[gentoo-commits] gentoo-x86 commit in sci-chemistry/apbs/files/apbs-1.3: 0014-apbs-1.3-pythonlib-fix.patch 0006-apbs-1.3-clean-targets.patch 0005-apbs-1.3-linking.patch 0008-apbs-1.3-broken-test.patch 0015-apbs-1.3-pythonlib-fix.patch 0007-apbs-1.3-configure.patch 0011-apbs-1.3-shared-linking.patch 0002-python-linking.patch 0004-apbs-1.3-system-zlib.patch 0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch 0012-apbs-1.3-python-linking-correction.patch 0001-autoconf-2.68.patch 0013-apbs-1.3-tools-installation.patch 0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch 0003-apbs-1.3-pkg-config-file.patch

[Justin Lecher (jlec)]

jlec        12/01/04 17:25:25

  Added:                0014-apbs-1.3-pythonlib-fix.patch
                        0006-apbs-1.3-clean-targets.patch
                        0005-apbs-1.3-linking.patch
                        0008-apbs-1.3-broken-test.patch
                        0015-apbs-1.3-pythonlib-fix.patch
                        0007-apbs-1.3-configure.patch
                        0011-apbs-1.3-shared-linking.patch
                        0002-python-linking.patch
                        0004-apbs-1.3-system-zlib.patch
                        0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch
                        0012-apbs-1.3-python-linking-correction.patch
                        0001-autoconf-2.68.patch
                        0013-apbs-1.3-tools-installation.patch
                        0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch
                        0003-apbs-1.3-pkg-config-file.patch
  Log:
  Rewrite build, rely on pkg-config when possible, move to autotools-utils.eclass, handle static-libs correctly
  
  (Portage version: 2.2.0_alpha84/cvs/Linux x86_64)

Revision  Changes    Path
1.1                  sci-chemistry/apbs/files/apbs-1.3/0014-apbs-1.3-pythonlib-fix.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0014-apbs-1.3-pythonlib-fix.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0014-apbs-1.3-pythonlib-fix.patch?rev=1.1&content-type=text/plain

Index: 0014-apbs-1.3-pythonlib-fix.patch
===================================================================
From 86ae9a75144d1d9600e7a9045e1154fb2f481efb Mon Sep 17 00:00:00 2001
Message-Id: <86ae9a75144d1d9600e7a9045e1154fb2f481efb.1325691465.git.jlec@g.o>
In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Wed, 4 Jan 2012 14:05:22 +0100
Subject: [PATCH 14/15] apbs 1.3 pythonlib fix

---
 tools/python/Makefile.am |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am
index 6a09644..aecd6ed 100644
--- a/tools/python/Makefile.am
+++ b/tools/python/Makefile.am
@@ -13,7 +13,7 @@ CCLD             = $(PY_CC)
 CLEANFILES       = _apbslib.so
 SUBDIRS          = vgrid 
 
-noinst_PROGRAMS       = _apbslib.so
+pyexec_LTLIBRARIES    = _apbslib.so
 _apbslib_so_SOURCES   = apbslib.c
 _apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
 _apbslib_so_LDADD     = -L${top_builddir}/bin/.libs/ -lapbsmainroutines -L${top_builddir}/src/aaa_lib/.libs/ -lapbs $(PY_LDFLAGS) ${z_lib} @maloc_lib@ @mc_lib@
-- 
1.7.8.2




1.1                  sci-chemistry/apbs/files/apbs-1.3/0006-apbs-1.3-clean-targets.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0006-apbs-1.3-clean-targets.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0006-apbs-1.3-clean-targets.patch?rev=1.1&content-type=text/plain

Index: 0006-apbs-1.3-clean-targets.patch
===================================================================
From e000438cebba988300c1210bc92a62635ba2ddf8 Mon Sep 17 00:00:00 2001
Message-Id: <e000438cebba988300c1210bc92a62635ba2ddf8.1325691465.git.jlec@g.o>
In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Tue, 3 Jan 2012 20:49:24 +0100
Subject: [PATCH 06/15] apbs 1.3 clean targets

---
 Makefile.am |   32 +++++++++++++++++++++++++++-----
 1 files changed, 27 insertions(+), 5 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index 437402d..af3a3a3 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -16,6 +16,9 @@ SUFFIXES = .H .h .C .cc .c .f .o
 
 SUBDIRS = contrib src bin @apbs_do_tools@ 
 
+pkgconfigdir = @pkgconfigdir@
+pkgconfig_DATA = apbs.pc
+
 distclean-local: clean-local
 
 clean-local: clean-ac
@@ -27,11 +30,30 @@ clean-ac:
 install-exec-local:
 	-rm -f ./bin/apbs
 
-install-data-local:
-	mkdir -p ${prefix}/share
-	-cp -rf examples ${prefix}/share 
-	-cp -rf doc ${prefix}/share 
-	-cp -rf tools ${prefix}/share
+install-data-local: install-cleanup
+	-rm -f doc/LICENSE.txt
+
+install-cleanup:
+	-rm -f tools/manip/*.pyc
+	-rm -f tools/**/*.o
+	-rm -f tools/**/*.c
+	-rm -f tools/**/*.f
+	-rm -f tools/**/*Makefile*
+	-rm -f tools/**/**/*.o
+	-rm -f tools/**/**/*.c
+	-rm -f tools/**/**/*.f
+	-rm -f tools/**/**/*Makefile*
+	-rm -f tools/*Makefile*
+	-rm -f examples/*Makefile*
+	-rm -f examples/**/*Makefile*
+
+install-tools:
+	mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools
+	-cp -rf tools $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
+
+install-examples:
+	mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/examples 
+	-cp -rf examples $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
 
 test:
 	cd examples; make test
-- 
1.7.8.2




1.1                  sci-chemistry/apbs/files/apbs-1.3/0005-apbs-1.3-linking.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0005-apbs-1.3-linking.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0005-apbs-1.3-linking.patch?rev=1.1&content-type=text/plain

