diff options
| author |   Justin Lecher <jlec@gentoo.org> | 2015-07-28 07:59:11 +0000 |
|---|---|---|
| committer | Justin Lecher <jlec@gentoo.org> | 2015-07-28 07:59:11 +0000 |
| commit | eca6abf3eb57390dc84216e7165e10c7d29819fc (patch) | |
| tree | 30e63040db273822124d9e762c96d2d85bcebd66 /sci-chemistry | |
| parent | Drop old (diff) | |
| download | gentoo-2-eca6abf3eb57390dc84216e7165e10c7d29819fc.tar.gz gentoo-2-eca6abf3eb57390dc84216e7165e10c7d29819fc.tar.bz2 gentoo-2-eca6abf3eb57390dc84216e7165e10c7d29819fc.zip | |
Drop old
(Portage version: 2.2.20/cvs/Linux x86_64, signed Manifest commit with key E9402A79B03529A2!)
Diffstat (limited to 'sci-chemistry')
34 files changed, 28 insertions, 1621 deletions
diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog index 15035c3e6039..79b9e428f498 100644 --- a/sci-chemistry/apbs/ChangeLog +++ b/sci-chemistry/apbs/ChangeLog @@ -1,6 +1,33 @@ # ChangeLog for sci-chemistry/apbs # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.78 2015/07/04 19:37:27 zlogene Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.79 2015/07/28 07:59:11 jlec Exp $ + + 28 Jul 2015; Justin Lecher <jlec@gentoo.org> -apbs-1.2.1b-r4.ebuild, + -files/apbs-1.2.0-contrib.patch, -files/apbs-1.2.0-link.patch, + -files/apbs-1.2.1b-autoconf-2.64.patch, -files/apbs-1.2.1b-install-fix.patch, + -files/apbs-1.2.1b-multilib.patch, -files/apbs-1.2.1b-openmp.patch, + -files/apbs-1.2.1b-parallelbuild.patch, -files/apbs-1.2.1b-shared.patch, + -files/apbs-1.3-blas.patch, -files/apbs-1.3-contrib.patch, + -files/apbs-1.3-link.patch, -files/apbs-1.3-mainroutines.patch, + -files/apbs-1.3-openmp.patch, -files/apbs-1.3-python.patch, + -files/apbs-1.3-shared.patch, -files/apbs-1.3-zlib.patch, + -files/apbs-1.3/0001-autoconf-2.68.patch, + -files/apbs-1.3/0002-python-linking.patch, + -files/apbs-1.3/0003-apbs-1.3-pkg-config-file.patch, + -files/apbs-1.3/0004-apbs-1.3-system-zlib.patch, + -files/apbs-1.3/0005-apbs-1.3-linking.patch, + -files/apbs-1.3/0006-apbs-1.3-clean-targets.patch, + -files/apbs-1.3/0007-apbs-1.3-configure.patch, + -files/apbs-1.3/0008-apbs-1.3-broken-test.patch, + -files/apbs-1.3/0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch, + -files/apbs-1.3/0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch, + -files/apbs-1.3/0011-apbs-1.3-shared-linking.patch, + -files/apbs-1.3/0012-apbs-1.3-python-linking-correction.patch, + -files/apbs-1.3/0013-apbs-1.3-tools-installation.patch, + -files/apbs-1.3/0014-apbs-1.3-pythonlib-fix.patch, + -files/apbs-1.3/0015-apbs-1.3-pythonlib-fix.patch, + -files/apbs-1.3/0016-apbs-1.3-apbs.pc-in-AC_CONFIG_FILES.patch: + Drop old 04 Jul 2015; Mikle Kolyada <zlogene@gentoo.org> apbs-1.4.1-r2.ebuild: amd64 stable wrt bug #534692 diff --git a/sci-chemistry/apbs/apbs-1.2.1b-r4.ebuild b/sci-chemistry/apbs/apbs-1.2.1b-r4.ebuild deleted file mode 100644 index d083881ab707..000000000000 --- a/sci-chemistry/apbs/apbs-1.2.1b-r4.ebuild +++ /dev/null @@ -1,142 +0,0 @@ -# Copyright 1999-2013 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-r4.ebuild,v 1.17 2013/04/23 14:01:32 jlec Exp $ - -EAPI="3" - -PYTHON_DEPEND="python? 2" - -inherit autotools eutils flag-o-matic fortran-2 python toolchain-funcs versionator - -MY_PV=$(get_version_component_range 1-3) -MY_P="${PN}-${MY_PV}" - -DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems" -HOMEPAGE="http://www.poissonboltzmann.org/apbs/" -SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz" - -SLOT="0" -LICENSE="BSD" -IUSE="arpack doc mpi openmp python tools" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" - -RDEPEND=" - dev-libs/maloc[mpi=] - virtual/blas - sys-libs/readline - arpack? ( sci-libs/arpack ) - tools? ( !sci-libs/gts ) - mpi? ( virtual/mpi )" -DEPEND="${DEPEND} - virtual/pkgconfig" - -S="${WORKDIR}"/"${MY_P}-source" - -pkg_setup() { - fortran-2_pkg_setup - use python && python_set_active_version 2 -} - -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-openmp.patch \ - "${FILESDIR}"/${P}-install-fix.patch \ - "${FILESDIR}"/${PN}-1.2.0-contrib.patch \ - "${FILESDIR}"/${PN}-1.2.0-link.patch \ - "${FILESDIR}"/${P}-autoconf-2.64.patch \ - "${FILESDIR}"/${P}-shared.patch \ - "${FILESDIR}"/${P}-multilib.patch \ - "${FILESDIR}"/${P}-parallelbuild.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/${PF}" - use arpack && myconf="${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="${myconf} --enable-tools" - fi - - econf \ - --disable-maloc-rebuild \ - --enable-shared \ - --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \ - $(use_enable openmp) \ - $(use_enable python) \ - $(use_enable tools) \ - ${myconf} -} - -src_test() { - export LC_NUMERIC=C - cd examples && make test \ - || die "Tests failed" - grep -q 'FAILED' "${S}"/examples/TESTRESULTS.log && 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-1.2.0-contrib.patch b/sci-chemistry/apbs/files/apbs-1.2.0-contrib.patch deleted file mode 100644 index 6bfc9ffaa790..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.2.0-contrib.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- contrib/Makefile.am 2009-03-05 21:30:09.000000000 +0100 -+++ contrib/Makefile.am.new 2009-04-24 19:08:39.000000000 +0200 -@@ -9,6 +9,6 @@ - AUTOMAKE_OPTIONS = no-dependencies - SUFFIXES = .H .h .C .c .f .o - --always_built_SUBDIRS = @apbs_do_blas@ @apbs_do_maloc@ pmgZ aqua opal -+always_built_SUBDIRS = @apbs_do_blas@ @apbs_do_maloc@ pmgZ aqua - - SUBDIRS = $(always_built_SUBDIRS) . diff --git a/sci-chemistry/apbs/files/apbs-1.2.0-link.patch b/sci-chemistry/apbs/files/apbs-1.2.0-link.patch deleted file mode 100644 index ae64793423b7..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.2.0-link.patch +++ /dev/null @@ -1,23 +0,0 @@ -diff -Naur apbs-1.2-source/tools/python/Makefile.am apbs-1.2-source.new/tools/python/Makefile.am ---- apbs-1.2-source/tools/python/Makefile.am 2009-10-14 13:20:57.000000000 -0400 -+++ apbs-1.2-source.new/tools/python/Makefile.am 2009-10-29 16:08:18.000000000 -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_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS) -+_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 $(PY_LDFLAGS) -diff -Naur apbs-1.2-source/tools/python/vgrid/Makefile.am apbs-1.2-source.new/tools/python/vgrid/Makefile.am ---- apbs-1.2-source/tools/python/vgrid/Makefile.am 2009-10-14 13:20:57.000000000 -0400 -+++ apbs-1.2-source.new/tools/python/vgrid/Makefile.am 2009-10-29 16:08:29.000000000 -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_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@ -+ _vgrid_so_LINK = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED) -+ _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a @lib_list@ - endif diff --git a/sci-chemistry/apbs/files/apbs-1.2.1b-autoconf-2.64.patch b/sci-chemistry/apbs/files/apbs-1.2.1b-autoconf-2.64.patch deleted file mode 100644 index ab7015126f9b..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.2.1b-autoconf-2.64.patch +++ /dev/null @@ -1,23 +0,0 @@ -diff -Naur apbs-1.2.1-source/acinclude.m4 apbs-1.2.1-source.new/acinclude.m4 ---- apbs-1.2.1-source/acinclude.m4 2009-12-01 09:20:23.000000000 -0500 -+++ apbs-1.2.1-source.new/acinclude.m4 2009-12-03 22:56:47.000000000 -0500 -@@ -54,14 +54,11 @@ - AC_LANG_C - ac_save_LIBS="$LIBS" - LIBS="mangle-func.o $LIBS" --AC_TRY_LINK(,foobar();, -- ac_f77_mangle_type=lowercase, -- AC_TRY_LINK(,foobar_();, -- ac_f77_mangle_type=lowercase-underscore, -- AC_TRY_LINK(,FOOBAR();, -- ac_f77_mangle_type=uppercase, -- AC_TRY_LINK(,FOOBAR_();, -- ac_f77_mangle_type=uppercase-underscore)))) -+AC_TRY_LINK(,foobar();,ac_f77_mangle_type=lowercase) -+AC_TRY_LINK(,foobar_();,ac_f77_mangle_type=lowercase-underscore) -+AC_TRY_LINK(,FOOBAR();,ac_f77_mangle_type=uppercase) -+AC_TRY_LINK(,FOOBAR_();,ac_f77_mangle_type=uppercase-underscore) -+ - LIBS="$ac_save_LIBS" - AC_LANG_RESTORE - AC_MSG_RESULT($ac_f77_mangle_type) diff --git a/sci-chemistry/apbs/files/apbs-1.2.1b-install-fix.patch b/sci-chemistry/apbs/files/apbs-1.2.1b-install-fix.patch deleted file mode 100644 index 636c685f1b9a..