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-rw-r--r--sci-chemistry/Manifest.gzbin9199 -> 9186 bytes
-rw-r--r--sci-chemistry/autodock_vina/Manifest3
-rw-r--r--sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild3
-rw-r--r--sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-boost-1.85.patch21
-rw-r--r--sci-chemistry/molmol/Manifest2
-rw-r--r--sci-chemistry/molmol/molmol-2k_p2-r9.ebuild2
-rw-r--r--sci-chemistry/vmd/Manifest1
-rw-r--r--sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild263
-rw-r--r--sci-chemistry/wxmacmolplt/Manifest3
-rw-r--r--sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch11
-rw-r--r--sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild48
-rw-r--r--sci-chemistry/xds-bin/Manifest6
-rw-r--r--sci-chemistry/xds-bin/xds-bin-20240831.ebuild (renamed from sci-chemistry/xds-bin/xds-bin-20170930.ebuild)24
13 files changed, 311 insertions, 76 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 4e4ba7251c80..dbbd5c59e90e 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
Binary files differ
diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest
index 8cd80f22576c..6f84dbd72847 100644
--- a/sci-chemistry/autodock_vina/Manifest
+++ b/sci-chemistry/autodock_vina/Manifest
@@ -1,9 +1,10 @@
AUX 1.1.2-gentoo.patch 2448 BLAKE2B f63add1d0fec8716672672af78fe8f34053bf060044e78fcf30ca6054e4075a5f12ac3a903812c9cd619dc34fa854603c8369c8acfcf17130d1b24b50b3d5373 SHA512 d8165d88f3e91064c74f1506a7f58473a74f6ebf993165827694d78170b29227dc378c61a7f096a3c49708b713583aca3d5714827d1fe43a5bb37f3d648d2613
AUX autodock_vina-1.1.2-boost-filesystem.patch 2936 BLAKE2B 70c55e95e9728221ba80177989fde0cc6c93b479779aa0dda45dcad79b97018fe934ea56b4ede4af20ce867b6ed39c3958a5529b8f286aec33ec7ea53d339ada SHA512 4226fb0d7196362a02afa4e0b0616146ef816a439dd63e1bffbfef183975fe7e6260318f919e9d9835d2d47973542b5340e93ad35b070467e42c0990f9a635f7
AUX autodock_vina-1.1.2-missing-debug-decl.patch 365 BLAKE2B 959b46facdce27850a1f9fd6c66ecc297e4ad089e79896b9fe2127e425bd1bfcfce5d676cf2e4336c47d3a72b0e8319c791fdf1a5807f244cf5b4528de8cbb25 SHA512 ddbdca76fca16b46fd042b57eb941b7ba67f59f46c35dc18428ea6873c8ed5f03051247b8c667a08af8de40fccb0caf851848bb9082536225cacf8eb3e313c98
+AUX autodock_vina-1.2.5-boost-1.85.patch 733 BLAKE2B 4163ff875f28ba883a0a0b98f23ba8341f1eb7fd29831e3654c7bb739605dfb1edf2c40867289fb7eaf3c59cd9220d856d914f55dbaa211acdf016789c8e10e8 SHA512 2bcabc02d3456b461a118e1d14932c8c2a091e8176cd927c1b423bf24aefecfb82e0a446f66d97830bebdee7b56fc7c1bc4d45512ddfd81bb827b43b897a1696
AUX autodock_vina-1.2.5-gentoo.patch 2803 BLAKE2B a365f3c83e5cfa366e458ce87e0d1e0a305b137040fbf3e0c0b2549e3cfde617c6934aaa4da6a992440400fbaa3f73b42faa665b1a5d1464f2a8d103b5469af3 SHA512 46b5c10123cf721eb80c6fa8d87f2d8405d269915d6bfec3eff5f1d5ee870e301608748ae245f7997f5c8a4b7c27e50fa222eff192c84ec4c82946c1783fa44b
