Version bump (fixes bug #219599). Changed license to BSD since it most closely matches the apbs license.

Package-Manager: portage-2.1.5_rc6

6 files changed, 197 insertions, 2 deletions

diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
index dabe9c5f4a6f..71d140fdbafe 100644
--- a/sci-chemistry/apbs/ChangeLog
+++ b/sci-chemistry/apbs/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-chemistry/apbs
 # Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.17 2008/03/23 11:39:18 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.18 2008/04/29 22:21:19 markusle Exp $
+
+*apbs-1.0.0 (29 Apr 2008)
+
+  29 Apr 2008; Markus Dittrich <markusle@gentoo.org>
+  +files/apbs-1.0.0-install-fix.patch,
+  +files/apbs-1.0.0-libmaloc-noinstall.patch,
+  +files/apbs-1.0.0-openmpi.patch, +apbs-1.0.0.ebuild:
+  Version bump (fixes bug #219599). Changed license to BSD since
+  it most closely matches the apbs license.
 
   23 Mar 2008; Markus Dittrich <markusle@gentoo.org> apbs-0.5.1.ebuild:
   Changed to unversioned install location in /usr/share (see bug #213616).
diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
index 7ef1a4121036..6dfe6635583d 100644
--- a/sci-chemistry/apbs/Manifest
+++ b/sci-chemistry/apbs/Manifest
@@ -1,8 +1,13 @@
+AUX apbs-1.0.0-install-fix.patch 742 RMD160 a062de26fd9441b7f25402abec87b1efbbf78f9b SHA1 6491839f6ac825dd2e18c3847dc70073e5a4a89a SHA256 9e1517407b28c314b319431644347b8ee01bec15e0c5136a5b2e66af8c3300f5
+AUX apbs-1.0.0-libmaloc-noinstall.patch 2230 RMD160 983d431fbe8af9aab163f3160521339fa0fc68d9 SHA1 9d5f2685d78c73f404899eca24cee4d1e5cb140d SHA256 729b836d5539a3c6328905c5e69403fd9386eb85199eb5702c90b5ec88bc5ef0
+AUX apbs-1.0.0-openmpi.patch 1458 RMD160 27e786dcb212348e14400442d11543038a1015b4 SHA1 40e45496d78c72a8b9169af623924ee74c5ff2a5 SHA256 ab2e1303c3bdcfc78c11b13ea2f99c4a8e81cb6d6f89c008815ecc20150863bf
 AUX apbs-examples-gentoo.patch 1446 RMD160 f0468219d3295cbaf90de7c0e3489d443f1ea144 SHA1 906197ecc9ee745cb0573ed2798a671cccd7b5a4 SHA256 1b12fdf855c4e80bb6e88d6b9c433a4c18eb406a5a6d1671146be897452863d4
 AUX apbs-gcc4-gentoo.patch 1080 RMD160 88138dc27c2fa17e558dc3a5c8c41e52bd2f0309 SHA1 c102e23f81627891552194896f2769f2cb7f0d6e SHA256 9077f4ffc41a2af28eed4193a2e56d20b668e2bc280ca2740d3a8803e28c48d6
 DIST apbs-0.5.0-source-2.tar.gz 10171621 RMD160 31a00f89052cc32d0fdf3272c214f2145ac62067 SHA1 4d3376a62169e3965a2d3b49a2b4b1014bf7721e SHA256 5f99cc6141d34800cf9e93e0e23215b3f740f6e208318698e7011602e1630a08
