[apbs/el6/master] update to 1.2.1
Timothy Fenn
timfenn at fedoraproject.org
Thu Aug 26 20:37:05 UTC 2010
commit 7de5b913893874060648b14ef0c5343ef2f90aa4
Author: Tim Fenn <fenn at stanford.edu>
Date: Thu Aug 26 13:36:49 2010 -0700
update to 1.2.1
.gitignore | 1 +
apbs-configure.ac.patch | 43 ++++++++++++++--
apbs-makefile.am.patch | 122 ++++++++++++++++++++++++++---------------------
apbs.spec | 23 +++++++--
sources | 2 +-
5 files changed, 125 insertions(+), 66 deletions(-)
---
diff --git a/.gitignore b/.gitignore
index dad4ed2..fe06b17 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
apbs-1.1.0-source.tar.gz
+/apbs-1.2.1-source.tar.gz
diff --git a/apbs-configure.ac.patch b/apbs-configure.ac.patch
index 162d141..7f882f7 100644
--- a/apbs-configure.ac.patch
+++ b/apbs-configure.ac.patch
@@ -1,6 +1,37 @@
---- configure.ac_orig 2009-07-10 11:37:12.000000000 -0700
-+++ configure.ac 2009-07-10 16:02:33.000000000 -0700
-@@ -390,7 +390,7 @@
+--- configure.ac_orig 2009-11-25 12:23:02.275659561 -0800
++++ configure.ac 2009-11-29 23:16:42.319661207 -0800
+@@ -230,14 +230,16 @@
+ CXXFLAGS=`echo ${CXXFLAGS} | sed 's/-g//g'`;
+ fi
+ fi
+-AC_F77_NOFORMAIN
++# AC_F77_NOFORMAIN
+ FFLAGS="${FLIBS} ${FFLAGS}"
+-if test "${CC}" != "icl"; then
+- AC_F77_FCN_MANGLE()
+-fi
++# this macro is broken, so be sure to set -DVF77_ONEUNDERSCORE
++# if test "${CC}" != "icl"; then
++# AC_F77_FCN_MANGLE()
++# fi
+ AC_LANG_C
+ AC_PROG_CPP
+-AC_DISABLE_SHARED
++# AC_DISABLE_SHARED
++AC_DISABLE_STATIC
+ AM_PROG_LIBTOOL
+
+ dnl ##########################################################################
+@@ -308,7 +310,7 @@
+ dnl # HANDLE COMPILER FLOATING POINT ERROR
+ dnl # ------------------------------------
+
+-AC_FPERROR
++# AC_FPERROR
+
+ dnl ##########################################################################
+ dnl 8. checks for library functions
+@@ -390,7 +392,7 @@
if test -n "${USE_FETK_LIBRARY}"; then
maloc_lib_path="${fetk_library_path}"
@@ -9,7 +40,7 @@
if test -z "${maloc_lib}"; then
AC_MSG_ERROR([Error... Couldn't find FETK library files in the location you specified])
fi
-@@ -806,7 +806,7 @@
+@@ -810,7 +812,7 @@
fi
LDFLAGS=${LDFLAGS_SAVE};
CPPFLAGS=${CPPFLAGS_SAVE};
@@ -18,7 +49,7 @@
dnl # BEGIN FETK LIBRARY/HEADER TEST BLOCK
dnl # -----------------------
-@@ -1028,6 +1028,7 @@
+@@ -1032,6 +1034,7 @@
blas_lib=${contrib_path}/blas/.libs/libapbsblas.a
fi
AC_SUBST(apbs_do_blas)
@@ -26,7 +57,7 @@
dnl # -----------------------
dnl # If using Portland compilers, do not compile
-@@ -1206,7 +1207,9 @@
+@@ -1258,7 +1261,9 @@
else
apbs_build_libraries="${top_apbsdir}/bin/libapbsmainroutines.la \
${top_apbsdir}/src/aaa_lib/libapbs.la \
diff --git a/apbs-makefile.am.patch b/apbs-makefile.am.patch
index 9f8bda0..16463fc 100644
--- a/apbs-makefile.am.patch
+++ b/apbs-makefile.am.patch
@@ -1,24 +1,33 @@
---- ./tools/python/Makefile.am_orig 2009-07-23 12:08:49.000000000 -0700
-+++ ./tools/python/Makefile.am 2009-07-23 13:20:16.000000000 -0700
-@@ -16,4 +16,5 @@