Index: 0005-apbs-1.3-linking.patch
===================================================================
From 071473a3ead25df253236329511dcc4c63c3b53a Mon Sep 17 00:00:00 2001
Message-Id: <071473a3ead25df253236329511dcc4c63c3b53a.1325691465.git.jlec@g.o>
In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Tue, 3 Jan 2012 20:48:36 +0100
Subject: [PATCH 05/15] apbs 1.3 linking

---
 bin/Makefile.am         |    8 +++-----
 src/aaa_lib/Makefile.am |    6 +++---
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/bin/Makefile.am b/bin/Makefile.am
index 7b2f3ee..9dae096 100644
--- a/bin/Makefile.am
+++ b/bin/Makefile.am
@@ -15,7 +15,7 @@ build_libraries = @apbs_build_libraries@
 bindir = ${prefix}/bin
 bin_PROGRAMS     = apbs
 apbs_SOURCES     = main.c 
-apbs_LDADD       = ${build_libraries}
+apbs_LDADD       = ${build_libraries} -L../src/aaa_lib/.libs/ libapbsmainroutines.la
 
 # This is a hack I suspect, but needed to force apbs to be
 # rebuilt anytime the make command is issued
@@ -27,9 +27,9 @@ BUILT_SOURCES	 = rm.apbs
 rm.apbs: Makefile
 	-rm -f apbs
 
-libdir = ${prefix}/lib
 lib_LTLIBRARIES = libapbsmainroutines.la
 libapbsmainroutines_la_SOURCES = routines.c
+libapbsmainroutines_la_LIBADD = -L../src/aaa_lib/.libs/ -lapbs @mc_lib@
 libapbsmainroutines_la_LDFLAGS = -version-info ${APBS_VERSION}
 
 INCLUDES = @inc_list@
@@ -40,6 +40,4 @@ 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
-	-rm -f ${prefix}/bin/wsdl2py 
\ No newline at end of file
+	-rm -f $(DESTDIR)${prefix}/bin/wsdl2py 
diff --git a/src/aaa_lib/Makefile.am b/src/aaa_lib/Makefile.am
index 2c5026b..2495246 100644
--- a/src/aaa_lib/Makefile.am
+++ b/src/aaa_lib/Makefile.am
@@ -16,13 +16,13 @@ FEM_LIBS  = ${top_builddir}/src/fem/libapbsfem.la
 MG_LIBS  = ${top_builddir}/src/mg/libapbsmg.la
 PMGZ_LIBS = ${top_builddir}/contrib/pmgZ/libapbspmgz.la
 AQUA_LIBS = ${top_builddir}/contrib/aqua/libapbsaqua.la
-BLAS_LIBS = @blas_lib@
+BLAS_LIBS = @BLAS_LIBS@
 
-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_LIBADD  = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS} \
+		     @OPENMP_LIBS@ @maloc_lib@ @mc_lib@ @z_lib@
 libapbs_la_LDFLAGS = -version-info ${APBS_VERSION}
 
 INCLUDES         = -I${top_srcdir}/src/generic -I${top_srcdir}/src/mg -I${top_srcdir}/src/fem @inc_list@
-- 
1.7.8.2




1.1                  sci-chemistry/apbs/files/apbs-1.3/0008-apbs-1.3-broken-test.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0008-apbs-1.3-broken-test.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0008-apbs-1.3-broken-test.patch?rev=1.1&content-type=text/plain

Index: 0008-apbs-1.3-broken-test.patch
===================================================================
From 6bcd14554262bf366aa371873c22cccb21b32850 Mon Sep 17 00:00:00 2001
Message-Id: <6bcd14554262bf366aa371873c22cccb21b32850.1325691465.git.jlec@g.o>
In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Tue, 3 Jan 2012 20:59:43 +0100
Subject: [PATCH 08/15] apbs 1.3 broken test

---
 examples/Makefile.am |    3 ---
 1 files changed, 0 insertions(+), 3 deletions(-)

diff --git a/examples/Makefile.am b/examples/Makefile.am
index 6cf5664..adf901f 100644
--- a/examples/Makefile.am
+++ b/examples/Makefile.am
@@ -22,7 +22,6 @@ clean:
 	cd born; make clean
 	cd FKBP; make clean
 	cd hca-bind; make clean
-	cd ion-pmf; make clean
 	cd ion-protein; make clean
 	cd ionize; make clean
 	cd pka-lig; make clean
@@ -39,7 +38,6 @@ test:
 	cd born; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
 	cd FKBP; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
 	cd hca-bind; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
-	cd ion-pmf; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
 	cd ion-protein; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
 	cd ionize; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
 	cd pka-lig; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
@@ -56,7 +54,6 @@ testocd:
 	cd born; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log
 	cd FKBP; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log
 	cd hca-bind; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log
-	cd ion-pmf; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log
 	cd ion-protein; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log
 	cd ionize; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log
 	cd pka-lig; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log
-- 
1.7.8.2




