diff -Nurd -x'*~' openbabel-2.2.3.orig/Makefile.am openbabel-2.2.3/Makefile.am --- openbabel-2.2.3.orig/Makefile.am 2008-12-01 12:42:48.000000000 -0500 +++ openbabel-2.2.3/Makefile.am 2015-02-15 23:42:19.000000000 -0500 @@ -1,5 +1,5 @@ # Use our libtool macros -ACLOCAL_AMFLAGS='-Iautoconf' +ACLOCAL_AMFLAGS=-I autoconf # only build in the scripts subdirectory if possible (perl, python, swig, etc.) if BUILD_SCRIPTS diff -Nurd -x'*~' openbabel-2.2.3.orig/configure.in openbabel-2.2.3/configure.in --- openbabel-2.2.3.orig/configure.in 2009-07-28 21:05:04.000000000 -0400 +++ openbabel-2.2.3/configure.in 2015-02-16 00:48:53.000000000 -0500 @@ -2,7 +2,7 @@ AC_INIT([Open Babel], 2.2.3, openbabel-discuss@lists.sourceforge.net, openbabel) AC_PREREQ([2.61]) AC_CONFIG_SRCDIR(src/zipstreamimpl.h) -AM_INIT_AUTOMAKE([foreign no-define]) +AM_INIT_AUTOMAKE([foreign no-define subdir-objects]) AM_MAINTAINER_MODE AX_MAINTAINER_MODE_AUTO_SILENT AM_CONFIG_HEADER(src/config.h) @@ -239,8 +239,11 @@ AM_PATH_XML2(2.6.5) AM_CONDITIONAL(BUILD_XML, test x"$XML_LIBS" != "x") -AC_CHECK_LIB(inchi, GetINCHI, LIBINCHI="-linchi", LIBINCHI="") -AM_CONDITIONAL(BUILD_INCHI, test x"$LIBINCHI" = "x" -o "$inchi" = "yes") +AC_CHECK_LIB(stdinchi, GetStdINCHI, LIBSTDINCHI="-lstdinchi", LIBSTDINCHI="") +dnl AC_CHECK_LIB(inchi, GetINCHI, LIBINCHI="-linchi", LIBINCHI="") +AM_CONDITIONAL(HAVE_INCHI, test x"$LIBINCHI" != "x" -o x"$LIBSTDINCHI" != "x" -o "$inchi" = "yes") +AM_CONDITIONAL(HAVE_STDINCHI, test x"$LIBSTDINCHI" != "x") +AM_CONDITIONAL(BUILD_INCHI, test "$inchi" = "yes") 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]) diff -Nurd -x'*~' openbabel-2.2.3.orig/src/GUI/Makefile.am openbabel-2.2.3/src/GUI/Makefile.am --- openbabel-2.2.3.orig/src/GUI/Makefile.am 2008-12-01 12:41:44.000000000 -0500 +++ openbabel-2.2.3/src/GUI/Makefile.am 2015-02-15 23:58:08.000000000 -0500 @@ -1,9 +1,7 @@ EXTRA_DIST = OBGUI.h optswx.h selformats.h stdwx.h \ OpenBabelGUI.html babel.xpm babel2.ico OBGUI.rc -INCLUDES = -I$(top_builddir)/include -I$(top_srcdir)/data -I$(top_srcdir)/include - -AM_CPPFLAGS = @WX_CPPFLAGS@ +AM_CPPFLAGS = -I$(top_builddir)/include -I$(top_srcdir)/data -I$(top_srcdir)/include @WX_CPPFLAGS@ AM_CXXFLAGS = @WX_CXXFLAGS@ bin_PROGRAMS = wxbabel diff -Nurd -x'*~' openbabel-2.2.3.orig/src/Makefile.am openbabel-2.2.3/src/Makefile.am --- openbabel-2.2.3.orig/src/Makefile.am 2009-07-28 21:05:03.000000000 -0400 +++ openbabel-2.2.3/src/Makefile.am 2015-02-15 23:57:45.000000000 -0500 @@ -10,7 +10,8 @@ SUBDIRS += GUI endif -INCLUDES = -I$(top_builddir)/include -I$(top_srcdir)/data/ -I$(top_srcdir)/include +our_includes = -I$(top_builddir)/include -I$(top_srcdir)/data/ -I$(top_srcdir)/include +AM_CPPFLAGS = $(our_includes) lib_LTLIBRARIES = libopenbabel.la @@ -51,7 +52,7 @@ libopenbabel_la_LDFLAGS = -version-info 3:3:0 -no-undefined if BUILD_SHARED -AM_CPPFLAGS = -DOB_MODULE_PATH=\"$(pkglibdir)/$(VERSION)\" -DUSING_DYNAMIC_LIBS +AM_CPPFLAGS += -DOB_MODULE_PATH=\"$(pkglibdir)/$(VERSION)\" -DUSING_DYNAMIC_LIBS libopenbabel_la_LIBADD = math/libmath.la fingerprints/libfingerprints.la \ forcefields/libforcefields.la ops/libops.la \ @@ -65,7 +66,7 @@ if BUILD_PCH BUILT_SOURCES = all.h.gch -PCHFLAGS=-Winvalid-pch -x c++-header $(CPPFLAGS) $(INCLUDES) +PCHFLAGS=-Winvalid-pch -x c++-header $(CPPFLAGS) $(our_includes) all.h.gch: all.h Makefile \ $(srcdir)/../include/openbabel/babelconfig.h \ $(srcdir)/../include/openbabel/base.h \ diff -Nurd -x'*~' openbabel-2.2.3.orig/src/formats/Makefile.am openbabel-2.2.3/src/formats/Makefile.am --- openbabel-2.2.3.orig/src/formats/Makefile.am 2009-07-09 09:05:02.000000000 -0400 +++ openbabel-2.2.3/src/formats/Makefile.am 2015-02-15 