- noinst_PROGRAMS = _apbslib.so
- _apbslib_so_SOURCES = apbslib.c
- _apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
--_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS)
-+_apbslib_so_LDFLAGS = @maloc_lib@ @blas_lib@ $(PY_LDFLAGS)
-+_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.so ${top_builddir}/src/aaa_lib/.libs/libapbs.so
---- ./tools/python/vgrid/Makefile.am_orig 2009-03-05 12:30:03.000000000 -0800
-+++ ./tools/python/vgrid/Makefile.am 2009-07-23 13:20:08.000000000 -0700
-@@ -16,5 +16,6 @@
- noinst_PROGRAMS = _vgrid.so
- _vgrid_so_SOURCES = vgridlib.c
- _vgrid_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
-- _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${top_builddir}/contrib/lib/libmaloc.a @lib_list@
-+ _vgrid_so_LDFLAGS = $(PY_LDFLAGS) @maloc_lib@ @lib_list@
-+ _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.so ${top_builddir}/src/aaa_lib/.libs/libapbs.so
- endif
---- ./tools/arpack/Makefile.am_orig 2009-07-23 13:20:45.000000000 -0700
-+++ ./tools/arpack/Makefile.am 2009-07-23 13:20:47.000000000 -0700
+--- ./contrib/opal/Makefile.am_orig 2009-11-24 18:56:20.564534299 -0800
++++ ./contrib/opal/Makefile.am 2009-11-24 18:59:57.836534326 -0800
+@@ -9,7 +9,7 @@
+ AUTOMAKE_OPTIONS = no-dependencies
+ SUFFIXES = .H .h .C .c .f .o
+
+-always_built_SUBDIRS = ZSI
++# always_built_SUBDIRS = ZSI
+
+ SUBDIRS = $(always_built_SUBDIRS) .
+
+--- ./src/aaa_lib/Makefile.am_orig 2009-11-24 18:57:31.108534078 -0800
++++ ./src/aaa_lib/Makefile.am 2009-11-29 22:09:14.931662428 -0800
+@@ -18,12 +18,12 @@
+ AQUA_LIBS = ${top_builddir}/contrib/aqua/libapbsaqua.la
+ BLAS_LIBS = @blas_lib@
+
+-libdir = ${prefix}/lib
++# libdir = ${prefix}/lib
+ lib_LTLIBRARIES = libapbs.la
+
+ libapbs_la_SOURCES = apbs_link.c
+ libapbs_la_LIBADD = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS}
+-libapbs_la_LDFLAGS = -version-info ${APBS_VERSION}
++libapbs_la_LDFLAGS = @maloc_lib@ -version-info ${APBS_VERSION}
+
+ INCLUDES = -I${top_srcdir}/src/generic -I${top_srcdir}/src/mg -I${top_srcdir}/src/fem @inc_list@
+ AM_CFLAGS = @wall_pedantic@
+--- ./tools/arpack/Makefile.am_orig 2009-11-24 18:57:41.564534258 -0800
++++ ./tools/arpack/Makefile.am 2009-11-24 18:59:57.837534477 -0800
@@ -12,7 +12,7 @@
noinst_PROGRAMS = driver
@@ -27,10 +36,29 @@
+driver_LDADD = ../../src/aaa_lib/libapbs.la @arpack_lib@ @apbs_build_libraries@ -latlas
INCLUDES = @inc_list@
AM_CFLAGS = @CFLAGS@
- AM_LDFLAGS = @LDFLAGS@ @FFLAGS@
---- ./bin/Makefile.am_orig 2009-07-22 22:08:44.000000000 -0700
-+++ ./bin/Makefile.am 2009-07-22 22:11:07.000000000 -0700
-@@ -12,24 +12,24 @@
+ AM_LDFLAGS = @LDFLAGS@
+--- ./tools/python/vgrid/Makefile.am_orig 2009-11-24 18:57:54.604534072 -0800
++++ ./tools/python/vgrid/Makefile.am 2009-11-24 18:59:57.837534477 -0800
+@@ -16,5 +16,6 @@
+ noinst_PROGRAMS = _vgrid.so
+ _vgrid_so_SOURCES = vgridlib.c
+ _vgrid_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
+- _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${top_builddir}/contrib/lib/libmaloc.a @lib_list@