1.1                  sci-chemistry/apbs/files/apbs-1.3/0015-apbs-1.3-pythonlib-fix.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0015-apbs-1.3-pythonlib-fix.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0015-apbs-1.3-pythonlib-fix.patch?rev=1.1&content-type=text/plain

Index: 0015-apbs-1.3-pythonlib-fix.patch
===================================================================
From 013f5770202f705df7c522dcb123da86ac62e901 Mon Sep 17 00:00:00 2001
Message-Id: <013f5770202f705df7c522dcb123da86ac62e901.1325691465.git.jlec@g.o>
In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Wed, 4 Jan 2012 14:28:14 +0100
Subject: [PATCH 15/15] apbs 1.3 pythonlib fix

---
 configure.ac             |    1 +
 tools/python/Makefile.am |   11 ++++++-----
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/configure.ac b/configure.ac
index 9837a57..d39a0a5 100644
--- a/configure.ac
+++ b/configure.ac
@@ -161,6 +161,7 @@ AC_ARG_ENABLE(
 if test x"$enable_python" != "xno"; then
 	AC_MSG_RESULT([yes])
 	AC_MSG_NOTICE([Python linkage requires GNU compilers])
+	AM_PATH_PYTHON
 	cclist="gcc"
 	f77list="gfortran g95 g77"
 	apbs_do_python="python"
diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am
index aecd6ed..7d661b1 100644
--- a/tools/python/Makefile.am
+++ b/tools/python/Makefile.am
@@ -10,10 +10,11 @@ AUTOMAKE_OPTIONS = no-dependencies
 SUFFIXES         = .c .C .o .so
 INCLUDES         = @inc_list@ $(PY_CFLAGS) -I${top_srcdir}/bin 
 CCLD             = $(PY_CC)
-CLEANFILES       = _apbslib.so
+CLEANFILES       = _apbs.so
 SUBDIRS          = vgrid 
 
-pyexec_LTLIBRARIES    = _apbslib.so
-_apbslib_so_SOURCES   = apbslib.c
-_apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
-_apbslib_so_LDADD     = -L${top_builddir}/bin/.libs/ -lapbsmainroutines -L${top_builddir}/src/aaa_lib/.libs/ -lapbs $(PY_LDFLAGS) ${z_lib} @maloc_lib@ @mc_lib@
+pkgpyexec_LTLIBRARIES    = _apbs.la
+_apbs_la_SOURCES   = apbslib.c
+#_apbs_la_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
+_apbs_la_LDFLAGS   = -module -avoid-version -shared
+_apbs_la_LIBADD    = ${top_builddir}/bin/.libs/libapbsmainroutines.la ${top_builddir}/src/aaa_lib/.libs/libapbs.la $(PY_LDFLAGS) ${z_lib} @maloc_lib@ @mc_lib@
-- 
1.7.8.2




1.1                  sci-chemistry/apbs/files/apbs-1.3/0007-apbs-1.3-configure.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0007-apbs-1.3-configure.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0007-apbs-1.3-configure.patch?rev=1.1&content-type=text/plain

Index: 0007-apbs-1.3-configure.patch
===================================================================
From b196b6b83a969e6c7ee60e3cdfe03b76eb87bd11 Mon Sep 17 00:00:00 2001
Message-Id: <b196b6b83a969e6c7ee60e3cdfe03b76eb87bd11.1325691465.git.jlec@g.o>
In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Tue, 3 Jan 2012 20:50:19 +0100
Subject: [PATCH 07/15] apbs 1.3 configure

---
 configure.ac |  117 +++++++++++++++------------------------------------------
 1 files changed, 31 insertions(+), 86 deletions(-)

diff --git a/configure.ac b/configure.ac
index 6020fbf..c91abb5 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-1.3dnl ##########################################################################
+dnl ##########################################################################
 dnl APBS -- Adaptive Poisson-Boltzmann Solver
 dnl 
 dnl Nathan A. Baker (nathan.baker@×××.gov)
@@ -71,6 +71,10 @@ AM_CONFIG_HEADER(src/aaa_inc/apbscfg.h)
 AC_CONFIG_AUX_DIR(config)
 AC_PREFIX_DEFAULT(${HOME})
 AC_CANONICAL_SYSTEM
+LT_INIT
+LT_LANG([Fortran 77])
+AC_F77_DUMMY_MAIN
+AC_F77_LIBRARY_LDFLAGS
 
 dnl ##########################################################################
 dnl 1. automake initialization (uncomment only if rebuilding Makefile.in's)
@@ -152,8 +156,7 @@ dnl ##########################################################################
 AC_MSG_CHECKING([for --enable-python])
 AC_ARG_ENABLE(
 	[python],
-	AS_HELP_STRING([--enable-python],[enables Python wrapper compilation]),,
-	[enable_python=no]
+	AS_HELP_STRING([--enable-python],[enables Python wrapper compilation])
 )
 if test x"$enable_python" != "xno"; then
 	AC_MSG_RESULT([yes])
@@ -582,6 +585,7 @@ if test x"$enable_python" != "xno"; then
 			PY_SHARED="-shared"
 			CC="${CC} -fPIC"
 			F77="${F77} -fPIC"
+			PY_LDFLAGS="-lpython$PY_VERSION"
 			;;
 		irix*) 
 			PY_SHARED="-shared"
@@ -717,8 +721,7 @@ if test -z "${USE_FETK}";  then
 	AC_MSG_CHECKING([for --disable-maloc-rebuild])
 	AC_ARG_ENABLE(
 		[maloc-rebuild],
-		AS_HELP_STRING([--disable-maloc-rebuild], [disable rebuilding maloc]),,
-		[enable_maloc_rebuild=yes]
+		AS_HELP_STRING([--disable-maloc-rebuild], [disable rebuilding maloc])
 	)
 	