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.2.1b-install-fix.patch +++ /dev/null @@ -1,53 +0,0 @@ -diff --git a/Makefile.am b/Makefile.am -index 437402d..b400095 100644 ---- a/Makefile.am -+++ b/Makefile.am -@@ -27,11 +27,30 @@ clean-ac: - install-exec-local: - -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 -+install-data-local: install-cleanup -+ -rm -f doc/LICENSE.txt -+ -+install-cleanup: -+ -rm -f tools/manip/*.pyc -+ -rm -f tools/**/*.o -+ -rm -f tools/**/*.c -+ -rm -f tools/**/*.f -+ -rm -f tools/**/*Makefile* -+ -rm -f tools/**/**/*.o -+ -rm -f tools/**/**/*.c -+ -rm -f tools/**/**/*.f -+ -rm -f tools/**/**/*Makefile* -+ -rm -f tools/*Makefile* -+ -rm -f examples/*Makefile* -+ -rm -f examples/**/*Makefile* -+ -+install-tools: -+ mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools -+ -cp -rf tools $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/ -+ -+install-examples: -+ mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/examples -+ -cp -rf examples $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/ - - test: - cd examples; make test -diff --git a/bin/Makefile.am b/bin/Makefile.am -index 7b2f3ee..0470525 100644 ---- a/bin/Makefile.am -+++ b/bin/Makefile.am -@@ -40,6 +40,4 @@ includedir = ${prefix}/include/apbs - include_HEADERS = routines.h - - install-data-local: -- -cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin -- -chmod 755 ${prefix}/bin/ApbsClient.py -- -rm -f ${prefix}/bin/wsdl2py -\ No newline at end of file -+ -rm -f $(DESTDIR)${prefix}/bin/wsdl2py diff --git a/sci-chemistry/apbs/files/apbs-1.2.1b-multilib.patch b/sci-chemistry/apbs/files/apbs-1.2.1b-multilib.patch deleted file mode 100644 index b52a629056a1..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.2.1b-multilib.patch +++ /dev/null @@ -1,22 +0,0 @@ -Respect multilib directories - ---- src/aaa_lib/Makefile.am -+++ src/aaa_lib/Makefile.am -@@ -18,7 +18,6 @@ - AQUA_LIBS = ${top_builddir}/contrib/aqua/libapbsaqua.la - BLAS_LIBS = @blas_lib@ - --libdir = ${prefix}/lib - lib_LTLIBRARIES = libapbs.la - - libapbs_la_SOURCES = apbs_link.c ---- bin/Makefile.am -+++ bin/Makefile.am -@@ -27,7 +27,6 @@ - rm.apbs: Makefile - -rm -f apbs - --libdir = ${prefix}/lib - lib_LTLIBRARIES = libapbsmainroutines.la - libapbsmainroutines_la_SOURCES = routines.c - libapbsmainroutines_la_LDFLAGS = -version-info ${APBS_VERSION} diff --git a/sci-chemistry/apbs/files/apbs-1.2.1b-openmp.patch b/sci-chemistry/apbs/files/apbs-1.2.1b-openmp.patch deleted file mode 100644 index b3e521bf9d3d..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.2.1b-openmp.patch +++ /dev/null @@ -1,51 +0,0 @@ ---- configure.ac -+++ configure.ac -@@ -976,7 +976,6 @@ - AC_ARG_ENABLE( - [tools], - AS_HELP_STRING([--disable-tools],[disable tool compilation]),, -- [enable_tools=yes] - ) - apbs_do_tools="" - if test x"$enable_tools" != "xno"; then -@@ -1134,32 +1133,32 @@ - AC_ARG_ENABLE( - [openmp], - AS_HELP_STRING([--disable-openmp],[disables OpenMP compiler support]),, -- [disable_openmp=yes] - ) --if test x"$disable_openmp" != "xyes"; then -- AC_MSG_RESULT([yes]) --else -+if test x"$enable_openmp" != "xno"; then - AC_MSG_RESULT([no]) - if [[ "${CC}" = "icc" ] && [ "${F77}" = "ifort" ]]; then - CFLAGS="${CFLAGS} -openmp" - FFLAGS="${FFLAGS} -openmp -assume cc_omp" - LDFLAGS="${LDFLAGS} -static-intel" - fi -- -- if [[ "${CC}" = "gcc" ] && [ "${F77}" = "gfortran" ]]; then -- gcc_version=`gcc --version` -+ if [[[ "${CC}" = *gcc* ]]] && [[[ "${F77}" = *gfortran* ]]]; then -+ gcc_version=`${CC} --version` - gcc_complete_version=`echo ${gcc_version} | awk '{printf("%s",$3)}' | awk -F'.' '{print $1$2}'` -- - if test ["${gcc_complete_version}" -ge 42]; then - CFLAGS="${CFLAGS} -fopenmp" - FFLAGS="${FFLAGS} -fopenmp" -+ OPENMP_LIBS="-lgomp" - else - AC_MSG_RESULT([WARNING]) - AC_MSG_RESULT([WARNING Version of gcc/gfortran does not support OpenMP. Disabling.]) - AC_MSG_RESULT([WARNING]) - fi - fi -+else -+ AC_MSG_RESULT([yes]) -+ disable_openmp=yes - fi -+AC_SUBST(OPENMP_LIBS) - - dnl # ----------------------- - dnl # CHECK FOR WINDOWS SPECIFIC LIBRARIES diff --git a/sci-chemistry/apbs/files/apbs-1.2.1b-parallelbuild.patch b/sci-chemistry/apbs/files/apbs-1.2.1b-parallelbuild.patch deleted file mode 100644 index f19ad6498a65..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.2.1b-parallelbuild.patch +++ /dev/null @@ -1,13 +0,0 @@ -Fix parallel build issues - ---- bin/Makefile.am -+++ bin/Makefile.am -@@ -15,7 +15,7 @@ - bindir = ${prefix}/bin - bin_PROGRAMS = apbs - apbs_SOURCES = main.c --apbs_LDADD = ${build_libraries} -+apbs_LDADD = ${build_libraries} libapbsmainroutines.la - - # This is a hack I suspect, but needed to force apbs to be - # rebuilt anytime the make command is issued diff --git a/sci-chemistry/apbs/files/apbs-1.2.1b-shared.patch b/sci-chemistry/apbs/files/apbs-1.2.1b-shared.patch deleted file mode 100644 index 8d8b05115af1..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.2.1b-shared.patch +++ /dev/null @@ -1,90 +0,0 @@ -Added shared libraries and create .pc file - ---- configure.ac -+++ configure.ac -@@ -72,7 +72,10 @@ - AC_CONFIG_AUX_DIR(config) - AC_PREFIX_DEFAULT(${HOME}) - AC_CANONICAL_SYSTEM -- -+LT_INIT -+LT_LANG([Fortran 77]) -+AC_F77_DUMMY_MAIN -+AC_F77_LIBRARY_LDFLAGS - dnl ########################################################################## - dnl 1. automake initialization (uncomment only if rebuilding Makefile.in's) - dnl ########################################################################## -@@ -1031,7 +1031,7 @@ - blas_lib=${contrib_path}/blas/.libs/libapbsblas.a - fi - AC_SUBST(apbs_do_blas) -- -+AC_SUBST(blas_lib) - dnl # ----------------------- - dnl # If using Portland compilers, do not compile - dnl # tools/mesh/uhbd_asc2bin.f -@@ -1258,6 +1258,17 @@ - fi - AC_SUBST(apbs_build_libraries) - -+# Additional arguments (and substitutions) -+# Allow the pkg-config directory to be set -+AC_ARG_WITH(pkgconfigdir, -+ AC_HELP_STRING([--with-pkgconfigdir], -+ [Use the specified pkgconfig dir (default is libdir/pkgconfig)]), -+ [pkgconfigdir=${withval}], -+ [pkgconfigdir='${libdir}/pkgconfig']) -+ -+AC_SUBST([pkgconfigdir]) -+AC_MSG_NOTICE([pkgconfig directory is ${pkgconfigdir}]) -+ - dnl ########################################################################## - dnl 11. generate the makefiles - dnl ########################################################################## -@@ -1305,6 +1316,8 @@ - - bin/Makefile - -+ apbs.pc:apbs.pc.in -+ - ]) - AC_OUTPUT - ---- src/aaa_lib/Makefile.am -+++ src/aaa_lib/Makefile.am -@@ -22,7 +22,8 @@ - lib_LTLIBRARIES = libapbs.la - - libapbs_la_SOURCES = apbs_link.c --libapbs_la_LIBADD = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS} -+libapbs_la_LIBADD = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS} \ -+ @OPENMP_LIBS@ @maloc_lib@ - libapbs_la_LDFLAGS = -version-info ${APBS_VERSION} - - INCLUDES = -I${top_srcdir}/src/generic -I${top_srcdir}/src/mg -I${top_srcdir}/src/fem @inc_list@ ---- apbs.pc.in -+++ apbs.pc.in -@@ -0,0 +1,11 @@ -+prefix=@prefix@ -+exec_prefix=@exec_prefix@ -+libdir=@libdir@ -+includedir=@includedir@/apbs -+ -+Name: apbs -+Description: apbs -+Version: @PACKAGE_VERSION@ -+Libs: -L${libdir} -lapbsmainroutines -lapbs -+Libs.private: @LIBS@ -+Cflags: -I${includedir} ---- Makefile.am -+++ Makefile.am -@@ -16,6 +16,9 @@ - - SUBDIRS = contrib src bin @apbs_do_tools@ - -+pkgconfigdir = @pkgconfigdir@ -+pkgconfig_DATA = apbs.pc -+ - distclean-local: clean-local - - clean-local: clean-ac diff --git a/sci-chemistry/apbs/files/apbs-1.3-blas.patch b/sci-chemistry/apbs/files/apbs-1.3-blas.patch deleted file mode 100644 index 08d99ce6a277..