gentoo auto-resync : 09:04:2025 - 08:43:18

5 files changed, 18 insertions, 271 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 914785333bd2..0ff13fb551e0 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 11f25cc2ac7d..facc56d53f30 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,5 +1,5 @@
+AUX vmd-1.9.4_alpha57-fltk-null.patch 355 BLAKE2B 0828d0672b0b06fd3fba3154b0b1765446b1c64e02c3dc392407447b8556a958bc89aef90b971c87448d8f3bdb7c96080e8ca3ba34845a81fa3c34ccb2a7b131 SHA512 d30c1e053031babaf5b012aa22673cc3811b4dd779f1c3a7fd62e5f512da923f7567721643c55bbf6af000b55ea035543693de6dfcc31941c297ea673da6b30f
 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-r2.ebuild 7505 BLAKE2B 5c1d9dfa81a3201181049a89ba5c0f948bbb9e792a919a20ccc2811c28b9706524404625372c3742ebeef799b69784324cf7e6255ce80295bfca6f5925c9853a SHA512 17f987b251a18705d735d53ac0b608f50471bcac31bd7b4cf1ff6933762c083f8adf070d82f369cdd472d45496c41759b29ca31f438a825e0c04b4dcafc37f0b
-EBUILD vmd-1.9.4_alpha57-r3.ebuild 7396 BLAKE2B 98dc5ec7b07e0707e59d890bb132dbdeeac84217bce9d7f930084b14abd6fda791eadd8f308d6756df30ce5cac48c5d88233fd5258a1db8934bc8c2904d6f39b SHA512 12a02d51473572fc9a5d56b0d6dcd5201e5d4b701259a72eead0d277001edfdb32ff07e2f1c2167c6551e491222a981df6db9bb63618bd632692a6541a5ff62b
+EBUILD vmd-1.9.4_alpha57-r3.ebuild 7474 BLAKE2B 3a018d0d47c9c3ae1f8c3e2890b79b101ad707d9099b0cef3b1fc5d81423d2c675b98baeacb815eaf6ba25c4105e299b805d802cc7255ad2a4e73535d23d541a SHA512 a8516b40eb5a0800788143f51baf879292d28474794d3f8fd63b78186220701e9ccaf41121d6f7c7f973f83a2e64efbe9c06c5b9e8d9c74341f15a53ad21efd3
 MISC metadata.xml 697 BLAKE2B fe7fd00b1802dba4e503212cf8e0a91723dd6d255e346bca099bb2eb8cdb6291b27d1cbe9229e652c6f113e93cc3285bbf346977647d186f5403bd153a2c6d17 SHA512 f1bacf679ce42835e525265af48429d58d65a9aedc268e699cba731a1ea0bbe481777c726c2e1fd6a0ad7465c0e666f8f58145619d985cd0675eb1aff6b15472
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4_alpha57-fltk-null.patch b/sci-chemistry/vmd/files/vmd-1.9.4_alpha57-fltk-null.patch
new file mode 100644
index 000000000000..9207af9b2dee
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.4_alpha57-fltk-null.patch
@@ -0,0 +1,11 @@
+--- a/src/SelectionBuilder.C	2022-04-27 15:21:15.000000000 +0900
++++ b/src/SelectionBuilder.C	2025-03-20 15:02:33.086330280 +0900
+@@ -182,7 +182,7 @@
+ 
+   int line = self->macrobrowser->value();
+   if (!line) {
+-    self->macrooutput->value(NULL);
++    self->macrooutput->value("");
+     return;
+   }
+   const char *name = self->macrobrowser->text(line);
diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r2.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r2.ebuild
deleted file mode 100644
index 9addf38da980..000000000000
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r2.ebuild
+++ /dev/null
@@ -1,267 +0,0 @@
-# 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}
-	$(python_gen_cond_dep '
-		dev-python/numpy[${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=
-	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) -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 "${WORKDIR}"/${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)"
-		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-patches/vmd.png
-	eprefixify "${WORKDIR}"/vmd-patches/vmd.desktop
-	domenu "${WORKDIR}"/vmd-patches/vmd.desktop
-}
diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r3.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r3.ebuild
index cc5a157bf69a..23ba511a9c90 100644
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r3.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r3.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{10..13} )
 
 inherit cuda desktop prefix python-single-r1 toolchain-funcs xdg
 
@@ -120,6 +120,9 @@ src_prepare() {
 	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32122.html
 	eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4-tmpdir.patch
 
+	# https://bugs.gentoo.org/947213
+	eapply "${FILESDIR}"/${P}-fltk-null.patch
+
 	# PREFIX
 	sed \
 		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \