Adding shared libs, fix parallel build, fix install paths on multilib

Package-Manager: portage-2.1.8.3/cvs/Linux x86_64

8 files changed, 309 insertions, 14 deletions

diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
index b487a7b503b1..c40083e11373 100644
--- a/sci-chemistry/apbs/ChangeLog
+++ b/sci-chemistry/apbs/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-chemistry/apbs
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.31 2010/06/09 06:37:14 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.32 2010/06/15 18:02:51 xarthisius Exp $
+
+*apbs-1.2.1b-r4 (15 Jun 2010)
+
+  15 Jun 2010; Kacper Kowalik <xarthisius@gentoo.org>
+  +apbs-1.2.1b-r4.ebuild, +files/apbs-1.2.1b-multilib.patch,
+  files/apbs-1.2.1b-openmp.patch, +files/apbs-1.2.1b-parallelbuild.patch,
+  +files/apbs-1.2.1b-shared.patch, metadata.xml:
+  Adding shared libs, fix parallel build, fix install paths on multilib
 
   09 Jun 2010; Justin Lecher <jlec@gentoo.org> -apbs-1.2.0.ebuild,
   -files/apbs-1.2.0-install-fix.patch, -apbs-1.2.1b.ebuild,
diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
index baa0299b9359..2f75bde2c901 100644
--- a/sci-chemistry/apbs/Manifest
+++ b/sci-chemistry/apbs/Manifest
@@ -9,17 +9,23 @@ AUX apbs-1.2.0-contrib.patch 382 RMD160 4c0c75e57fb6a0c298606d87785a5b9daa8db457
 AUX apbs-1.2.0-link.patch 1716 RMD160 904e7123d32f628171aa728a761c9d7fd95e967d SHA1 63265d0c7c636749292d90efe6a989e7e48251b6 SHA256 37faa758d6439f22853aa9d4524e3e8770437d3986e00649a193b0a97f369bba
 AUX apbs-1.2.1b-autoconf-2.64.patch 952 RMD160 80ed2f351c52764b1c3221b4f5f0e152652c8637 SHA1 dbe725035299182efe82d6ab4a8dcb721601592c SHA256 d9855b84b5b3ca404c463ad9ada7d75d7076d11a929b53bd61f42ed427be9984
 AUX apbs-1.2.1b-install-fix.patch 1467 RMD160 0ed57415822554b888f642b4e3afb296418ead1e SHA1 b7de15116e16c440c7b689182fa465c55fb4a628 SHA256 f67dfdbdff6f89c616c01890efcb059e104be94a33bc8a538275fa4360831d9f
-AUX apbs-1.2.1b-openmp.patch 1431 RMD160 d72a7dad56c1d2ce4e13c4eb03b2cb5e58ebcdf0 SHA1 94ca5f758749c3d71ab783041624256b8d4e8092 SHA256 ae6ba8acc1de36372e3e2af00bac23beca6354cbfbcf2140d9c65bf8e2c3bff6
+AUX apbs-1.2.1b-multilib.patch 762 RMD160 24093fa4dec54c95882c77113dd37e59fc0ba5f1 SHA1 3de61489da2cacbef395602ec41596d26f7a88b3 SHA256 d55b62bdade6077e848d3b56f5d38fe937b8ed2779ac639ced5555cf4a6792db
+AUX apbs-1.2.1b-openmp.patch 1471 RMD160 456d2b1b74a3cb403c7e77814bcb017e7726b578 SHA1 386ffbe0e68398168ede30a33706227e6da64e48 SHA256 ba91c8e780035c884e344c6c84c7bdbd606f3c9919a9aa803ff831d6f41bc905
+AUX apbs-1.2.1b-parallelbuild.patch 371 RMD160 22369e3923307f5cc17602a4cab0326131ac3b72 SHA1 d0b775bf826cc96a799bf1ef9273b79de64164d0 SHA256 907caa55463f5dd0bfc3bbc890c0f97f70bab782c3f76938b59b03e34a9e448c
