From 7e0fa199c33ea466ae2abe893bf15f07d3046d22 Mon Sep 17 00:00:00 2001 From: Sascha Steinbiss Date: Wed, 9 Dec 2015 23:31:53 +0000 Subject: [PATCH 1/4] add support for kFreeBSD --- configure.ac | 8 ++++++-- src/Makefile.am | 6 ++++++ 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/configure.ac b/configure.ac index 58bc6ce..a8b7ec4 100644 --- a/configure.ac +++ b/configure.ac @@ -1,7 +1,7 @@ AC_INIT([snp-sites], [1]) 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 @@ -10,15 +10,19 @@ case $host_os in *linux*) HOST_OS=linux ;; + *freebsd*) + HOST_OS=freebsd + ;; *) ;; esac AM_CONDITIONAL([HOST_LINUX],[test x$HOST_OS = xlinux]) +AM_CONDITIONAL([HOST_FREEBSD],[test x$HOST_OS = xfreebsd]) AC_CHECK_HEADERS([zlib.h math.h]) AC_PROG_LIBTOOL -AC_PROG_CC +AC_PROG_CC AC_PROG_CXX AC_CONFIG_FILES([Makefile src/Makefile]) diff --git a/src/Makefile.am b/src/Makefile.am index 869b72e..32e1495 100644 --- a/src/Makefile.am +++ b/src/Makefile.am @@ -9,6 +9,9 @@ snp_sites_LDADD =-lm libsnp-sites.la -lz -lpthread if HOST_LINUX snp_sites_LDADD += -lrt endif +if HOST_FREEBSD +snp_sites_LDADD += -lrt +endif # libsnp_sites.so is our library lib_LTLIBRARIES = libsnp-sites.la @@ -29,3 +32,6 @@ run_all_tests_LDADD = -lm -lcheck libsnp-sites.la -lz -lpthread if HOST_LINUX run_all_tests_LDADD += -lrt endif +if HOST_FREEBSD +run_all_tests_LDADD += -lrt +endif From 01250cc7da130a7318a57b333dca5261c71a02d1 Mon Sep 17 00:00:00 2001 From: Sascha Steinbiss Date: Thu, 10 Dec 2015 12:54:20 +0000 Subject: [PATCH 2/4] rework build system to use autotools --- configure.ac | 17 ++--- m4/m4_ax_check_zlib.m4 | 142 +++++++++++++++++++++++++++++++++++++++++ src/Makefile.am | 21 +----- 3 files changed, 150 insertions(+), 30 deletions(-) create mode 100644 m4/m4_ax_check_zlib.m4 diff --git a/configure.ac b/configure.ac index a8b7ec4..3609975 100644 --- a/configure.ac +++ b/configure.ac @@ -6,20 +6,13 @@ AC_CONFIG_MACRO_DIR([m4]) AC_CANONICAL_HOST -case $host_os in - *linux*) - HOST_OS=linux - ;; - *freebsd*) - HOST_OS=freebsd - ;; - *) ;; -esac - -AM_CONDITIONAL([HOST_LINUX],[test x$HOST_OS = xlinux]) -AM_CONDITIONAL([HOST_FREEBSD],[test x$HOST_OS = xfreebsd]) +PKG_CHECK_MODULES([CHECK],[check >= 0.8.2],[have_check="yes"], + AC_MSG_WARN(['Check' unit testing framework not found. It would be impossible to run unit tests!"]) + [have_check="no"]) AC_CHECK_HEADERS([zlib.h math.h]) +AC_CHECK_LIB(m, floor) +AX_CHECK_ZLIB AC_PROG_LIBTOOL AC_PROG_CC diff --git a/m4/m4_ax_check_zlib.m4 b/m4/m4_ax_check_zlib.m4 new file mode 100644 index 0000000..ae5705f --- /dev/null +++ b/m4/m4_ax_check_zlib.m4 @@ -0,0 +1,142 @@ +# =========================================================================== +# http://www.gnu.org/software/autoconf-archive/ax_check_zlib.html +# =========================================================================== +# +# SYNOPSIS +# +# AX_CHECK_ZLIB([action-if-found], [action-if-not-found]) +# +# DESCRIPTION +# +# This macro searches for an installed zlib library. If nothing was +# specified when calling configure, it searches first in /usr/local and +# then in /usr, /opt/local and /sw. If the --with-zlib=DIR is specified, +# it will try to find it in DIR/include/zlib.h and DIR/lib/libz.a. If +# --without-zlib is specified, the library is not searched at all. +# +# If either the header file (zlib.h) or the library (libz) is not found, +# shell commands 'action-if-not-found' is run. If 'action-if-not-found' is +# not specified, the configuration exits on error, asking for a valid zlib +# installation directory or --without-zlib. +# +# If both header file and library are found, shell commands +# 'action-if-found' is run. If 'action-if-found' is not specified, the +# default action appends '-I${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 +# #endif /* HAVE_LIBZ */ +# +# LICENSE +# +# Copyright (c) 2008 Loic Dachary +# Copyright (c) 2010 Bastien Chevreux +# +# 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 . +# +# 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 +]) diff --git a/src/Makefile.am b/src/Makefile.am index 32e1495..9d5773b 100644 --- a/src/Makefile.am +++ b/src/Makefile.am @@ -3,15 +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 -if HOST_FREEBSD -snp_sites_LDADD += -lrt -endif +snp_sites_LDADD = libsnp-sites.la -lpthread # libsnp_sites.so is our library lib_LTLIBRARIES = libsnp-sites.la @@ -26,12 +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 -if HOST_FREEBSD -run_all_tests_LDADD += -lrt -endif +run_all_tests_CFLAGS = $(CHECK_CFLAGS) $(CFLAGS) +run_all_tests_LDADD = libsnp-sites.la -lpthread $(CHECK_LIBS) From 1930a2a7a104fef74dc85d77600c1baacab80586 Mon Sep 17 00:00:00 2001 From: Sascha Steinbiss Date: Thu, 10 Dec 2015 13:01:05 +0000 Subject: [PATCH 3/4] remove dependency on libsubunit-dev --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 7954a93..c4b8953 100644 --- a/.travis.yml +++ b/.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 From 5ad48826819186682c766a7b2435f3a819f1798d Mon Sep 17 00:00:00 2001 From: Sascha Steinbiss Date: Thu, 10 Dec 2015 13:31:07 +0000 Subject: [PATCH 4/4] version bump also fills in version information in main.c automatically --- VERSION | 2 +- configure.ac | 4 ++-- src/main.c | 3 ++- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/VERSION b/VERSION index 7ec1d6d..3e3c2f1 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -2.1.0 +2.1.1 diff --git a/configure.ac b/configure.ac index 3609975..cc5e631 100644 --- a/configure.ac +++ b/configure.ac @@ -1,4 +1,4 @@ -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]) @@ -7,7 +7,7 @@ AC_CONFIG_MACRO_DIR([m4]) AC_CANONICAL_HOST 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!"]) + 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]) diff --git a/src/main.c b/src/main.c index 7a60132..1c67070 100644 --- a/src/main.c +++ b/src/main.c @@ -24,9 +24,10 @@ #include #include #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() {