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John Tate
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Merge pull request #38 from satta/check_deps
Autotoolize checking for dependencies
2 parents d62351a + 5ad4882 commit 5f6addf

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6 files changed

+157
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6 files changed

+157
-26
lines changed

.travis.yml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,5 +4,5 @@ compiler:
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- clang
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before_install:
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- sudo apt-get update -qq
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- sudo apt-get install -qq check libsubunit-dev
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- sudo apt-get install -qq check
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script: autoreconf -i && ./configure && make && make check

VERSION

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Original file line numberDiff line numberDiff line change
@@ -1 +1 @@
1-
2.1.0
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2.1.1

configure.ac

Lines changed: 8 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,24 +1,21 @@
1-
AC_INIT([snp-sites], [1])
1+
AC_INIT([snp-sites], m4_esyscmd([tr -d '\n' < VERSION]))
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AM_INIT_AUTOMAKE([foreign subdir-objects])
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AC_CONFIG_SRCDIR([configure.ac])
4-
AC_CONFIG_HEADERS([config.h])
4+
AC_CONFIG_HEADERS([config.h])
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AC_CONFIG_MACRO_DIR([m4])
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77
AC_CANONICAL_HOST
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9-
case $host_os in
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*linux*)
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HOST_OS=linux
12-
;;
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*) ;;
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esac
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AM_CONDITIONAL([HOST_LINUX],[test x$HOST_OS = xlinux])
9+
PKG_CHECK_MODULES([CHECK],[check >= 0.8.2],[have_check="yes"],
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AC_MSG_WARN(["'Check' unit testing framework not found. It would be impossible to run unit tests!"])
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[have_check="no"])
1712

1813
AC_CHECK_HEADERS([zlib.h math.h])
14+
AC_CHECK_LIB(m, floor)
15+
AX_CHECK_ZLIB
1916

2017
AC_PROG_LIBTOOL
21-
AC_PROG_CC
18+
AC_PROG_CC
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AC_PROG_CXX
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AC_CONFIG_FILES([Makefile src/Makefile])

