VSEARCH 1.8.1: OS X 1.7 and QIIME compatibility fixes

configure.ac

@@ -2,16 +2,14 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.63])
-AC_INIT([vsearch], [1.8.0], [[email protected]])
+AC_INIT([vsearch], [1.8.1], [[email protected]])
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C++])
 AC_CONFIG_SRCDIR([src/vsearch.cc])
 AC_CONFIG_HEADERS([config.h])
 
-# disable default CXXFLAGS
-if test -z $CXXFLAGS; then
-  CXXFLAGS=''
-fi
+AC_SUBST(MACOSX_DEPLOYMENT_TARGET)
+MACOSX_DEPLOYMENT_TARGET="10.7"
 
 # Checks for programs.
 AC_PROG_CXX

src/Makefile.am

@@ -1,19 +1,24 @@
 bin_PROGRAMS = $(top_builddir)/bin/vsearch
 
-AM_CXXFLAGS=-I${srcdir}/cityhash -O3 -mtune=native -Wall -Wsign-compare -g
+AM_CXXFLAGS=-Wall -Wsign-compare
+AM_CFLAGS=$(AM_CXXFLAGS)
+
+export MACOSX_DEPLOYMENT_TARGET
 
 libcpu_sse2_a_SOURCES = cpu.cc
-libcpu_sse2_a_CXXFLAGS = -msse2
+libcpu_sse2_a_CXXFLAGS = $(AM_CXXFLAGS) -msse2
 
 libcpu_ssse3_a_SOURCES = cpu.cc
-libcpu_ssse3_a_CXXFLAGS = -mssse3 -DSSSE3
+libcpu_ssse3_a_CXXFLAGS = $(AM_CXXFLAGS) -mssse3 -DSSSE3
+
+libcityhash_a_SOURCES = cityhash/city.cc
+libcityhash_a_CXXFLAGS = $(AM_CXXFLAGS) -Wno-sign-compare -Icityhash
 
-noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a
+noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a libcityhash.a
 
-__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a libcpu_sse2.a
+__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a libcpu_sse2.a libcityhash.a
 
-__top_builddir__bin_vsearch_SOURCES = cityhash/city.h \
-cityhash/config.h \
+__top_builddir__bin_vsearch_SOURCES = \
 abundance.h \
 align.h \
 align_simd.h \
@@ -53,7 +58,6 @@ userfields.h \
 util.h \
 vsearch.h \
 xstring.h \
-cityhash/city.cc \
 abundance.cc \
 align.cc \
 align_simd.cc \

src/vsearch.cc

@@ -880,7 +880,7 @@ void args_init(int argc, char **argv)
           break;
 
         case 13:
-          opt_threads = args_getlong(optarg);
+          opt_threads = (long) args_getdouble(optarg);
           break;
 
         case 14: