From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: <gentoo-commits+bounces-1189577-garchives=archives.gentoo.org@lists.gentoo.org> Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id E0CF6138359 for <garchives@archives.gentoo.org>; Tue, 21 Jul 2020 09:54:45 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 03BF3E0908; Tue, 21 Jul 2020 09:54:45 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id C9E9DE0908 for <gentoo-commits@lists.gentoo.org>; Tue, 21 Jul 2020 09:54:44 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 9A4E334F461 for <gentoo-commits@lists.gentoo.org>; Tue, 21 Jul 2020 09:54:43 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 16670253 for <gentoo-commits@lists.gentoo.org>; Tue, 21 Jul 2020 09:54:42 +0000 (UTC) From: "Pacho Ramos" <pacho@gentoo.org> To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Pacho Ramos" <pacho@gentoo.org> Message-ID: <1595325278.ca543cde3fd9c01494d9f33fe40c55b16d98a91f.pacho@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/, sci-chemistry/vmd/files/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-chemistry/vmd/Manifest sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch sci-chemistry/vmd/vmd-1.9.2.ebuild sci-chemistry/vmd/vmd-1.9.3-r1.ebuild sci-chemistry/vmd/vmd-1.9.3-r4.ebuild sci-chemistry/vmd/vmd-1.9.3.ebuild X-VCS-Directories: sci-chemistry/vmd/files/ sci-chemistry/vmd/ X-VCS-Committer: pacho X-VCS-Committer-Name: Pacho Ramos X-VCS-Revision: ca543cde3fd9c01494d9f33fe40c55b16d98a91f X-VCS-Branch: master Date: Tue, 21 Jul 2020 09:54:42 +0000 (UTC) Precedence: bulk List-Post: <mailto:gentoo-commits@lists.gentoo.org> List-Help: <mailto:gentoo-commits+help@lists.gentoo.org> List-Unsubscribe: <mailto:gentoo-commits+unsubscribe@lists.gentoo.org> List-Subscribe: <mailto:gentoo-commits+subscribe@lists.gentoo.org> List-Id: Gentoo Linux mail <gentoo-commits.gentoo.org> X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: d84cd760-7272-47b5-b21b-3d62f1779c84 X-Archives-Hash: c14d6ea82cfcb7e07925351d24a1fe46 commit: ca543cde3fd9c01494d9f33fe40c55b16d98a91f Author: Pacho Ramos <pacho <AT> gentoo <DOT> org> AuthorDate: Tue Jul 21 09:54:29 2020 +0000 Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org> CommitDate: Tue Jul 21 09:54:38 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ca543cde sci-chemistry/vmd: Drop old Package-Manager: Portage-3.0.0, Repoman-2.3.23 Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org> sci-chemistry/vmd/Manifest | 2 - .../vmd/files/vmd-1.9.1-cuda-device_ptr.patch | 28 --- .../vmd/files/vmd-1.9.2-format-security.patch | 16 -- sci-chemistry/vmd/vmd-1.9.2.ebuild | 256 ------------------- sci-chemistry/vmd/vmd-1.9.3-r1.ebuild | 267 -------------------- sci-chemistry/vmd/vmd-1.9.3-r4.ebuild | 271 --------------------- sci-chemistry/vmd/vmd-1.9.3.ebuild | 255 ------------------- 7 files changed, 1095 deletions(-) diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest index 49868a8280d..977dcfa66a2 100644 --- a/sci-chemistry/vmd/Manifest +++ b/sci-chemistry/vmd/Manifest @@ -1,4 +1,2 @@ -DIST vmd-1.9.2-gentoo-patches.tar.xz 14896 BLAKE2B eb7c7fb982602f37bd8374bf8458a0a2ea2202161248caffd0d4e0f8124d627755304bb778976e1cf5598b6bfbbe5d8c8e6016c9ec562204d6782aaaf179b185 SHA512 0516b9e57b256ce822a64df420ebf3ab7391722757caeaa7e615526242043e9375fee8f4ee86fb4eb8de7a50d5cfc8f8d973ace5fa082e6f9010eb692cd6ee51 -DIST vmd-1.9.2.src.tar.gz 34903084 BLAKE2B f7f7048ef7bb72a8b0dcae955c7f90691085158c38a59229d5b929a4b52d3148bdb2f40084cf8c4544f01cb8bcb57de1d98a90bd17568a07c4ebb8f6985cec9b SHA512 b232b743d4ea97dcf76e3005e1c8716d7138602edc078c4846026ab67759c8559af956182cb1acf3c85890db10b6f658ac9c269d432f2595612cf376d6d505ef DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1 DIST vmd-1.9.3.src.tar 129566720 BLAKE2B 848f3280d51765dcd18722dd233e0cdee3b7c0ac3dd48324260ebe1604ba781ca0a1fe4cae6652501d23d5d41712020e17dbb6bc21a1856eb3289a4aab6b774b SHA512 0502df1e8b60c570ca88b779b4153acfaa599a78df53fa96fca36301bab902864118332b5524ae7d170d3a9e429cf1e13d69e1197268b5e841afc0bb56a737ba diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch deleted file mode 100644 index 67eb11bbd36..00000000000 --- a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch +++ /dev/null @@ -1,28 +0,0 @@ - vmd-1.9.1/src/CUDAMarchingCubes.cu | 1 + - vmd-1.9.1/src/CUDAQuickSurf.cu | 1 + - 2 files changed, 2 insertions(+) - -diff --git a/vmd-1.9.1/src/CUDAMarchingCubes.cu b/vmd-1.9.1/src/CUDAMarchingCubes.cu -index 5bfe7bf..36faaf0 100755 ---- a/src/CUDAMarchingCubes.cu -+++ b/src/CUDAMarchingCubes.cu -@@ -45,6 +45,7 @@ - #include "CUDAMarchingCubes.h" - #include <thrust/scan.h> - #include <thrust/functional.h> -+#include <thrust/device_ptr.h> - - // The number of threads to use for triangle generation - // (limited by shared memory size) -diff --git a/vmd-1.9.1/src/CUDAQuickSurf.cu b/vmd-1.9.1/src/CUDAQuickSurf.cu -index a21ebde..56a42c8 100755 ---- a/src/CUDAQuickSurf.cu -+++ b/src/CUDAQuickSurf.cu -@@ -22,6 +22,7 @@ - #include <stdlib.h> - #include <string.h> - #include <cuda.h> -+#include <thrust/device_ptr.h> - - #if CUDART_VERSION < 4000 - #error The VMD QuickSurf feature requires CUDA 4.0 or later diff --git a/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch b/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch deleted file mode 100644 index 3f9ea5c8c2e..00000000000 --- a/sci-chemistry/vmd/files/vmd-1.9.2-format-security.patch +++ /dev/null @@ -1,16 +0,0 @@ - plugins/molfile_plugin/src/maeffplugin.cxx | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/plugins/molfile_plugin/src/maeffplugin.cxx b/plugins/molfile_plugin/src/maeffplugin.cxx -index cfe1223..41d92bb 100644 ---- a/plugins/molfile_plugin/src/maeffplugin.cxx -+++ b/plugins/molfile_plugin/src/maeffplugin.cxx -@@ -1979,7 +1979,7 @@ namespace { - } - } - catch (std::exception &e) { -- fprintf(stderr, e.what()); -+ fprintf(stderr, "%s", e.what()); - return MOLFILE_ERROR; - } - return MOLFILE_SUCCESS; diff --git a/sci-chemistry/vmd/vmd-1.9.2.ebuild b/sci-chemistry/vmd/vmd-1.9.2.ebuild deleted file mode 100644 index 92daf030477..00000000000 --- a/sci-chemistry/vmd/vmd-1.9.2.ebuild +++ /dev/null @@ -1,256 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs - -DESCRIPTION="Visual Molecular Dynamics" -HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" -SRC_URI=" - https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz - ${P}.src.tar.gz" - -SLOT="0" -LICENSE="vmd" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="cuda gromacs msms povray sqlite tachyon xinerama" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RESTRICT="fetch" - -# currently, tk-8.5* with USE=truetype breaks some -# tk apps such as Sequence Viewer or Timeline. -CDEPEND=" - >=dev-lang/tk-8.6.1 - dev-lang/perl - dev-libs/expat - $(python_gen_cond_dep ' - || ( - dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}] - dev-python/numpy[${PYTHON_MULTI_USEDEP}] - ) - ') - sci-libs/netcdf:0= - virtual/opengl - >=x11-libs/fltk-1.1.10-r2:1 - x11-libs/libXft - x11-libs/libXi - ${PYTHON_DEPS} - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) - gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1[tng] ) - sqlite? ( dev-db/sqlite:3= ) - tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) - xinerama? ( x11-libs/libXinerama )" -DEPEND="${CDEPEND} - virtual/pkgconfig - dev-lang/swig" -RDEPEND="${CDEPEND} - sci-biology/stride - sci-chemistry/surf - x11-terms/xterm - msms? ( sci-chemistry/msms-bin ) - povray? ( media-gfx/povray ) - " - -VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" -# Binary only plugin!! -QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" -QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" -QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" - -pkg_nofetch() { - elog "Please download ${P}.src.tar.gz from" - elog "${VMD_DOWNLOAD}" - elog "after agreeing to the license and get" - elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" - elog "Place both into your DISTDIR directory" -} - -src_prepare() { - use cuda && cuda_sanitize - - epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch - - cd "${WORKDIR}"/plugins || die - - epatch \ - "${WORKDIR}"/${P}-gentoo-plugins.patch \ - "${FILESDIR}"/${P}-format-security.patch - - [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) - - sed \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CXX = g++:CXX = $(tc-getCXX):" \ - -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ - -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ - -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ - -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ - -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ - -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ - -e "s:-ltcl8.5:-ltcl:" \ - -i Make-arch || die "Failed to set up plugins Makefile" - - sed \ - -e '/^AR /s:=:?=:g' \ - -e '/^RANLIB /s:=:?