+AUX apbs-1.2.1b-shared.patch 2508 RMD160 e122f33b7a64a70ebb17631e93085f982ff48074 SHA1 84d835d823e8fa82bc9aa7e274d63c59a4998a12 SHA256 9d35a22be4ea3cd1a0c821b25fbcaf0c44212a2004581e14a8245af4338d73f8
 DIST apbs-1.0.0-source.tar.gz 11541303 RMD160 1eeb79f93a591835281bf8395308cddc065dac93 SHA1 fbcfe664defb09165e0eae3ff913a9d5a17cb27e SHA256 bd3803183ffb2bede9fca242d5432acb60b3cb8668eeccdbbced69aaf7a57604
 DIST apbs-1.2.1b-source.tar.gz 40647966 RMD160 4ba1f72a7f9adcf7b283dc18743488143025b398 SHA1 dc3e6933a987ff9fdf88db510db79b3dacb100d6 SHA256 7d088def1ed7689127eb64014ea44069b9d7bfc995941fe5800ff753d48c87be
 EBUILD apbs-1.0.0-r1.ebuild 1995 RMD160 0efbe531fe27749a65a23d17958c411bcd15ad74 SHA1 9ff5761e0d8d01cdb49518cdf5d3372977c0f9ad SHA256 34b2bd026da29cec1224c91d9b4c86bdac3bec95747e167b2127aa329de2f4b2
 EBUILD apbs-1.2.1b-r3.ebuild 3447 RMD160 779c3a7076ae8d907b6076ff14538d6aad5eb753 SHA1 92911c7a777bbfddd709d5dd2ad58b415b56f30d SHA256 ac3222c4c52f9bb2c66cf11f76180a9cc93863a1d8c21a6a2dfcf6d34203ea74
-MISC ChangeLog 5423 RMD160 c0a79801a7d9dbe0b2c4cd65a7386f169fe6062b SHA1 3a8c3e878710f92b351cd0c891b2a8c2c5dda1e2 SHA256 96d9312e020742d808b06d0954ac901fea98dce6555b29b1aae2cc9af5216b4d
-MISC metadata.xml 547 RMD160 7df9b626591272a0875025ac69614734ebeaa886 SHA1 7fb86e4654460def273914edb38551efbee4facc SHA256 49c4f98a836f53297ed0efc680613a595f149b92a864ed3e7e329f93ea17116f
+EBUILD apbs-1.2.1b-r4.ebuild 3557 RMD160 be26f87ed195ca9f36bcfb1224ede7ef4d415171 SHA1 e9be58798586f2a768442480524c5aa95b3c08fa SHA256 af8ab3bdac40086bec961cb54b5a445cc86dc732351b222729c8320b2e80dccb
+MISC ChangeLog 5771 RMD160 433c0a4c05df4fbcd3d55e7fa8756cb35814591b SHA1 abc1619713b46de98cd31bca74f15dc9a9c4888e SHA256 22cb9cce01ed2ee9a684afcda1a0c1997888168f0882801885a3f94d4ca44003
+MISC metadata.xml 623 RMD160 2b62b6245e7ba05198d3f73d1548bddaf43f2221 SHA1 43d5621c91d4d8ff14e4faff680d8998f4917885 SHA256 26fc548a18df9cca13bc53c103333a49c1042f112356a5f7d6b557e3a0d67cbf
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.15 (GNU/Linux)
 
-iEYEARECAAYFAkwPNp8ACgkQgAnW8HDreRZJrgCfQ5+X/0aGjP9e43K9gT59k6Zt
-d5AAoLn+udD4hVej+eVQmmwlRWlEyoEJ
-=eQT+
+iJwEAQECAAYFAkwXwFQACgkQIiMqcbOVdxQgVAQAjhFRx6ifLqsRg+K7iWHJ3lbe
+efA8SORxIP42GS3O73JMZoGytmQVbm1njPB6NfPUBpCVtOBMmB5AEQTPsqqJyxbK
+9ThSYsnjSZVPfCJWNqknxV/Ym0XFzbplNJuY6AHKfbmW5cQ8wF+2l7KJsMGGLP5R
+xoZH+hv+8tSQBQSp/9k=
+=NXvw
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/apbs/apbs-1.2.1b-r4.ebuild b/sci-chemistry/apbs/apbs-1.2.1b-r4.ebuild
new file mode 100644
index 000000000000..a223b2adcb92
--- /dev/null
+++ b/sci-chemistry/apbs/apbs-1.2.1b-r4.ebuild
@@ -0,0 +1,142 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.2.1b-r4.ebuild,v 1.1 2010/06/15 18:02:51 xarthisius Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="python? 2"
+FORTRAN="g77 gfortran ifc"
+
+inherit autotools eutils flag-o-matic fortran python versionator
+
