peter Johansson
12# Copyright (C) 2013 Peter Johansson
13#
14# This file is part of the yat library, http://dev.thep.lu.se/yat
15#
16# The yat library is free software; you can redistribute it
17# and/or modify it under the terms of the GNU General Public License as
18# published by the Free Software Foundation; either version 3 of the
19# License, or (at your option) any later version.
20#
21# The yat library is distributed in the hope that it will be useful,
22# but WITHOUT ANY WARRANTY; without even the implied warranty of
23# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
24# General Public License for more details.
25#
26# You should have received a copy of the GNU General Public License
27# along with yat. If not, see <http://www.gnu.org/licenses/>.
28#
29# If you grabbed the source from the subversion repository you should,
30# at top-level, execute:
31#     ./bootstrap
32# To push subsequent changes of this file into the build scripts you
33# must issue:
34#     autoreconf
35
36
37m4_include([m4/version.m4])
38AC_INIT([yat],[my_VERSION],[libyat-users@lists.sourceforge.net],,
39        [http://dev.thep.lu.se/yat])
40MY_VERSION
41AC_PREREQ(2.63)
42AC_CONFIG_SRCDIR([yat/utility/Matrix.h])
43AC_CONFIG_AUX_DIR([autotools])
44dnl arg below should be the same as in Makefile.am
45AC_CONFIG_MACRO_DIR([m4])
46AC_PREFIX_DEFAULT([/usr/local])
47
48# Set default htmldir to ${docdir}/html
49AS_IF([test $htmldir = '${docdir}'], [htmldir='${docdir}/html'])
50
51dnl FIXME remove when we assume autoconf 2.64
52m4_ifndef([AC_PACKAGE_URL],
53          [AC_DEFINE([PACKAGE_URL], ["http://dev.thep.lu.se/yat"],
54                     [Define to home page for this package])
55           AC_SUBST([PACKAGE_URL], ["http://dev.thep.lu.se/yat"])])
56
57AC_SUBST([YAT_LT_VERSION], [YAT_LT_VERSION_INFO])
58AC_DEFINE([YAT_VERSION], ["my_VERSION"], [version])
59
60AC_CONFIG_HEADERS([config.h])
61AM_INIT_AUTOMAKE([1.11 std-options color-tests parallel-tests
62                  silent-rules subdir-objects])
63
64dnl When fatal error are detected we use macro YAT_MSG_ERROR that
65dnl collects all error messages and aborts configure [just] before
66dnl creating output files with this message below plus collected
67dnl messages from YAT_MSG_ERROR calls.
68YAT_MSG_ERROR_PREPARE([
69        Some pre-requisites were not fulfilled, aborting configure.
70        Please consult the 'README' file for more information about what
71        is needed to compile yat and refer to messages below.
72])
73
74
75# Set default programming language
76AC_LANG(C++)
77
78# propagate selected configure variables to DISTCHECK_CONFIGURE_FLAGS
79for var in CPPFLAGS CXX CXXFLAGS CXXCPP LDFLAGS LIBS; do
80  eval isset=\${$var+set}
81  if test "$isset" = 'set' ; then
82    eval val=$`echo $var`
83    DISTCHECK_CONFIGURE_FLAGS="${DISTCHECK_CONFIGURE_FLAGS}'${var}=${val}' "
84  fi
85done
86AC_SUBST(DISTCHECK_CONFIGURE_FLAGS)
87
88# record if CXXFLAGS was set by user for further use below
89AS_IF([test "${CXXFLAGS+set}" = set], [
90  CXXFLAGS_set_by_user=yes
91],[
92  CXXFLAGS_set_by_user=no
93  # set CXXFLAGS to avoid expansion in AC_PROG_CXX
94  CXXFLAGS=
95])
96
97# Checks for programs.
