Merge pull request #38 from satta/check_deps

Autotoolize checking for dependencies

.travis.yml

@@ -4,5 +4,5 @@ compiler:
   - clang
 before_install:
  - sudo apt-get update -qq
- - sudo apt-get install -qq check libsubunit-dev
+ - sudo apt-get install -qq check 
 script: autoreconf -i && ./configure && make && make check

VERSION

@@ -1 +1 @@
-2.1.0
+2.1.1

configure.ac

@@ -1,24 +1,21 @@
-AC_INIT([snp-sites], [1])
+AC_INIT([snp-sites], m4_esyscmd([tr -d '\n' < VERSION]))
 AM_INIT_AUTOMAKE([foreign subdir-objects])
 AC_CONFIG_SRCDIR([configure.ac])
-AC_CONFIG_HEADERS([config.h])   
+AC_CONFIG_HEADERS([config.h])
 AC_CONFIG_MACRO_DIR([m4])
 
 AC_CANONICAL_HOST
 
-case $host_os in
-	*linux*)
-		HOST_OS=linux
-		;;
-	*) ;;
-esac
-
-AM_CONDITIONAL([HOST_LINUX],[test x$HOST_OS = xlinux])
+PKG_CHECK_MODULES([CHECK],[check >= 0.8.2],[have_check="yes"],
+  AC_MSG_WARN(["'Check' unit testing framework not found. It would be impossible to run unit tests!"])
+  [have_check="no"])
 
 AC_CHECK_HEADERS([zlib.h math.h])
+AC_CHECK_LIB(m, floor)
+AX_CHECK_ZLIB
 
 AC_PROG_LIBTOOL
-AC_PROG_CC                                   
+AC_PROG_CC
 AC_PROG_CXX
 
 AC_CONFIG_FILES([Makefile src/Makefile])

