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authorJustin Lecher <jlec@gentoo.org>2010-07-09 16:03:33 +0000
committerJustin Lecher <jlec@gentoo.org>2010-07-09 16:03:33 +0000
commit03f3265b496a1fd171ccec24000fc1b1cd1aa014 (patch)
treeaa58e86302e3c762fca6e0213ba2d39b2ca1ae5c /sci-chemistry/apbs
parentstable amd64, bug 327525 (diff)
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Cleaned old after stabilization
(Portage version: 2.2_rc67/cvs/Linux x86_64)
Diffstat (limited to 'sci-chemistry/apbs')
-rw-r--r--sci-chemistry/apbs/ChangeLog8
-rw-r--r--sci-chemistry/apbs/apbs-1.0.0-r1.ebuild72
-rw-r--r--sci-chemistry/apbs/apbs-1.2.1b-r3.ebuild134
-rw-r--r--sci-chemistry/apbs/files/apbs-1.0.0-LDFLAGS.patch21
-rw-r--r--sci-chemistry/apbs/files/apbs-1.0.0-install-fix.patch27
-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
7 files changed, 7 insertions, 342 deletions
diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
index 2b295857a1af..9c6029b1cc7a 100644
--- a/sci-chemistry/apbs/ChangeLog
+++ b/sci-chemistry/apbs/ChangeLog
@@ -1,6 +1,12 @@
# 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 1.38 2010/07/09 13:36:47 fauli Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.39 2010/07/09 16:03:33 jlec Exp $
+
+ 09 Jul 2010; Justin Lecher <jlec@gentoo.org> -apbs-1.0.0-r1.ebuild,
+ -files/apbs-1.0.0-LDFLAGS.patch, -files/apbs-1.0.0-install-fix.patch,
+ -files/apbs-1.0.0-libmaloc-noinstall.patch,
+ -files/apbs-1.0.0-openmpi.patch, -apbs-1.2.1b-r3.ebuild:
+ Cleaned old after stabilization
09 Jul 2010; Christian Faulhammer <fauli@gentoo.org>
apbs-1.2.1b-r4.ebuild:
diff --git a/sci-chemistry/apbs/apbs-1.0.0-r1.ebuild b/sci-chemistry/apbs/apbs-1.0.0-r1.ebuild
deleted file mode 100644
index c3c0b64565d6..000000000000
--- a/sci-chemistry/apbs/apbs-1.0.0-r1.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# 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-1.0.0-r1.ebuild,v 1.4 2010/06/17 01:48:33 jsbronder Exp $
-
-inherit eutils fortran autotools
-
-MY_P="${P}-source"
-S="${WORKDIR}"/"${MY_P}"
-
-DESCRIPTION=" Software for evaluating the electrostatic properties of nanoscale biomolecular systems"
-LICENSE="BSD"
-HOMEPAGE="http://apbs.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-IUSE="blas mpi python doc"
-KEYWORDS="amd64 ~ppc x86"
-
-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
- epatch "${FILESDIR}"/${P}-LDFLAGS.patch
- eautoreconf
-}
-
-src_compile() {
- local myconf="--docdir=/usr/share/doc/${PF}"
- use blas && myconf="${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/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"
- dodoc AUTHORS INSTALL README NEWS ChangeLog \
- || die "Failed to install docs"
-}
diff --git a/sci-chemistry/apbs/apbs-1.2.1b-r3.ebuild b/sci-chemistry/apbs/apbs-1.2.1b-r3.ebuild
deleted file mode 100644
index 3156a5a51131..000000000000
--- a/sci-chemistry/apbs/apbs-1.2.1b-r3.ebuild
+++ /dev/null
@@ -1,134 +0,0 @@
-# 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-r3.ebuild,v 1.5 2010/06/22 19:25:14 mr_bones_ 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}/${P}-source.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-IUSE="arpack blas doc mpi openmp python tools"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-
-DEPEND="
- dev-libs/maloc[mpi=]
- blas? ( virtual/blas )
- sys-libs/readline
- arpack? ( sci-libs/arpack )
- mpi? ( virtual/mpi )"
-RDEPEND="${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
- epatch "${FILESDIR}"/${P}-install-fix.patch
- epatch "${FILESDIR}"/${PN}-1.2.0-contrib.patch
- epatch "${FILESDIR}"/${PN}-1.2.0-link.patch