m4/m4_ax_check_zlib.m4

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@@ -0,0 +1,142 @@
1+
# ===========================================================================
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# http://www.gnu.org/software/autoconf-archive/ax_check_zlib.html
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# ===========================================================================
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#
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# SYNOPSIS
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#
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# AX_CHECK_ZLIB([action-if-found], [action-if-not-found])
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#
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# DESCRIPTION
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#
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# This macro searches for an installed zlib library. If nothing was
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# specified when calling configure, it searches first in /usr/local and
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# then in /usr, /opt/local and /sw. If the --with-zlib=DIR is specified,
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# it will try to find it in DIR/include/zlib.h and DIR/lib/libz.a. If
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# --without-zlib is specified, the library is not searched at all.
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#
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# If either the header file (zlib.h) or the library (libz) is not found,
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# shell commands 'action-if-not-found' is run. If 'action-if-not-found' is
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# not specified, the configuration exits on error, asking for a valid zlib
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# installation directory or --without-zlib.
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#
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# If both header file and library are found, shell commands
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# 'action-if-found' is run. If 'action-if-found' is not specified, the
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# default action appends '-I${ZLIB_HOME}/include' to CPFLAGS, appends
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# '-L$ZLIB_HOME}/lib' to LDFLAGS, prepends '-lz' to LIBS, and calls
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# AC_DEFINE(HAVE_LIBZ). You should use autoheader to include a definition
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# for this symbol in a config.h file. Sample usage in a C/C++ source is as
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# follows:
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#
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# #ifdef HAVE_LIBZ
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# #include <zlib.h>
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# #endif /* HAVE_LIBZ */
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#
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# LICENSE
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#
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# Copyright (c) 2008 Loic Dachary <loic@senga.org>
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# Copyright (c) 2010 Bastien Chevreux <bach@chevreux.org>
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#
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# This program is free software; you can redistribute it and/or modify it
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# under the terms of the GNU General Public License as published by the
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# Free Software Foundation; either version 2 of the License, or (at your
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# option) any later version.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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# Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program. If not, see <http://www.gnu.org/licenses/>.
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#
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# As a special exception, the respective Autoconf Macro's copyright owner
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# gives unlimited permission to copy, distribute and modify the configure
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# scripts that are the output of Autoconf when processing the Macro. You
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# need not follow the terms of the GNU General Public License when using
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# or distributing such scripts, even though portions of the text of the
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# Macro appear in them. The GNU General Public License (GPL) does govern
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# all other use of the material that constitutes the Autoconf Macro.
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#
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# This special exception to the GPL applies to versions of the Autoconf
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# Macro released by the Autoconf Archive. When you make and distribute a
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# modified version of the Autoconf Macro, you may extend this special
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# exception to the GPL to apply to your modified version as well.
64+
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#serial 14
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67+
AU_ALIAS([CHECK_ZLIB], [AX_CHECK_ZLIB])
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AC_DEFUN([AX_CHECK_ZLIB],
69+
#
70+
# Handle user hints
71+
#
72+
[AC_MSG_CHECKING(if zlib is wanted)
73+
zlib_places="/usr/local /usr /opt/local /sw"
74+
AC_ARG_WITH([zlib],
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[ --with-zlib=DIR root directory path of zlib installation @<:@defaults to
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/usr/local or /usr if not found in /usr/local@:>@
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--without-zlib to disable zlib usage completely],
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[if test "$withval" != no ; then
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AC_MSG_RESULT(yes)
80+
if test -d "$withval"
81+
then
82+
zlib_places="$withval $zlib_places"
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else
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AC_MSG_WARN([Sorry, $withval does not exist, checking usual places])
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fi
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else
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zlib_places=
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AC_MSG_RESULT(no)
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fi],
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[AC_MSG_RESULT(yes)])
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#
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# Locate zlib, if wanted
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#
95+
if test -n "${zlib_places}"
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then
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# check the user supplied or any other more or less 'standard' place:
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# Most UNIX systems : /usr/local and /usr
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# MacPorts / Fink on OSX : /opt/local respectively /sw
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for ZLIB_HOME in ${zlib_places} ; do
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if test -f "${ZLIB_HOME}/include/zlib.h"; then break; fi
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ZLIB_HOME=""
103+
done
104+
105+
ZLIB_OLD_LDFLAGS=$LDFLAGS
106+
ZLIB_OLD_CPPFLAGS=$CPPFLAGS
107+
if test -n "${ZLIB_HOME}"; then
108+
LDFLAGS="$LDFLAGS -L${ZLIB_HOME}/lib"
109+
CPPFLAGS="$CPPFLAGS -I${ZLIB_HOME}/include"
110+
fi
111+
AC_LANG_SAVE
112+
AC_LANG_C
113+
AC_CHECK_LIB([z], [inflateEnd], [zlib_cv_libz=yes], [zlib_cv_libz=no])
114+
AC_CHECK_HEADER([zlib.h], [zlib_cv_zlib_h=yes], [zlib_cv_zlib_h=no])
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AC_LANG_RESTORE
116+
if test "$zlib_cv_libz" = "yes" && test "$zlib_cv_zlib_h" = "yes"
117+
then
118+
#
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# If both library and header were found, action-if-found
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#
121+
m4_ifblank([$1],[
122+
CPPFLAGS="$CPPFLAGS -I${ZLIB_HOME}/include"
123+
LDFLAGS="$LDFLAGS -L${ZLIB_HOME}/lib"
124+
LIBS="-lz $LIBS"
125+
AC_DEFINE([HAVE_LIBZ], [1],
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[Define to 1 if you have `z' library (-lz)])
127+
],[
128+
# Restore variables
129+
LDFLAGS="$ZLIB_OLD_LDFLAGS"
130+
CPPFLAGS="$ZLIB_OLD_CPPFLAGS"
131+
$1
132+
])
133+
else
134+
#
135+
# If either header or library was not found, action-if-not-found
136+
#
137+
m4_default([$2],[
138+
AC_MSG_ERROR([either specify a valid zlib installation with --with-zlib=DIR or disable zlib usage with --without-zlib])
139+
])
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fi
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fi
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])

src/Makefile.am

Lines changed: 3 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -3,12 +3,7 @@ snpsitesinclude_HEADERS=alignment-file.h vcf.h phylib-of-snp-sites.h snp-sites.
33

44
bin_PROGRAMS = snp-sites
55
snp_sites_SOURCES = main.c
6-
7-
8-
snp_sites_LDADD =-lm libsnp-sites.la -lz -lpthread
9-
if HOST_LINUX
10-
snp_sites_LDADD += -lrt
11-
endif
6+
snp_sites_LDADD = libsnp-sites.la -lpthread
127

138
# libsnp_sites.so is our library
149
lib_LTLIBRARIES = libsnp-sites.la
@@ -23,9 +18,5 @@ run_all_tests_SOURCES = \
2318
../tests/check-vcf.c \
2419
../tests/helper-methods.c \
2520
../tests/run-all-tests.c
26-
run_all_tests_CFLAGS = -I../tests
27-
28-
run_all_tests_LDADD = -lm -lcheck libsnp-sites.la -lz -lpthread
29-
if HOST_LINUX
30-
run_all_tests_LDADD += -lrt
31-
endif
21+
run_all_tests_CFLAGS = $(CHECK_CFLAGS) $(CFLAGS)
22+
run_all_tests_LDADD = libsnp-sites.la -lpthread $(CHECK_LIBS)

src/main.c

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@@ -24,9 +24,10 @@
2424
#include <ctype.h>
2525
#include <unistd.h>
2626
#include "snp-sites.h"
27+
#include "config.h"
2728

2829
#define PROGRAM_NAME "snp-sites"
29-
#define PROGRAM_VERSION "2.1.0"
30+
#define PROGRAM_VERSION PACKAGE_VERSION
3031

3132
static void print_usage()
3233
{

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