=:g' \ - -i ../plugins/*/Makefile || die - - tc-export AR RANLIB - - sed \ - -e "s:\$(CXXFLAGS)::g" \ - -i hesstrans/Makefile || die - - # prepare vmd itself - cd "${S}" || die - - epatch "${WORKDIR}"/${P}-gentoo-base.patch - - # PREFIX - sed \ - -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ - -i configure || die - - sed \ - -e "s:gentoo-bindir:${ED}/usr/bin:g" \ - -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ - -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ - -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-gcc:$(tc-getCC):g" \ - -e "s:gentoo-g++:$(tc-getCXX):g" \ - -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ - -e "s:gentoo-cflags:${CFLAGS}:g" \ - -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ - -e "s:gentoo-nvflags::g" \ - -e "s:gentoo-ldflags:${LDFLAGS}:g" \ - -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ - -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ - -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ - -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ - -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -i configure || die - - if use cuda; then - sed \ - -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ - -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ - -i configure src/Makefile || die - sed \ - -e '/compute_/d' \ - -i configure || die - sed \ - -e 's:-gencode .*code=sm_..::' \ - -i src/Makefile || die - fi - - sed \ - -e "s:LINUXPPC:LINUX:g" \ - -e "s:LINUXALPHA:LINUX:g" \ - -e "s:LINUXAMD64:LINUX:g" \ - -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ - -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ - -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ - -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" - - EMAKEOPTS=( - TCLINC="-I${EPREFIX}/usr/include" - TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" - TCLLDFLAGS="-shared" - NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" - NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf) ${EPREFIX}/usr/include" - NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" - NETCDFDYNAMIC=1 - EXPATINC="-I${EPREFIX}/usr/include" - EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" - EXPATLDFLAGS="-shared" - EXPATDYNAMIC=1 - ) - if use gromacs; then - EMAKEOPTS+=( - TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" - TNGINC="-I${EPREFIX}/usr/include" - TNGLDFLAGS="-shared" - TNGDYNAMIC=1 - ) - fi - if use sqlite; then - EMAKEOPTS+=( - SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" - SQLITEINC="-I${EPREFIX}/usr/include" - SQLITELDFLAGS="-shared" - SQLITEDYNAMIC=1 - ) - fi -} - -src_configure() { - local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" - rm -f configure.options && echo $myconf >> configure.options - - use cuda && myconf+=" CUDA" -# use mpi && myconf+=" MPI" - use tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon" - use xinerama && myconf+=" XINERAMA" - - export \ - PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ - PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ - PYTHON_LIBRARY="$(python_get_LIBS)" \ - NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ - NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" - - perl ./configure LINUX \ - ${myconf} || die -} - -src_compile() { - # build plugins - cd "${WORKDIR}"/plugins || die - - emake \ - ${EMAKEOPTS[@]} \ - LINUX - - # build vmd - cd "${S}"/src || die - emake -} - -src_install() { - # install plugins - cd "${WORKDIR}"/plugins || die - emake \ - PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ - distrib - - # install vmd - cd "${S}"/src || die - emake install - - # install docs - cd "${S}" || die - dodoc Announcement README doc/ig.pdf doc/ug.pdf - - # remove some of the things we don't want and need in - # /usr/lib - cd "${ED}"/usr/$(get_libdir)/vmd || die - rm -fr doc README Announcement LICENSE || \ - die "failed to clean up /usr/lib/vmd directory" - - # adjust path in vmd wrapper - sed \ - -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ - -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ - || die "failed to set up vmd wrapper script" - - # install icon and generate desktop entry - insinto /usr/share/pixmaps - doins "${WORKDIR}"/vmd.png - eprefixify "${WORKDIR}"/vmd.desktop - sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die - domenu "${WORKDIR}"/vmd.desktop -} diff --git a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild deleted file mode 100644 index f42cb4d104f..00000000000 --- a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild +++ /dev/null @@ -1,267 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -PYTHON_COMPAT=( python2_7 ) - -inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs - -DESCRIPTION="Visual Molecular Dynamics" -HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" -SRC_URI=" - https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz - ${P}.src.tar -" - -SLOT="0" -LICENSE="vmd" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="cuda gromacs msms povray sqlite tachyon xinerama" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RESTRICT="fetch" - -# currently, tk-8.5* with USE=truetype breaks some -# tk apps such as Sequence Viewer or Timeline. -CDEPEND=" - >=dev-lang/tk-8.6.1:0= - dev-lang/perl - dev-libs/expat - $(python_gen_cond_dep ' - || ( - dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}] - dev-python/numpy[${PYTHON_MULTI_USEDEP}] - ) - ') - sci-libs/netcdf:0= - virtual/opengl - >=x11-libs/fltk-1.1.10-r2:1 - x11-libs/libXft - x11-libs/libXi - ${PYTHON_DEPS} - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) - gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) - sqlite? ( dev-db/sqlite:3= ) - tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) - xinerama? ( x11-libs/libXinerama ) -" -DEPEND="${CDEPEND}" -BDEPEND=" - virtual/pkgconfig - dev-lang/swig -" -RDEPEND="${CDEPEND} - sci-biology/stride - sci-chemistry/surf - x11-terms/xterm - msms? ( sci-chemistry/msms-bin ) - povray? ( media-gfx/povray ) -" - -VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" -# Binary only plugin!! -QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" -QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" -QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" - -pkg_nofetch() { - elog "Please download ${P}.src.tar from" - elog "${VMD_DOWNLOAD}" - elog "after agreeing to the license and get" - elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" - elog "Place both into your DISTDIR directory" - elog - elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources" - elog "file may get downloaded as a compressed tarball or not. In that case" - elog "you will need to ensure you uncompress the file and rename it" - elog "as ${P}.src.tar" -} - -src_prepare() { - default - - use cuda && cuda_sanitize - - eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch - - cd "${WORKDIR}"/plugins || die - - eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch - - [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) - - sed \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CXX = g++:CXX = $(tc-getCXX):" \ - -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ - -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ - -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ - -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ - -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ - -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ - -e "s:-ltcl8.5:-ltcl:" \ - -i Make-arch || die "Failed to set up plugins Makefile" - - sed \ - -e '/^AR /s:=:?=:g' \ - -e '/^RANLIB /s:=:?=:g' \ - -i ../plugins/*/Makefile || die - - tc-export AR RANLIB - - sed \ - -e "s:\$(CXXFLAGS)::g" \ - -i hesstrans/Makefile || die - - # prepare vmd itself - cd "${S}" || die - - eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch - eapply "${FILESDIR}"/${P}-configure-libtachyon.patch - - # PREFIX - sed \ - -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ - -i configure || die - - sed \ - -e "s:gentoo-bindir:${ED}/usr/bin:g" \ - -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ - -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ - -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-gcc:$(tc-getCC):g" \ - -e "s:gentoo-g++:$(tc-getCXX):g" \ - -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ - -e "s:gentoo-cflags:${CFLAGS}:g" \ - -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ - -e "s:gentoo-nvflags::g" \ - -e "s:gentoo-ldflags:${LDFLAGS}:g" \ - -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ - -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ - -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ - -e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \ - -e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ - -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -i configure || die - - if use cuda; then - sed \ - -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ - -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ - -i configure src/Makefile || die - sed \ - -e '/compute_/d' \ - -i configure || die - sed \ - -e 's:-gencode .*code=sm_..::' \ - -i src/Makefile || die - fi - - sed \ - -e "s:LINUXPPC:LINUX:g" \ - -e "s:LINUXALPHA:LINUX:g" \ - -e "s:LINUXAMD64:LINUX:g" \ - -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ - -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ - -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ - -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" - - EMAKEOPTS=( - TCLINC="-I${EPREFIX}/usr/include" - TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" - TCLLDFLAGS="-shared" - NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" - NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include" - NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" - NETCDFDYNAMIC=1 - EXPATINC="-I${EPREFIX}/usr/include" - EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" - EXPATLDFLAGS="-shared" - EXPATDYNAMIC=1 - ) - if use gromacs; then - EMAKEOPTS+=( - TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" - TNGINC="-I${EPREFIX}/usr/include" - TNGLDFLAGS="-shared" - TNGDYNAMIC=1 - ) - fi - if use sqlite; then - EMAKEOPTS+=( - SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" - SQLITEINC="-I${EPREFIX}/usr/include" - SQLITELDFLAGS="-shared" - SQLITEDYNAMIC=1 - ) - fi -} - -src_configure() { - local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" - rm -f configure.options && echo $myconf >> configure.options - - use cuda && myconf+=" CUDA" -# use mpi && myconf+=" MPI" - use tachyon && myconf+=" LIBTACHYON" - use xinerama && myconf+=" XINERAMA" - - export \ - PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ - PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ - PYTHON_LIBRARY="$(python_get_LIBS)" \ - NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ - NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" - - perl ./configure LINUX \ - ${myconf} || die -} - -src_compile() { - # build plugins - cd "${WORKDIR}"/plugins || die - - emake \ - ${EMAKEOPTS[@]} \ - LINUX - - # build vmd - cd "${S}"/src || die - emake -} - -src_install() { - # install plugins - cd "${WORKDIR}"/plugins || die - emake \ - PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ - distrib - - # install vmd - cd "${S}"/src || die - emake install - - # install docs - cd "${S}" || die - dodoc Announcement README doc/ig.pdf doc/ug.pdf - - # remove some of the things we don't want and need in - # /usr/lib - cd "${ED}"/usr/$(get_libdir)/vmd || die - rm -fr doc README Announcement LICENSE || \ - die "failed to clean up /usr/lib/vmd directory" - - # adjust path in vmd wrapper - sed \ - -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ - -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ - || die "failed to set up vmd wrapper script" - - # install icon and generate desktop entry - insinto /usr/share/pixmaps - doins "${WORKDIR}"/vmd.png - eprefixify "${WORKDIR}"/vmd.desktop - sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die - domenu "${WORKDIR}"/vmd.desktop -} diff --git a/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild deleted file mode 100644 index 39e7a9751ce..00000000000 --- a/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild +++ /dev/null @@ -1,271 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -PYTHON_COMPAT=( python2_7 ) - -inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg - -DESCRIPTION="Visual Molecular Dynamics" -HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" -SRC_URI=" - https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz - ${P}.src.tar -" - -SLOT="0" -LICENSE="vmd" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="cuda gromacs msms povray sqlite tachyon xinerama" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RESTRICT="fetch" - -# currently, tk-8.5* with USE=truetype breaks some -# tk apps such as Sequence Viewer or Timeline. -CDEPEND=" - >=dev-lang/tk-8.6.1:0= - dev-lang/perl - dev-libs/expat - $(python_gen_cond_dep ' - || ( - dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}] - dev-python/numpy[${PYTHON_MULTI_USEDEP}] - ) - ') - sci-libs/netcdf:0= - virtual/opengl - >=x11-libs/fltk-1.1.10-r2:1 - x11-libs/libXft - x11-libs/libXi - ${PYTHON_DEPS} - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) - gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) - sqlite? ( dev-db/sqlite:3= ) - tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) - xinerama? ( x11-libs/libXinerama ) -" -DEPEND="${CDEPEND}" -BDEPEND=" - virtual/pkgconfig - dev-lang/swig -" -RDEPEND="${CDEPEND} - sci-biology/stride - sci-chemistry/chemical-mime-data - sci-chemistry/surf - x11-terms/xterm - msms? ( sci-chemistry/msms-bin ) - povray? ( media-gfx/povray ) -" - -VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" -# Binary only plugin!! -QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" -QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" -QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" - -pkg_nofetch() { - elog "Please download ${P}.src.tar from" - elog "${VMD_DOWNLOAD}" - elog "after agreeing to the license and get" - elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" - elog "Place both into your DISTDIR directory" - elog - elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources" - elog "file may get downloaded as a compressed tarball or not. In that case" - elog "you will need to ensure you uncompress the file and rename it" - elog "as ${P}.src.tar" -} - -src_prepare() { - xdg_src_prepare - - use cuda && cuda_sanitize - - eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch - - cd "${WORKDIR}"/plugins || die - - eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch - - [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) - - sed \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CXX = g++:CXX = $(tc-getCXX):" \ - -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ - -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ - -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ - -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ - -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ - -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ - -e "s:-ltcl8.5:-ltcl:" \ - -i Make-arch || die "Failed to set up plugins Makefile" - - sed \ - -e '/^AR /s:=:?=:g' \ - -e '/^RANLIB /s:=:?=:g' \ - -i ../plugins/*/Makefile || die - - tc-export AR RANLIB - - sed \ - -e "s:\$(CXXFLAGS)::g" \ - -i hesstrans/Makefile || die - - # prepare vmd itself - cd "${S}" || die - - eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch - eapply "${FILESDIR}"/${P}-configure-libtachyon.patch - eapply "${FILESDIR}"/${P}-tmpdir.patch - - # PREFIX - sed \ - -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ - -i configure || die - - sed \ - -e "s:gentoo-bindir:${ED}/usr/bin:g" \ - -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ - -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ - -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-gcc:$(tc-getCC):g" \ - -e "s:gentoo-g++:$(tc-getCXX):g" \ - -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ - -e "s:gentoo-cflags:${CFLAGS}:g" \ - -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ - -e "s:gentoo-nvflags::g" \ - -e "s:gentoo-ldflags:${LDFLAGS}:g" \ - -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ - -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ - -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ - -e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \ - -e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ - -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -i configure || die - - if use cuda; then - sed \ - -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ - -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ - -i configure src/Makefile || die - sed \ - -e '/compute_/d' \ - -i configure || die - sed \ - -e 's:-gencode .*code=sm_..::' \ - -i src/Makefile || die - fi - - sed \ - -e "s:LINUXPPC:LINUX:g" \ - -e "s:LINUXALPHA:LINUX:g" \ - -e "s:LINUXAMD64:LINUX:g" \ - -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ - -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ - -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ - -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" - - EMAKEOPTS=( - TCLINC="-I${EPREFIX}/usr/include" - TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" - TCLLDFLAGS="-shared" - NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" - NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include" - NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" - NETCDFDYNAMIC=1 - EXPATINC="-I${EPREFIX}/usr/include" - EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" - EXPATLDFLAGS="-shared" - EXPATDYNAMIC=1 - ) - if use gromacs; then - EMAKEOPTS+=( - TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" - TNGINC="-I${EPREFIX}/usr/include" - TNGLDFLAGS="-shared" - TNGDYNAMIC=1 - ) - fi - if use sqlite; then - EMAKEOPTS+=( - SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" - SQLITEINC="-I${EPREFIX}/usr/include" - SQLITELDFLAGS="-shared" - SQLITEDYNAMIC=1 - ) - fi -} - -src_configure() { - local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" - rm -f configure.options && echo $myconf >> configure.options - - use cuda && myconf+=" CUDA" -# use mpi && myconf+=" MPI" - use tachyon && myconf+=" LIBTACHYON" - use xinerama && myconf+=" XINERAMA" - - export \ - PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ - PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ - PYTHON_LIBRARY="$(python_get_LIBS)" \ - NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ - NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" - - perl ./configure LINUX \ - ${myconf} || die -} - -src_compile() { - # build plugins - cd "${WORKDIR}"/plugins || die - - emake \ - ${EMAKEOPTS[@]} \ - LINUX - - # build vmd - cd "${S}"/src || die - emake -} - -src_install() { - # install plugins - cd "${WORKDIR}"/plugins || die - emake \ - PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ - distrib - - # install vmd - cd "${S}"/src || die - emake install - - # install docs - cd "${S}" || die - dodoc Announcement README doc/ig.pdf doc/ug.pdf - - # remove some of the things we don't want and need in - # /usr/lib - cd "${ED}"/usr/$(get_libdir)/vmd || die - rm -fr doc README Announcement LICENSE || \ - die "failed to clean up /usr/lib/vmd directory" - - # adjust path in vmd wrapper - sed \ - -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ - -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ - || die "failed to set up vmd wrapper script" - - # install icon and generate desktop entry - insinto /usr/share/pixmaps - doins "${WORKDIR}"/vmd.png - eprefixify "${WORKDIR}"/vmd.desktop - sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die - # Open PDB files with VMD - echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die - domenu "${WORKDIR}"/vmd.desktop -} diff --git a/sci-chemistry/vmd/vmd-1.9.3.ebuild b/sci-chemistry/vmd/vmd-1.9.3.ebuild deleted file mode 100644 index 88394af1970..00000000000 --- a/sci-chemistry/vmd/vmd-1.9.3.ebuild +++ /dev/null @@ -1,255 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs - -DESCRIPTION="Visual Molecular Dynamics" -HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" -SRC_URI=" - https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz - ${P}.src.tar" - -SLOT="0" -LICENSE="vmd" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="cuda gromacs msms povray sqlite tachyon xinerama" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RESTRICT="fetch" - -# currently, tk-8.5* with USE=truetype breaks some -# tk apps such as Sequence Viewer or Timeline. -CDEPEND=" - >=dev-lang/tk-8.6.1 - dev-lang/perl - dev-libs/expat - $(python_gen_cond_dep ' - || ( - dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}] - dev-python/numpy[${PYTHON_MULTI_USEDEP}] - ) - ') - sci-libs/netcdf:0= - virtual/opengl - >=x11-libs/fltk-1.1.10-r2:1 - x11-libs/libXft - x11-libs/libXi - ${PYTHON_DEPS} - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) - gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) - sqlite? ( dev-db/sqlite:3= ) - tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) - xinerama? ( x11-libs/libXinerama )" -DEPEND="${CDEPEND} - virtual/pkgconfig - dev-lang/swig" -RDEPEND="${CDEPEND} - sci-biology/stride - sci-chemistry/surf - x11-terms/xterm - msms? ( sci-chemistry/msms-bin ) - povray? ( media-gfx/povray ) - " - -VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" -# Binary only plugin!! -QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" -QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" -QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" - -pkg_nofetch() { - elog "Please download ${P}.src.tar.gz from" - elog "${VMD_DOWNLOAD}" - elog "after agreeing to the license and get" - elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" - elog "Place both into your DISTDIR directory" -} - -src_prepare() { - use cuda && cuda_sanitize - - epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch - - cd "${WORKDIR}"/plugins || die - - epatch \ - "${WORKDIR}"/${P}-gentoo-plugins.patch - - [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) - - sed \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CXX = g++:CXX = $(tc-getCXX):" \ - -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ - -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ - -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ - -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ - -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ - -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ - -e "s:-ltcl8.5:-ltcl:" \ - -i Make-arch || die "Failed to set up plugins Makefile" - - sed \ - -e '/^AR /s:=:?