- epatch "${FILESDIR}"/${P}-autoconf-2.64.patch
- sed "s:GENTOO_PKG_NAME:${PN}:g" \
- -i Makefile.am || die "Cannot correct package name"
- # this test is broken
- sed '/ion-pmf/d' -i examples/Makefile.am || die
- eautoreconf
- find . -name "._*" -exec rm -f '{}' \;
-}
-
-src_configure() {
- local myconf="--docdir=${EPREFIX}/usr/share/doc/${PF}"
- use blas && myconf="${myconf} --with-blas=-lblas"
- 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=${EPREFIX}/usr"
- elif has_version sys-cluster/openmpi; then
- myconf="${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 \
- $(use_enable openmp) \
- $(use_enable python) \
- $(use_enable tools) \
- ${myconf}
-}
-
-src_test() {
- cd examples && make test \
- || die "Tests failed"
-}
-
-src_install() {
- emake -j1 DESTDIR="${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-1.0.0-LDFLAGS.patch b/sci-chemistry/apbs/files/apbs-1.0.0-LDFLAGS.patch
deleted file mode 100644
index 4fde1c4883b0..000000000000
--- a/sci-chemistry/apbs/files/apbs-1.0.0-LDFLAGS.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff -Naur apbs-1.0.0-source/tools/python/Makefile.am apbs-1.0.0-source.new/tools/python/Makefile.am
---- apbs-1.0.0-source/tools/python/Makefile.am 2008-04-17 16:41:08.000000000 -0400
-+++ apbs-1.0.0-source.new/tools/python/Makefile.am 2008-10-11 11:54:17.000000000 -0400
-@@ -15,5 +15,5 @@
-
- noinst_PROGRAMS = _apbslib.so
- _apbslib_so_SOURCES = apbslib.c
--_apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
-+_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 ${top_builddir}/contrib/lib/libmaloc.a $(PY_LDFLAGS)
-diff -Naur apbs-1.0.0-source/tools/python/vgrid/Makefile.am apbs-1.0.0-source.new/tools/python/vgrid/Makefile.am
---- apbs-1.0.0-source/tools/python/vgrid/Makefile.am 2008-04-17 16:41:08.000000000 -0400
-+++ apbs-1.0.0-source.new/tools/python/vgrid/Makefile.am 2008-10-11 12:02:02.000000000 -0400
-@@ -15,6 +15,6 @@
- if PY_PRESENT
- noinst_PROGRAMS = _vgrid.so
- _vgrid_so_SOURCES = vgridlib.c
-- _vgrid_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
-+ _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 $(PY_LDFLAGS) ${top_builddir}/contrib/lib/libmaloc.a @lib_list@
- endif
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
deleted file mode 100644
index 6efd4e16a1f5..000000000000
--- a/sci-chemistry/apbs/files/apbs-1.0.0-install-fix.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-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 2008-10-11 13:02:42.000000000 -0400
-@@ -16,6 +16,8 @@
-
- SUBDIRS = contrib src bin @apbs_do_tools@
-
-+example_dir = $(datarootdir)/@PACKAGE@
-+
- distclean-local: clean-local
-
- clean-local: clean-ac
-@@ -28,7 +30,10 @@
- -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
-+ $(mkinstalldirs) $(DESTDIR)$(docdir)
-+ $(mkinstalldirs) $(DESTDIR)$(example_dir)/examples
-+ $(mkinstalldirs) $(DESTDIR)$(example_dir)/tools
-+ rm -f doc/LICENSE.txt doc/README
-+ -cp -rf doc $(DESTDIR)$(docdir)/html
-+ -cp -rf examples/* $(DESTDIR)$(example_dir)/examples
-+ -cp -rf tools/* $(DESTDIR)$(example_dir)/tools
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
deleted file mode 100644
index f15bab64872d..000000000000
--- a/sci-chemistry/apbs/files/apbs-1.0.0-libmaloc-noinstall.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-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
deleted file mode 100644
index 8c9e95a1d173..000000000000
--- a/sci-chemistry/apbs/files/apbs-1.0.0-openmpi.patch
+++ /dev/null
@@ -1,49 +0,0 @@
-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)