DIST autodock_vina-1.2.5.tar.gz 24158966 BLAKE2B c11493fcb35d409b97f639c4da48967d5df450781d412d80a951b95162555f4b1dfba809a01062136a7f0664c0b9a01a42b5403ee1d278a57afd669cf1f96321 SHA512 d36908e5833d22bcbc4dae353ef32b905d6eb46511302f7583a291398bfadff5e75fc99ce7b380860578b2257e5c32434cc75b1ca51fafb4b5f12d9477a878e9
DIST autodock_vina_1_1_2.tgz 67366 BLAKE2B dc754bf522795ebfbfcf89a2df4e3761d941c1f0ce05cf56898720c1e855f5dd00fd2a583f5a8d218fa2e738d37e014a9b3239b9aa989b9018a6a33f8f0bd02c SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9
EBUILD autodock_vina-1.1.2-r1.ebuild 972 BLAKE2B aaad2df1b51bdd684ca5fd9aaa54353b161e4e5d72b59210919349993fb6ad2c796f8b6bff4d420ad64e52273a26bf9f7d9b90f95387db5f7814352ebdb5be1c SHA512 123083cc13a05fd10627f9750274de9f7070e4068b718b4407230f9af22ead0a4f6ef33cda4b86a2d1e08856c31a58f8cc0d0ef8d861f196275332095885e44b
-EBUILD autodock_vina-1.2.5.ebuild 1034 BLAKE2B a123bd340d3c5763d39cad3e2d9d7afbd6e4e0d96d1041736978af88295c58645e3ea53e634f1bb41e905d54afa94e8baa784fd27d6a6f577915e8c3635acdcc SHA512 383fa58b584f9f3ec6e1eb403b1845d3e7cfd66e88b89e857ffedc4847444caede2953f581f20b7414d5a9ec20e3f8bc4c864ded5206b182eb5c9ea38055401e
+EBUILD autodock_vina-1.2.5.ebuild 1070 BLAKE2B 69e0e7fce39fa45ed6cf5dc01fef51a575353bfdd2cb5c333c2d2269cc38dccf20bac1c1b3caa273929e4848e9c66add90336dba767a9adc269d3d455a4428da SHA512 1bd3e7de0795caf8379a03becb1db12f7a24a83efa26336ac07355c09bda4633e36604dd52afe906064dcd479c93d30a1e664699be820ba9e92cf706bea75e6e
MISC metadata.xml 1002 BLAKE2B 775eb10f8c916ff2b5655243224d1608a865228b1e300b636c793c1c86a4634a33fdda3bf4a8f56f43ad8bb734413963e490b738d2baf69168bb8dea6e3e6106 SHA512 0ea67a95d4bb8f90323ceeeced2d47f4732ee5fb3daa45d8690c13b71daf67729b33cdf3024a4706d2ee9e296b67474141125e95801b9f799228391571395532
diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
index e9edf1f9c991..dd396732c357 100644
--- a/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.2.5.ebuild
@@ -15,7 +15,7 @@ S="${WORKDIR}/${MY_PN}-${PV}/build/linux/release"
LICENSE="Apache-2.0"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="amd64 ~x86"
IUSE="debug"
RDEPEND="dev-libs/boost:="
@@ -23,6 +23,7 @@ DEPEND="${RDEPEND}"
PATCHES=(
"${FILESDIR}"/${P}-gentoo.patch
+ "${FILESDIR}"/${P}-boost-1.85.patch
)
src_prepare() {
diff --git a/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-boost-1.85.patch b/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-boost-1.85.patch
new file mode 100644
index 000000000000..55906b093a49
--- /dev/null
+++ b/sci-chemistry/autodock_vina/files/autodock_vina-1.2.5-boost-1.85.patch
@@ -0,0 +1,21 @@
+https://bugs.gentoo.org/932237
+--- a/src/lib/vina.h
++++ b/src/lib/vina.h
+@@ -35,7 +35,6 @@
+ #include <boost/program_options.hpp>
+ #include <boost/filesystem/fstream.hpp>
+ #include <boost/filesystem/exception.hpp>
+-#include <boost/filesystem/convenience.hpp> // filesystem::basename
+ #include <boost/thread/thread.hpp> // hardware_concurrency // FIXME rm ?