98dnl FIXME remove m4_ifdef when we assume Automake 1.12
99m4_ifdef([AM_PROG_AR], [AM_PROG_AR])
100AC_PROG_CXX
101AC_PROG_SED
102AC_PROG_LIBTOOL
103
104# find the compiler vendor: gnu, intel, etc
105AX_COMPILER_VENDOR
106
107have_doxygen=no
108AC_PATH_PROG([DOXYGEN], [doxygen], [no])
109if test "$DOXYGEN" = "no"; then
110   AC_MSG_WARN([unable to find doxygen application])
111else
112   doxygen_min_version=1.5
113   AC_MSG_CHECKING([if doxygen is at least $doxygen_min_version])
114   doxygen_version=`$DOXYGEN --version`
115   AX_COMPARE_VERSION([$doxygen_version], [ge], [$doxygen_min_version],
116                      [have_doxygen=yes], [have_doxygen=old])
117   AC_MSG_RESULT([$doxygen_version])
118fi
119
120AC_SUBST(have_doxygen)
121AM_CONDITIONAL([DX_ENABLE_HTML], [test x$have_doxygen = xyes])
122
123# check for quiet_NaN support in OS
124# Check at run-time, but if we are cross-compiling fall back on a
125# compilation test
126AC_MSG_CHECKING([if std::numeric_limits<>::has_quiet_NaN is true])
127AC_RUN_IFELSE(
128  [AC_LANG_PROGRAM(
129    [@%:@include <limits>],
130    [return !std::numeric_limits<double>::has_quiet_NaN])],
131  [quiet_nan=yes
132   AC_MSG_RESULT($quiet_nan)],
133  [quiet_nan=no
134   AC_MSG_RESULT($quiet_nan)],
135  # if we are cross-compiling fall back on compilation test
136  [AC_MSG_RESULT(cross-compiling)
137   AC_MSG_CHECKING([for std::numeric_limits<>::quiet_NaN()])
138    AC_COMPILE_IFELSE(
139     [AC_LANG_PROGRAM(
140        [@%:@include <limits>
141         extern void f(double);],
142        [f(std::numeric_limits<double>::quiet_NaN())])],
143     [quiet_nan=yes],
144     [quiet_nan=no])
145   AC_MSG_RESULT($quiet_nan)])
146# No support for quiet NAN is fatal -- sub-sequent compilation, or execution
147# of created binary, will fail.
148AS_IF([test x"$quiet_nan" = x"no"], [
149  YAT_MSG_ERROR([dnl
150Support for quiet NAN required. yat will not work on this system!])
151])
152
153# Check for infinity support for doubles in OS
154# Check at run-time, but if we are cross-compiling fall back on a
155# compilation test
156AC_MSG_CHECKING([if std::numeric_limits<>::has_infinity is true])
157AC_RUN_IFELSE(
158  [AC_LANG_PROGRAM(
159    [@%:@include <limits>],
160    [return !std::numeric_limits<double>::has_infinity])],
161  [has_infinity=yes
162   AC_MSG_RESULT($has_infinity)],
163  [has_infinity=no
164   AC_MSG_RESULT($has_infinity)],
165  # if we are cross-compiling fall back on compilation test
166  [AC_MSG_RESULT(cross-compiling)
167   AC_MSG_CHECKING([for std::numeric_limits<>::infinity()])
168    AC_COMPILE_IFELSE(
169     [AC_LANG_PROGRAM(
170        [@%:@include <limits>
171         extern void f(double);],
172        [f(std::numeric_limits<double>::infinity())])],
173     [has_infinity=yes],
174     [has_infinity=no])
175   AC_MSG_RESULT($has_infinity)])
176# No support for infinity is fatal -- sub-sequent compilation, or execution
177# of created binary, will fail.
178AS_IF([test x"${has_infinity}" = x"no"], [
179YAT_MSG_ERROR([dnl
180Support for infinity required. yat will not work on this system!])
181])
182
183
184AC_MSG_CHECKING([g++ deprecation attribute])
185AC_COMPILE_IFELSE(
186   [AC_LANG_PROGRAM([[void f() __attribute__ ((deprecated));]],)],
187   [AC_DEFINE([YAT_HAVE_GCC_DEPRECATED], [1],
188              [Define if compiler supports deprecated attribute, as in g++ 4.0])
189    AC_MSG_RESULT([yes])],
190   [AC_MSG_RESULT([no])] )
191
192AC_MSG_CHECKING([if std::multiset::iterator is mutable])
193AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[@%:@include <set>
194                                     @%:@include <vector>]],
195                                   [[std::set<std::vector<double> > s;
196                                     std::vector<double> v;
197                                     s.insert(v);
198                                     s.begin()->reserve(100);
199                                   ]])],
200                  [AC_DEFINE([MULTISET_ITERATOR_IS_MUTABLE], [1],
201                             [Define if std::multiset::iterator is mutable])
202                   AC_MSG_RESULT([yes])
203                  ],
204                  [AC_MSG_RESULT([no])] )
205
206# Save user-defined environment settings for later restoration
207APR_SAVE_THE_ENVIRONMENT(CPPFLAGS)
208APR_SAVE_THE_ENVIRONMENT(CXXFLAGS)
209APR_SAVE_THE_ENVIRONMENT(LDFLAGS)
210APR_SAVE_THE_ENVIRONMENT(LIBS)
211
212# Checks for libraries.