 	if test x"$enable_maloc_rebuild" = "xno"; then
@@ -981,8 +984,7 @@ dnl # -----------------------
 AC_MSG_CHECKING([for --disable-tools])
 AC_ARG_ENABLE(
 	[tools],
-	AS_HELP_STRING([--disable-tools],[disable tool compilation]),,
-	[enable_tools=yes]
+	AS_HELP_STRING([--disable-tools],[disable tool compilation])
 )
 apbs_do_tools=""
 if test x"$enable_tools" != "xno"; then
@@ -999,45 +1001,10 @@ AC_SUBST(apbs_do_tools)
 dnl # -----------------------
 dnl # HANDLE THE BLAS LIBRARIES
 dnl # -----------------------
-blas_lib=""
-AC_ARG_WITH(
-	    [blas], 
-	    AS_HELP_STRING([--with-blas=LDFLAGS], [link to user-specified BLAS (specify flags to pass to ld)])
-	    )
-AC_MSG_CHECKING([for --with-blas])
-if test x"$with_blas" != "xno" -a -n "$with_blas"; then
-	blas_lib="${with_blas}"
-	AC_MSG_RESULT([${blas_lib}])
- 	AC_ARG_WITH(
-		    [blas_name], 
-		    AS_HELP_STRING([--with-blas-name=NAME], [name of BLAS library, defaults to blas]),, 
-		    [with_blas_name="blas"]
-		    )
-	if test x"$with_blas_name" != "xno" -a -n "$with_blas_name"; then
-		blas_name="${with_blas_name}"
-	fi
- 	AC_MSG_NOTICE([checking ${blas_name} using ${blas_lib}])
-	AC_LANG_FORTRAN77
-	LDFLAGS_SAVE=${LDFLAGS};
-	CPPFLAGS_SAVE=${CPPFLAGS};
-	LDFLAGS="-L${maloc_lib_path} ${blas_lib}";
-	AC_CHECK_LIB(${blas_name},dscal,
-		[blas_found="yes"],
-		[blas_found=""],
-		[${blas_lib} ${socket_lib} ${nsl_lib} ${math_lib}])
-	LDFLAGS=${LDFLAGS_SAVE};
-	CPPFLAGS=${CPPFLAGS_SAVE};
-	if test -z "${blas_found}"; then
-		AC_MSG_ERROR([BLAS libraries or headers missing:  exiting on error!])
-	fi
-	apbs_do_blas=""
-	AC_LANG_C
-else
-	AC_MSG_RESULT([no])
-	apbs_do_blas="blas"
-	blas_lib=${contrib_path}/blas/.libs/libapbsblas.a
-fi
+apbs_do_blas=""
+PKG_CHECK_MODULES([BLAS],[blas])
 AC_SUBST(apbs_do_blas)
+AC_SUBST([BLAS_LIBS])
 
 dnl # --------------------------------
 dnl # HANDLE ZLIB COMPILATION
@@ -1047,13 +1014,12 @@ z_lib=
 AC_MSG_CHECKING([--disable-zlib])
 AC_ARG_ENABLE(
 	[zlib],
-	AS_HELP_STRING([--disable-zlib], [disable zlib compilation]),,
-	[disable_zlib=no]
+	AS_HELP_STRING([--disable-zlib], [disable zlib compilation])
 )
-if test x"$disable_zlib" == "xno"; then
+if test x"$disable_zlib" != "xno"; then
 	AC_MSG_RESULT([yes])
 	zlib="zlib"
-	z_lib=${contrib_path}/zlib/.libs/libz.a
+	z_lib=-lz
 	AC_DEFINE([HAVE_ZLIB], [], [have zlib compression enabled])
 fi
 AC_SUBST(zlib)
@@ -1143,8 +1109,7 @@ dnl # -----------------------
 AC_MSG_CHECKING([for --enable-abps-quiet])
 AC_ARG_ENABLE(
 	[abps-quiet],
-	AS_HELP_STRING([--enable-abps-quiet],[prevent APBS diagnostic messages from displaying to stdout]),,
-	[enable_apbs_quiet=no]
+	AS_HELP_STRING([--enable-abps-quiet],[prevent APBS diagnostic messages from displaying to stdout])
 )
 if test x"$enable_apbs_quiet" != "xno"; then
     AC_MSG_RESULT([yes])
@@ -1156,36 +1121,7 @@ fi
 dnl # -----------------------
 dnl # CHECK WHETHER YOU WANT TO DISABLE OPENMP SUPPORT
 dnl # -----------------------
-AC_MSG_CHECKING([for --disable-openmp])
-AC_ARG_ENABLE(
-	[openmp],
-	AS_HELP_STRING([--disable-openmp],[disables OpenMP compiler support]),,
-	[disable_openmp=yes]
-)
-if test x"$disable_openmp" != "xyes"; then
-    AC_MSG_RESULT([yes])
-else
-    AC_MSG_RESULT([no])
-	if [[ "${CC}" = "icc" ] && [ "${F77}" = "ifort" ]]; then
-		CFLAGS="${CFLAGS} -openmp"
-		FFLAGS="${FFLAGS} -openmp -assume cc_omp"
-		LDFLAGS="${LDFLAGS} -static-intel"
-	fi
-	
-	if [[ "${CC}" = "gcc" ] && [ "${F77}" = "gfortran" ]]; then
-		gcc_version=`gcc --version`
-		gcc_complete_version=`echo ${gcc_version} | awk '{printf("%s",$3)}' | awk -F'.' '{print $1$2}'`
-		
-		if test ["${gcc_complete_version}" -ge 42]; then
-			CFLAGS="${CFLAGS} -fopenmp"
-			FFLAGS="${FFLAGS} -fopenmp"
-		else
-		    AC_MSG_RESULT([WARNING])
-			AC_MSG_RESULT([WARNING Version of gcc/gfortran does not support OpenMP. Disabling.])
-			AC_MSG_RESULT([WARNING])
-		fi
-	fi
-fi
+AC_OPENMP
 