 DIST apbs-0.5.1-source.tgz 10952600 RMD160 d738f88252193dff64ca692d895d1359445d5eda SHA1 50d88392f4cf2cadf1627828aeffeb165ef49f0e SHA256 28828a56d474d644f1e0940b9f232c92ccf2bc123ae402bd70976cf018564903
+DIST apbs-1.0.0-source.tar.gz 11541303 RMD160 1eeb79f93a591835281bf8395308cddc065dac93 SHA1 fbcfe664defb09165e0eae3ff913a9d5a17cb27e SHA256 bd3803183ffb2bede9fca242d5432acb60b3cb8668eeccdbbced69aaf7a57604
 EBUILD apbs-0.5.0.ebuild 1761 RMD160 d680a39910bbacb86dfd1829f244da763539f5b0 SHA1 d2622fafd3ae540f3bc3a8350e7e20dbbecf165b SHA256 2820f64797fb4955b632be053bda14aa78d837cc94dc9f239d8be0d4dd780e16
 EBUILD apbs-0.5.1.ebuild 1904 RMD160 52436392ef003b55abd8f1f29d763c87588f219b SHA1 57f0bd16b7f06f37bc52fd4b82a5412b80b30a1b SHA256 ebe9e800f22ab4ec0e81e481aa2d8753f2fbdfe9e05f2fa759c6c9925b90a864
-MISC ChangeLog 2397 RMD160 b90920146db1cb410414b1c3b8a2848e4cbd6599 SHA1 41e0dbd2309d571321fdadfcd7f8884a8e7c21f2 SHA256 d7e5eaab188a8c2b0b7537f5877bcc30aacc1e0d080d728bddb8df8a98a4eb36
+EBUILD apbs-1.0.0.ebuild 1934 RMD160 fa2cae1b54bf10fb8ed78f8d5833605439b439f0 SHA1 1c322768613ea82579c963a551fddbc458a43ef8 SHA256 dc60699fb9e6159cc72e82a84c6f9d33c3ddfc22fdcca5057f9c078971fbff88
+MISC ChangeLog 2727 RMD160 8ccf4bdb4502a763280a85d3848eacb1a323a95c SHA1 aeab4abcd9afea8ca457c63bb9aab057d003eb12 SHA256 fe4dad9858776ec4898dbba0d7778d875b7df125971b2555a6a813d5b206e7a4
 MISC metadata.xml 282 RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 SHA1 7f42dcea44641b8a77ab9644791344ec6ed6c327 SHA256 3c1785eb4ab63774ed3a6b1bddd602ef24cd6795f690bb3289d5a980bca06349
diff --git a/sci-chemistry/apbs/apbs-1.0.0.ebuild b/sci-chemistry/apbs/apbs-1.0.0.ebuild
new file mode 100644
index 000000000000..db8d5545bd09
--- /dev/null
+++ b/sci-chemistry/apbs/apbs-1.0.0.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.0.0.ebuild,v 1.1 2008/04/29 22:21:19 markusle Exp $
+
+inherit eutils fortran autotools
+
+MY_P="${P}-source"
+S="${WORKDIR}"/"${MY_P}"
+
+DESCRIPTION=" Software for evaluating the electrostatic properties of nanoscale biomolecular systems"
+LICENSE="BSD"
+HOMEPAGE="http://agave.wustl.edu/apbs/"
+SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
+
+SLOT="0"
+IUSE="blas mpi python doc"
+KEYWORDS="~ppc ~x86 ~amd64"
+
+DEPEND="blas? ( virtual/blas )
+		python? ( dev-lang/python )
+		sys-libs/readline
+		mpi? ( virtual/mpi )"
+
+FORTRAN="g77 gfortran"
+
+pkg_setup() {
+	# It is important that you use the same compiler to compile
+	# APBS that you used when compiling MPI.