+ #include <boost/algorithm/string.hpp>
+ //#include <openbabel/mol.h>
+--- a/src/split/split.cpp
++++ b/src/split/split.cpp
+@@ -30,7 +30,6 @@
+ #include <boost/program_options.hpp>
+ #include <boost/filesystem/fstream.hpp>
+ #include <boost/filesystem/exception.hpp>
+-#include <boost/filesystem/convenience.hpp> // filesystem::basename
+
+ #include "file.h"
+ #include "parse_error.h"
diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest
index 5fdb76ae39ea..76e5c78f437b 100644
--- a/sci-chemistry/molmol/Manifest
+++ b/sci-chemistry/molmol/Manifest
@@ -4,5 +4,5 @@ DIST molmol-2k.2.0-src.tar.gz 1088805 BLAKE2B cd649604f6ee491d3a4485391ecdaa48dc
DIST molmol-patches.tbz2 17528 BLAKE2B b91270a980f290edc169be00639e86b3272281c9fe237750f5778eab1605ed482c09bdaf90660a5edf74bd04b3e31adc755e77e39aea6c75d88b6db9bf47a6d6 SHA512 bd94baf0a378f40f854f396963edd9b9e4afc5c56462ee6f8b68889290afdb4c5d9b10878aa5619d0a70153453fe6ee8e7540064522c6db0291ae9162bba9287
DIST molmol_256.png 22668 BLAKE2B c7d75b8e0d738b48790bea25e21ec60d57a8181253518c70d6f18d93c64eef3c9acf90213fdbdf2dde272e85a04a6442e4e4a9c375829f369380d88c9c0ca57c SHA512 5e7975f54a7462161dc630ee973e9a8126b9c120e0d8d6b62007384c970ce39792e52300edc25dc7a85209845801d749d9ecba02899f3e18b18f5a5fdbc28a97
EBUILD molmol-2k_p2-r8.ebuild 2284 BLAKE2B fa9954fca3dd8b52450beb1c0901abc71743672d7a76e2daa2bb05f52280ecf7dec5c401da24ce3e72f429cb69b27738117e33d41b49a96836b1b407efef67f0 SHA512 d813743572479b5eb0ed4181d42743402c4bd0a5a8e012f32bad03c4be68f38329722b749abc91845ba9c25642b19f5e2c4b5578ed9d3f7d03beaabbaa3345f5
-EBUILD molmol-2k_p2-r9.ebuild 2314 BLAKE2B f54b8793c88c3e5d14a128e922d9d22dcc5ad861c76a205b84a0a4d8f36ccdf8e6259955e71257689424ac48819fcd3350105e4472202681e8a9bc80c43d9d21 SHA512 56e0839d1f3d971d549c2bcde64115b17e3b7adccaf63b75e7221247684c7b7ee40df89d30c2b0d0acd28aa4e147523644f34ce496cf6a9e51ff540616123bda
+EBUILD molmol-2k_p2-r9.ebuild 2313 BLAKE2B fecc271cadf3eb73478b1adc674a6d369ee7bbb05c38e10ae78ebbc886782962f7c33ea07ef4d065e643ee7f5a71e99801f72c290cb7ab437833141dcfe80a99 SHA512 d173ed8f60c833485bf639fa8fc0ace5ff1ae46316be319d2cd1feb5f5201484ed9e8bba46054dfc91303d71051b52d4fa943638ecf6b843514fa9585bc421a5
MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild
index 29769cede153..14378809c07a 100644
--- a/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild
+++ b/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild
@@ -25,7 +25,7 @@ S="${WORKDIR}"
LICENSE="molmol"
SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
RDEPEND="
|| (
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index b87d6941446e..1135f253ff10 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,4 +1,5 @@
