# 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:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
-AUX apbs-1.0.0-LDFLAGS.patch 1423 RMD160 d802bbcfda969f86a799847ec323f786b25e9d75 SHA1 c4d4ce34fe72e9b54f553abf0fdec2ed979cdf8f SHA256 2dae2123d325b0bee45544fe681afb0b82616983d82fa1e9a16b4f9fbb4f2e33
-AUX apbs-1.0.0-install-fix.patch 890 RMD160 64e4d2247e23fd4d67b43ae91e1470d4cd2b8b02 SHA1 a5d618d37601bdafce0f7c3a58c399454955fdb0 SHA256 e30f2396261d7320aa0bbcc873689cc3368fe3bcc670806c6f2e399e66439b14
-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-1.2.0-contrib.patch 382 RMD160 4c0c75e57fb6a0c298606d87785a5b9daa8db457 SHA1 653295c9ff7ac075613dd82ce332b41b0e2ea37e SHA256 0b2a1c518c66de6010954f101c1622cfd570bbfcc4774d98607174e57e67f1b3
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-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 1915 RMD160 342778cd4ab7f862da9688c941f5183b0dcda1a6 SHA1 13f1b57cc5f0ee564546050ff6f5280a9ded188a SHA256 ad9eebe4ec97ce5796e2800436b48df314f1de73e143b35cd9af8abea29b63cc
-EBUILD apbs-1.2.1b-r3.ebuild 3380 RMD160 fa5078bd74b143c62a92369d0e0b7aca3505f184 SHA1 36f082abbe94e6edeabfc9a2a3833775b3eaa3f9 SHA256 94de1c8c2ef9403f2b492867d6eee19d4ee8b6b149d3c90839ffbad51b587df3
EBUILD apbs-1.2.1b-r4.ebuild 3771 RMD160 b61cbde00fbbe895143bf7e8b0fdf7c8be939f58 SHA1 c0324578dace543dc40af6176787d1593d963d40 SHA256 4b2c56077d308ba2643c536bf2a0c12b0448f2795d0787292e3dffee8149fd06
-MISC ChangeLog 6494 RMD160 eff2614cc1612e051eadbaffa2fccfa6f0ed285f SHA1 e78e73eb66173cfd746dcd7a4be509510704dadb SHA256 3c1f4520b7eb648a37600a06c8826d9de7e9b1439e129bf589208cffb0aa584c
+MISC ChangeLog 6775 RMD160 4795d2fb9c465242c39fec6ba100c88f242e7c8f SHA1 b78fbd2575aa971591abee1d55c1e28ce714d55e SHA256 38ce0a7702498c74732659d20e67a74d1846b5efac8007806903c2d63f3e2421
MISC metadata.xml 623 RMD160 2b62b6245e7ba05198d3f73d1548bddaf43f2221 SHA1 43d5621c91d4d8ff14e4faff680d8998f4917885 SHA256 26fc548a18df9cca13bc53c103333a49c1042f112356a5f7d6b557e3a0d67cbf
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+++ /dev/null
-# 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"
-}
+++ /dev/null
-# 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}
-}
+++ /dev/null
-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
+++ /dev/null
-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
+++ /dev/null
-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
-
+++ /dev/null
-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)
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