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3-blas.patch +++ /dev/null @@ -1,16 +0,0 @@ - configure.ac | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 6020fbf..65dd770 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -1021,7 +1021,7 @@ if test x"$with_blas" != "xno" -a -n "$with_blas"; then - LDFLAGS_SAVE=${LDFLAGS}; - CPPFLAGS_SAVE=${CPPFLAGS}; - LDFLAGS="-L${maloc_lib_path} ${blas_lib}"; -- AC_CHECK_LIB(${blas_name},dscal, -+ AC_CHECK_LIB(m,dscal, - [blas_found="yes"], - [blas_found=""], - [${blas_lib} ${socket_lib} ${nsl_lib} ${math_lib}]) diff --git a/sci-chemistry/apbs/files/apbs-1.3-contrib.patch b/sci-chemistry/apbs/files/apbs-1.3-contrib.patch deleted file mode 100644 index 9971f032dcbc..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3-contrib.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/contrib/Makefile.am b/contrib/Makefile.am -index bddb563..6a882ca 100644 ---- a/contrib/Makefile.am -+++ b/contrib/Makefile.am -@@ -9,6 +9,6 @@ - AUTOMAKE_OPTIONS = no-dependencies - SUFFIXES = .H .h .C .c .f .o - --always_built_SUBDIRS = @apbs_do_blas@ @apbs_do_maloc@ pmgZ aqua opal @zlib@ -+always_built_SUBDIRS = @apbs_do_blas@ @apbs_do_maloc@ pmgZ aqua - - SUBDIRS = $(always_built_SUBDIRS) . diff --git a/sci-chemistry/apbs/files/apbs-1.3-link.patch b/sci-chemistry/apbs/files/apbs-1.3-link.patch deleted file mode 100644 index 54b66235a2d0..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3-link.patch +++ /dev/null @@ -1,25 +0,0 @@ -diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am -index 73d25f7..431640c 100644 ---- a/tools/python/Makefile.am -+++ b/tools/python/Makefile.am -@@ -15,5 +15,5 @@ SUBDIRS = vgrid - - noinst_PROGRAMS = _apbslib.so - _apbslib_so_SOURCES = apbslib.c --_apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -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 ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS) ${z_lib} -+_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 $(PY_LDFLAGS) ${z_lib} -diff --git a/tools/python/vgrid/Makefile.am b/tools/python/vgrid/Makefile.am -index b573268..b31c9b6 100644 ---- a/tools/python/vgrid/Makefile.am -+++ b/tools/python/vgrid/Makefile.am -@@ -15,6 +15,6 @@ CLEANFILES = _vgrid.so - if PY_PRESENT - noinst_PROGRAMS = _vgrid.so - _vgrid_so_SOURCES = vgridlib.c -- _vgrid_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -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@ -+ _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 @lib_list@ - endif diff --git a/sci-chemistry/apbs/files/apbs-1.3-mainroutines.patch b/sci-chemistry/apbs/files/apbs-1.3-mainroutines.patch deleted file mode 100644 index fa8678a971fd..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3-mainroutines.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/bin/Makefile.am b/bin/Makefile.am -index 15158ca..f73d276 100644 ---- a/bin/Makefile.am -+++ b/bin/Makefile.am -@@ -29,6 +29,7 @@ rm.apbs: Makefile - - lib_LTLIBRARIES = libapbsmainroutines.la - libapbsmainroutines_la_SOURCES = routines.c -+libapbsmainroutines_la_LIBADD = -L../src/aaa_lib/.libs/ -lapbs @mc_lib@ - libapbsmainroutines_la_LDFLAGS = -version-info ${APBS_VERSION} - - INCLUDES = @inc_list@ diff --git a/sci-chemistry/apbs/files/apbs-1.3-openmp.patch b/sci-chemistry/apbs/files/apbs-1.3-openmp.patch deleted file mode 100644 index d5aefd893325..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3-openmp.patch +++ /dev/null @@ -1,61 +0,0 @@ -diff --git a/configure.ac b/configure.ac -index 6020fbf..73fbe21 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -982,7 +982,6 @@ AC_MSG_CHECKING([for --disable-tools]) - AC_ARG_ENABLE( - [tools], - AS_HELP_STRING([--disable-tools],[disable tool compilation]),, -- [enable_tools=yes] - ) - apbs_do_tools="" - if test x"$enable_tools" != "xno"; then -@@ -1048,7 +1047,6 @@ AC_MSG_CHECKING([--disable-zlib]) - AC_ARG_ENABLE( - [zlib], - AS_HELP_STRING([--disable-zlib], [disable zlib compilation]),, -- [disable_zlib=no] - ) - if test x"$disable_zlib" == "xno"; then - AC_MSG_RESULT([yes]) -@@ -1160,11 +1158,8 @@ AC_MSG_CHECKING([for --disable-openmp]) - AC_ARG_ENABLE( - [openmp], - AS_HELP_STRING([--disable-openmp],[disables OpenMP compiler support]),, -- [disable_openmp=yes] - ) --if test x"$disable_openmp" != "xyes"; then -- AC_MSG_RESULT([yes]) --else -+if test x"$disable_openmp" != "xno"; then - AC_MSG_RESULT([no]) - if [[ "${CC}" = "icc" ] && [ "${F77}" = "ifort" ]]; then - CFLAGS="${CFLAGS} -openmp" -@@ -1172,20 +1167,25 @@ else - LDFLAGS="${LDFLAGS} -static-intel" - fi - -- if [[ "${CC}" = "gcc" ] && [ "${F77}" = "gfortran" ]]; then -- gcc_version=`gcc --version` -+ if [[[ "${CC}" = *gcc* ]]] && [[[ "${F77}" = *gfortran* ]]]; then -+ gcc_version=`${CC} --version` - gcc_complete_version=`echo ${gcc_version} | awk '{printf("%s",$3)}' | awk -F'.' '{print $1$2}'` - - if test ["${gcc_complete_version}" -ge 42]; then - CFLAGS="${CFLAGS} -fopenmp" - FFLAGS="${FFLAGS} -fopenmp" -+ OPENMP_LIBS="-lgomp" - else - AC_MSG_RESULT([WARNING]) - AC_MSG_RESULT([WARNING Version of gcc/gfortran does not support OpenMP. Disabling.]) - AC_MSG_RESULT([WARNING]) - fi - fi -+else -+ AC_MSG_RESULT([yes]) -+ disable_openmp=yes - fi -+AC_SUBST(OPENMP_LIBS) - - dnl # ----------------------- - dnl # CHECK FOR WINDOWS SPECIFIC LIBRARIES diff --git a/sci-chemistry/apbs/files/apbs-1.3-python.patch b/sci-chemistry/apbs/files/apbs-1.3-python.patch deleted file mode 100644 index 66dec34d32a9..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3-python.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff --git a/configure.ac b/configure.ac -index 31a0053..7301f0f 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -585,6 +585,7 @@ if test x"$enable_python" != "xno"; then - PY_SHARED="-shared" - CC="${CC} -fPIC" - F77="${F77} -fPIC" -+ PY_LDFLAGS="-lpython$PY_VERSION" - ;; - irix*) - PY_SHARED="-shared" -diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am -index 431640c..2c1fbea 100644 ---- a/tools/python/Makefile.am -+++ b/tools/python/Makefile.am -@@ -16,4 +16,4 @@ SUBDIRS = vgrid - noinst_PROGRAMS = _apbslib.so - _apbslib_so_SOURCES = apbslib.c - _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 $(PY_LDFLAGS) ${z_lib} -+_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${z_lib} @OPENMP_LIBS@ @maloc_lib@ @mc_lib@ diff --git a/sci-chemistry/apbs/files/apbs-1.3-shared.patch b/sci-chemistry/apbs/files/apbs-1.3-shared.patch deleted file mode 100644 index 2b6688697f5e..