DIST vmd-1.9.4_alpha57-gentoo-patches.tar.xz 14612 BLAKE2B e50a2fc734038207174dd5cc525f01824ce324a65b8ce604f83862ce50be6b1950d199188a717e2368b2b050256a4705662009e3530d621b19c52bb109b6a844 SHA512 6283076e47dfcd780bbc94f9ca2b044a028a472c09d78616d373813d81ec764bf1697e56a8f487f9f0999cf409c0f141bf248156f60851073347d1b640a6953c
DIST vmd-1.9.4a57.src.tar.gz 43155120 BLAKE2B de0da96f6681c24e7b1d38890f109088187198cbdddb3d86d783322e837b7a71224085699f3addf2833cf293ab2689f06ab47df284b8fbe080162740094ae844 SHA512 0a3726d8fa279ac62c368cd18724cd09535618454ff6e299d147291ef5d4198ad9d58a94f0b05699ec8a23128753c55e7397c95a5ce194e36d3fabef1bcf454c
+EBUILD vmd-1.9.4_alpha57-r1.ebuild 7407 BLAKE2B a2dd25449e23acbb09181e939b27c0bd5fd81344ffb1d64f49dc26a1bc89a8e550418c27bf436d291bb91cda4f1ce3d0b520ac43e5eba065ddc3ae54154f77db SHA512 480b04d19e75c51f6ecc77e2decca4b9e645985f5d4f2f7ee5f441a6c8530658e5c8d588fd3f77457c9cce8e4b43203281eb295cb985a926907a62459cb25557
EBUILD vmd-1.9.4_alpha57.ebuild 7516 BLAKE2B 3694b45e09af9f1ca33854543a902230bef3b72f1c2b0cf0f0e446b0e1276720e84da17eee0c0bb70eb4321c7602bdb7e2490e619a260f616d9d664c53ac4127 SHA512 80d1c81faca51066b5a4c3e6f3bf437b3ac3e5c01c0b4d156d6bac219f4dc90e1652ef77032539cfff73e62b9e19a381ec30a8a77a0de32d724c32faf39730bf
MISC metadata.xml 697 BLAKE2B fe7fd00b1802dba4e503212cf8e0a91723dd6d255e346bca099bb2eb8cdb6291b27d1cbe9229e652c6f113e93cc3285bbf346977647d186f5403bd153a2c6d17 SHA512 f1bacf679ce42835e525265af48429d58d65a9aedc268e699cba731a1ea0bbe481777c726c2e1fd6a0ad7465c0e666f8f58145619d985cd0675eb1aff6b15472
diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild
new file mode 100644
index 000000000000..18bdb88a4c0c
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild
@@ -0,0 +1,263 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit cuda desktop prefix python-single-r1 toolchain-funcs xdg
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+
+MY_PV="${PV/_alpha/a}"
+MY_P="${PN}-${MY_PV}"
+SRC_URI="
+ ${MY_P}.src.tar.gz
+ fetch+https://dev.gentoo.org/~pacho/${PN}/${PN}-1.9.4_alpha57-gentoo-patches.tar.xz
+"
+S="${WORKDIR}/${MY_P}"
+LICENSE="vmd"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RESTRICT="fetch"
+
+CDEPEND="${PYTHON_DEPS}
+ $(python_gen_cond_dep '
+ >=dev-python/numpy-2[${PYTHON_USEDEP}]
+ ')
+ >=dev-lang/tk-8.6.1:0=
+ dev-lang/perl
+ dev-libs/expat
+ sci-libs/netcdf:0=
+ virtual/opengl
+ >=x11-libs/fltk-1.1.10-r2:1
+ x11-libs/libXft
+ x11-libs/libXi
+ 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-misc/xdg-utils
+ 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/intersurf/bin/intersurf.so"
+QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil/volutil"
+QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil/volutil"
+
+pkg_nofetch() {
+ elog "Please download ${MY_P}.src.tar.gz from"
+ elog "${VMD_DOWNLOAD}"
+ elog "after agreeing to the license."
+ elog "Place it into your DISTDIR directory."
