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-rw-r--r--sci-chemistry/apbs/ChangeLog11
-rw-r--r--sci-chemistry/apbs/apbs-1.0.0.ebuild76
-rw-r--r--sci-chemistry/apbs/files/apbs-1.0.0-install-fix.patch18
-rw-r--r--sci-chemistry/apbs/files/apbs-1.0.0-libmaloc-noinstall.patch38
-rw-r--r--sci-chemistry/apbs/files/apbs-1.0.0-openmpi.patch49
5 files changed, 191 insertions, 1 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/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)