diff options
| author |   Justin Lecher <jlec@gentoo.org> | 2012-01-04 17:25:25 +0000 |
|---|---|---|
| committer | Justin Lecher <jlec@gentoo.org> | 2012-01-04 17:25:25 +0000 |
| commit | 6b7e14a060ffd4f91debc1a7ea11efc549a6ebc0 (patch) | |
| tree | b4afab1ed84cc471d864139f620a68b2c9c183aa /sci-chemistry | |
| parent | Stable for AMD64, wrt bug #396913 (diff) | |
| download | historical-6b7e14a060ffd4f91debc1a7ea11efc549a6ebc0.tar.gz historical-6b7e14a060ffd4f91debc1a7ea11efc549a6ebc0.tar.bz2 historical-6b7e14a060ffd4f91debc1a7ea11efc549a6ebc0.zip | |
Rewrite build, rely on pkg-config when possible, move to autotools-utils.eclass, handle static-libs correctly
Package-Manager: portage-2.2.0_alpha84/cvs/Linux x86_64
Diffstat (limited to 'sci-chemistry')
18 files changed, 1070 insertions, 6 deletions
diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog index f9b4465ddb85..0c4db73650ac 100644 --- a/sci-chemistry/apbs/ChangeLog +++ b/sci-chemistry/apbs/ChangeLog @@ -1,6 +1,27 @@ # ChangeLog for sci-chemistry/apbs -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.53 2011/12/13 14:25:50 jlec Exp $ +# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.54 2012/01/04 17:25:25 jlec Exp $ + +*apbs-1.3-r2 (04 Jan 2012) + + 04 Jan 2012; Justin Lecher <jlec@gentoo.org> +apbs-1.3-r2.ebuild, + +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: + Rewrite build, rely on pkg-config when possible, move to + autotools-utils.eclass, handle static-libs correctly 13 Dec 2011; Justin Lecher <jlec@gentoo.org> apbs-1.2.1b-r4.ebuild, apbs-1.3.ebuild, apbs-1.3-r1.ebuild: diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest index 4294982dff28..599e303ee03a 100644 --- a/sci-chemistry/apbs/Manifest +++ b/sci-chemistry/apbs/Manifest @@ -17,17 +17,33 @@ AUX apbs-1.3-openmp.patch 1843 RMD160 58030d378e217752c56b925e7e17ec4b4eb43e52 S AUX apbs-1.3-python.patch 985 RMD160 03562872ec1996a93c54bcfce16f4dbf15e7adf4 SHA1 1ea3b38334062c09f91b12edc54c5ed4de915e2e SHA256 fc0ba045bc0fb9b9913c5fa04e1d58f92c5c6df29c1586e7198f17d81d3876ec AUX apbs-1.3-shared.patch 2888 RMD160 89d7e36f6a361753a178111ce87d01616ccd9864 SHA1 f2178cf365e6c1930fc7a6c661c87064663db7c3 SHA256 f3965767dcdc17e4d97663d2febb7ede717d55736d4ba8554039dda5fd357c93 AUX apbs-1.3-zlib.patch 1231 RMD160 a0278f6883bf045de59aae921072a756495587b9 SHA1 2635e07429e4ad110c347beeaf0cea1f1d279a85 SHA256 77e4752ccd3c466efcadb95c50004c2f62147e9f220d10a871ec7a72d30eb2be +AUX apbs-1.3/0001-autoconf-2.68.patch 1224 RMD160 74a9085bfd103518a785354bc83d397bd7b6ffa3 SHA1 5f54ba17a18bf7fcbc02bf276197667f46331f75 SHA256 676ef592fb52cef75fa7f53e0ca159471c9d70551324e653868e421f0915f520 +AUX apbs-1.3/0002-python-linking.patch 2212 RMD160 b6c6950ea7b3474122e2229109fce4af6dc8396a SHA1 75549cd23965b4ddebc0155e9c92ab5ca006de32 SHA256 f3a6fc3d73ff105db72cd82827ab6812e0dc1b6071d19a978dbb08c9130b11c7 +AUX apbs-1.3/0003-apbs-1.3-pkg-config-file.patch 927 RMD160 8456047f9428f6df78ce2ec217d69310f3015f70 SHA1 f4a117114c85a77aad748a6ffa5aed0aca04e6b7 SHA256 b5585885d8b1cd15927e3240f8085970639e265c23b464825d2e5a9fd6fa6cee +AUX apbs-1.3/0004-apbs-1.3-system-zlib.patch 999 RMD160 6eb46534bc2489253439f5f263df67c372b22a26 SHA1 fdb8d06fc07255a5db248627668420aefccd74b4 SHA256 51f7dc4d11dda4922f76620ca9b929f280d7136c50813c5218982927912be046 +AUX apbs-1.3/0005-apbs-1.3-linking.patch 2673 RMD160 ede2d6190cd7a446f9c8e77002cf0ecc26eb3216 SHA1 f5f6b599cafaf732f4d7966e1687791d2044f79a SHA256 4a078632f656739dea24a8160f4f516fadba0678bf61b5cc06186dd0c6c593fb +AUX apbs-1.3/0006-apbs-1.3-clean-targets.patch 1826 RMD160 5e98a95bdce0d5b1f866b05bb7371c6c9a9674ef SHA1 73ce6084dfc39afbfe75f5d6c9b4b1d1c0e8afa7 SHA256 2f931428eac36022b07a8856c48917e1b7cf4c9dfddcfb311a28e9c4b7cb350e +AUX apbs-1.3/0007-apbs-1.3-configure.patch 7735 RMD160 401f5901e91f7081994b60c6bb2047843574b8d9 SHA1 5202acec11032c38c21023013a54df8584b79b33 SHA256 8371e3dbb1570b83c9f1ccd8654997d129e14510c55c28652d9447981a088eb1 +AUX apbs-1.3/0008-apbs-1.3-broken-test.patch 1896 RMD160 d0ac81396a6794a7c46c2af0b8a88a2dd12ac424 SHA1 69b711a2ec22c36a55b1942ae3c3e3789bc1760f SHA256 395b3780799b6dc0efe12db39bbd7039339b89ac35602206b0777214d18f7369 +AUX apbs-1.3/0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch 1247 RMD160 f1ec05b871a19bd115d1e034f66d69ad245c9ac9 SHA1 92a1317c605acbcdec4de52865dda9a6a9775093 SHA256 25356fff07091ff6d13f5f2cefbe61639cad5581c3feccb1fb070f990d1bb5cc +AUX apbs-1.3/0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch 1819 RMD160 c82c67fe47d99665707a158cf32e65564866e493 SHA1 fa7d1a6d73cec31c76398916c75af666fe0419b1 SHA256 3cf0dfea9c1faacd4620e75a5861cf9fb561702a2e081d79c0beef1a0b80adeb +AUX apbs-1.3/0011-apbs-1.3-shared-linking.patch 1197 RMD160 999f31b2056622a4258e84a477e9b4b873d67704 SHA1 d12f41a9597a7f3a94aa8ed90349611aedcc9192 SHA256 b17024321c8eaa9f016039a1bb10aeb826436a22a5b1d9683cfde75e1ed59c4b +AUX apbs-1.3/0012-apbs-1.3-python-linking-correction.patch 2862 RMD160 b3e78f77f7d2252e6346dc751957515c29f4bb82 SHA1 957f40ab90b1cd4ad462b2902b4f7d0b76a6b799 SHA256 ad8c92ccef3ed56e18a2de313c18ed2fb5e18f1d6cf61d5b5794d86cd003a458 +AUX apbs-1.3/0013-apbs-1.3-tools-installation.patch 2683 RMD160 4a6bd9310002d4ff3686cda8ff908f21ea35ca95 SHA1 7bb596b8d6cad278529f593883bd77dbd1f743a7 SHA256 fd1f4345977b1c714b2408e2cf9b2124e5fe0c2ea760e78f0da3ca390132c1f2 +AUX apbs-1.3/0014-apbs-1.3-pythonlib-fix.patch 1170 RMD160 9c0c56bbf1db22b6fc743602445cdb4bdd3371c5 SHA1 186d8690718c055e07ba1aeec724701b924520f6 SHA256 e092594f4bab6b4c41ff34b7b4ca8cdd5410352ea12f3e74d4277dd1805f9adb +AUX apbs-1.3/0015-apbs-1.3-pythonlib-fix.patch 2055 RMD160 dd424aa44e3bc1d08a56fcd507731a38025a8473 SHA1 d7f678de1b05dacba0d2b7a33baa9b225cc66441 SHA256 7855076f6e70c462c84a65870d6984a367f0050b5400e780907faf9879857e6a DIST apbs-1.2.1b-source.tar.gz 40647966 RMD160 4ba1f72a7f9adcf7b283dc18743488143025b398 SHA1 dc3e6933a987ff9fdf88db510db79b3dacb100d6 SHA256 7d088def1ed7689127eb64014ea44069b9d7bfc995941fe5800ff753d48c87be DIST apbs-1.3-source.tar.gz 48625351 RMD160 c075a747dc28f382f3a383a0944a1b20e0c8a9f1 SHA1 1494f36e35f2e4b1a18d4b22516fad4948c6391f SHA256 5fa5b597f7d5a3d9bb55429ec4fefc69e7d0f918d568c3c4a288088c0fde9ef2 