 dnl # -----------------------
 dnl # CHECK FOR WINDOWS SPECIFIC LIBRARIES
@@ -1217,7 +1153,7 @@ dnl # COMPILATIONS
 dnl # -----------------------
 top_srcdir="`pwd`"
 base_list="${FLIBS} ${tree_lib} ${vmetis_lib} ${vor_lib} ${mcx_lib} ${mc_lib} \ 
-	   ${thread_lib} ${mpi_lib} ${math_lib} ${rl_lib} ${socket_lib} ${nsl_lib} ${blas_lib} ${z_lib}"
+	   ${thread_lib} ${mpi_lib} ${math_lib} ${rl_lib} ${socket_lib} ${nsl_lib} ${BLAS_LIBS} ${z_lib}"
 
 case $host_os in
 
@@ -1284,6 +1220,17 @@ else
 fi
 AC_SUBST(apbs_build_libraries)
 
+# Additional arguments (and substitutions)
+# Allow the pkg-config directory to be set
+AC_ARG_WITH(pkgconfigdir,
+        AC_HELP_STRING([--with-pkgconfigdir],
+        [Use the specified pkgconfig dir (default is libdir/pkgconfig)]),
+        [pkgconfigdir=${withval}],
+        [pkgconfigdir='${libdir}/pkgconfig'])
+
+AC_SUBST([pkgconfigdir])
+AC_MSG_NOTICE([pkgconfig directory is ${pkgconfigdir}])
+
 dnl ##########################################################################
 dnl 11. generate the makefiles
 dnl ##########################################################################
@@ -1292,12 +1239,8 @@ AC_CONFIG_FILES([
     Makefile
 
     contrib/Makefile
-    contrib/blas/Makefile
     contrib/pmgZ/Makefile
     contrib/aqua/Makefile
-    contrib/opal/Makefile
-    contrib/opal/ZSI/Makefile
-    contrib/zlib/Makefile	
 	
     tools/Makefile
     tools/mesh/Makefile
@@ -1332,6 +1275,8 @@ AC_CONFIG_FILES([
     
     bin/Makefile
 
+    apbs.pc:apbs.pc.in
+
 ])
 AC_OUTPUT
 
-- 
1.7.8.2




1.1                  sci-chemistry/apbs/files/apbs-1.3/0011-apbs-1.3-shared-linking.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0011-apbs-1.3-shared-linking.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0011-apbs-1.3-shared-linking.patch?rev=1.1&content-type=text/plain

Index: 0011-apbs-1.3-shared-linking.patch
===================================================================
From 0f26ce7c0c5013ba72c6bf5fcf04004240e79d26 Mon Sep 17 00:00:00 2001
Message-Id: <0f26ce7c0c5013ba72c6bf5fcf04004240e79d26.1325691465.git.jlec@g.o>
In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Wed, 4 Jan 2012 11:36:56 +0100
Subject: [PATCH 11/15] apbs 1.3 shared linking

---
 tools/python/vgrid/Makefile.am |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/tools/python/vgrid/Makefile.am b/tools/python/vgrid/Makefile.am
index b31c9b6..50c09ac 100644
--- a/tools/python/vgrid/Makefile.am
+++ b/tools/python/vgrid/Makefile.am
@@ -16,5 +16,5 @@ if PY_PRESENT
    noinst_PROGRAMS     = _vgrid.so
    _vgrid_so_SOURCES   = vgridlib.c
    _vgrid_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
-   _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a @lib_list@
+   _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.la ${top_builddir}/src/aaa_lib/.libs/libapbs.la @lib_list@
 endif
-- 
1.7.8.2




1.1                  sci-chemistry/apbs/files/apbs-1.3/0002-python-linking.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0002-python-linking.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0002-python-linking.patch?rev=1.1&content-type=text/plain

Index: 0002-python-linking.patch
===================================================================
From 5b208a6ef5fc706b699b3b33bd9248126c54a034 Mon Sep 17 00:00:00 2001
Message-Id: <5b208a6ef5fc706b699b3b33bd9248126c54a034.1325691465.git.jlec@g.o>
In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Tue, 3 Jan 2012 20:45:58 +0100
Subject: [PATCH 02/15] python linking

---
 tools/python/Makefile.am       |    4 ++--
 tools/python/vgrid/Makefile.am |    4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am
index 73d25f7..2c1fbea 100644
--- a/tools/python/Makefile.am
+++ b/tools/python/Makefile.am
@@ -15,5 +15,5 @@ SUBDIRS          = vgrid
 
