[ssm] * Thu Jun 20 2013 Tim Fenn <tim.fenn at gmail.com> - 1.3-1 - update to 1.3 - update to new upstream URL

Wed Jul 24 06:03:22 UTC 2013

commit 0dd37e1bea66e7354011d481f16cbfdb22edc8f3
Author: Tim Fenn <tim.fenn at gmail.com>
Date:   Tue Jul 23 23:02:44 2013 -0700

    * Thu Jun 20 2013 Tim Fenn <tim.fenn at gmail.com> - 1.3-1
    - update to 1.3
    - update to new upstream URL

 .gitignore             |    1 +
 sources                |    2 +-
 ssm-configure.ac.patch |   43 ++++++++++++++++++++++++++++++-------------
 ssm-makefile.am.patch  |   33 +++++++++++++++++++++++++--------
 ssm.pc.in              |   12 ++++++++++++
 ssm.spec               |   32 +++++++++++++++++---------------
 6 files changed, 86 insertions(+), 37 deletions(-)
---

diff --git a/.gitignore b/.gitignore
index f58fb29..6178a3c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@ ssm-configure.ac.patch
 ssm-makefile.am.patch
 ssm-ssm.pc.in.patch
 /ssm-1.1.tar.gz
+/ssm-1.3.tar.bz2
diff --git a/sources b/sources
index 6bf46a9..7dc95ee 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-fa67a91d9b481b737fa266fe73a0772e  ssm-1.1.tar.gz
+a7f4eee0ccb4831d2d5d0e06f9327041  ssm-1.3.tar.bz2
diff --git a/ssm-configure.ac.patch b/ssm-configure.ac.patch
index cd51c96..5beece0 100644
--- a/ssm-configure.ac.patch
+++ b/ssm-configure.ac.patch
@@ -1,15 +1,32 @@
---- configure.ac_orig	2011-02-25 16:20:48.000000000 -0800
-+++ configure.ac	2011-02-25 16:21:19.000000000 -0800
-@@ -27,8 +27,10 @@
- AC_STRUCT_TM
+--- configure.ac_orig	2013-07-07 12:42:29.284908451 -0700
++++ configure.ac	2013-07-07 12:59:43.970008464 -0700
+@@ -19,18 +19,20 @@
+ AC_SEARCH_LIBS([cos], [m], [], [AC_MSG_ERROR([need math library])])
  
- dnl Check for MMDB.
--AM_PATH_MMDB([echo Found mmdb], [echo Error locating necessary mmdb; exit 1])
--
-+# AM_PATH_MMDB([echo Found mmdb], [echo Error locating necessary mmdb; exit 1])
-+PKG_CHECK_MODULES(MMDB, mmdb >= 1.23)
-+AC_SUBST(MMDB_CFLAGS)
-+AC_SUBST(MMDB_LIBS)
+ AC_LANG_PUSH([C++])
+-AC_CHECK_LIB(mmdb, MMDB_CCIF_Init, [dummy=yes],
+-             AC_MSG_WARN([mmdb library not found.]))
+-AC_CHECK_HEADER(mmdb/mmdb_manager.h, [dummy=yes],
+-                AC_MSG_ERROR([mmdb headers not found.]))
++PKG_CHECK_MODULES(MMDB, mmdb >= 1.12)
++#AC_CHECK_LIB(mmdb, MMDB_CCIF_Init, [dummy=yes],
++#             AC_MSG_WARN([mmdb library not found.]))
++#AC_CHECK_HEADER(mmdb/mmdb_manager.h, [dummy=yes],
++#                AC_MSG_ERROR([mmdb headers not found.]))
+ AC_LANG_POP([C++])
  
- # Checks for library functions.
- AC_FUNC_STRTOD
+ if test "x$enable_ccp4" = "xyes"; then
+-  AC_CHECK_LIB(ccp4c, ccp4_banner, :,
+-               AC_MSG_WARN([ccp4c library not found.]))
+-  AC_CHECK_HEADER(ccp4/ccp4_general.h, :,
+-                  AC_MSG_ERROR([libccp4 headers not found.]))
++   PKG_CHECK_MODULES(CCP4, libccp4c > 6.3)
++  #AC_CHECK_LIB(ccp4c, ccp4_banner, :,
++  #             AC_MSG_WARN([ccp4c library not found.]))
++  #AC_CHECK_HEADER(ccp4/ccp4_general.h, :,
++  #                AC_MSG_ERROR([libccp4 headers not found.]))
+ fi
+ AM_CONDITIONAL([USE_LIBCCP4], [test "x$enable_ccp4" = "xyes"])
+ 
+-AC_OUTPUT([Makefile])
++AC_OUTPUT([Makefile ssm.pc])
diff --git a/ssm-makefile.am.patch b/ssm-makefile.am.patch
index facaed6..8229182 100644
--- a/ssm-makefile.am.patch
+++ b/ssm-makefile.am.patch
@@ -1,12 +1,29 @@
---- src/Makefile.am_orig	2007-09-03 13:58:00.000000000 -0700
-+++ src/Makefile.am	2008-11-10 01:38:24.000000000 -0800
-@@ -5,7 +5,8 @@
+--- Makefile.am_orig	2013-07-07 12:50:49.698886451 -0700
++++ Makefile.am	2013-07-07 12:57:30.271384925 -0700
+@@ -1,19 +1,23 @@
+ ACLOCAL_AMFLAGS = -I m4
  