++ _vgrid_so_LDFLAGS = $(PY_LDFLAGS) @maloc_lib@ @lib_list@
++ _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.so ${top_builddir}/src/aaa_lib/.libs/libapbs.so
+ endif
+--- ./tools/python/Makefile.am_orig 2009-11-24 18:58:01.740534012 -0800
++++ ./tools/python/Makefile.am 2009-11-24 18:59:57.838534348 -0800
+@@ -16,4 +16,5 @@
+ noinst_PROGRAMS = _apbslib.so
+ _apbslib_so_SOURCES = apbslib.c
+ _apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
+-_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS)
++_apbslib_so_LDFLAGS = @maloc_lib@ @blas_lib@ $(PY_LDFLAGS)
++_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.so ${top_builddir}/src/aaa_lib/.libs/libapbs.so
+--- ./bin/Makefile.am_orig 2009-11-24 18:58:07.772534219 -0800
++++ ./bin/Makefile.am 2009-11-24 19:09:09.452534035 -0800
+@@ -12,34 +12,35 @@
build_libraries = @apbs_build_libraries@
@@ -41,7 +69,21 @@
-apbs_LDADD = ${build_libraries}
+apbs_LDADD = ${build_libraries} ./libapbsmainroutines.la
+ # This is a hack I suspect, but needed to force apbs to be
+ # rebuilt anytime the make command is issued
+ # Problem before is that there is no dependency between source file
+ # recompilation and relinking the binary. There is probably
+ # a cleaner way to do this, I can't find it, however.
+-BUILT_SOURCES = rm.apbs
+
+-rm.apbs: Makefile
+- -rm -f apbs
++# BUILT_SOURCES = rm.apbs
+
-libdir = ${prefix}/lib
++# rm.apbs: Makefile
++# -rm -f apbs
++
+# libdir = ${prefix}/lib
lib_LTLIBRARIES = libapbsmainroutines.la
libapbsmainroutines_la_SOURCES = routines.c
@@ -56,7 +98,7 @@
-include_HEADERS = routines.h
+# includedir = ${prefix}/include/apbs
+# include_HEADERS = routines.h
-
+
-install-data-local:
- -cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin
- -chmod 755 ${prefix}/bin/ApbsClient.py
@@ -66,31 +108,3 @@
+# -cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin
+# -chmod 755 ${prefix}/bin/ApbsClient.py
+# -rm -f ${prefix}/bin/wsdl2py
---- ./src/aaa_lib/Makefile.am_orig 2009-07-22 22:08:57.000000000 -0700
-+++ ./src/aaa_lib/Makefile.am 2009-07-22 22:12:12.000000000 -0700
-@@ -18,12 +18,12 @@
- AQUA_LIBS = ${top_builddir}/contrib/aqua/libapbsaqua.la
- BLAS_LIBS = @blas_lib@
-
--libdir = ${prefix}/lib
-+# libdir = ${prefix}/lib
- lib_LTLIBRARIES = libapbs.la
-
- libapbs_la_SOURCES = apbs_link.c
- libapbs_la_LIBADD = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS}
--libapbs_la_LDFLAGS = -version-info ${APBS_VERSION}
-+libapbs_la_LDFLAGS = @maloc_lib@ -version-info ${APBS_VERSION}
-
- INCLUDES = -I${top_srcdir}/src/generic -I${top_srcdir}/src/mg -I${top_srcdir}/src/fem @inc_list@
- AM_CFLAGS = @wall_pedantic@
---- ./contrib/opal/Makefile.am_orig 2009-07-23 17:40:40.000000000 -0700
-+++ ./contrib/opal/Makefile.am 2009-07-23 17:40:08.000000000 -0700
-@@ -9,7 +9,7 @@
- AUTOMAKE_OPTIONS = no-dependencies
- SUFFIXES = .H .h .C .c .f .o
-
--always_built_SUBDIRS = ZSI
-+# always_built_SUBDIRS = ZSI
-
- SUBDIRS = $(always_built_SUBDIRS) .