+	fortran_pkg_setup
+}
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${P}-openmpi.patch
+	epatch "${FILESDIR}"/${P}-install-fix.patch
+	epatch "${FILESDIR}"/${P}-libmaloc-noinstall.patch
+
+	sed -e "s:GENTOO_PKG_NAME:${PN}:" -i Makefile.am \
+		|| die "Failed to fix Makefile.am"
+
+	eautoreconf
+}
+
+src_compile() {
+	local myconf
+	use blas && myconf="${myconf} --with-blas=-lblas"
+
+	# check which mpi version is installed and tell configure
+	if use mpi; then
+		if has_version sys-cluster/mpich; then
+	 		myconf="${myconf} --with-mpich=/usr"
+		elif has_version sys-cluster/mpich2; then
+			myconf="${myconf} --with-mpich2=/usr"
+		elif has_version sys-cluster/lam-mpi; then
+			myconf="${myconf} --with-lam=/usr"
+		elif has_version sys-cluster/openmpi; then
+			myconf="${myconf} --with-openmpi=/usr"
+		fi
+	fi || die "Failed to select proper mpi implementation"
+
+	econf $(use_enable python) \
+		${myconf} || die "configure failed"
+
+	emake -j1 || die "make failed"
+}
+
+src_test() {
+	cd examples && make test \
+		|| die "Tests failed"
+}
+
+
+src_install() {
+	make DESTDIR="${D}" install || die "make install failed"
+}
diff --git a/sci-chemistry/apbs/files/apbs-1.0.0-install-fix.patch b/sci-chemistry/apbs/files/apbs-1.0.0-install-fix.patch
new file mode 100644
index 000000000000..d9c5a808f0fe
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.0.0-install-fix.patch
@@ -0,0 +1,18 @@
+diff -Naur apbs-1.0.0-source/Makefile.am apbs-1.0.0-source.new/Makefile.am
+--- apbs-1.0.0-source/Makefile.am	2008-04-17 16:44:51.000000000 -0400
++++ apbs-1.0.0-source.new/Makefile.am	2008-04-28 18:51:14.000000000 -0400
+@@ -28,7 +28,10 @@
+ 	-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
++	mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/examples 
++	mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools
++	-rm -f doc/LICENSE.txt
++	-rm -f tools/manip/*.pyc
++	-cp -rf doc $(DESTDIR)${prefix}/share
++	-cp -rf examples $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
++	-cp -rf tools $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
diff --git a/sci-chemistry/apbs/files/apbs-1.0.0-libmaloc-noinstall.patch b/sci-chemistry/apbs/files/apbs-1.0.0-libmaloc-noinstall.patch
new file mode 100644
index 000000000000..f15bab64872d
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.0.0-libmaloc-noinstall.patch
@@ -0,0 +1,38 @@
+diff -Naur apbs-1.0.0-source/contrib/maloc/src/aaa_inc/maloc/Makefile.in apbs-1.0.0-source.new/contrib/maloc/src/aaa_inc/maloc/Makefile.in
+--- apbs-1.0.0-source/contrib/maloc/src/aaa_inc/maloc/Makefile.in	2008-04-17 16:40:56.000000000 -0400
++++ apbs-1.0.0-source.new/contrib/maloc/src/aaa_inc/maloc/Makefile.in	2008-04-29 13:32:58.000000000 -0400
+@@ -265,12 +265,12 @@
+ uninstall-info-am:
+ install-includeHEADERS: $(include_HEADERS)
+ 	@$(NORMAL_INSTALL)
+-	test -z "$(includedir)" || $(mkdir_p) "$(DESTDIR)$(includedir)"
++	test -z "$(includedir)" || $(mkdir_p) "$(includedir)"
+ 	@list='$(include_HEADERS)'; for p in $$list; do \
+ 	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+ 	  f="`echo $$p | sed -e 's|^.*/||'`"; \
+-	  echo " $(includeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(includedir)/$$f'"; \