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3-shared.patch +++ /dev/null @@ -1,96 +0,0 @@ -diff --git a/Makefile.am b/Makefile.am -index b400095..af3a3a3 100644 ---- a/Makefile.am -+++ b/Makefile.am -@@ -16,6 +16,9 @@ SUFFIXES = .H .h .C .cc .c .f .o - - SUBDIRS = contrib src bin @apbs_do_tools@ - -+pkgconfigdir = @pkgconfigdir@ -+pkgconfig_DATA = apbs.pc -+ - distclean-local: clean-local - - clean-local: clean-ac -diff --git a/apbs.pc.in b/apbs.pc.in -new file mode 100644 -index 0000000..c177512 ---- /dev/null -+++ b/apbs.pc.in -@@ -0,0 +1,11 @@ -+prefix=@prefix@ -+exec_prefix=@exec_prefix@ -+libdir=@libdir@ -+includedir=@includedir@/apbs -+ -+Name: apbs -+Description: apbs -+Version: @PACKAGE_VERSION@ -+Libs: -L${libdir} -lapbsmainroutines -lapbs -+Libs.private: @LIBS@ -+Cflags: -I${includedir} -diff --git a/configure.ac b/configure.ac -index 73fbe21..31a0053 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -71,7 +71,10 @@ AM_CONFIG_HEADER(src/aaa_inc/apbscfg.h) - AC_CONFIG_AUX_DIR(config) - AC_PREFIX_DEFAULT(${HOME}) - AC_CANONICAL_SYSTEM -- -+LT_INIT -+LT_LANG([Fortran 77]) -+AC_F77_DUMMY_MAIN -+AC_F77_LIBRARY_LDFLAGS - dnl ########################################################################## - dnl 1. automake initialization (uncomment only if rebuilding Makefile.in's) - dnl ########################################################################## -@@ -1037,6 +1040,7 @@ else - blas_lib=${contrib_path}/blas/.libs/libapbsblas.a - fi - AC_SUBST(apbs_do_blas) -+AC_SUBST(blas_lib) - - dnl # -------------------------------- - dnl # HANDLE ZLIB COMPILATION -@@ -1284,6 +1288,17 @@ else - fi - AC_SUBST(apbs_build_libraries) - -+# Additional arguments (and substitutions) -+# Allow the pkg-config directory to be set -+AC_ARG_WITH(pkgconfigdir, -+ AC_HELP_STRING([--with-pkgconfigdir], -+ [Use the specified pkgconfig dir (default is libdir/pkgconfig)]), -+ [pkgconfigdir=${withval}], -+ [pkgconfigdir='${libdir}/pkgconfig']) -+ -+AC_SUBST([pkgconfigdir]) -+AC_MSG_NOTICE([pkgconfig directory is ${pkgconfigdir}]) -+ - dnl ########################################################################## - dnl 11. generate the makefiles - dnl ########################################################################## -@@ -1332,6 +1347,8 @@ AC_CONFIG_FILES([ - - bin/Makefile - -+ apbs.pc:apbs.pc.in -+ - ]) - AC_OUTPUT - -diff --git a/src/aaa_lib/Makefile.am b/src/aaa_lib/Makefile.am -index 0064aaa..8b33f70 100644 ---- a/src/aaa_lib/Makefile.am -+++ b/src/aaa_lib/Makefile.am -@@ -21,7 +21,8 @@ BLAS_LIBS = @blas_lib@ - lib_LTLIBRARIES = libapbs.la - - libapbs_la_SOURCES = apbs_link.c --libapbs_la_LIBADD = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS} -+libapbs_la_LIBADD = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS} \ -+ @OPENMP_LIBS@ @maloc_lib@ @mc_lib@ @z_lib@ - libapbs_la_LDFLAGS = -version-info ${APBS_VERSION} - - INCLUDES = -I${top_srcdir}/src/generic -I${top_srcdir}/src/mg -I${top_srcdir}/src/fem @inc_list@ diff --git a/sci-chemistry/apbs/files/apbs-1.3-zlib.patch b/sci-chemistry/apbs/files/apbs-1.3-zlib.patch deleted file mode 100644 index c7ce0bcc589e..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3-zlib.patch +++ /dev/null @@ -1,43 +0,0 @@ -diff --git a/configure.ac b/configure.ac -index 31a0053..7301f0f 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -1052,10 +1053,10 @@ AC_ARG_ENABLE( - [zlib], - AS_HELP_STRING([--disable-zlib], [disable zlib compilation]),, - ) --if test x"$disable_zlib" == "xno"; then -+if test x"$disable_zlib" == "xyes"; then - AC_MSG_RESULT([yes]) - zlib="zlib" -- z_lib=${contrib_path}/zlib/.libs/libz.a -+ z_lib=-lz - AC_DEFINE([HAVE_ZLIB], [], [have zlib compression enabled]) - fi - AC_SUBST(zlib) -@@ -1307,12 +1308,8 @@ AC_CONFIG_FILES([ - Makefile - - contrib/Makefile -- contrib/blas/Makefile - contrib/pmgZ/Makefile - contrib/aqua/Makefile -- contrib/opal/Makefile -- contrib/opal/ZSI/Makefile -- contrib/zlib/Makefile - - tools/Makefile - tools/mesh/Makefile -diff --git a/src/mg/vgrid.c b/src/mg/vgrid.c -index d183bb2..e0669ab 100644 ---- a/src/mg/vgrid.c -+++ b/src/mg/vgrid.c -@@ -432,7 +432,7 @@ VPUBLIC int Vgrid_gradient(Vgrid *thee, double pt[3], double grad[3]) { - /////////////////////////////////////////////////////////////////////////// */ - #ifdef HAVE_ZLIB - #define off_t long --#include "../../contrib/zlib/zlib.h" -+#include <zlib.h> - #endif - VPUBLIC int Vgrid_readGZ(Vgrid *thee, const char *fname) { - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0001-autoconf-2.68.patch b/sci-chemistry/apbs/files/apbs-1.3/0001-autoconf-2.68.patch deleted file mode 100644 index ea6a27479c57..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0001-autoconf-2.68.patch +++ /dev/null @@ -1,37 +0,0 @@ -From 89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea Mon Sep 17 00:00:00 2001 -Message-Id: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Tue, 3 Jan 2012 20:25:55 +0100 -Subject: [PATCH 01/15] autoconf 2.68 - ---- - acinclude.m4 | 13 +++++-------- - 1 files changed, 5 insertions(+), 8 deletions(-) - -diff --git a/acinclude.m4 b/acinclude.m4 -index 3701ceb..34602e3 100644 ---- a/acinclude.m4 -+++ b/acinclude.m4 -@@ -54,14 +54,11 @@ AC_LANG_SAVE - AC_LANG_C - ac_save_LIBS="$LIBS" - LIBS="mangle-func.o $LIBS" --AC_TRY_LINK(,foobar();, -- ac_f77_mangle_type=lowercase, -- AC_TRY_LINK(,foobar_();, -- ac_f77_mangle_type=lowercase-underscore, -- AC_TRY_LINK(,FOOBAR();, -- ac_f77_mangle_type=uppercase, -- AC_TRY_LINK(,FOOBAR_();, -- ac_f77_mangle_type=uppercase-underscore)))) -+AC_TRY_LINK(,foobar();,ac_f77_mangle_type=lowercase) -+AC_TRY_LINK(,foobar_();,ac_f77_mangle_type=lowercase-underscore) -+AC_TRY_LINK(,FOOBAR();,ac_f77_mangle_type=uppercase) -+AC_TRY_LINK(,FOOBAR_();,ac_f77_mangle_type=uppercase-underscore) -+ - LIBS="$ac_save_LIBS" - AC_LANG_RESTORE - AC_MSG_RESULT($ac_f77_mangle_type) --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0002-python-linking.patch b/sci-chemistry/apbs/files/apbs-1.3/0002-python-linking.patch deleted file mode 100644 index 4c699ad19f07..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0002-python-linking.patch +++ /dev/null @@ -1,41 +0,0 @@ -From 5b208a6ef5fc706b699b3b33bd9248126c54a034 Mon Sep 17 00:00:00 2001 -Message-Id: <5b208a6ef5fc706b699b3b33bd9248126c54a034.1325691465.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Tue, 3 Jan 2012 20:45:58 +0100 -Subject: [PATCH 02/15] python linking - ---- - tools/python/Makefile.am | 4 ++-- - tools/python/vgrid/Makefile.am | 4 ++-- - 2 files changed, 4 insertions(+), 4 deletions(-) - -diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am -index 73d25f7..2c1fbea 100644 ---- a/tools/python/Makefile.am -+++ b/tools/python/Makefile.am -@@ -15,5 +15,5 @@ SUBDIRS = vgrid - - noinst_PROGRAMS = _apbslib.so - _apbslib_so_SOURCES = apbslib.c --_apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -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 ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS) ${z_lib} -+_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 $(PY_LDFLAGS) ${z_lib} @OPENMP_LIBS@ @maloc_lib@ @mc_lib@ -diff --git a/tools/python/vgrid/Makefile.am b/tools/python/vgrid/Makefile.am -index b573268..b31c9b6 100644 ---- a/tools/python/vgrid/Makefile.am -+++ b/tools/python/vgrid/Makefile.am -@@ -15,6 +15,6 @@ CLEANFILES = _vgrid.so - if PY_PRESENT - noinst_PROGRAMS = _vgrid.so - _vgrid_so_SOURCES = vgridlib.c -- _vgrid_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -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@ -+ _vgrid_so_LINK = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED) -+ _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a @lib_list@ - endif --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0003-apbs-1.3-pkg-config-file.patch b/sci-chemistry/apbs/files/apbs-1.3/0003-apbs-1.3-pkg-config-file.patch deleted file mode 100644 index 9ae90d2977cb..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0003-apbs-1.3-pkg-config-file.patch +++ /dev/null @@ -1,32 +0,0 @@ -From 9876050808e5d43c02d3c703e998a82f7502275d Mon Sep 17 00:00:00 2001 -Message-Id: <9876050808e5d43c02d3c703e998a82f7502275d.1325691465.