213AC_MSG_NOTICE([checking for libraries])
214AC_CHECK_LIBM
215LIBS="$LIBM $LIBS"
216
217# find library implementing BLAS C API, or use gslcblas
218YAT_LIB_CBLAS([YAT_CBLAS_LIB=$CBLAS_LIB], [YAT_CBLAS_LIB=-lgslcblas])
219LIBS="$YAT_CBLAS_LIB $LIBS"
220
221# GNU Scientific Library, GSL http://www.gnu.org/software/gsl/, checks
222# Including AX_PATH_GSL macro from gsl.m4 distributed by GSL
223gsl_version="1.8"
224AC_SUBST(gsl_version)
225YAT_CHECK_GSL([$gsl_version],[LIBS="-lgsl $LIBS"],[YAT_MSG_ERROR([dnl
226GSL $gsl_version (or newer) not found. The GNU Scientific Library
227(GSL) library cannot be found. Please make sure GSL is
228installed. Please refer to warnings above for more details])
229])
230
231# Boost http://www.boost.org
232boost_version=1.35
233AC_SUBST(boost_version)
234AX_BOOST_BASE(["$boost_version"], [], [YAT_MSG_ERROR([dnl
235Boost ${boost_version} (or newer) not found. Please install boost, or provide
236CPPFLAGS=-I/path/to/boost])
237])
238# skip boost link tests if boost is not wanted (--without-boost)
239AS_IF([test x"$want_boost" = x"yes"],[
240  AX_BOOST_THREAD
241  AX_BOOST_SYSTEM
242  YAT_CPP_ADD_FLAG([CPPFLAGS], [$BOOST_CPPFLAGS])
243  YAT_LD_ADD_FLAG([LDFLAGS], [$BOOST_LDFLAGS])
244  # boost tests above only test compilation, so let's try link in the libs
245  LIBS="$LIBS $BOOST_THREAD_LIB $BOOST_SYSTEM_LIB"
246  AC_MSG_CHECKING([for thread_specific_ptr])
247  AC_LINK_IFELSE([AC_LANG_PROGRAM([@%:@include <boost/thread/tss.hpp>],
248                                  [boost::thread_specific_ptr<int> x;
249                                   x.reset(new int(1));])],
250                 [AC_MSG_RESULT([yes])],
251                 [AC_MSG_RESULT([no])
252                  YAT_MSG_ERROR([Boost thread library not found. Please install library boost-thread.])
253                 ])
254])
255
256# see tickets #648 #687
257AC_MSG_CHECKING([whether constructor in boost concept is supported])
258AC_COMPILE_IFELSE([
259  AC_LANG_PROGRAM(
260    [
261     @%:@include <boost/concept_check.hpp>
262     template <typename T>
263     class MyConcept
264     {
265     public:
266       MyConcept(void) {}
267       BOOST_CONCEPT_USAGE(MyConcept){}
268     };
269    ],[
270     MyConcept<double> x;
271     x = x;
272    ])
273  ],
274  [AC_MSG_RESULT([yes])
275   AC_DEFINE([YAT_HAVE_BOOST_CONCEPT_WITH_CONSTRUCTOR],[1],
276             [define if compiler supports boost concept with constructor])
277  ],
278  [AC_MSG_RESULT([no])]
279)
280
281
282# samtools API from http://samtools.sourceforge.net
283AC_ARG_WITH([samtools],
284            [AS_HELP_STRING([--without-samtools],
285                            [disable samtools support])],
286            [],
287            [with_samtools=yes])
288
289AS_IF([test x"$with_samtools" != x"no"], [
290  AC_CHECK_HEADER([zlib.h], [],
291    [YAT_MSG_ERROR([Header file 'zlib.h' was not found])])
292  AC_SEARCH_LIBS([inflateEnd], [z], [],
293    [YAT_MSG_ERROR([Library 'libz' was not found])])
294  YAT_CHECK_HEADER_BAM([],[YAT_MSG_ERROR([Header file 'bam.h' was not found])])
295  # try link against libbam
296  YAT_CHECK_LIBBAM([LIBS="$BAM_LIBS $LIBS"
297                    AC_DEFINE([HAVE_LIBBAM], [1],
298                              [Define to 1 if libbam is available])],
299    [YAT_MSG_ERROR([Library 'libbam' was not found])])
300  AC_PATH_PROG([SAMTOOLS], [samtools], [false])
301  AC_ARG_VAR([SAMTOOLS], [Tools for alignment in the SAM format])
302], [
303  SAMTOOLS=false
304])