m4/m4_ax_check_zlib.m4

@@ -0,0 +1,142 @@
+# ===========================================================================
+#       http://www.gnu.org/software/autoconf-archive/ax_check_zlib.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+#   AX_CHECK_ZLIB([action-if-found], [action-if-not-found])
+#
+# DESCRIPTION
+#
+#   This macro searches for an installed zlib library. If nothing was
+#   specified when calling configure, it searches first in /usr/local and
+#   then in /usr, /opt/local and /sw. If the --with-zlib=DIR is specified,
+#   it will try to find it in DIR/include/zlib.h and DIR/lib/libz.a. If
+#   --without-zlib is specified, the library is not searched at all.
+#
+#   If either the header file (zlib.h) or the library (libz) is not found,
+#   shell commands 'action-if-not-found' is run. If 'action-if-not-found' is
+#   not specified, the configuration exits on error, asking for a valid zlib
+#   installation directory or --without-zlib.
+#
+#   If both header file and library are found, shell commands
+#   'action-if-found' is run. If 'action-if-found' is not specified, the
+#   default action appends '-I${ZLIB_HOME}/include' to CPFLAGS, appends
+#   '-L$ZLIB_HOME}/lib' to LDFLAGS, prepends '-lz' to LIBS, and calls
+#   AC_DEFINE(HAVE_LIBZ). You should use autoheader to include a definition
+#   for this symbol in a config.h file. Sample usage in a C/C++ source is as
+#   follows:
+#
+#     #ifdef HAVE_LIBZ
+#     #include <zlib.h>
+#     #endif /* HAVE_LIBZ */
+#
+# LICENSE
+#
+#   Copyright (c) 2008 Loic Dachary <[email protected]>
+#   Copyright (c) 2010 Bastien Chevreux <[email protected]>
+#
+#   This program is free software; you can redistribute it and/or modify it
+#   under the terms of the GNU General Public License as published by the
+#   Free Software Foundation; either version 2 of the License, or (at your
+#   option) any later version.
+#
+#   This program is distributed in the hope that it will be useful, but
+#   WITHOUT ANY WARRANTY; without even the implied warranty of
+#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
+#   Public License for more details.
+#
+#   You should have received a copy of the GNU General Public License along
+#   with this program. If not, see <http://www.gnu.org/licenses/>.
+#
+#   As a special exception, the respective Autoconf Macro's copyright owner
+#   gives unlimited permission to copy, distribute and modify the configure
+#   scripts that are the output of Autoconf when processing the Macro. You
+#   need not follow the terms of the GNU General Public License when using
+#   or distributing such scripts, even though portions of the text of the
+#   Macro appear in them. The GNU General Public License (GPL) does govern
+#   all other use of the material that constitutes the Autoconf Macro.
+#
+#   This special exception to the GPL applies to versions of the Autoconf
+#   Macro released by the Autoconf Archive. When you make and distribute a
+#   modified version of the Autoconf Macro, you may extend this special
+#   exception to the GPL to apply to your modified version as well.
+
+#serial 14
+
+AU_ALIAS([CHECK_ZLIB], [AX_CHECK_ZLIB])
+AC_DEFUN([AX_CHECK_ZLIB],
+#
+# Handle user hints
+#
+[AC_MSG_CHECKING(if zlib is wanted)
+zlib_places="/usr/local /usr /opt/local /sw"
+AC_ARG_WITH([zlib],
+[  --with-zlib=DIR         root directory path of zlib installation @<:@defaults to
+                          /usr/local or /usr if not found in /usr/local@:>@
+  --without-zlib          to disable zlib usage completely],
+[if test "$withval" != no ; then
+  AC_MSG_RESULT(yes)
+  if test -d "$withval"
+  then
+    zlib_places="$withval $zlib_places"
+  else
+    AC_MSG_WARN([Sorry, $withval does not exist, checking usual places])
+  fi
+else
+  zlib_places=
+  AC_MSG_RESULT(no)
+fi],
+[AC_MSG_RESULT(yes)])
+
+#
+# Locate zlib, if wanted
+#
+if test -n "${zlib_places}"
+then
+	# check the user supplied or any other more or less 'standard' place:
+	#   Most UNIX systems      : /usr/local and /usr
+	#   MacPorts / Fink on OSX : /opt/local respectively /sw
+	for ZLIB_HOME in ${zlib_places} ; do
+	  if test -f "${ZLIB_HOME}/include/zlib.h"; then break; fi
+	  ZLIB_HOME=""
+	done
+
+  ZLIB_OLD_LDFLAGS=$LDFLAGS
+  ZLIB_OLD_CPPFLAGS=$CPPFLAGS
+  if test -n "${ZLIB_HOME}"; then
+        LDFLAGS="$LDFLAGS -L${ZLIB_HOME}/lib"
+        CPPFLAGS="$CPPFLAGS -I${ZLIB_HOME}/include"
+  fi
+  AC_LANG_SAVE
+  AC_LANG_C
+  AC_CHECK_LIB([z], [inflateEnd], [zlib_cv_libz=yes], [zlib_cv_libz=no])
+  AC_CHECK_HEADER([zlib.h], [zlib_cv_zlib_h=yes], [zlib_cv_zlib_h=no])
+  AC_LANG_RESTORE
+  if test "$zlib_cv_libz" = "yes" && test "$zlib_cv_zlib_h" = "yes"
+  then
+    #
+    # If both library and header were found, action-if-found
+    #
+    m4_ifblank([$1],[
+                CPPFLAGS="$CPPFLAGS -I${ZLIB_HOME}/include"
+                LDFLAGS="$LDFLAGS -L${ZLIB_HOME}/lib"
+                LIBS="-lz $LIBS"
+                AC_DEFINE([HAVE_LIBZ], [1],
+                          [Define to 1 if you have `z' library (-lz)])
+               ],[
+                # Restore variables
+                LDFLAGS="$ZLIB_OLD_LDFLAGS"
+                CPPFLAGS="$ZLIB_OLD_CPPFLAGS"
+                $1
+               ])
+  else
+    #
+    # If either header or library was not found, action-if-not-found
+    #
+    m4_default([$2],[
+                AC_MSG_ERROR([either specify a valid zlib installation with --with-zlib=DIR or disable zlib usage with --without-zlib])
+                ])
+  fi
+fi
+])

src/Makefile.am

@@ -3,12 +3,7 @@ snpsitesinclude_HEADERS=alignment-file.h  vcf.h phylib-of-snp-sites.h snp-sites.
 
 bin_PROGRAMS = snp-sites
 snp_sites_SOURCES = main.c
-
-
-snp_sites_LDADD =-lm libsnp-sites.la -lz -lpthread
-if HOST_LINUX
-snp_sites_LDADD += -lrt
-endif
+snp_sites_LDADD = libsnp-sites.la -lpthread
 
 # libsnp_sites.so is our library
 lib_LTLIBRARIES = libsnp-sites.la
@@ -23,9 +18,5 @@ run_all_tests_SOURCES = \
 	../tests/check-vcf.c \
 	../tests/helper-methods.c \
 	../tests/run-all-tests.c
-run_all_tests_CFLAGS = -I../tests
-
-run_all_tests_LDADD = -lm -lcheck libsnp-sites.la -lz -lpthread
-if HOST_LINUX
-run_all_tests_LDADD += -lrt
-endif
+run_all_tests_CFLAGS = $(CHECK_CFLAGS) $(CFLAGS)
+run_all_tests_LDADD = libsnp-sites.la -lpthread $(CHECK_LIBS)

src/main.c

@@ -24,9 +24,10 @@
 #include <ctype.h>
 #include <unistd.h>
 #include "snp-sites.h"
+#include "config.h"
 
 #define PROGRAM_NAME "snp-sites"
-#define PROGRAM_VERSION "2.1.0"
+#define PROGRAM_VERSION PACKAGE_VERSION
 
 static void print_usage()
 {