-
diff --git a/apbs.spec b/apbs.spec
index 46a0a17..c3cf1d7 100644
--- a/apbs.spec
+++ b/apbs.spec
@@ -2,13 +2,13 @@
Name: apbs
Summary: Adaptive Poisson Boltzmann Solver
-Version: 1.1.0
-Release: 7%{?dist}
+Version: 1.2.1
+Release: 2%{?dist}
# License of pmgZ, aqua and contrib/blas/mblasd.f is LGPLv2+, the rest is BSD.
License: LGPLv2+ and BSD
Group: Applications/Engineering
URL: http://apbs.sourceforge.net/
-Source0: http://downloads.sourceforge.net/apbs/%{name}-%{version}-source.tar.gz
+Source0: http://downloads.sourceforge.net/apbs/%{name}-1.2.1-source.tar.gz
Source1: LGPL_V2
# adds blas_lib to AC_SUBST so Makefiles are complete
Patch0: apbs-configure.ac.patch
@@ -69,9 +69,10 @@ development using the adaptive poisson boltzmann (APBS) solver
library.
%prep
-%setup -q -n %{name}-%{version}-source
+%setup -q -n %{name}-1.2.1-source
%patch0 -p0
%patch1 -p0
+rm acinclude.m4
libtoolize --automake
aclocal
autoheader
@@ -91,7 +92,7 @@ rm doc/programmer/html/vpee_8h__incl.map
rm doc/programmer/html/dummy_8c__incl.map
%build
-%configure --with-blas='-L%{_libdir}/atlas -lf77blas -latlas -lblas' --with-fetk-include=%{_includedir} --with-fetk-library=%{_libdir} --with-arpack=%{_libdir}/atlas --enable-python --enable-shared --disable-static FFLAGS="-I/usr/include/atlas"
+%configure --with-blas='-L%{_libdir}/atlas -lf77blas -latlas -lblas' --with-fetk-include=%{_includedir} --with-fetk-library=%{_libdir} --with-arpack=%{_libdir}/atlas --enable-python --enable-shared FFLAGS="${RPM_OPT_FLAGS} -I/usr/include/atlas" CFLAGS="${RPM_OPT_FLAGS} -DVF77_ONEUNDERSCORE"
# die, rpath, die.
sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
@@ -172,6 +173,18 @@ rm -rf %{buildroot}
%doc doc/programmer/
%changelog
+* Tue Dec 01 2009 Tim Fenn <fenn at stanford.edu> - 1.2.1-2
+- add RPM_OPT_FLAGS
+
+* Wed Nov 25 2009 Tim Fenn <fenn at stanford.edu> - 1.2.1-1
+- update to 1.2.1
+
+* Tue Nov 24 2009 Tim Fenn <fenn at stanford.edu> - 1.2.0-2
+- fix broken source
+
+* Thu Nov 04 2009 Tim Fenn <fenn at stanford.edu> - 1.2.0-1
+- update to 1.2.0
+
* Mon Jul 27 2009 Tim Fenn <fenn at stanford.edu> - 1.1.0-7
- remove python byte compiled files in bindir
- loop to add tools
diff --git a/sources b/sources
index ca113f8..a83d832 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-ca31ba09714e4fc9acce91e7961569cd apbs-1.1.0-source.tar.gz
+831d85e90083ec639451657195ff90da apbs-1.2.1-source.tar.gz
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