305AM_CONDITIONAL([HAVE_LIBBAM], [test x"$with_samtools" = x"yes"])
306have_libbam=$with_samtools
307AC_SUBST([have_libbam])
308AM_CONDITIONAL([HAVE_SAMTOOLS], [test x"$SAMTOOLS" != x"false"])
309AC_SUBST([SAMTOOLS])
310AS_IF([test x"$SAMTOOLS" = x"false"], [], [
311  AC_DEFINE([HAVE_SAMTOOLS], [1], [Define if samtools executable is available])
312])
313
314#support for large files
315AC_SYS_LARGEFILE
316if test "$enable_largefile" = "no"; then
317  AC_DEFINE([YAT_LFS_DISABLED], 1,
318            [defined to 1 if large file support is disabled])
319fi
320
321AC_DEFINE([HAVE_INLINE], [1], [Define if inline is available on system])
322AC_ARG_ENABLE([debug],
323  [AS_HELP_STRING([--enable-debug],[turn on debug options and code])])
324
325# If neither --enable-assert nor --disable-assert, set enable_assert
326# to same as enable_debug
327AC_ARG_ENABLE([assert],
328              [AS_HELP_STRING([--enable-assert], [turn on assertions])],
329              [], [enable_assert=$enable_debug])
330
331# we use prefix INTERNAL_ for variables that are solely needed for
332# building yat, i.e., they are not needed for a user of yat and are
333# not propagated to yat-config or yat.m4.
334AS_IF([test "${enable_debug}" = "yes"], [
335  AC_DEFINE([YAT_DEBUG], [1], [Define to activate yat assertioons])
336  YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS], [-Wall -pedantic -g -O])
337], [
338  # avoid defining GSL_RANGE_CHECK_OFF if GSL_RANGE_CHECK is already defined
339  AC_CHECK_DECL([GSL_RANGE_CHECK],[],
340                [AC_DEFINE([GSL_RANGE_CHECK_OFF], [1],
341                           [Define to turn off GSL range checks])])
342  # If CXXFLAGS not set by user, set it to default value
343  AS_IF([test x$CXXFLAGS_set_by_user != xyes], [
344    YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS],[-O3])
345  ])
346])
347
348AS_IF([test x"$enable_assert" = x"no"], [
349  AC_DEFINE([NDEBUG], [1], [Define to turn off assertions])
350])
351
352# turn off compiler warning #654 from intel compiler
353AS_IF([test x"$ax_cv_cxx_compiler_vendor" = x"intel"], [
354  YAT_CXX_ADD_FLAG([CXXFLAGS], ['-diag-disable 654'])
355])
356
357# Turns warnings to errors in compilation tests. Only put tests that
358# should be warning sensitive below this point. Can't find any
359# mechanism to revert AC_LANG_WERROR
360AC_LANG_WERROR
361
362# GCC 4.0.1 on OSX complains about -pthread (issue #713)
363AS_IF([AS_ECHO(["$CPPFLAGS"]) | $GREP '\-pthread' > /dev/null],
364  [AX_CHECK_PREPROC_FLAG([-pthread], [],
365     [CPPFLAGS=`AS_ECHO(["$CPPFLAGS"]) | $SED 's%-pthread%%'`],
366     [$INTERNAL_CPPFLAGS])
367])
368
369AS_IF([test x$enable_debug = xyes], [
370  # some versions of boost uses long long - turn off compiler warnings
371  # with -Wno-long-long
372  yat_save_CXXFLAGS=$CXXFLAGS
373  AC_MSG_CHECKING([whether boost uses long long])
374  CXXFLAGS="$INTERNAL_CXXFLAGS $CXXFLAGS"
375  AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
376    [
377      @%:@include <boost/iterator/transform_iterator.hpp>
378      @%:@include <boost/thread.hpp>
379      @%:@include <cmath>
380      @%:@include <functional>
381      @%:@include <vector>
382    ],[
383      using namespace boost;
384      typedef std::pointer_to_unary_function<double, double> F;
385      std::vector<double> vec;
386      transform_iterator<F, std::vector<double>::iterator>
387        i(vec.begin(), std::ptr_fun(fabs));
388      int x = boost::thread::hardware_concurrency();
389      ++x;