EBUILD apbs-1.2.1b-r4.ebuild 3605 RMD160 9cc3a6e31fef129da866bf90f6a6eeb97710a111 SHA1 c8df66903bcaf4e2cd39715112b9b83280513820 SHA256 38dc067d4a8efd351a15d292b3d00424e3782871e1ff8caada78a8ab2772bfac EBUILD apbs-1.3-r1.ebuild 4543 RMD160 ad848dd2f7f9f02dc13bbd1ac4b98ccccbb20c8e SHA1 d3140513caa7d5ea77472d560e040a3f38024849 SHA256 04edd7a4849302039b34cbbad5623eeaaf163eb32b20d84fa5253126b85f0f99 +EBUILD apbs-1.3-r2.ebuild 3797 RMD160 0c43f05fe04db4488802b2a8b8815e700b0a6000 SHA1 a08887dd834dd8891dc07e76cc917c065dd42fd2 SHA256 556e07abeb74313aa5a8fdc69c72b6994a3abb2ae9082722672a01dbca4632dc EBUILD apbs-1.3.ebuild 4358 RMD160 c3897181791ca3715ed77f30031af6a811f2beac SHA1 17c656a149e83de4a8158145ded80423f4fe5d3a SHA256 d3683ca49b49838368d70658a0e28b30f6a172de1709983d11a33bd1dc042cde -MISC ChangeLog 8992 RMD160 f7012914ac84ddd21f6ddd837569aaf16db2cdb1 SHA1 d35a7d688b8442d94cc309b4a1dbe2d5a6287bf6 SHA256 1d10d93f0c21f6656ffe567787e0686d53505ed8f2339652f69a17d569a569c0 +MISC ChangeLog 10034 RMD160 a3b6a30b63574cba316726a47922371dcf5152fc SHA1 3a0ad2e4445cfea90257708f7e7e19c3ba10531d SHA256 1aea2cdf6aa2ee002bb57063907da7df81d00f3d73239764064aab41b15e8624 MISC metadata.xml 871 RMD160 e50499e926ad62fc924b5c48f6d6fd56519c7cf7 SHA1 fe5335ee3c033f9f0b336663c4065ba4af3f9c8b SHA256 510d88fd555af07b55320109b1a56718980f6eb9e3569f9c39d88c82268cf56f -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.18 (GNU/Linux) -iEYEAREKAAYFAk7nYHMACgkQgAnW8HDreRad5ACgmPMNryL1Lsbc/9SdpXJ7wXTi -NA4AoJDqFHzWfBXSzxAfH4SDSSqqAXbE -=J17d +iEYEAREKAAYFAk8Ei5AACgkQgAnW8HDreRa18ACeNgsXOGQeeQ2mETxlRp2H6OBp +l1YAnRvZKKAqxtq4dYbDiKKc04855w+Y +=rlk6 -----END PGP SIGNATURE----- diff --git a/sci-chemistry/apbs/apbs-1.3-r2.ebuild b/sci-chemistry/apbs/apbs-1.3-r2.ebuild new file mode 100644 index 000000000000..e4145b592a25 --- /dev/null +++ b/sci-chemistry/apbs/apbs-1.3-r2.ebuild @@ -0,0 +1,149 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.3-r2.ebuild,v 1.1 2012/01/04 17:25:25 jlec Exp $ + +EAPI=4 + +PYTHON_DEPEND="python? 2" + +inherit autotools-utils eutils fortran-2 python toolchain-funcs versionator + +MY_PV=$(get_version_component_range 1-3) +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="For evaluation of electrostatic properties of nanoscale biomolecular systems" +HOMEPAGE="http://apbs.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="arpack doc examples fetk mpi openmp python static-libs tools" +REQUIRED_USE="mpi? ( !python )" + +DEPEND=" + dev-libs/maloc[mpi=] + virtual/blas + sys-libs/readline + virtual/fortran + arpack? ( sci-libs/arpack ) + tools? ( !sci-libs/gts ) + fetk? ( + sci-libs/fetk + sci-libs/amd + sci-libs/umfpack + sci-libs/superlu ) + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/"${MY_P}-source" + +AUTOTOOLS_IN_SOURCE_BUILD=1 +MAKEOPTS+=" -j1" + +pkg_setup() { + fortran-2_pkg_setup + use python && python_set_active_version 2 && python_pkg_setup + if [[ -z ${MAXMEM} ]]; then + einfo "You can specify the max amount of RAM used" + einfo "by setting MAXMEM=\"your size in MB\"" + else + einfo "Settings