+}
+
+src_prepare() {
+ # Apply user patches from ${WORKDIR} to allow patching on patches
+ # subdir too
+ cd "${WORKDIR}"
+ default
+
+ # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32121.html
+ # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32116.html
+ eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4a51-gentoo-plugins.patch
+
+ use cuda && cuda_sanitize
+
+ # Prepare plugins
+ cd plugins || die
+
+ 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):" \
+ -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX):" \
+ -e "s:-ltcl8.5:-ltcl:" \
+ -i Make-arch || die "Failed to set up plugins Makefile"
+
+ sed \
+ -e '/^AR /s:=:?=:g' \
+ -e '/^RANLIB /s:=:?=:g' \
+ -i ../plugins/*/Makefile || die
+
+ tc-export AR RANLIB
+
+ sed \
+ -e "s:\$(CXXFLAGS)::g" \
+ -i hesstrans/Makefile || die
+
+ # prepare vmd itself
+ cd "${S}" || die
+
+ eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4a51-gentoo-paths.patch
+
+ # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32122.html
+ eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4-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)"
+ 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)"
+ EXPATDYNAMIC=1
+ )
+ if use gromacs; then
+ EMAKEOPTS+=(
+ TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
+ TNGINC="-I${EPREFIX}/usr/include"
+ TNGDYNAMIC=1
+ )
+ fi
+ if use sqlite; then
+ EMAKEOPTS+=(
+ SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
+ SQLITEINC="-I${EPREFIX}/usr/include"
+ 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-patches/vmd.png
+ eprefixify "${WORKDIR}"/vmd-patches/vmd.desktop
+ domenu "${WORKDIR}"/vmd-patches/vmd.desktop
+}
diff --git a/sci-chemistry/wxmacmolplt/Manifest b/sci-chemistry/wxmacmolplt/Manifest
index 15e8ec679986..eed90ecfb010 100644
--- a/sci-chemistry/wxmacmolplt/Manifest
+++ b/sci-chemistry/wxmacmolplt/Manifest
@@ -1,6 +1,3 @@
-AUX wxmacmolplt-7.5-glew.patch 232 BLAKE2B 9e0bd2849cc20664ca4a6b6678d2d78a723ae3e730225355dd70db0cac56d501c14aaa34d86d2ff87932feb950178a7245a943b763bde728f64a07a49ed4ba29 SHA512 cf1f77f9a86224b866f55154316a044314fda47a82de9b5be4ee58ed4ea8f4a07f9540e7060f477249b773e147739f15f43df293110045bdbca9567c60fbd5dc
-DIST wxmacmolplt-7.5.tar.gz 1965376 BLAKE2B 01033266ae66a215582a62690e792ca4ae82c8a8885fe277e2e77ee67ff70f02f6a9c10467ea6f3cee15933c6c89ba3c6137c9d29e47322ac4f395a3efd41383 SHA512 a1064d5068136b2a91328c7f912ff57d4741081d6d61437e7b4567fbf732917485b391493d637b8892bdad50b539363cfa9c778bb35407a9c0a2bfed20e42bc0
DIST wxmacmolplt-7.7.2.tar.gz 2012054 BLAKE2B 0e419d9700dd6461a4520722f43cc36cdaa2f51920868a868bdd58db169ed92f88c71d4ce0d79446c4c564eb794f7327b0eef5f87d9ab5a639829287b29482d6 SHA512 bf4b3126bbc8657a604f8dee8b022a17dbf4633a877318ceb45d803456acb0da007c2edae23f581fb6eeafd6ea411d147fbc076acb07aba3dcb8ee55b9c486fa
-EBUILD wxmacmolplt-7.5-r1.ebuild 986 BLAKE2B 67cccea1d2e7886ee67f78ac54548047c2fe889dedfef45956a4614149d5597fd0376f0f01fd59085c9f925faa2284c2c22d4bae2d8ee98f2eca3be6b06e96ed SHA512 6e1d9051621a36deb7aeb997aa93a0b5becea1b3f7512fc56d2ee97788b5a9bedace25fb40a7a7b4e77a76830e7f8aa61ad0c32ea3e1afdb66b744197d50daf0