 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) ${z_lib} 
+_apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
+_apbslib_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${z_lib} @OPENMP_LIBS@ @maloc_lib@ @mc_lib@
diff --git a/tools/python/vgrid/Makefile.am b/tools/python/vgrid/Makefile.am
index b573268..b31c9b6 100644
--- a/tools/python/vgrid/Makefile.am
+++ b/tools/python/vgrid/Makefile.am
@@ -15,6 +15,6 @@ CLEANFILES       = _vgrid.so
 if PY_PRESENT
    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_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
+   _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a @lib_list@
 endif
-- 
1.7.8.2




1.1                  sci-chemistry/apbs/files/apbs-1.3/0004-apbs-1.3-system-zlib.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0004-apbs-1.3-system-zlib.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0004-apbs-1.3-system-zlib.patch?rev=1.1&content-type=text/plain

Index: 0004-apbs-1.3-system-zlib.patch
===================================================================
From 7abe31a7006c97e908ec717f5f85dddd4cd36110 Mon Sep 17 00:00:00 2001
Message-Id: <7abe31a7006c97e908ec717f5f85dddd4cd36110.1325691465.git.jlec@g.o>
In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Tue, 3 Jan 2012 20:47:58 +0100
Subject: [PATCH 04/15] apbs 1.3 system zlib

---
 src/mg/vgrid.c |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/src/mg/vgrid.c b/src/mg/vgrid.c
index d183bb2..e0669ab 100644
--- a/src/mg/vgrid.c
+++ b/src/mg/vgrid.c
@@ -432,7 +432,7 @@ VPUBLIC int Vgrid_gradient(Vgrid *thee, double pt[3], double grad[3]) {
  /////////////////////////////////////////////////////////////////////////// */
 #ifdef HAVE_ZLIB
 #define off_t long
-#include "../../contrib/zlib/zlib.h"
+#include <zlib.h>
 #endif
 VPUBLIC int Vgrid_readGZ(Vgrid *thee, const char *fname) {
 
-- 
1.7.8.2




1.1                  sci-chemistry/apbs/files/apbs-1.3/0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch?rev=1.1&content-type=text/plain

Index: 0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch
===================================================================
From a7705f4957dca398031f1b6f3a74494004588c4d Mon Sep 17 00:00:00 2001
Message-Id: <a7705f4957dca398031f1b6f3a74494004588c4d.1325691465.git.jlec@g.o>
In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Wed, 4 Jan 2012 10:52:29 +0100
Subject: [PATCH 09/15] apbs 1.3 use pkg-config for zlib detection

---
 configure.ac |   15 ++++-----------
 1 files changed, 4 insertions(+), 11 deletions(-)

diff --git a/configure.ac b/configure.ac
index c91abb5..53deb06 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1011,17 +1011,10 @@ dnl # HANDLE ZLIB COMPILATION
 dnl # --------------------------------
 disable_zlib=yes
 z_lib=
-AC_MSG_CHECKING([--disable-zlib])
-AC_ARG_ENABLE(
-	[zlib],
-	AS_HELP_STRING([--disable-zlib], [disable zlib compilation])
-)
-if test x"$disable_zlib" != "xno"; then
-	AC_MSG_RESULT([yes])
-	zlib="zlib"
-	z_lib=-lz
-	AC_DEFINE([HAVE_ZLIB], [], [have zlib compression enabled])
-fi
+zlib=
+PKG_CHECK_MODULES([ZLIB],[zlib])
+z_lib=$(ZLIB_LIBS)
+AC_DEFINE([HAVE_ZLIB], [], [have zlib compression enabled])
 AC_SUBST(zlib)
 AC_SUBST(z_lib)
 
-- 
1.7.8.2




1.1                  sci-chemistry/apbs/files/apbs-1.3/0012-apbs-1.3-python-linking-correction.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0012-apbs-1.3-python-linking-correction.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0012-apbs-1.3-python-linking-correction.patch?rev=1.1&content-type=text/plain

Index: 0012-apbs-1.3-python-linking-correction.patch
===================================================================
From 73a1f1d63d7617fea85c10990b1f35c9567a3573 Mon Sep 17 00:00:00 2001
Message-Id: <73a1f1d63d7617fea85c10990b1f35c9567a3573.1325691465.git.jlec@g.o>
In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Wed, 4 Jan 2012 11:49:50 +0100
Subject: [PATCH 12/15] apbs 1.3 python linking correction

---
 bin/Makefile.am                |    4 ++--
 tools/python/Makefile.am       |    2 +-
 tools/python/vgrid/Makefile.am |    2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/bin/Makefile.am b/bin/Makefile.am
index 9dae096..574be3d 100644
--- a/bin/Makefile.am
+++ b/bin/Makefile.am
@@ -15,7 +15,7 @@ build_libraries = @apbs_build_libraries@
 bindir = ${prefix}/bin
 bin_PROGRAMS     = apbs
 apbs_SOURCES     = main.c 
-apbs_LDADD       = ${build_libraries} -L../src/aaa_lib/.libs/ libapbsmainroutines.la
+apbs_LDADD       = ${build_libraries} .libs/libapbsmainroutines.la
 
 # This is a hack I suspect, but needed to force apbs to be
 # rebuilt anytime the make command is issued
@@ -29,7 +29,7 @@ rm.apbs: Makefile
 
 lib_LTLIBRARIES = libapbsmainroutines.la
 libapbsmainroutines_la_SOURCES = routines.c
-libapbsmainroutines_la_LIBADD = -L../src/aaa_lib/.libs/ -lapbs @mc_lib@
+libapbsmainroutines_la_LIBADD = ../src/aaa_lib/.libs/libapbs.la @mc_lib@
 libapbsmainroutines_la_LDFLAGS = -version-info ${APBS_VERSION}
 