23:59:57.000000000 -0500 @@ -1,4 +1,5 @@ -INCLUDES = -I$(top_builddir)/include -I$(top_srcdir)/data -I$(top_srcdir)/include +our_includes = -I$(top_builddir)/include -I$(top_srcdir)/data -I$(top_srcdir)/include +AM_CPPFLAGS = $(our_includes) # KFc.h and ArrayList.h for ADF formats EXTRA_DIST = exampleformat.cpp ArrayList.h CMakeLists.txt @@ -18,7 +19,7 @@ if BUILD_PCH BUILT_SOURCES = all.h.gch -PCHFLAGS=-Winvalid-pch -x c++-header $(CPPFLAGS) $(INCLUDES) +PCHFLAGS=-Winvalid-pch -x c++-header $(CPPFLAGS) $(our_includes) all.h.gch: all.h Makefile \ $(srcdir)/../../include/openbabel/babelconfig.h \ $(srcdir)/../../include/openbabel/base.h \ @@ -39,11 +40,17 @@ if !BUILD_SHARED noinst_LTLIBRARIES = libformats.la +if HAVE_INCHI if BUILD_INCHI libformats_la_LIBADD = inchi102/libinchi.la else +if HAVE_STDINCHI +libformats_la_LIBADD = -lstdinchi +else libformats_la_LIBADD = -linchi endif +endif +endif libformats_la_SOURCES = \ APIInterface.cpp MCDLformat.cpp \ CSRformat.cpp PQSformat.cpp alchemyformat.cpp \ @@ -124,7 +131,7 @@ formats_LTLIBRARIES += chemdrawcdxformat.la chemkinformat.la \ rxnformat.la rsmiformat.la endif -if BUILD_INCHI +if HAVE_INCHI formats_LTLIBRARIES += inchiformat.la endif if BUILD_ZLIB @@ -261,12 +268,18 @@ hinformat_la_LDFLAGS = -module -avoid-version -no-undefined $(win32ldflags) ../libopenbabel.la inchiformat_la_SOURCES = inchiformat.cpp getinchi.cpp +if HAVE_INCHI if BUILD_INCHI inchiformat_la_LDFLAGS = -module -avoid-version -no-undefined $(win32ldflags) ../libopenbabel.la inchi102/libinchi.la else inchiformat_la_LDFLAGS = -module -avoid-version -no-undefined $(win32ldflags) ../libopenbabel.la +if HAVE_STDINCHI +inchiformat_la_LIBADD = -lstdinchi +else inchiformat_la_LIBADD = -linchi endif +endif +endif jaguarformat_la_SOURCES = jaguarformat.cpp jaguarformat_la_LDFLAGS = -module -avoid-version -no-undefined $(win32ldflags) ../libopenbabel.la diff -Nurd -x'*~' openbabel-2.2.3.orig/src/formats/inchi102/Makefile.am openbabel-2.2.3/src/formats/inchi102/Makefile.am --- openbabel-2.2.3.orig/src/formats/inchi102/Makefile.am 2009-06-14 23:05:02.000000000 -0400 +++ openbabel-2.2.3/src/formats/inchi102/Makefile.am 2015-02-16 00:00:04.000000000 -0500 @@ -1,5 +1,5 @@ EXTRA_DIST = CMakeLists.txt -INCLUDES = -I$(top_srcdir)/include/inchi102 +AM_CPPFLAGS = -I$(top_srcdir)/include/inchi102 noinst_LTLIBRARIES = libinchi.la @@ -12,4 +12,4 @@ ichirvr6.c ichirvr7.c ichisort.c ichister.c ichitaut.c \ ikey_base26.c ikey_dll.c inchi_dll.c inchi_dll_a.c \ inchi_dll_a2.c inchi_dll_main.c runichi.c sha2.c \ - strutil.c util.c \ No newline at end of file + strutil.c util.c diff -Nurd -x'*~' openbabel-2.2.3.orig/src/formats/xml/Makefile.am openbabel-2.2.3/src/formats/xml/Makefile.am --- openbabel-2.2.3.orig/src/formats/xml/Makefile.am 2008-12-01 12:42:01.000000000 -0500 +++ openbabel-2.2.3/src/formats/xml/Makefile.am 2015-02-15 23:59:23.000000000 -0500 @@ -1,5 +1,4 @@ -INCLUDES = -I$(top_builddir)/include -I$(top_srcdir)/include -AM_CPPFLAGS = @XML_CPPFLAGS@ +AM_CPPFLAGS = -I$(top_builddir)/include -I$(top_srcdir)/include @XML_CPPFLAGS@ AM_LDFLAGS = @LIBS@ @XML_LIBS@ ../../libopenbabel.la if USE_BOOST_FLAGS diff -Nurd -x'*~' openbabel-2.2.3.orig/test/Makefile.am openbabel-2.2.3/test/Makefile.am --- openbabel-2.2.3.orig/test/Makefile.am 2009-07-28 19:05:03.000000000 -0400 +++ openbabel-2.2.3/test/Makefile.am 2015-02-16 00:25:25.000000000 -0500 @@ -18,7 +18,7 @@ else # Standard automake tests (if we don't have prove) TESTS = cansmi invalidsmarts invalidsmiles smarts rings unitcell \ - $(top_srcdir)/test/cml.sh $(top_srcdir)/test/test-set.sh + test/cml.sh test/test-set.sh endif LDADD = ../src/libopenbabel.la @LIBDL@