EBUILD wxmacmolplt-7.7.2.ebuild 982 BLAKE2B edc3b4383a20ec6039472319273947988aa77de31622a40bd604857560684612d79dd6743c2048fc423e928c5a9c8b45e38899568a68de32069591b7593ef2b7 SHA512 99e5cf215f4ef74d6c7480b9aa1732cc1eda079634e2e09e61b83f080b9093febea8d48c77d4e5dbf20bc32c3eecfef9e26b233ec7e549818b3714b13e8ac82f
MISC metadata.xml 717 BLAKE2B e2344ebd6332d01a309edb0951483adff1342584fd1a9a6b6890c4cae7bba86f8e9f874b4200726845c1aed7712a4459fddda27ae544ee98da63098e897b499e SHA512 169c1aa0ff6cdfe7ed5e155bd1bdb2ea817c59501dde6c7caa1d25bc4826341516731e3082bf7960cc6f87fdf2a26983c04e26baea21b7bdff815eef45e4521b
diff --git a/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch b/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch
deleted file mode 100644
index 809d7723cbb0..000000000000
--- a/sci-chemistry/wxmacmolplt/files/wxmacmolplt-7.5-glew.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/configure.ac
-+++ b/configure.ac
-@@ -20,7 +20,7 @@
- ;;
- *)
- HOST=LINUX
-- LIBGL="-lGL -lGLU"
-+ LIBGL=`${PKG_CONFIG} --libs glu glew`
- ;;
- esac
- AM_CONDITIONAL(HOST_IS_MSW, [test "x$HOST" == xMSW])
diff --git a/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild b/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild
deleted file mode 100644
index d100dad51cbc..000000000000
--- a/sci-chemistry/wxmacmolplt/wxmacmolplt-7.5-r1.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-WX_GTK_VER=3.0
-inherit autotools desktop toolchain-funcs wxwidgets
-
-DESCRIPTION="Chemical 3D graphics program with GAMESS input builder"
-HOMEPAGE="http://www.scl.ameslab.gov/MacMolPlt/"
-SRC_URI="https://wxmacmolplt.googlecode.com/files/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- media-libs/glew:0=
- media-libs/mesa[X(+)]
- x11-libs/wxGTK:${WX_GTK_VER}[X,opengl]"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-PATCHES=( "${FILESDIR}"/${P}-glew.patch )
-
-src_prepare() {
- default
- sed \
- -e "/^dist_doc_DATA/d" \
- -i Makefile.am || die "Failed to disable installation of LICENSE file"
- eautoreconf
-}
-
-src_configure() {
- tc-export PKG_CONFIG
-
- setup-wxwidgets unicode
- econf \
- --with-glew \
- --without-ming
-}
-
-src_install() {
- default
-
- doicon resources/${PN}.png
- make_desktop_entry ${PN} wxMacMolPlt ${PN} "Science;DataVisualization;"
-}
diff --git a/sci-chemistry/xds-bin/Manifest b/sci-chemistry/xds-bin/Manifest
index f4e1a6e0072a..09c641ceac9d 100644
--- a/sci-chemistry/xds-bin/Manifest
+++ b/sci-chemistry/xds-bin/Manifest
@@ -1,4 +1,4 @@
-DIST XDS-INTEL64_Linux_x86_64-20170930.tar.gz 9501598 BLAKE2B 33eea09210e9196859f62e66770aef3b34ace7d0cbe50607ef03ba37943fdb13ddf570b53cb2a7e668e650284ff245767a9cca9f6595de9fdb1815bb9625b56e SHA512 8da1d75633e8bf8495c30926a622f57aa0a51ea3b724101c96da6fae0a303860a4a4a8eaf3ecdf66948f18e702211aab3800760ca498c4562e947e3f94c25a4d
-DIST XDS_html_doc-20170930.tar.gz 117249 BLAKE2B 81e0c216eee38f21acc4dba299a20c4790f4aa1dc58e2d0dab5474784bf01842db41ab869b6d36cdfc9a31771e0bcad41b062bbf000771552c7de36f36a2291e SHA512 bbc24eeb0f8a63e6186906b0c0ee67efa83d1cdd169b091878c323455e2448ee6cb1667467bc9701b4e1839af2d10d4cb3e8f8d080b7dd5e449fda03c2aa8f89
-EBUILD xds-bin-20170930.ebuild 1174 BLAKE2B 9a5a18719f52eab2f114ce58ba6ade158ae138b70c092967d5ed0adeae6867963c4cf6391f6bdedd0296a56fad46ab1214cde0faa02c4dab701d572268f3b8f6 SHA512 47963c7d31eaa1d6f2eaf172ef67a7d448e3bec36a9e6da35f85532bb878996ef6791977efd06874e0d3d790820306214e190af1ea07bca30f3320ed64605470
