diff options
author | Justin Lecher <jlec@gentoo.org> | 2010-07-09 16:03:33 +0000 |
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committer | Justin Lecher <jlec@gentoo.org> | 2010-07-09 16:03:33 +0000 |
commit | 03f3265b496a1fd171ccec24000fc1b1cd1aa014 (patch) | |
tree | aa58e86302e3c762fca6e0213ba2d39b2ca1ae5c /sci-chemistry/apbs | |
parent | stable amd64, bug 327525 (diff) | |
download | gentoo-2-03f3265b496a1fd171ccec24000fc1b1cd1aa014.tar.gz gentoo-2-03f3265b496a1fd171ccec24000fc1b1cd1aa014.tar.bz2 gentoo-2-03f3265b496a1fd171ccec24000fc1b1cd1aa014.zip |
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/ChangeLog | 8 | ||||
-rw-r--r-- | sci-chemistry/apbs/apbs-1.0.0-r1.ebuild | 72 | ||||
-rw-r--r-- | sci-chemistry/apbs/apbs-1.2.1b-r3.ebuild | 134 | ||||
-rw-r--r-- | sci-chemistry/apbs/files/apbs-1.0.0-LDFLAGS.patch | 21 | ||||
-rw-r--r-- | sci-chemistry/apbs/files/apbs-1.0.0-install-fix.patch | 27 | ||||
-rw-r--r-- | sci-chemistry/apbs/files/apbs-1.0.0-libmaloc-noinstall.patch | 38 | ||||
-rw-r--r-- | sci-chemistry/apbs/files/apbs-1.0.0-openmpi.patch | 49 |
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) |