+MY_PV=$(get_version_component_range 1-3)
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="Software for evaluating the electrostatic properties of nanoscale biomolecular systems"
+HOMEPAGE="http://apbs.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+IUSE="arpack doc mpi openmp python tinker tools"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+
+DEPEND="dev-libs/maloc[mpi=]
+	virtual/blas
+	sys-libs/readline
+	arpack? ( sci-libs/arpack )
+	mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/"${MY_P}-source"
+
+pkg_setup() {
+	use python && python_set_active_version 2
+	fortran_pkg_setup
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-openmp.patch \
+		"${FILESDIR}"/${P}-install-fix.patch \
+		"${FILESDIR}"/${PN}-1.2.0-contrib.patch \
+		"${FILESDIR}"/${PN}-1.2.0-link.patch \
+		"${FILESDIR}"/${P}-autoconf-2.64.patch \
+		"${FILESDIR}"/${P}-shared.patch \
+		"${FILESDIR}"/${P}-multilib.patch \
+		"${FILESDIR}"/${P}-parallelbuild.patch
+	sed "s:GENTOO_PKG_NAME:${PN}:g" \
+		-i Makefile.am || die "Cannot correct package name"
+	eautoreconf
+	find . -name "._*" -exec rm -f '{}' \;
+}
+
+src_configure() {
+	local myconf="--docdir=${EPREFIX}/usr/share/doc/${PF}"
+	use arpack && myconf="${myconf} --with-arpack=${EPREFIX}/usr/$(get_libdir)"
+
+	# check which mpi version is installed and tell configure
+	if use mpi; then
+		export CC="${EPREFIX}/usr/bin/mpicc"
+		export F77="${EPREFIX}/usr/bin/mpif77"
+
+		if has_version sys-cluster/mpich; then
+	 		myconf="${myconf} --with-mpich=${EPREFIX}/usr"
+		elif has_version sys-cluster/mpich2; then
+			myconf="${myconf} --with-mpich2=${EPREFIX}/usr"
+		elif has_version sys-cluster/lam-mpi; then
+			myconf="${myconf} --with-lam=${EPREFIX}/usr"
+		elif has_version sys-cluster/openmpi; then
+			myconf="${myconf} --with-openmpi=${EPREFIX}/usr"
+		fi
+	fi || die "Failed to select proper mpi implementation"
+
+	# we need the tools target for python
+	if use python && ! use tools; then
+		myconf="${myconf} --enable-tools"
+	fi
+
+	econf \
+		--disable-maloc-rebuild \
+		--enable-shared \
+		--with-blas=-lblas \
+		$(use_enable openmp) \
+		$(use_enable python) \
+		$(use_enable tinker) \
+		$(use_enable tools) \
+		${myconf}
+}
+
+src_compile() {
+	emake || die "make failed"
+}
+
+src_test() {
+	cd examples && make test \
+		|| die "Tests failed"
+}
+
+src_install() {
+	emake -j1 DESTDIR="${D}" install \
+		|| die "make install failed"
+
+	if use tools; then
+		mv tools/mesh/{,mesh-}analysis || die
+		dobin tools/mesh/* || die
+
+		if use arpack; then
+			dobin tools/arpack/* || die
+		fi
+
+		insinto /usr/share/${PN}
+		doins -r tools/conversion || die
+		doins -r tools/visualization/opendx || die
+
+		dobin tools/manip/{born,coulomb} || die
+
+		doins -r tools/matlab || die
+	fi
+
+	insinto $(python_get_sitedir)/${PN}