+-	  $(includeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(includedir)/$$f"; \
++	  echo " $(includeHEADERS_INSTALL) '$$d$$p' '$(includedir)/$$f'"; \
++	  $(includeHEADERS_INSTALL) "$$d$$p" "$(includedir)/$$f"; \
+ 	done
+ 
+ uninstall-includeHEADERS:
+diff -Naur apbs-1.0.0-source/contrib/maloc/src/aaa_lib/Makefile.in apbs-1.0.0-source.new/contrib/maloc/src/aaa_lib/Makefile.in
+--- apbs-1.0.0-source/contrib/maloc/src/aaa_lib/Makefile.in	2008-04-17 16:40:54.000000000 -0400
++++ apbs-1.0.0-source.new/contrib/maloc/src/aaa_lib/Makefile.in	2008-04-29 09:13:08.000000000 -0400
+@@ -283,12 +283,12 @@
+ 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+ install-libLTLIBRARIES: $(lib_LTLIBRARIES)
+ 	@$(NORMAL_INSTALL)
+-	test -z "$(libdir)" || $(mkdir_p) "$(DESTDIR)$(libdir)"
++	test -z "$(libdir)" || $(mkdir_p) "$(libdir)"
+ 	@list='$(lib_LTLIBRARIES)'; for p in $$list; do \
+ 	  if test -f $$p; then \
+ 	    f="`echo $$p | sed -e 's|^.*/||'`"; \
+-	    echo " $(LIBTOOL) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) '$$p' '$(DESTDIR)$(libdir)/$$f'"; \
+-	    $(LIBTOOL) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) "$$p" "$(DESTDIR)$(libdir)/$$f"; \
++	    echo " $(LIBTOOL) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) '$$p' '$(libdir)/$$f'"; \
++	    $(LIBTOOL) --mode=install $(libLTLIBRARIES_INSTALL) $(INSTALL_STRIP_FLAG) "$$p" "$(libdir)/$$f"; \
+ 	  else :; fi; \
+ 	done
+ 
diff --git a/sci-chemistry/apbs/files/apbs-1.0.0-openmpi.patch b/sci-chemistry/apbs/files/apbs-1.0.0-openmpi.patch
new file mode 100644
index 000000000000..8c9e95a1d173
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.0.0-openmpi.patch
@@ -0,0 +1,49 @@
+diff -Naur apbs-1.0.0-source/configure.ac apbs-1.0.0-source.new/configure.ac
+--- apbs-1.0.0-source/configure.ac	2008-04-17 16:44:51.000000000 -0400
++++ apbs-1.0.0-source.new/configure.ac	2008-04-28 17:51:47.000000000 -0400
+@@ -521,28 +521,27 @@
+ 		fi
+ 	fi
+ 	
+-#	if test -n "${USE_OPMI}"; then
+-#		AC_CHECK_FILE(${mpi_path}/lib/libmpi.a, [HAS_MPI_LIB="yes"], [])
+-#		AC_CHECK_FILE(${mpi_path}/lib/libmpi.so, [HAS_MPI_LIB="yes"], [])
+-#		AC_CHECK_FILE(${mpi_path}/lib/liblam.dylib, [HAS_MPI_LIB="yes"], [])
+-#		if test -n "${HAS_MPI_LIB}"; then
+-#			mpi_lib="-L${mpi_path}/lib -lmpi"
+-#		else
+-#			AC_MSG_ERROR([Error...Could not find LAM-MPI libraries in ${mpi_path}/lib], 0)
+-#		fi
+-#	fi
++	if test -n "${USE_OPMI}"; then
++		AC_CHECK_FILE(${mpi_path}/lib/libmpi.a, [HAS_MPI_LIB="yes"], [])
++		AC_CHECK_FILE(${mpi_path}/lib/libmpi.so, [HAS_MPI_LIB="yes"], [])
++		if test -n "${HAS_MPI_LIB}"; then
++			mpi_lib="-L${mpi_path}/lib -lmpi"
++		else
++			AC_MSG_ERROR([Error...Could not find OPEN-MPI libraries in ${mpi_path}/lib], 0)
++		fi
++	fi
+ 
+ 	USE_MPI="yes"
+ fi
+ 
+-if test -n "${USE_OPMI}"; then
+-  	HAS_MPI_LIB="yes"
+-	HAS_MPI_INC="yes"
+-	mpi_inc=""
+-	mpi_lib=""
+-	AC_DEFINE([HAVE_MPI_H], [], [have the MPI library])
+-	USE_MPI="yes"
+-fi	
++#if test -n "${USE_OPMI}"; then
++#  	HAS_MPI_LIB="yes"
++#	HAS_MPI_INC="yes"
++#	mpi_inc=""
++#	mpi_lib=""
++#	AC_DEFINE([HAVE_MPI_H], [], [have the MPI library])
++#	USE_MPI="yes"
++#fi	
+ 
+ AC_SUBST(mpi_lib)
+ AC_SUBST(mpi_inc)