+DIST XDS-INTEL64_Linux_x86_64-20240831.tar.gz 11067644 BLAKE2B d8687af54aad5694937cc633f511766147bb52616a388f03d0d052239a0f81b6e3692be0f234ea012905c89e13f2ef45e0254babe1e23598d954b2e65ed93d20 SHA512 773f074237311c8ea2d6dda974250cf906f84db02589bb40b646ff77afac2ee7d978d272993ab5f9b9f55c9dde7965b8e4fba7222349bf3665679f90ec6ef658
+DIST XDS_html_doc-20240831.tar.gz 151503 BLAKE2B c559d1a7b4ca75b00d5d37d2c9248fea177cca6a2dac5a9b42443430477337f8bc99add4f89f9eac2d57592b6b5843e167d4e86c6c3ce0ccbb5ba91234d534d8 SHA512 5d3a20dd0b6458c5bfd8ed46f4963fd53f59208fff72278acac19237c988537bae9d7b3c993342c8a9abc03e2ab5aed98a002caeb853fb87c19ae19a32f05faa
+EBUILD xds-bin-20240831.ebuild 1459 BLAKE2B a03054c1af3d8ad3b972a08ca0bf6e07d252b047ad3fea490e8e71d751d33e9969d7853f1b00b6ee2080d5e10bfefd8a0e085a9eb4f25cbbf9f39ad3a55ff445 SHA512 4af84bc488142b629636b3a9516d3b56944b4078c865ab10c5acc0a8898b105c5677ad9bb588cc58823a6d34275dd8c6eb9610116ff748e3c55fc31ce75a2c79
MISC metadata.xml 272 BLAKE2B 531e98b72776bbe9126811b70943add0f6f43141b01cb75b17ac2c8d1cfb6a9b349022fd411894d2b8eeb0612a73db10aed4ba71f9624bd6dbd172a05fca2c76 SHA512 04f5575703aaaa95e575460ae3de428d3da173b3b741ab52b4aad31e381fef78b325f49f99622ec26a65024437759ea013fc525bd63ee553003c71afcc40d10c
diff --git a/sci-chemistry/xds-bin/xds-bin-20170930.ebuild b/sci-chemistry/xds-bin/xds-bin-20240831.ebuild
index 4e609092fa03..4fcd833d3071 100644
--- a/sci-chemistry/xds-bin/xds-bin-20170930.ebuild
+++ b/sci-chemistry/xds-bin/xds-bin-20240831.ebuild
@@ -1,21 +1,31 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=8
DESCRIPTION="Software for processing single-crystal X-ray monochromatic diffraction data"
-HOMEPAGE="http://xds.mpimf-heidelberg.mpg.de/"
+HOMEPAGE="https://xds.mr.mpg.de"
SRC_URI="
- ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz -> XDS-INTEL64_Linux_x86_64-${PV}.tar.gz
- ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS_html_doc.tar.gz -> XDS_html_doc-${PV}.tar.gz"
+ https://xds.mr.mpg.de/XDS-INTEL64_Linux_x86_64.tar.gz -> XDS-INTEL64_Linux_x86_64-${PVR}.tar.gz
+ https://xds.mr.mpg.de/XDS_html_doc.tar.gz -> XDS_html_doc-${PVR}.tar.gz"
LICENSE="free-noncomm"
SLOT="0"
KEYWORDS="-* ~amd64"
IUSE="smp"
+RESTRICT="fetch"
QA_PREBUILT="opt/xds-bin/*"
+# The web site uses a certificate that is not in the system certificate store.
+# Use a web browser to download, instead.
+pkg_nofetch() {
+ elog "Please visit"
+ elog "https://xds.mr.mpg.de/html_doc/downloading.html"
+ elog "and download XDS-INTEL64_Linux_x86_64.tar.gz and XDS_html_doc.tar.gz."
+ elog "Please save them as: ${A}. in your \${DISTDIR}"
+}
+
src_unpack() {
default
mv XDS-* "${S}" || die
@@ -33,7 +43,7 @@ src_install() {
dosym ../${PN}/${i}${suffix} /opt/bin/${i}
done
- for i in 2cbf cellparm forkcolspot forkintegrate merge2cbf pix2lab xdsconv; do
+ for i in 2cbf cellparm forkxds merge2cbf pix2lab xdsconv; do
dosym ../${PN}/${i} /opt/bin/${i}
done
@@ -42,5 +52,5 @@ src_install() {
}
pkg_postinst() {
- elog "This package will expire on September 30, 2017"
+ elog "This package will expire on August 31, 2024"
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-18 17:05:16 +0000