=:g' \ - -e '/^RANLIB /s:=:?=:g' \ - -i ../plugins/*/Makefile || die - - tc-export AR RANLIB - - sed \ - -e "s:\$(CXXFLAGS)::g" \ - -i hesstrans/Makefile || die - - # prepare vmd itself - cd "${S}" || die - - epatch "${WORKDIR}"/${P}-gentoo-base.patch - - # PREFIX - sed \ - -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ - -i configure || die - - sed \ - -e "s:gentoo-bindir:${ED}/usr/bin:g" \ - -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ - -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ - -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-gcc:$(tc-getCC):g" \ - -e "s:gentoo-g++:$(tc-getCXX):g" \ - -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ - -e "s:gentoo-cflags:${CFLAGS}:g" \ - -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ - -e "s:gentoo-nvflags::g" \ - -e "s:gentoo-ldflags:${LDFLAGS}:g" \ - -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ - -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ - -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ - -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ - -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -i configure || die - - if use cuda; then - sed \ - -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ - -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ - -i configure src/Makefile || die - sed \ - -e '/compute_/d' \ - -i configure || die - sed \ - -e 's:-gencode .*code=sm_..::' \ - -i src/Makefile || die - fi - - sed \ - -e "s:LINUXPPC:LINUX:g" \ - -e "s:LINUXALPHA:LINUX:g" \ - -e "s:LINUXAMD64:LINUX:g" \ - -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ - -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ - -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ - -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" - - EMAKEOPTS=( - TCLINC="-I${EPREFIX}/usr/include" - TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" - TCLLDFLAGS="-shared" - NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf) ${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" - NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf) ${EPREFIX}/usr/include" - NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" - NETCDFDYNAMIC=1 - EXPATINC="-I${EPREFIX}/usr/include" - EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" - EXPATLDFLAGS="-shared" - EXPATDYNAMIC=1 - ) - if use gromacs; then - EMAKEOPTS+=( - TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" - TNGINC="-I${EPREFIX}/usr/include" - TNGLDFLAGS="-shared" - TNGDYNAMIC=1 - ) - fi - if use sqlite; then - EMAKEOPTS+=( - SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" - SQLITEINC="-I${EPREFIX}/usr/include" - SQLITELDFLAGS="-shared" - SQLITEDYNAMIC=1 - ) - fi -} - -src_configure() { - local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" - rm -f configure.options && echo $myconf >> configure.options - - use cuda && myconf+=" CUDA" -# use mpi && myconf+=" MPI" - use tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon" - use xinerama && myconf+=" XINERAMA" - - export \ - PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ - PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ - PYTHON_LIBRARY="$(python_get_LIBS)" \ - NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ - NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" - - perl ./configure LINUX \ - ${myconf} || die -} - -src_compile() { - # build plugins - cd "${WORKDIR}"/plugins || die - - emake \ - ${EMAKEOPTS[@]} \ - LINUX - - # build vmd - cd "${S}"/src || die - emake -} - -src_install() { - # install plugins - cd "${WORKDIR}"/plugins || die - emake \ - PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ - distrib - - # install vmd - cd "${S}"/src || die - emake install - - # install docs - cd "${S}" || die - dodoc Announcement README doc/ig.pdf doc/ug.pdf - - # remove some of the things we don't want and need in - # /usr/lib - cd "${ED}"/usr/$(get_libdir)/vmd || die - rm -fr doc README Announcement LICENSE || \ - die "failed to clean up /usr/lib/vmd directory" - - # adjust path in vmd wrapper - sed \ - -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ - -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ - || die "failed to set up vmd wrapper script" - - # install icon and generate desktop entry - insinto /usr/share/pixmaps - doins "${WORKDIR}"/vmd.png - eprefixify "${WORKDIR}"/vmd.desktop - sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die - domenu "${WORKDIR}"/vmd.desktop -}