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Tue, 3 Jan 2012 20:47:13 +0100 -Subject: [PATCH 03/15] apbs 1.3 pkg-config file - ---- - apbs.pc.in | 11 +++++++++++ - 1 files changed, 11 insertions(+), 0 deletions(-) - -diff --git a/apbs.pc.in b/apbs.pc.in -new file mode 100644 -index 0000000..c177512 ---- /dev/null -+++ b/apbs.pc.in -@@ -0,0 +1,11 @@ -+prefix=@prefix@ -+exec_prefix=@exec_prefix@ -+libdir=@libdir@ -+includedir=@includedir@/apbs -+ -+Name: apbs -+Description: apbs -+Version: @PACKAGE_VERSION@ -+Libs: -L${libdir} -lapbsmainroutines -lapbs -+Libs.private: @LIBS@ -+Cflags: -I${includedir} --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0004-apbs-1.3-system-zlib.patch b/sci-chemistry/apbs/files/apbs-1.3/0004-apbs-1.3-system-zlib.patch deleted file mode 100644 index 1a668132f350..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0004-apbs-1.3-system-zlib.patch +++ /dev/null @@ -1,28 +0,0 @@ -From 7abe31a7006c97e908ec717f5f85dddd4cd36110 Mon Sep 17 00:00:00 2001 -Message-Id: <7abe31a7006c97e908ec717f5f85dddd4cd36110.1325691465.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Tue, 3 Jan 2012 20:47:58 +0100 -Subject: [PATCH 04/15] apbs 1.3 system zlib - ---- - src/mg/vgrid.c | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) - -diff --git a/src/mg/vgrid.c b/src/mg/vgrid.c -index d183bb2..e0669ab 100644 ---- a/src/mg/vgrid.c -+++ b/src/mg/vgrid.c -@@ -432,7 +432,7 @@ VPUBLIC int Vgrid_gradient(Vgrid *thee, double pt[3], double grad[3]) { - /////////////////////////////////////////////////////////////////////////// */ - #ifdef HAVE_ZLIB - #define off_t long --#include "../../contrib/zlib/zlib.h" -+#include <zlib.h> - #endif - VPUBLIC int Vgrid_readGZ(Vgrid *thee, const char *fname) { - --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0005-apbs-1.3-linking.patch b/sci-chemistry/apbs/files/apbs-1.3/0005-apbs-1.3-linking.patch deleted file mode 100644 index dd3f286eff23..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0005-apbs-1.3-linking.patch +++ /dev/null @@ -1,70 +0,0 @@ -From 071473a3ead25df253236329511dcc4c63c3b53a Mon Sep 17 00:00:00 2001 -Message-Id: <071473a3ead25df253236329511dcc4c63c3b53a.1325691465.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Tue, 3 Jan 2012 20:48:36 +0100 -Subject: [PATCH 05/15] apbs 1.3 linking - ---- - bin/Makefile.am | 8 +++----- - src/aaa_lib/Makefile.am | 6 +++--- - 2 files changed, 6 insertions(+), 8 deletions(-) - -diff --git a/bin/Makefile.am b/bin/Makefile.am -index 7b2f3ee..9dae096 100644 ---- a/bin/Makefile.am -+++ b/bin/Makefile.am -@@ -15,7 +15,7 @@ build_libraries = @apbs_build_libraries@ - bindir = ${prefix}/bin - bin_PROGRAMS = apbs - apbs_SOURCES = main.c --apbs_LDADD = ${build_libraries} -+apbs_LDADD = ${build_libraries} -L../src/aaa_lib/.libs/ libapbsmainroutines.la - - # This is a hack I suspect, but needed to force apbs to be - # rebuilt anytime the make command is issued -@@ -27,9 +27,9 @@ BUILT_SOURCES = rm.apbs - rm.apbs: Makefile - -rm -f apbs - --libdir = ${prefix}/lib - lib_LTLIBRARIES = libapbsmainroutines.la - libapbsmainroutines_la_SOURCES = routines.c -+libapbsmainroutines_la_LIBADD = -L../src/aaa_lib/.libs/ -lapbs @mc_lib@ - libapbsmainroutines_la_LDFLAGS = -version-info ${APBS_VERSION} - - INCLUDES = @inc_list@ -@@ -40,6 +40,4 @@ includedir = ${prefix}/include/apbs - include_HEADERS = routines.h - - install-data-local: -- -cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin -- -chmod 755 ${prefix}/bin/ApbsClient.py -- -rm -f ${prefix}/bin/wsdl2py -\ No newline at end of file -+ -rm -f $(DESTDIR)${prefix}/bin/wsdl2py -diff --git a/src/aaa_lib/Makefile.am b/src/aaa_lib/Makefile.am -index 2c5026b..2495246 100644 ---- a/src/aaa_lib/Makefile.am -+++ b/src/aaa_lib/Makefile.am -@@ -16,13 +16,13 @@ FEM_LIBS = ${top_builddir}/src/fem/libapbsfem.la - MG_LIBS = ${top_builddir}/src/mg/libapbsmg.la - PMGZ_LIBS = ${top_builddir}/contrib/pmgZ/libapbspmgz.la - AQUA_LIBS = ${top_builddir}/contrib/aqua/libapbsaqua.la --BLAS_LIBS = @blas_lib@ -+BLAS_LIBS = @BLAS_LIBS@ - --libdir = ${prefix}/lib - lib_LTLIBRARIES = libapbs.la - - libapbs_la_SOURCES = apbs_link.c --libapbs_la_LIBADD = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS} -+libapbs_la_LIBADD = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS} \ -+ @OPENMP_LIBS@ @maloc_lib@ @mc_lib@ @z_lib@ - libapbs_la_LDFLAGS = -version-info ${APBS_VERSION} - - INCLUDES = -I${top_srcdir}/src/generic -I${top_srcdir}/src/mg -I${top_srcdir}/src/fem @inc_list@ --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0006-apbs-1.3-clean-targets.patch b/sci-chemistry/apbs/files/apbs-1.3/0006-apbs-1.3-clean-targets.patch deleted file mode 100644 index b157252647e8..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0006-apbs-1.3-clean-targets.patch +++ /dev/null @@ -1,65 +0,0 @@ -From e000438cebba988300c1210bc92a62635ba2ddf8 Mon Sep 17 00:00:00 2001 -Message-Id: <e000438cebba988300c1210bc92a62635ba2ddf8.1325691465.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Tue, 3 Jan 2012 20:49:24 +0100 -Subject: [PATCH 06/15] apbs 1.3 clean targets - ---- - Makefile.am | 32 +++++++++++++++++++++++++++----- - 1 files changed, 27 insertions(+), 5 deletions(-) - -diff --git a/Makefile.am b/Makefile.am -index 437402d..af3a3a3 100644 ---- a/Makefile.am -+++ b/Makefile.am -@@ -16,6 +16,9 @@ SUFFIXES = .H .h .C .cc .c .f .o - - SUBDIRS = contrib src bin @apbs_do_tools@ - -+pkgconfigdir = @pkgconfigdir@ -+pkgconfig_DATA = apbs.pc -+ - distclean-local: clean-local - - clean-local: clean-ac -@@ -27,11 +30,30 @@ clean-ac: - install-exec-local: - -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 -+install-data-local: install-cleanup -+ -rm -f doc/LICENSE.txt -+ -+install-cleanup: -+ -rm -f tools/manip/*.pyc -+ -rm -f tools/**/*.o -+ -rm -f tools/**/*.c -+ -rm -f tools/**/*.f -+ -rm -f tools/**/*Makefile* -+ -rm -f tools/**/**/*.o -+ -rm -f tools/**/**/*.c -+ -rm -f tools/**/**/*.f -+ -rm -f tools/**/**/*Makefile* -+ -rm -f tools/*Makefile* -+ -rm -f examples/*Makefile* -+ -rm -f examples/**/*Makefile* -+ -+install-tools: -+ mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools -+ -cp -rf tools $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/ -+ -+install-examples: -+ mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/examples -+ -cp -rf examples $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/ - - test: - cd examples; make test --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0007-apbs-1.3-configure.patch b/sci-chemistry/apbs/files/apbs-1.3/0007-apbs-1.3-configure.patch deleted file mode 100644 index 38c1cb8d7934..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0007-apbs-1.3-configure.patch +++ /dev/null @@ -1,237 +0,0 @@ -From b196b6b83a969e6c7ee60e3cdfe03b76eb87bd11 Mon Sep 17 00:00:00 2001 -Message-Id: <b196b6b83a969e6c7ee60e3cdfe03b76eb87bd11.1325691465.