 INCLUDES = @inc_list@
diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am
index 2c1fbea..6a09644 100644
--- a/tools/python/Makefile.am
+++ b/tools/python/Makefile.am
@@ -16,4 +16,4 @@ SUBDIRS          = vgrid
 noinst_PROGRAMS       = _apbslib.so
 _apbslib_so_SOURCES   = apbslib.c
 _apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
-_apbslib_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${z_lib} @OPENMP_LIBS@ @maloc_lib@ @mc_lib@
+_apbslib_so_LDADD     = -L${top_builddir}/bin/.libs/ -lapbsmainroutines -L${top_builddir}/src/aaa_lib/.libs/ -lapbs $(PY_LDFLAGS) ${z_lib} @maloc_lib@ @mc_lib@
diff --git a/tools/python/vgrid/Makefile.am b/tools/python/vgrid/Makefile.am
index 50c09ac..165cd4d 100644
--- a/tools/python/vgrid/Makefile.am
+++ b/tools/python/vgrid/Makefile.am
@@ -16,5 +16,5 @@ if PY_PRESENT
    noinst_PROGRAMS     = _vgrid.so
    _vgrid_so_SOURCES   = vgridlib.c
    _vgrid_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
-   _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.la ${top_builddir}/src/aaa_lib/.libs/libapbs.la @lib_list@
+   _vgrid_so_LDADD     = -L${top_builddir}/bin/.libs/ -lapbsmainroutines -L${top_builddir}/src/aaa_lib/.libs/ -lapbs @lib_list@
 endif
-- 
1.7.8.2




1.1                  sci-chemistry/apbs/files/apbs-1.3/0001-autoconf-2.68.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0001-autoconf-2.68.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0001-autoconf-2.68.patch?rev=1.1&content-type=text/plain

Index: 0001-autoconf-2.68.patch
===================================================================
From 89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea Mon Sep 17 00:00:00 2001
Message-Id: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Tue, 3 Jan 2012 20:25:55 +0100
Subject: [PATCH 01/15] autoconf 2.68

---
 acinclude.m4 |   13 +++++--------
 1 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/acinclude.m4 b/acinclude.m4
index 3701ceb..34602e3 100644
--- a/acinclude.m4
+++ b/acinclude.m4
@@ -54,14 +54,11 @@ AC_LANG_SAVE
 AC_LANG_C
 ac_save_LIBS="$LIBS"
 LIBS="mangle-func.o $LIBS"
-AC_TRY_LINK(,foobar();,
-     ac_f77_mangle_type=lowercase,
-     AC_TRY_LINK(,foobar_();,
-          ac_f77_mangle_type=lowercase-underscore,
-          AC_TRY_LINK(,FOOBAR();,
-               ac_f77_mangle_type=uppercase,
-               AC_TRY_LINK(,FOOBAR_();,
-                    ac_f77_mangle_type=uppercase-underscore))))
+AC_TRY_LINK(,foobar();,ac_f77_mangle_type=lowercase)
+AC_TRY_LINK(,foobar_();,ac_f77_mangle_type=lowercase-underscore)
+AC_TRY_LINK(,FOOBAR();,ac_f77_mangle_type=uppercase)
+AC_TRY_LINK(,FOOBAR_();,ac_f77_mangle_type=uppercase-underscore)
+
 LIBS="$ac_save_LIBS"
 AC_LANG_RESTORE
 AC_MSG_RESULT($ac_f77_mangle_type)
-- 
1.7.8.2




1.1                  sci-chemistry/apbs/files/apbs-1.3/0013-apbs-1.3-tools-installation.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0013-apbs-1.3-tools-installation.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0013-apbs-1.3-tools-installation.patch?rev=1.1&content-type=text/plain

Index: 0013-apbs-1.3-tools-installation.patch
===================================================================
From 4fd349da80e63c6fd3fbb2f015d8d802c326508e Mon Sep 17 00:00:00 2001
Message-Id: <4fd349da80e63c6fd3fbb2f015d8d802c326508e.1325691465.git.jlec@g.o>
In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Wed, 4 Jan 2012 13:29:19 +0100
Subject: [PATCH 13/15] apbs 1.3 tools installation

---
 Makefile.am              |    2 +-
 tools/arpack/Makefile.am |    2 +-
 tools/manip/Makefile.am  |    2 +-
 tools/mesh/Makefile.am   |    2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index af3a3a3..60ba9bd 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -49,7 +49,7 @@ install-cleanup:
 
 install-tools:
 	mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools
-	-cp -rf tools $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
+	-cp -rf tools/conversion tools/visualization tools/matlab $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools
 
 install-examples:
 	mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/examples 
diff --git a/tools/arpack/Makefile.am b/tools/arpack/Makefile.am
index 6c05f4a..2362114 100644
--- a/tools/arpack/Makefile.am
+++ b/tools/arpack/Makefile.am
@@ -10,7 +10,7 @@ AUTOMAKE_OPTIONS = no-dependencies
 SUFFIXES = .H .h .C .c .f .o
 CCLD = $(F77)
 