++INCLUDES = $(MMDB_CFLAGS)
  lib_LTLIBRARIES = libssm.la
+ libssm_la_SOURCES = ssm_superpose.cpp ssm_csia.cpp ssm_vxedge.cpp \
+ 		    ssm_align.cpp ssm_malign.cpp ssm_graph.cpp
+-libssm_la_LIBADD = -lmmdb
++libssm_la_LIBADD = $(MMDB_LIBS)
+ libssm_la_LDFLAGS = -no-undefined -version-info 1:0:0
  
--INCLUDES = $(MMDB_CXXFLAGS)
-+AM_CPPFLAGS = @MMDB_CFLAGS@
-+AM_LDFLAGS = @MMDB_LIBS@
- 
- libssm_h_sources = ss_csia.h ss_graph.h ssm_align.h ssm_superpose.h ss_vxedge.h
+ pkginclude_HEADERS = ssm_graph.h ssm_superpose.h ssm_csia.h ssm_vxedge.h \
+                      ssm_align.h ssm_malign.h ssm_defs.h
  
++pkgconfigdir = $(libdir)/pkgconfig
++pkgconfig_DATA = ssm.pc
++
+ bin_PROGRAMS = superpose
+ superpose_SOURCES = superpose.cpp sup_pairwise.cpp sup_multiple.cpp \
+                     sup_pairwise.h sup_multiple.h sup_defs.h
+ superpose_LDADD = libssm.la -lmmdb
+ if USE_LIBCCP4
+-superpose_CPPFLAGS = -D_ccp4_
+-superpose_LDADD += -lccp4c
++superpose_CPPFLAGS = -D_ccp4_ $(CCP4_CFLAGS)
++superpose_LDADD += $(CCP4_LIBS)
+ endif
diff --git a/ssm.pc.in b/ssm.pc.in
new file mode 100644
index 0000000..8403bce
--- /dev/null
+++ b/ssm.pc.in
@@ -0,0 +1,12 @@
+prefix=@prefix@
+exec_prefix=@exec_prefix@
+libdir=@libdir@
+includedir=@includedir@
+
+Name: ssm
+Description: Macromolecular superposition library
+Version: @VERSION@
+Requires: mmdb
+Conflicts:
+Libs: -L${libdir} -lssm
+Cflags: -I${includedir}
diff --git a/ssm.spec b/ssm.spec
index 758616a..1e0b1f0 100644
--- a/ssm.spec
+++ b/ssm.spec
@@ -2,20 +2,20 @@
 
 Summary: Macromolecular coordinate superposition library
 Name: ssm
-Version: 1.1
-Release: 5%{?dist}
-License: LGPLv2+
+Version: 1.3
+Release: 1%{?dist}
+License: LGPLv3
 Group: System Environment/Libraries
-URL: https://launchpad.net/ssm
-Source0: http://launchpad.net/%{name}/trunk/%{version}/+download/%{name}-%{version}.tar.gz
+URL: ftp://ftp.ccp4.ac.uk/opensource/
+Source0: ftp://ftp.ccp4.ac.uk/opensource/%{name}-%{version}.tar.bz2
+Source1: ssm.pc.in
 Patch0: ssm-configure.ac.patch
 Patch1: ssm-makefile.am.patch
-Patch2: ssm-ssm.pc.in.patch
-Patch3: ssm-mattype.patch
 BuildRequires: autoconf
 BuildRequires: automake
 BuildRequires: libtool
 BuildRequires: mmdb-devel
+BuildRequires: libccp4-devel
 
 %description
 SSM is a macromolecular coordinate superposition library, written by 
@@ -48,17 +48,16 @@ development using SSM.
 
 %prep
 %setup -q
+cp %{SOURCE1} ./
 %patch0 -p0
 %patch1 -p0
-%patch2 -p0
-%patch3 -p0
 aclocal
 libtoolize --automake --copy
 autoconf
 automake --copy --add-missing --gnu
 
 %build
-%configure --disable-static
+%configure --enable-shared --disable-static --enable-ccp4
 make %{?_smp_mflags}
 
 %install
@@ -76,18 +75,21 @@ rm -f $RPM_BUILD_ROOT%{_libdir}/*.la
 rm -rf %{buildroot}
 
 %files
-%defattr(-,root,root,-)
-%doc AUTHORS COPYING README
-%{_libdir}/libssm.so.0.0.0
-%{_libdir}/libssm.so.0
+%doc AUTHORS COPYING.LESSER
+%{_bindir}/superpose
+%{_libdir}/libssm.so.1.0.0
+%{_libdir}/libssm.so.1
 
 %files devel
-%defattr(-,root,root,-)
 %{_libdir}/libssm.so
 %{_includedir}/ssm/
 %{_libdir}/pkgconfig/%{name}.pc
 
 %changelog
+* Thu Jun 20 2013 Tim Fenn <tim.fenn at gmail.com> - 1.3-1
+- update to 1.3
+- update to new upstream URL
+
 * Fri Feb 15 2013 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 1.1-5
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
 
