Merge pull request #47 from smithlabcode/update-build-system

Updating the build system

Author: andrewdavidsmith

Makefile

@@ -18,8 +18,11 @@ EXTRA_DIST = README.md
 
 ACLOCAL_AMFLAGS = -I m4
 
-CXXFLAGS = -Wall -Wextra -Wpedantic
-CXXFLAGS += -O3 -DNDEBUG
+# For thing we don't want users to override
+AM_CXXFLAGS = -Wall -Wextra -Wpedantic
+
+# Users can override this; by default it would get -O2 -g
+CXXFLAGS = -O3 -DNDEBUG
 
 lib_LIBRARIES = libsmithlab_cpp.a
 

Makefile.am

@@ -0,0 +1,37 @@
+#!/bin/sh
+#
+# Run 'autoreconf -i' to generate 'configure', 'Makefile.in', etc.
+#
+# The first time this is run on a new cloned git repo the configure
+# script will not be present, only the configure.ac and
+# Makefile.am. The rest must be generated by `autoreconf -i`.
+#
+# If you are working with a distribution (file ending with ".tar.gz"
+# or similar) then this script should not be needed, and should not be
+# present, as all the files should already exist. You should only run
+# this script if you know what you are doing with autoreconf.
+#
+# This script will only work with an argument to confirm the help
+# message has been read.
+
+runautoreconf() {
+    autoreconf -i;
+}
+
+if test -d .git && test "$(basename "${PWD}")" = "smithlab_cpp"
+then
+    runautoreconf
+    exit 0
+else
+    echo "  It seems you are either attempting to run this script       "
+    echo "  from the wrong directory, or in a source tree that was      "
+    echo "  not obtained by cloning the smithlab_cpp git repo.          "
+    echo "                                                              "
+    echo "  ./autogen.sh generates the configure script. Only run       "
+    echo "                                                              "
+    echo "  this if you know what you are doing with autoreconf and     "
+    echo "  are simply avoiding doing that. If you just want to use     "
+    echo "  the software, download a release and this script will       "
+    echo "  not be needed.                                              "
+    exit 1
+fi

autogen.sh

@@ -50,6 +50,7 @@ AM_CONDITIONAL([ENABLE_HTS], [test "x$enable_hts" = "xyes"])
 
 dnl check for required libraries
 AC_CHECK_LIB([z],[zlibVersion])
+AC_CHECK_HEADERS([zlib.h], , [echo "Did not find zlib.h header"; exit -1])
 
 AC_CONFIG_FILES([Makefile])
 AC_OUTPUT