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Tue, 3 Jan 2012 20:50:19 +0100 -Subject: [PATCH 07/15] apbs 1.3 configure - ---- - configure.ac | 117 +++++++++++++++------------------------------------------ - 1 files changed, 31 insertions(+), 86 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 6020fbf..c91abb5 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -1,4 +1,4 @@ --1.3dnl ########################################################################## -+dnl ########################################################################## - dnl APBS -- Adaptive Poisson-Boltzmann Solver - dnl - dnl Nathan A. Baker (nathan.baker@pnl.gov) -@@ -71,6 +71,10 @@ AM_CONFIG_HEADER(src/aaa_inc/apbscfg.h) - AC_CONFIG_AUX_DIR(config) - AC_PREFIX_DEFAULT(${HOME}) - AC_CANONICAL_SYSTEM -+LT_INIT -+LT_LANG([Fortran 77]) -+AC_F77_DUMMY_MAIN -+AC_F77_LIBRARY_LDFLAGS - - dnl ########################################################################## - dnl 1. automake initialization (uncomment only if rebuilding Makefile.in's) -@@ -152,8 +156,7 @@ dnl ########################################################################## - AC_MSG_CHECKING([for --enable-python]) - AC_ARG_ENABLE( - [python], -- AS_HELP_STRING([--enable-python],[enables Python wrapper compilation]),, -- [enable_python=no] -+ AS_HELP_STRING([--enable-python],[enables Python wrapper compilation]) - ) - if test x"$enable_python" != "xno"; then - AC_MSG_RESULT([yes]) -@@ -582,6 +585,7 @@ if test x"$enable_python" != "xno"; then - PY_SHARED="-shared" - CC="${CC} -fPIC" - F77="${F77} -fPIC" -+ PY_LDFLAGS="-lpython$PY_VERSION" - ;; - irix*) - PY_SHARED="-shared" -@@ -717,8 +721,7 @@ if test -z "${USE_FETK}"; then - AC_MSG_CHECKING([for --disable-maloc-rebuild]) - AC_ARG_ENABLE( - [maloc-rebuild], -- AS_HELP_STRING([--disable-maloc-rebuild], [disable rebuilding maloc]),, -- [enable_maloc_rebuild=yes] -+ AS_HELP_STRING([--disable-maloc-rebuild], [disable rebuilding maloc]) - ) - - if test x"$enable_maloc_rebuild" = "xno"; then -@@ -981,8 +984,7 @@ dnl # ----------------------- - AC_MSG_CHECKING([for --disable-tools]) - AC_ARG_ENABLE( - [tools], -- AS_HELP_STRING([--disable-tools],[disable tool compilation]),, -- [enable_tools=yes] -+ AS_HELP_STRING([--disable-tools],[disable tool compilation]) - ) - apbs_do_tools="" - if test x"$enable_tools" != "xno"; then -@@ -999,45 +1001,10 @@ AC_SUBST(apbs_do_tools) - dnl # ----------------------- - dnl # HANDLE THE BLAS LIBRARIES - dnl # ----------------------- --blas_lib="" --AC_ARG_WITH( -- [blas], -- AS_HELP_STRING([--with-blas=LDFLAGS], [link to user-specified BLAS (specify flags to pass to ld)]) -- ) --AC_MSG_CHECKING([for --with-blas]) --if test x"$with_blas" != "xno" -a -n "$with_blas"; then -- blas_lib="${with_blas}" -- AC_MSG_RESULT([${blas_lib}]) -- AC_ARG_WITH( -- [blas_name], -- AS_HELP_STRING([--with-blas-name=NAME], [name of BLAS library, defaults to blas]),, -- [with_blas_name="blas"] -- ) -- if test x"$with_blas_name" != "xno" -a -n "$with_blas_name"; then -- blas_name="${with_blas_name}" -- fi -- AC_MSG_NOTICE([checking ${blas_name} using ${blas_lib}]) -- AC_LANG_FORTRAN77 -- LDFLAGS_SAVE=${LDFLAGS}; -- CPPFLAGS_SAVE=${CPPFLAGS}; -- LDFLAGS="-L${maloc_lib_path} ${blas_lib}"; -- AC_CHECK_LIB(${blas_name},dscal, -- [blas_found="yes"], -- [blas_found=""], -- [${blas_lib} ${socket_lib} ${nsl_lib} ${math_lib}]) -- LDFLAGS=${LDFLAGS_SAVE}; -- CPPFLAGS=${CPPFLAGS_SAVE}; -- if test -z "${blas_found}"; then -- AC_MSG_ERROR([BLAS libraries or headers missing: exiting on error!]) -- fi -- apbs_do_blas="" -- AC_LANG_C --else -- AC_MSG_RESULT([no]) -- apbs_do_blas="blas" -- blas_lib=${contrib_path}/blas/.libs/libapbsblas.a --fi -+apbs_do_blas="" -+PKG_CHECK_MODULES([BLAS],[blas]) - AC_SUBST(apbs_do_blas) -+AC_SUBST([BLAS_LIBS]) - - dnl # -------------------------------- - dnl # HANDLE ZLIB COMPILATION -@@ -1047,13 +1014,12 @@ z_lib= - AC_MSG_CHECKING([--disable-zlib]) - AC_ARG_ENABLE( - [zlib], -- AS_HELP_STRING([--disable-zlib], [disable zlib compilation]),, -- [disable_zlib=no] -+ AS_HELP_STRING([--disable-zlib], [disable zlib compilation]) - ) --if test x"$disable_zlib" == "xno"; then -+if test x"$disable_zlib" != "xno"; then - AC_MSG_RESULT([yes]) - zlib="zlib" -- z_lib=${contrib_path}/zlib/.libs/libz.a -+ z_lib=-lz - AC_DEFINE([HAVE_ZLIB], [], [have zlib compression enabled]) - fi - AC_SUBST(zlib) -@@ -1143,8 +1109,7 @@ dnl # ----------------------- - AC_MSG_CHECKING([for --enable-abps-quiet]) - AC_ARG_ENABLE( - [abps-quiet], -- AS_HELP_STRING([--enable-abps-quiet],[prevent APBS diagnostic messages from displaying to stdout]),, -- [enable_apbs_quiet=no] -+ AS_HELP_STRING([--enable-abps-quiet],[prevent APBS diagnostic messages from displaying to stdout]) - ) - if test x"$enable_apbs_quiet" != "xno"; then - AC_MSG_RESULT([yes]) -@@ -1156,36 +1121,7 @@ fi - dnl # ----------------------- - dnl # CHECK WHETHER YOU WANT TO DISABLE OPENMP SUPPORT - dnl # ----------------------- --AC_MSG_CHECKING([for --disable-openmp]) --AC_ARG_ENABLE( -- [openmp], -- AS_HELP_STRING([--disable-openmp],[disables OpenMP compiler support]),, -- [disable_openmp=yes] --) --if test x"$disable_openmp" != "xyes"; then -- AC_MSG_RESULT([yes]) --else -- AC_MSG_RESULT([no]) -- if [[ "${CC}" = "icc" ] && [ "${F77}" = "ifort" ]]; then -- CFLAGS="${CFLAGS} -openmp" -- FFLAGS="${FFLAGS} -openmp -assume cc_omp" -- LDFLAGS="${LDFLAGS} -static-intel" -- fi -- -- if [[ "${CC}" = "gcc" ] && [ "${F77}" = "gfortran" ]]; then -- gcc_version=`gcc --version` -- gcc_complete_version=`echo ${gcc_version} | awk '{printf("%s",$3)}' | awk -F'.' '{print $1$2}'` -- -- if test ["${gcc_complete_version}" -ge 42]; then -- CFLAGS="${CFLAGS} -fopenmp" -- FFLAGS="${FFLAGS} -fopenmp" -- else -- AC_MSG_RESULT([WARNING]) -- AC_MSG_RESULT([WARNING Version of gcc/gfortran does not support OpenMP. Disabling.]) -- AC_MSG_RESULT([WARNING]) -- fi -- fi --fi -+AC_OPENMP - - dnl # ----------------------- - dnl # CHECK FOR WINDOWS SPECIFIC LIBRARIES -@@ -1217,7 +1153,7 @@ dnl # COMPILATIONS - dnl # ----------------------- - top_srcdir="`pwd`" - base_list="${FLIBS} ${tree_lib} ${vmetis_lib} ${vor_lib} ${mcx_lib} ${mc_lib} \ -- ${thread_lib} ${mpi_lib} ${math_lib} ${rl_lib} ${socket_lib} ${nsl_lib} ${blas_lib} ${z_lib}" -+ ${thread_lib} ${mpi_lib} ${math_lib} ${rl_lib} ${socket_lib} ${nsl_lib} ${BLAS_LIBS} ${z_lib}" - - case $host_os in - -@@ -1284,6 +1220,17 @@ else - fi - AC_SUBST(apbs_build_libraries) - -+# Additional arguments (and substitutions) -+# Allow the pkg-config directory to be set -+AC_ARG_WITH(pkgconfigdir, -+ AC_HELP_STRING([--with-pkgconfigdir], -+ [Use the specified pkgconfig dir (default is libdir/pkgconfig)]), -+ [pkgconfigdir=${withval}], -+ [pkgconfigdir='${libdir}/pkgconfig']) -+ -+AC_SUBST([pkgconfigdir]) -+AC_MSG_NOTICE([pkgconfig directory is ${pkgconfigdir}]) -+ - dnl ########################################################################## - dnl 11. generate the makefiles - dnl ########################################################################## -@@ -1292,12 +1239,8 @@ AC_CONFIG_FILES([ - Makefile - - contrib/Makefile -- contrib/blas/Makefile - contrib/pmgZ/Makefile - contrib/aqua/Makefile -- contrib/opal/Makefile -- contrib/opal/ZSI/Makefile -- contrib/zlib/Makefile - - tools/Makefile - tools/mesh/Makefile -@@ -1332,6 +1275,8 @@ AC_CONFIG_FILES([ - - bin/Makefile - -+ apbs.pc:apbs.pc.in -+ - ]) - AC_OUTPUT - --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0008-apbs-1.3-broken-test.patch b/sci-chemistry/apbs/files/apbs-1.3/0008-apbs-1.3-broken-test.patch deleted file mode 100644 index 4c481a574195..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0008-apbs-1.3-broken-test.patch +++ /dev/null @@ -1,43 +0,0 @@ -From 6bcd14554262bf366aa371873c22cccb21b32850 Mon Sep 17 00:00:00 2001 -Message-Id: <6bcd14554262bf366aa371873c22cccb21b32850.1325691465.