max memory usage to ${MAXMEM} MB" + fi +} + +# git clone ssh://woodpecker/home/jlec/apbs.git +PATCHES=( "${FILESDIR}"/${P}/00{01..15}* ) + +src_prepare() { + rm -rf contrib/{blas,maloc,opal,zlib} || die + find -name "._*" -delete || die + touch apbs.pc.in || die + + autotools-utils_src_prepare + + sed \ + -e "s:GENTOO_PKG_NAME:${PN}:g" \ + -i Makefile.am || die "Cannot correct package name" + sed \ + -e 's:libmaloc.a:libmaloc.so:g' \ + -e 's:-lblas::g' \ + -i configure.ac || die + sed -e 's:opal::g' -i contrib/Makefile.am || die + sed \ + -e 's:noinst_PROGRAMS:bin_PROGRAMS:g' \ + -i tools/*/Makefile.am || die + eautoreconf +} + +src_configure() { + local myeconfargs=( --docdir="${EPREFIX}/usr/share/doc/${PF}" ) + use arpack && myeconfargs+=( --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 + myeconfargs+=( --with-mpich="${EPREFIX}/usr" ) + elif has_version sys-cluster/mpich2; then + myeconfargs+=( --with-mpich2="${EPREFIX}/usr" ) + elif has_version sys-cluster/openmpi; then + myeconfargs+=( --with-openmpi="${EPREFIX}/usr" ) + fi + fi || die "Failed to select proper mpi implementation" + + if use fetk; then + myeconfargs+=( --with-fetk-include="${EPREFIX}/usr/include" --with-fetk-library="${EPREFIX}/usr/$(get_libdir)" ) + else + myeconfargs+=( --disable-fetk ) + fi + + [[ -n ${MAXMEM} ]] && myeconfargs+=( --with-maxmem=${MAXMEM} ) + + if use python; then + myeconfargs+=( --enable-tools ) + else + myeconfargs+=( $(use_enable tools) ) + fi + + myeconfargs+=( + --disable-maloc-rebuild + --enable-shared + $(use_enable openmp) + $(use_enable python) + ) + autotools-utils_src_configure +} + +src_test() { + export LC_NUMERIC=C + cd examples && make test \ + || die "Tests failed" + grep -q 'FAILED' "${S}"/examples/TESTRESULTS.log && die "Tests failed" +} + +src_install() { + autotools-utils_src_install + + use doc && dohtml -r doc/* + use examples && insinto /usr/share/${PN} && doins -r examples + use tools && emake DESTDIR="${D}" install-tools + + if use python && ! use mpi; then + insinto $(python_get_sitedir)/${PN} + doins tools/manip/*.py + doins tools/python/{*.py,*.pqr} + doins tools/python/*/{*.py,*.so} + python_clean_installation_image + fi +} + +pkg_postinst() { + use python && python_mod_optimize ${PN} +} + +pkg_postrm() { + use python && python_mod_cleanup ${PN} +} diff --git a/sci-chemistry/apbs/files/apbs-1.3/0001-autoconf-2.68.patch b/sci-chemistry/apbs/files/apbs-1.3/0001-autoconf-2.68.patch new file mode 100644 index 000000000000..ea6a27479c57 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0001-autoconf-2.68.patch @@ -0,0 +1,37 @@ +From 89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea Mon Sep 17 00:00:00 2001 +Message-Id: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> +From: Justin Lecher <jlec@gentoo.org> +Date: Tue, 3 Jan 2012 20:25:55 +0100 +Subject: [PATCH 01/15] autoconf 2.68 + +--- + acinclude.m4 | 13 +++++-------- + 1 files changed, 5 insertions(+), 8 deletions(-) + +diff --git a/acinclude.m4 b/acinclude.m4 +index 3701ceb..34602e3 100644 +--- a/acinclude.m4 ++++ b/acinclude.m4 +@@ -54,14 +54,11 @@ AC_LANG_SAVE + AC_LANG_C + ac_save_LIBS="$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 new file mode 100644 index 000000000000..4c699ad19f07 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0002-python-linking.patch @@ -0,0 +1,41 @@ +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 ${top_builddir}/src/aaa_lib/.libs/libapbs.a @lib_list@ + endif +-- +1.7.8.2 + diff --git a/sci-chemistry/apbs/files/apbs-1.3/0003-apbs-1.3-pkg-config-file.patch b/sci-chemistry/apbs/files/apbs-1.3/0003-apbs-1.3-pkg-config-file.patch new file mode 100644 index 000000000000..9ae90d2977cb --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0003-apbs-1.3-pkg-config-file.patch @@ -0,0 +1,32 @@ +From 9876050808e5d43c02d3c703e998a82f7502275d Mon Sep 17 00:00:00 2001 +Message-Id: <9876050808e5d43c02d3c703e998a82f7502275d.1325691465.git.jlec@gentoo.org> +In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> +References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> +From: Justin Lecher <jlec@gentoo.org> +Date: Tue, 3 Jan 2012 20:47:13 +0100 +Subject: [PATCH 03/15] apbs 1.3 pkg-config file + +--- + apbs.pc.in | 11 +++++++++++ + 1 files changed, 11 insertions(+), 0 deletions(-) + +diff --git a/apbs.pc.in b/apbs.pc.in +new file mode 100644 +index 0000000..c177512 +--- /dev/null ++++ b/apbs.pc.in +@@ -0,0 +1,11 @@ ++prefix=@prefix@ ++exec_prefix=@exec_prefix@ ++libdir=@libdir@ ++includedir=@includedir@/apbs ++ ++Name: apbs ++Description: apbs ++Version: @PACKAGE_VERSION@ ++Libs: -L${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 new file mode 100644 index 000000000000..1a668132f350 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0004-apbs-1.3-system-zlib.patch @@ -0,0 +1,28 @@ +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 new file mode 100644 index 000000000000..dd3f286eff23 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0005-apbs-1.3-linking.patch @@ -0,0 +1,70 @@ +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 new file mode 100644 index 000000000000..b157252647e8 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0006-apbs-1.3-clean-targets.patch @@ -0,0 +1,65 @@ +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 new file mode 100644 index 000000000000..38c1cb8d7934 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0007-apbs-1.3-configure.patch @@ -0,0 +1,237 @@ +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 new file mode 100644 index 000000000000..4c481a574195 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0008-apbs-1.3-broken-test.patch @@ -0,0 +1,43 @@ +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 new file mode 100644 index 000000000000..136d86bc8a18 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0009-apbs-1.3-use-pkg-config-for-zlib-detection.patch @@ -0,0 +1,41 @@ +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=$(ZLIB_LIBS) ++AC_DEFINE([HAVE_ZLIB], [], [have zlib compression enabled]) + AC_SUBST(zlib) + AC_SUBST(z_lib) + +-- +1.7.8.2 + diff --git a/sci-chemistry/apbs/files/apbs-1.3/0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch b/sci-chemistry/apbs/files/apbs-1.3/0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch new file mode 100644 index 000000000000..b955e9237668 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0010-apbs-1.3-use-OPENMP_CFLAGS-instead-of-OPENMP_LIBS.patch @@ -0,0 +1,51 @@ +From c09358a2aca006d93d8bc7525efe656f1b4f9c0a Mon Sep 17 00:00:00 2001 +Message-Id: <c09358a2aca006d93d8bc7525efe656f1b4f9c0a.1325691465.git.jlec@gentoo.org> +In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> +References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> +From: Justin Lecher <jlec@gentoo.org> +Date: Wed, 4 Jan 2012 11:05:04 +0100 +Subject: [PATCH 10/15] apbs 1.3 use OPENMP_CFLAGS instead of OPENMP_LIBS + +--- + configure.ac | 4 ++-- + src/aaa_lib/Makefile.am | 2 +- + 2 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 53deb06..9837a57 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -1013,7 +1013,7 @@ disable_zlib=yes + z_lib= + zlib= + PKG_CHECK_MODULES([ZLIB],[zlib]) +-z_lib=$(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 new file mode 100644 index 000000000000..f0c7259b0d2b --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0011-apbs-1.3-shared-linking.patch @@ -0,0 +1,26 @@ +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 new file mode 100644 index 000000000000..56a86d21d184 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0012-apbs-1.3-python-linking-correction.patch @@ -0,0 +1,60 @@ +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 new file mode 100644 index 000000000000..b52483f54e70 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0013-apbs-1.3-tools-installation.patch @@ -0,0 +1,70 @@ +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 new file mode 100644 index 000000000000..08e98276ca05 --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0014-apbs-1.3-pythonlib-fix.patch @@ -0,0 +1,28 @@ +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) ${z_lib} @maloc_lib@ @mc_lib@ +-- +1.7.8.2 + diff --git a/sci-chemistry/apbs/files/apbs-1.3/0015-apbs-1.3-pythonlib-fix.patch b/sci-chemistry/apbs/files/apbs-1.3/0015-apbs-1.3-pythonlib-fix.patch new file mode 100644 index 000000000000..a9dd87ba761b --- /dev/null +++ b/sci-chemistry/apbs/files/apbs-1.3/0015-apbs-1.3-pythonlib-fix.patch @@ -0,0 +1,49 @@ +From 013f5770202f705df7c522dcb123da86ac62e901 Mon Sep 17 00:00:00 2001 +Message-Id: <013f5770202f705df7c522dcb123da86ac62e901.1325691465.git.jlec@gentoo.org> +In-Reply-To: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> +References: <89d53654acb88cd8dbd4bc9eb388ca6e76d0d6ea.1325691465.git.jlec@gentoo.org> +From: Justin Lecher <jlec@gentoo.org> +Date: Wed, 4 Jan 2012 14:28:14 +0100 +Subject: [PATCH 15/15] apbs 1.3 pythonlib fix + +--- + configure.ac | 1 + + tools/python/Makefile.am | 11 ++++++----- + 2 files changed, 7 insertions(+), 5 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 9837a57..d39a0a5 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -161,6 +161,7 @@ AC_ARG_ENABLE( + if test x"$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 + |