+	doins tools/manip/*.py || die
+
+	if use python && ! use mpi; then
+		insinto $(python_get_sitedir)/${PN}
+		doins tools/python/{*.py,*.pqr,*.so} || die
+		doins tools/python/*/{*.py,*.so} || die
+	fi
+
+	dodoc AUTHORS INSTALL README NEWS ChangeLog \
+		|| die "Failed to install docs"
+
+	if use doc; then
+		dohtml -r doc/* || die "Failed to install html docs"
+	fi
+}
+
+pkg_postinst() {
+	python_mod_optimize ${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup ${PN}
+}
diff --git a/sci-chemistry/apbs/files/apbs-1.2.1b-multilib.patch b/sci-chemistry/apbs/files/apbs-1.2.1b-multilib.patch
new file mode 100644
index 000000000000..e0637349b551
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.2.1b-multilib.patch
@@ -0,0 +1,32 @@
+Respect multilib directories
+
+--- src/aaa_lib/Makefile.am
++++ src/aaa_lib/Makefile.am
+@@ -18,7 +18,6 @@
+ AQUA_LIBS = ${top_builddir}/contrib/aqua/libapbsaqua.la
+ BLAS_LIBS = @blas_lib@
+ 
+-libdir = ${prefix}/lib
+ lib_LTLIBRARIES = libapbs.la
+ 
+ libapbs_la_SOURCES = apbs_link.c
+--- bin/Makefile.am
++++ bin/Makefile.am
+@@ -27,7 +27,6 @@
+ rm.apbs: Makefile
+ 	-rm -f apbs
+ 
+-libdir = ${prefix}/lib
+ lib_LTLIBRARIES = libapbsmainroutines.la
+ libapbsmainroutines_la_SOURCES = routines.c
+ libapbsmainroutines_la_LDFLAGS = -version-info ${APBS_VERSION}
+--- contrib/maloc/src/aaa_lib/Makefile.am
++++ contrib/maloc/src/aaa_lib/Makefile.am
+@@ -49,7 +49,6 @@
+ LIBEFENCE =
+ endif
+ 
+-libdir = ${prefix}/lib
+ lib_LTLIBRARIES = libmaloc.la ${LIBEFENCE}
+ 
+ libmaloc_la_SOURCES =
diff --git a/sci-chemistry/apbs/files/apbs-1.2.1b-openmp.patch b/sci-chemistry/apbs/files/apbs-1.2.1b-openmp.patch
index e202725b6056..b3e521bf9d3d 100644
--- a/sci-chemistry/apbs/files/apbs-1.2.1b-openmp.patch
+++ b/sci-chemistry/apbs/files/apbs-1.2.1b-openmp.patch
@@ -1,8 +1,6 @@
-diff --git a/configure.ac b/configure.ac
-index 24748bd..bd1b608 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -976,7 +976,6 @@ AC_MSG_CHECKING([for --disable-tools])
+--- configure.ac
++++ configure.ac
+@@ -976,7 +976,6 @@
  AC_ARG_ENABLE(
  	[tools],
  	AS_HELP_STRING([--disable-tools],[disable tool compilation]),,
@@ -10,7 +8,7 @@ index 24748bd..bd1b608 100644
  )
  apbs_do_tools=""
  if test x"$enable_tools" != "xno"; then
-@@ -1134,22 +1133,17 @@ AC_MSG_CHECKING([for --disable-openmp])
+@@ -1134,32 +1133,32 @@
  AC_ARG_ENABLE(
  	[openmp],
  	AS_HELP_STRING([--disable-openmp],[disables OpenMP compiler support]),,
@@ -36,7 +34,10 @@ index 24748bd..bd1b608 100644
  		if test ["${gcc_complete_version}" -ge 42]; then
  			CFLAGS="${CFLAGS} -fopenmp"
  			FFLAGS="${FFLAGS} -fopenmp"
-@@ -1159,6 +1153,9 @@ else
++			OPENMP_LIBS="-lgomp"
+ 		else
+ 		    AC_MSG_RESULT([WARNING])
+ 			AC_MSG_RESULT([WARNING Version of gcc/gfortran does not support OpenMP. Disabling.])