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Tue, 3 Jan 2012 20:59:43 +0100 -Subject: [PATCH 08/15] apbs 1.3 broken test - ---- - examples/Makefile.am | 3 --- - 1 files changed, 0 insertions(+), 3 deletions(-) - -diff --git a/examples/Makefile.am b/examples/Makefile.am -index 6cf5664..adf901f 100644 ---- a/examples/Makefile.am -+++ b/examples/Makefile.am -@@ -22,7 +22,6 @@ clean: - cd born; make clean - cd FKBP; make clean - cd hca-bind; make clean -- cd ion-pmf; make clean - cd ion-protein; make clean - cd ionize; make clean - cd pka-lig; make clean -@@ -39,7 +38,6 @@ test: - cd born; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log - cd FKBP; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log - cd hca-bind; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log -- cd ion-pmf; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log - cd ion-protein; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log - cd ionize; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log - cd pka-lig; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log -@@ -56,7 +54,6 @@ testocd: - cd born; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log - cd FKBP; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log - cd hca-bind; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log -- cd ion-pmf; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log - cd ion-protein; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log - cd ionize; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log - cd pka-lig; make testocd; cat TESTRESULTS.log >> ../TESTRESULTS.log --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch b/sci-chemistry/apbs/files/apbs-1.3/0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch deleted file mode 100644 index 136d86bc8a18..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch +++ /dev/null @@ -1,41 +0,0 @@ -From a7705f4957dca398031f1b6f3a74494004588c4d Mon Sep 17 00:00:00 2001 -Message-Id: <a7705f4957dca398031f1b6f3a74494004588c4d.1325691465.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Wed, 4 Jan 2012 10:52:29 +0100 -Subject: [PATCH 09/15] apbs 1.3 use pkg-config for zlib detection - ---- - configure.ac | 15 ++++----------- - 1 files changed, 4 insertions(+), 11 deletions(-) - -diff --git a/configure.ac b/configure.ac -index c91abb5..53deb06 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -1011,17 +1011,10 @@ dnl # HANDLE ZLIB COMPILATION - dnl # -------------------------------- - disable_zlib=yes - z_lib= --AC_MSG_CHECKING([--disable-zlib]) --AC_ARG_ENABLE( -- [zlib], -- AS_HELP_STRING([--disable-zlib], [disable zlib compilation]) --) --if test x"$disable_zlib" != "xno"; then -- AC_MSG_RESULT([yes]) -- zlib="zlib" -- z_lib=-lz -- AC_DEFINE([HAVE_ZLIB], [], [have zlib compression enabled]) --fi -+zlib= -+PKG_CHECK_MODULES([ZLIB],[zlib]) -+z_lib=$(ZLIB_LIBS) -+AC_DEFINE([HAVE_ZLIB], [], [have zlib compression enabled]) - AC_SUBST(zlib) - AC_SUBST(z_lib) - --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch b/sci-chemistry/apbs/files/apbs-1.3/0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch deleted file mode 100644 index b955e9237668..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch +++ /dev/null @@ -1,51 +0,0 @@ -From c09358a2aca006d93d8bc7525efe656f1b4f9c0a Mon Sep 17 00:00:00 2001 -Message-Id: <c09358a2aca006d93d8bc7525efe656f1b4f9c0a.1325691465.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Wed, 4 Jan 2012 11:05:04 +0100 -Subject: [PATCH 10/15] apbs 1.3 use OPENMP_CFLAGS instead of OPENMP_LIBS - ---- - configure.ac | 4 ++-- - src/aaa_lib/Makefile.am | 2 +- - 2 files changed, 3 insertions(+), 3 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 53deb06..9837a57 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -1013,7 +1013,7 @@ disable_zlib=yes - z_lib= - zlib= - PKG_CHECK_MODULES([ZLIB],[zlib]) --z_lib=$(ZLIB_LIBS) -+z_lib=${ZLIB_LIBS} - AC_DEFINE([HAVE_ZLIB], [], [have zlib compression enabled]) - AC_SUBST(zlib) - AC_SUBST(z_lib) -@@ -1115,7 +1115,7 @@ dnl # ----------------------- - dnl # CHECK WHETHER YOU WANT TO DISABLE OPENMP SUPPORT - dnl # ----------------------- - AC_OPENMP -- -+CFLAGS+=" ${OPENMP_CFLAGS}" - dnl # ----------------------- - dnl # CHECK FOR WINDOWS SPECIFIC LIBRARIES - dnl # ----------------------- -diff --git a/src/aaa_lib/Makefile.am b/src/aaa_lib/Makefile.am -index 2495246..9fcbcaa 100644 ---- a/src/aaa_lib/Makefile.am -+++ b/src/aaa_lib/Makefile.am -@@ -22,7 +22,7 @@ lib_LTLIBRARIES = libapbs.la - - libapbs_la_SOURCES = apbs_link.c - libapbs_la_LIBADD = ${GEN_LIBS} ${FEM_LIBS} ${MG_LIBS} ${PMGZ_LIBS} ${AQUA_LIBS} ${BLAS_LIBS} \ -- @OPENMP_LIBS@ @maloc_lib@ @mc_lib@ @z_lib@ -+ @maloc_lib@ @mc_lib@ @z_lib@ - libapbs_la_LDFLAGS = -version-info ${APBS_VERSION} - - INCLUDES = -I${top_srcdir}/src/generic -I${top_srcdir}/src/mg -I${top_srcdir}/src/fem @inc_list@ --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0011-apbs-1.3-shared-linking.patch b/sci-chemistry/apbs/files/apbs-1.3/0011-apbs-1.3-shared-linking.patch deleted file mode 100644 index f0c7259b0d2b..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0011-apbs-1.3-shared-linking.patch +++ /dev/null @@ -1,26 +0,0 @@ -From 0f26ce7c0c5013ba72c6bf5fcf04004240e79d26 Mon Sep 17 00:00:00 2001 -Message-Id: <0f26ce7c0c5013ba72c6bf5fcf04004240e79d26.1325691465.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Wed, 4 Jan 2012 11:36:56 +0100 -Subject: [PATCH 11/15] apbs 1.3 shared linking - ---- - tools/python/vgrid/Makefile.am | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) - -diff --git a/tools/python/vgrid/Makefile.am b/tools/python/vgrid/Makefile.am -index b31c9b6..50c09ac 100644 ---- a/tools/python/vgrid/Makefile.am -+++ b/tools/python/vgrid/Makefile.am -@@ -16,5 +16,5 @@ if PY_PRESENT - noinst_PROGRAMS = _vgrid.so - _vgrid_so_SOURCES = vgridlib.c - _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 @lib_list@ -+ _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.la ${top_builddir}/src/aaa_lib/.libs/libapbs.la @lib_list@ - endif --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0012-apbs-1.3-python-linking-correction.patch b/sci-chemistry/apbs/files/apbs-1.3/0012-apbs-1.3-python-linking-correction.patch deleted file mode 100644 index 56a86d21d184..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0012-apbs-1.3-python-linking-correction.patch +++ /dev/null @@ -1,60 +0,0 @@ -From 73a1f1d63d7617fea85c10990b1f35c9567a3573 Mon Sep 17 00:00:00 2001 -Message-Id: <73a1f1d63d7617fea85c10990b1f35c9567a3573.1325691465.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Wed, 4 Jan 2012 11:49:50 +0100 -Subject: [PATCH 12/15] apbs 1.3 python linking correction - ---- - bin/Makefile.am | 4 ++-- - tools/python/Makefile.am | 2 +- - tools/python/vgrid/Makefile.am | 2 +- - 3 files changed, 4 insertions(+), 4 deletions(-) - -diff --git a/bin/Makefile.am b/bin/Makefile.am -index 9dae096..574be3d 100644 ---- a/bin/Makefile.am -+++ b/bin/Makefile.am -@@ -15,7 +15,7 @@ build_libraries = @apbs_build_libraries@ - bindir = ${prefix}/bin - bin_PROGRAMS = apbs - apbs_SOURCES = main.c --apbs_LDADD = ${build_libraries} -L../src/aaa_lib/.libs/ libapbsmainroutines.la -+apbs_LDADD = ${build_libraries} .libs/libapbsmainroutines.la - - # This is a hack I suspect, but needed to force apbs to be - # rebuilt anytime the make command is issued -@@ -29,7 +29,7 @@ rm.apbs: Makefile - - lib_LTLIBRARIES = libapbsmainroutines.la - libapbsmainroutines_la_SOURCES = routines.c --libapbsmainroutines_la_LIBADD = -L../src/aaa_lib/.libs/ -lapbs @mc_lib@ -+libapbsmainroutines_la_LIBADD = ../src/aaa_lib/.libs/libapbs.la @mc_lib@ - libapbsmainroutines_la_LDFLAGS = -version-info ${APBS_VERSION} - - INCLUDES = @inc_list@ -diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am -index 2c1fbea..6a09644 100644 ---- a/tools/python/Makefile.am -+++ b/tools/python/Makefile.am -@@ -16,4 +16,4 @@ SUBDIRS = vgrid - noinst_PROGRAMS = _apbslib.so - _apbslib_so_SOURCES = apbslib.c - _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 $(PY_LDFLAGS) ${z_lib} @OPENMP_LIBS@ @maloc_lib@ @mc_lib@ -+_apbslib_so_LDADD = -L${top_builddir}/bin/.libs/ -lapbsmainroutines -L${top_builddir}/src/aaa_lib/.libs/ -lapbs $(PY_LDFLAGS) ${z_lib} @maloc_lib@ @mc_lib@ -diff --git a/tools/python/vgrid/Makefile.am b/tools/python/vgrid/Makefile.am -index 50c09ac..165cd4d 100644 ---- a/tools/python/vgrid/Makefile.am -+++ b/tools/python/vgrid/Makefile.am -@@ -16,5 +16,5 @@ if PY_PRESENT - noinst_PROGRAMS = _vgrid.so - _vgrid_so_SOURCES = vgridlib.c - _vgrid_so_LINK = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED) -- _vgrid_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.la ${top_builddir}/src/aaa_lib/.libs/libapbs.la @lib_list@ -+ _vgrid_so_LDADD = -L${top_builddir}/bin/.libs/ -lapbsmainroutines -L${top_builddir}/src/aaa_lib/.libs/ -lapbs @lib_list@ - endif --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0013-apbs-1.3-tools-installation.patch b/sci-chemistry/apbs/files/apbs-1.3/0013-apbs-1.3-tools-installation.patch deleted file mode 100644 index b52483f54e70..