-noinst_PROGRAMS  = driver
+bin_PROGRAMS  = driver
 driver_SOURCES   = driver.c readhb.f ardriv.f
 driver_LDADD     = ../../src/aaa_lib/libapbs.la @arpack_lib@ @apbs_build_libraries@
 INCLUDES         = @inc_list@
diff --git a/tools/manip/Makefile.am b/tools/manip/Makefile.am
index f5f692b..f64f8fc 100644
--- a/tools/manip/Makefile.am
+++ b/tools/manip/Makefile.am
@@ -10,7 +10,7 @@ AUTOMAKE_OPTIONS = no-dependencies
 SUFFIXES = .H .h .C .c .f .o
 CCLD = $(CC)
 
-noinst_PROGRAMS  = coulomb born
+bin_PROGRAMS  = coulomb born
 coulomb_SOURCES  = coulomb.c 
 coulomb_LDADD    = ../../src/aaa_lib/libapbs.la @apbs_build_libraries@
 born_SOURCES     = born.c 
diff --git a/tools/mesh/Makefile.am b/tools/mesh/Makefile.am
index 8ad5cfb..3cd9268 100644
--- a/tools/mesh/Makefile.am
+++ b/tools/mesh/Makefile.am
@@ -21,7 +21,7 @@ uhbd_asc2bin_CCLD        = $(F77)
 else
 UHBD =
 endif
-noinst_PROGRAMS          = mgmesh dxmath mergedx mergedx2 $(UHBD) smooth value dx2mol dx2uhbd benchmark similarity analysis multivalue del2dx tensor2dx
+bin_PROGRAMS          = mgmesh dxmath mergedx mergedx2 $(UHBD) smooth value dx2mol dx2uhbd benchmark similarity analysis multivalue del2dx tensor2dx
 
 mgmesh_SOURCES				= mgmesh.c 
 mgmesh_LDADD				= ../../src/aaa_lib/libapbs.la @apbs_build_libraries@
-- 
1.7.8.2




1.1                  sci-chemistry/apbs/files/apbs-1.3/0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch?rev=1.1&content-type=text/plain

Index: 0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch
===================================================================
From c09358a2aca006d93d8bc7525efe656f1b4f9c0a Mon Sep 17 00:00:00 2001
Message-Id: <c09358a2aca006d93d8bc7525efe656f1b4f9c0a.1325691465.git.jlec@g.o>
In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Wed, 4 Jan 2012 11:05:04 +0100
Subject: [PATCH 10/15] apbs 1.3 use OPENMP_CFLAGS instead of OPENMP_LIBS

---
 configure.ac            |    4 ++--
 src/aaa_lib/Makefile.am |    2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/configure.ac b/configure.ac
index 53deb06..9837a57 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1013,7 +1013,7 @@ disable_zlib=yes
 z_lib=
 zlib=
 PKG_CHECK_MODULES([ZLIB],[zlib])
-z_lib=$(ZLIB_LIBS)
+z_lib=${ZLIB_LIBS}
 AC_DEFINE([HAVE_ZLIB], [], [have zlib compression enabled])
 AC_SUBST(zlib)
 AC_SUBST(z_lib)
@@ -1115,7 +1115,7 @@ dnl # -----------------------
 dnl # CHECK WHETHER YOU WANT TO DISABLE OPENMP SUPPORT
 dnl # -----------------------
 AC_OPENMP
-
+CFLAGS+=" ${OPENMP_CFLAGS}"
 dnl # -----------------------
 dnl # CHECK FOR WINDOWS SPECIFIC LIBRARIES
 dnl # -----------------------
diff --git a/src/aaa_lib/Makefile.am b/src/aaa_lib/Makefile.am
index 2495246..9fcbcaa 100644
--- a/src/aaa_lib/Makefile.am
+++ b/src/aaa_lib/Makefile.am
@@ -22,7 +22,7 @@ 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} \
-		     @OPENMP_LIBS@ @maloc_lib@ @mc_lib@ @z_lib@
+		     @maloc_lib@ @mc_lib@ @z_lib@
 libapbs_la_LDFLAGS = -version-info ${APBS_VERSION}
 
 INCLUDES         = -I${top_srcdir}/src/generic -I${top_srcdir}/src/mg -I${top_srcdir}/src/fem @inc_list@
-- 
1.7.8.2




1.1                  sci-chemistry/apbs/files/apbs-1.3/0003-apbs-1.3-pkg-config-file.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0003-apbs-1.3-pkg-config-file.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.3/0003-apbs-1.3-pkg-config-file.patch?rev=1.1&content-type=text/plain

Index: 0003-apbs-1.3-pkg-config-file.patch
===================================================================
From 9876050808e5d43c02d3c703e998a82f7502275d Mon Sep 17 00:00:00 2001
Message-Id: <9876050808e5d43c02d3c703e998a82f7502275d.1325691465.git.jlec@g.o>
In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@g.o>
From: Justin Lecher <jlec@g.o>
Date: Tue, 3 Jan 2012 20:47:13 +0100
Subject: [PATCH 03/15] apbs 1.3 pkg-config file

---
 apbs.pc.in |   11 +++++++++++
 1 files changed, 11 insertions(+), 0 deletions(-)

diff --git a/apbs.pc.in b/apbs.pc.in
new file mode 100644
index 0000000..c177512
--- /dev/null
+++ b/apbs.pc.in
@@ -0,0 +1,11 @@
+prefix=@prefix@
+exec_prefix=@exec_prefix@
+libdir=@libdir@
+includedir=@includedir@/apbs
+
+Name: apbs
+Description: apbs
+Version: @PACKAGE_VERSION@
+Libs: -L${libdir} -lapbsmainroutines -lapbs
+Libs.private: @LIBS@
+Cflags: -I${includedir}
-- 
1.7.8.2