  			AC_MSG_RESULT([WARNING])
  		fi
  	fi
@@ -44,5 +45,7 @@ index 24748bd..bd1b608 100644
 +    AC_MSG_RESULT([yes])
 +    disable_openmp=yes
  fi
++AC_SUBST(OPENMP_LIBS)
  
  dnl # -----------------------
+ dnl # CHECK FOR WINDOWS SPECIFIC LIBRARIES
diff --git a/sci-chemistry/apbs/files/apbs-1.2.1b-parallelbuild.patch b/sci-chemistry/apbs/files/apbs-1.2.1b-parallelbuild.patch
new file mode 100644
index 000000000000..f19ad6498a65
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.2.1b-parallelbuild.patch
@@ -0,0 +1,13 @@
+Fix parallel build issues
+
+--- bin/Makefile.am
++++ bin/Makefile.am
+@@ -15,7 +15,7 @@
+ bindir = ${prefix}/bin
+ bin_PROGRAMS     = apbs
+ apbs_SOURCES     = main.c 
+-apbs_LDADD       = ${build_libraries}
++apbs_LDADD       = ${build_libraries} libapbsmainroutines.la
+ 
+ # This is a hack I suspect, but needed to force apbs to be
+ # rebuilt anytime the make command is issued
diff --git a/sci-chemistry/apbs/files/apbs-1.2.1b-shared.patch b/sci-chemistry/apbs/files/apbs-1.2.1b-shared.patch
new file mode 100644
index 000000000000..8d8b05115af1
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.2.1b-shared.patch
@@ -0,0 +1,90 @@
+Added shared libraries and create .pc file
+
+--- configure.ac
++++ configure.ac
+@@ -72,7 +72,10 @@
+ AC_CONFIG_AUX_DIR(config)
+ AC_PREFIX_DEFAULT(${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)
+ dnl ##########################################################################
+@@ -1031,7 +1031,7 @@
+ 	blas_lib=${contrib_path}/blas/.libs/libapbsblas.a
+ fi
+ AC_SUBST(apbs_do_blas)
+-
++AC_SUBST(blas_lib)
+ dnl # -----------------------
+ dnl # If using Portland compilers, do not compile
+ dnl # tools/mesh/uhbd_asc2bin.f
+@@ -1258,6 +1258,17 @@
+ fi
+ AC_SUBST(apbs_build_libraries)
+ 
++# Additional arguments (and substitutions)
++# Allow the pkg-config directory to be set
++AC_ARG_WITH(pkgconfigdir,
++        AC_HELP_STRING([--with-pkgconfigdir],
++        [Use the specified pkgconfig dir (default is libdir/pkgconfig)]),
++        [pkgconfigdir=${withval}],
++        [pkgconfigdir='${libdir}/pkgconfig'])
++
++AC_SUBST([pkgconfigdir])
++AC_MSG_NOTICE([pkgconfig directory is ${pkgconfigdir}])
++
+ dnl ##########################################################################
+ dnl 11. generate the makefiles
+ dnl ##########################################################################
+@@ -1305,6 +1316,8 @@
+     
+     bin/Makefile
+ 
++    apbs.pc:apbs.pc.in
++
+ ])
+ AC_OUTPUT
+ 
+--- src/aaa_lib/Makefile.am
++++ src/aaa_lib/Makefile.am
+@@ -22,7 +22,8 @@
+ 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@
+ 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@
+--- apbs.pc.in
++++ 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}
+--- Makefile.am
++++ Makefile.am
+@@ -16,6 +16,9 @@
+ 
+ SUBDIRS = contrib src bin @apbs_do_tools@ 
+ 
++pkgconfigdir = @pkgconfigdir@
++pkgconfig_DATA = apbs.pc
++
+ distclean-local: clean-local
+ 
+ clean-local: clean-ac
diff --git a/sci-chemistry/apbs/metadata.xml b/sci-chemistry/apbs/metadata.xml
index b360b031c2e8..54d335b9d919 100644
--- a/sci-chemistry/apbs/metadata.xml
+++ b/sci-chemistry/apbs/metadata.xml
@@ -13,6 +13,7 @@
 	<herd>sci-chemistry</herd>
 	<use>
 		<flag name='arpack'>Include support for arpack libs</flag>
+        <flag name='tinker'>Provide support for sci-chemistry/tinker</flag>
 		<flag name='tools'>Install optional tools</flag>
 	</use>
 </pkgmetadata>