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0013-apbs-1.3-tools-installation.patch +++ /dev/null @@ -1,70 +0,0 @@ -From 4fd349da80e63c6fd3fbb2f015d8d802c326508e Mon Sep 17 00:00:00 2001 -Message-Id: <4fd349da80e63c6fd3fbb2f015d8d802c326508e.1325691465.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Wed, 4 Jan 2012 13:29:19 +0100 -Subject: [PATCH 13/15] apbs 1.3 tools installation - ---- - Makefile.am | 2 +- - tools/arpack/Makefile.am | 2 +- - tools/manip/Makefile.am | 2 +- - tools/mesh/Makefile.am | 2 +- - 4 files changed, 4 insertions(+), 4 deletions(-) - -diff --git a/Makefile.am b/Makefile.am -index af3a3a3..60ba9bd 100644 ---- a/Makefile.am -+++ b/Makefile.am -@@ -49,7 +49,7 @@ install-cleanup: - - install-tools: - mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools -- -cp -rf tools $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/ -+ -cp -rf tools/conversion tools/visualization tools/matlab $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools - - install-examples: - mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/examples -diff --git a/tools/arpack/Makefile.am b/tools/arpack/Makefile.am -index 6c05f4a..2362114 100644 ---- a/tools/arpack/Makefile.am -+++ b/tools/arpack/Makefile.am -@@ -10,7 +10,7 @@ AUTOMAKE_OPTIONS = no-dependencies - SUFFIXES = .H .h .C .c .f .o - CCLD = $(F77) - --noinst_PROGRAMS = driver -+bin_PROGRAMS = driver - driver_SOURCES = driver.c readhb.f ardriv.f - driver_LDADD = ../../src/aaa_lib/libapbs.la @arpack_lib@ @apbs_build_libraries@ - INCLUDES = @inc_list@ -diff --git a/tools/manip/Makefile.am b/tools/manip/Makefile.am -index f5f692b..f64f8fc 100644 ---- a/tools/manip/Makefile.am -+++ b/tools/manip/Makefile.am -@@ -10,7 +10,7 @@ AUTOMAKE_OPTIONS = no-dependencies - SUFFIXES = .H .h .C .c .f .o - CCLD = $(CC) - --noinst_PROGRAMS = coulomb born -+bin_PROGRAMS = coulomb born - coulomb_SOURCES = coulomb.c - coulomb_LDADD = ../../src/aaa_lib/libapbs.la @apbs_build_libraries@ - born_SOURCES = born.c -diff --git a/tools/mesh/Makefile.am b/tools/mesh/Makefile.am -index 8ad5cfb..3cd9268 100644 ---- a/tools/mesh/Makefile.am -+++ b/tools/mesh/Makefile.am -@@ -21,7 +21,7 @@ uhbd_asc2bin_CCLD = $(F77) - else - UHBD = - endif --noinst_PROGRAMS = mgmesh dxmath mergedx mergedx2 $(UHBD) smooth value dx2mol dx2uhbd benchmark similarity analysis multivalue del2dx tensor2dx -+bin_PROGRAMS = mgmesh dxmath mergedx mergedx2 $(UHBD) smooth value dx2mol dx2uhbd benchmark similarity analysis multivalue del2dx tensor2dx - - mgmesh_SOURCES = mgmesh.c - mgmesh_LDADD = ../../src/aaa_lib/libapbs.la @apbs_build_libraries@ --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0014-apbs-1.3-pythonlib-fix.patch b/sci-chemistry/apbs/files/apbs-1.3/0014-apbs-1.3-pythonlib-fix.patch deleted file mode 100644 index 08e98276ca05..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0014-apbs-1.3-pythonlib-fix.patch +++ /dev/null @@ -1,28 +0,0 @@ -From 86ae9a75144d1d9600e7a9045e1154fb2f481efb Mon Sep 17 00:00:00 2001 -Message-Id: <86ae9a75144d1d9600e7a9045e1154fb2f481efb.1325691465.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Wed, 4 Jan 2012 14:05:22 +0100 -Subject: [PATCH 14/15] apbs 1.3 pythonlib fix - ---- - tools/python/Makefile.am | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) - -diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am -index 6a09644..aecd6ed 100644 ---- a/tools/python/Makefile.am -+++ b/tools/python/Makefile.am -@@ -13,7 +13,7 @@ CCLD = $(PY_CC) - CLEANFILES = _apbslib.so - SUBDIRS = vgrid - --noinst_PROGRAMS = _apbslib.so -+pyexec_LTLIBRARIES = _apbslib.so - _apbslib_so_SOURCES = apbslib.c - _apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED) - _apbslib_so_LDADD = -L${top_builddir}/bin/.libs/ -lapbsmainroutines -L${top_builddir}/src/aaa_lib/.libs/ -lapbs $(PY_LDFLAGS) ${z_lib} @maloc_lib@ @mc_lib@ --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0015-apbs-1.3-pythonlib-fix.patch b/sci-chemistry/apbs/files/apbs-1.3/0015-apbs-1.3-pythonlib-fix.patch deleted file mode 100644 index a9dd87ba761b..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0015-apbs-1.3-pythonlib-fix.patch +++ /dev/null @@ -1,49 +0,0 @@ -From 013f5770202f705df7c522dcb123da86ac62e901 Mon Sep 17 00:00:00 2001 -Message-Id: <013f5770202f705df7c522dcb123da86ac62e901.1325691465.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Wed, 4 Jan 2012 14:28:14 +0100 -Subject: [PATCH 15/15] apbs 1.3 pythonlib fix - ---- - configure.ac | 1 + - tools/python/Makefile.am | 11 ++++++----- - 2 files changed, 7 insertions(+), 5 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 9837a57..d39a0a5 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -161,6 +161,7 @@ AC_ARG_ENABLE( - if test x"$enable_python" != "xno"; then - AC_MSG_RESULT([yes]) - AC_MSG_NOTICE([Python linkage requires GNU compilers]) -+ AM_PATH_PYTHON - cclist="gcc" - f77list="gfortran g95 g77" - apbs_do_python="python" -diff --git a/tools/python/Makefile.am b/tools/python/Makefile.am -index aecd6ed..7d661b1 100644 ---- a/tools/python/Makefile.am -+++ b/tools/python/Makefile.am -@@ -10,10 +10,11 @@ AUTOMAKE_OPTIONS = no-dependencies - SUFFIXES = .c .C .o .so - INCLUDES = @inc_list@ $(PY_CFLAGS) -I${top_srcdir}/bin - CCLD = $(PY_CC) --CLEANFILES = _apbslib.so -+CLEANFILES = _apbs.so - SUBDIRS = vgrid - --pyexec_LTLIBRARIES = _apbslib.so --_apbslib_so_SOURCES = apbslib.c --_apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED) --_apbslib_so_LDADD = -L${top_builddir}/bin/.libs/ -lapbsmainroutines -L${top_builddir}/src/aaa_lib/.libs/ -lapbs $(PY_LDFLAGS) ${z_lib} @maloc_lib@ @mc_lib@ -+pkgpyexec_LTLIBRARIES = _apbs.la -+_apbs_la_SOURCES = apbslib.c -+#_apbs_la_LINK = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED) -+_apbs_la_LDFLAGS = -module -avoid-version -shared -+_apbs_la_LIBADD = ${top_builddir}/bin/.libs/libapbsmainroutines.la ${top_builddir}/src/aaa_lib/.libs/libapbs.la $(PY_LDFLAGS) ${z_lib} @maloc_lib@ @mc_lib@ --- -1.7.8.2 - diff --git a/sci-chemistry/apbs/files/apbs-1.3/0016-apbs-1.3-apbs.pc-in-AC_CONFIG_FILES.patch b/sci-chemistry/apbs/files/apbs-1.3/0016-apbs-1.3-apbs.pc-in-AC_CONFIG_FILES.patch deleted file mode 100644 index 8a5e59d0a838..000000000000 --- a/sci-chemistry/apbs/files/apbs-1.3/0016-apbs-1.3-apbs.pc-in-AC_CONFIG_FILES.patch +++ /dev/null @@ -1,28 +0,0 @@ -From ba195e1ea7e023ab442c4699c9c329bacc646c6a Mon Sep 17 00:00:00 2001 -Message-Id: <ba195e1ea7e023ab442c4699c9c329bacc646c6a.1342692605.git.jlec@gentoo.org> -In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1342692605.git.jlec@gentoo.org> -References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1342692605.git.jlec@gentoo.org> -From: Justin Lecher <jlec@gentoo.org> -Date: Thu, 19 Jul 2012 12:07:59 +0200 -Subject: [PATCH 16/16] apbs 1.3 apbs.pc in AC_CONFIG_FILES - ---- - configure.ac | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) - -diff --git a/configure.ac b/configure.ac -index d39a0a5..6855929 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -1269,7 +1269,7 @@ AC_CONFIG_FILES([ - - bin/Makefile - -- apbs.pc:apbs.pc.in -+ apbs.pc - - ]) - AC_OUTPUT --- -1.7.8.6 - |