390    ])],
391  [AC_MSG_RESULT([no])],
392  [AC_MSG_RESULT([yes])
393   YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS], [-Wno-long-long])
394  ])
395  # restore CXXFLAGS
396  CXXFLAGS=$yat_save_CXXFLAGS
397])
398
399#doxygen stuff
400DX_HTML_OUTPUT=html
401AC_SUBST(DX_HTML_OUTPUT)
402
403AC_CONFIG_FILES([build_support/gen_yat_pc.sh],
404                [chmod +x build_support/gen_yat_pc.sh])
405AC_CONFIG_FILES([build_support/tag_and_release.sh],
406                [chmod +x-w build_support/tag_and_release.sh])
407AC_CONFIG_FILES([Makefile
408     doc/doxygen.config
409     doc/first_page.doxygen
410     test/common_defs.sh
411])
412
413AC_CONFIG_HEADERS([yat/utility/config_public.h])
414# for the test suite
415yat_abs_top_srcdir=`cd $srcdir && pwd`
416AC_DEFINE_UNQUOTED([YAT_ABS_TOP_SRCDIR], ["$yat_abs_top_srcdir"],
417                   [Define to absolute path to top yat src dir])
418
419# Reset flags
420APR_RESTORE_THE_ENVIRONMENT(CPPFLAGS, YAT_)
421APR_RESTORE_THE_ENVIRONMENT(CXXFLAGS, YAT_)
422APR_RESTORE_THE_ENVIRONMENT(LDFLAGS, YAT_)
423APR_RESTORE_THE_ENVIRONMENT(LIBS, YAT_)
424
425# YAT_LIBS minus cblas and math libraries
426YAT_PRIMARY_LIBS=
427for lib in $YAT_LIBS; do
428  AS_CASE([$lib], [$YAT_CBLAS_LIB], [],
429          [$LIBM], [],
430          [YAT_PRIMARY_LIBS="$YAT_PRIMARY_LIBS $lib"])
431done
432# workaround for ticket #736
433for lib in $BAM_LIBS; do
434  APR_REMOVEFROM([YAT_PRIMARY_LIBS], [$lib])
435done
436AC_SUBST(BAM_LIBS)
437AC_SUBST(YAT_PRIMARY_LIBS)
438AC_SUBST(YAT_LIBS)
439AC_SUBST(YAT_CBLAS_LIB)
440
441# set and AC_SUBST variables that are interpreted by Automake
442AM_CPPFLAGS="$INTERNAL_CPPFLAGS $YAT_CPPFLAGS"
443AM_CXXFLAGS="$INTERNAL_CXXFLAGS $YAT_CXXFLAGS"
444AM_LDFLAGS="$INTERNAL_LDFLAGS $YAT_LDFLAGS"
445
446AC_SUBST(AM_CPPFLAGS)
447AC_SUBST(AM_CXXFLAGS)
448AC_SUBST(AM_LDFLAGS)
449AC_SUBST(enable_static)
450
451YAT_SVN_RELEASE([am/maintainer.am])
452
453# set some variable for final message
454AS_CASE([$have_doxygen],
455        [yes], [doxygen_message=yes],
456        [no], [doxygen_message="no (doxygen not found)"],
457        [old], [doxygen_message="no (\`$DOXYGEN' too old)"],
458        [AC_MSG_WARN([unexpected value \$have_doxygen: '$have_doxygen'])
459         AS_BOX([Report this to ]AC_PACKAGE_BUGREPORT)
460        ])
461
462yat_gslcblas_message=
463AS_IF([test "x$YAT_CBLAS_LIB" = "x-lgslcblas"], [
464yat_gslcblas_message='
465  GSL CBLAS found. This is a reference implementation only.
466  Consider using hardware optimized BLAS.
467  ATLAS (http://math-atlas.sourceforge.net/) provides an
468  optimized BLAS library. It is supported by yat!
469'
470])
471
472# Create output.
473AC_OUTPUT
474
475
476# Some more messages.
477AC_MSG_RESULT([
478yat is configured as follows:
479
480  Build Shared Library: $enable_shared
481  Build Static Library: $enable_static
482  Build Documentation:  $doxygen_message
483  With Bam Support:     $with_samtools
484
485Options used to compile and link:
486  VERSION     = $VERSION
487  CXX         = $CXX
488  CPPFLAGS    = $CPPFLAGS
489  YAT_CPPFLAGS= $AM_CPPFLAGS
490  CXXFLAGS    = $CXXFLAGS
491  YAT_CXXFLAGS= $AM_CXXFLAGS
492  LD          = $LD
493  LDFLAGS     = $LDFLAGS
494  YAT_LDFLAGS = $AM_LDFLAGS
495  LIBS        = $LIBS
496  YAT_LIBS    = $YAT_LIBS
497${yat_gslcblas_message}dnl
498----------------------------------------------------------------
499Now type `make'. dnl
500])
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