commit: b32ac5d0ffb292ed37ebe39c0b5c158e70a95f32 Author: Alfred Wingate <parona <AT> protonmail <DOT> com> AuthorDate: Tue Nov 18 04:36:13 2025 +0000 Commit: Sam James <sam <AT> gentoo <DOT> org> CommitDate: Mon Dec 1 02:27:43 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b32ac5d0
sci-geosciences/grass: fix segfault if flexiblas used Bug: https://bugs.gentoo.org/965293 Signed-off-by: Alfred Wingate <parona <AT> protonmail.com> Part-of: https://github.com/gentoo/gentoo/pull/44664 Signed-off-by: Sam James <sam <AT> gentoo.org> .../grass/files/grass-8.4.1-fix-segfault.patch | 99 +++++++ sci-geosciences/grass/grass-8.4.1-r2.ebuild | 295 +++++++++++++++++++++ 2 files changed, 394 insertions(+) diff --git a/sci-geosciences/grass/files/grass-8.4.1-fix-segfault.patch b/sci-geosciences/grass/files/grass-8.4.1-fix-segfault.patch new file mode 100644 index 000000000000..a85b55752cb0 --- /dev/null +++ b/sci-geosciences/grass/files/grass-8.4.1-fix-segfault.patch @@ -0,0 +1,99 @@ +https://bugs.gentoo.org/965293 +https://github.com/OSGeo/grass/issues/3731 +https://github.com/OSGeo/grass/pull/6632 +https://github.com/OSGeo/grass/commit/66c1733a055484761c1c25bdec937ebf0b31f00e + +From 66c1733a055484761c1c25bdec937ebf0b31f00e Mon Sep 17 00:00:00 2001 +From: Nicklas Larsson <[email protected]> +Date: Mon, 17 Nov 2025 13:07:11 +0100 +Subject: [PATCH] r.geomorphon: rename variable 'dirname' (#6632) + +The name is conflicting with the namesake of POSIX's function, +causing segmentation fault on some systems. + +Closes #3731 +--- a/raster/r.geomorphon/local_proto.h ++++ b/raster/r.geomorphon/local_proto.h +@@ -86,7 +86,7 @@ const char *form_long_name(const FORMS); + + /* pattern */ + int calc_pattern(PATTERN *pattern, int row, int cur_row, int col, const int); +-extern const char *dirname[]; ++extern const char *direction_name[]; + + /* geom */ + void generate_ternary_codes(void); +--- a/raster/r.geomorphon/pattern.c ++++ b/raster/r.geomorphon/pattern.c +@@ -6,7 +6,8 @@ + * 5|6|7 */ + static int nextr[NUM_DIRS] = {-1, -1, -1, 0, 1, 1, 1, 0}; + static int nextc[NUM_DIRS] = {1, 0, -1, -1, -1, 0, 1, 1}; +-const char *dirname[NUM_DIRS] = {"NE", "N", "NW", "W", "SW", "S", "SE", "E"}; ++const char *direction_name[NUM_DIRS] = {"NE", "N", "NW", "W", ++ "SW", "S", "SE", "E"}; + + /* + * A more thorough comparison using a few factors of different priority +@@ -125,7 +126,7 @@ int calc_pattern(PATTERN *pattern, int row, int cur_row, int col, + zenith_easting = nadir_easting = target_easting; + pattern->e[i] = cur_easting; + pattern->n[i] = cur_northing; +- prof_sso(dirname[i]); ++ prof_sso(direction_name[i]); + } + while (cur_distance < search_distance) { + if (cur_row + j * nextr[i] < 0 || +--- a/raster/r.geomorphon/profile.c ++++ b/raster/r.geomorphon/profile.c +@@ -145,42 +145,42 @@ void prof_pattern(const double o_elevation, const PATTERN *p) + + prof_sso("pattern"); + for (i = 0; i < NUM_DIRS; i++) +- prof_int(dirname[i], p->pattern[i]); ++ prof_int(direction_name[i], p->pattern[i]); + prof_eso(); + + prof_sso("rel_elevation_m"); + for (i = 0; i < NUM_DIRS; i++) +- prof_mtr(dirname[i], p->elevation[i]); ++ prof_mtr(direction_name[i], p->elevation[i]); + prof_eso(); + + prof_sso("abs_elevation_m"); + for (i = 0; i < NUM_DIRS; i++) +- prof_mtr(dirname[i], o_elevation + p->elevation[i]); ++ prof_mtr(direction_name[i], o_elevation + p->elevation[i]); + prof_eso(); + + prof_sso("distance_m"); + for (i = 0; i < NUM_DIRS; i++) +- prof_mtr(dirname[i], p->distance[i]); ++ prof_mtr(direction_name[i], p->distance[i]); + prof_eso(); + + prof_sso("offset_easting_m"); + for (i = 0; i < NUM_DIRS; i++) +- prof_mtr(dirname[i], p->x[i]); ++ prof_mtr(direction_name[i], p->x[i]); + prof_eso(); + + prof_sso("offset_northing_m"); + for (i = 0; i < NUM_DIRS; i++) +- prof_mtr(dirname[i], p->y[i]); ++ prof_mtr(direction_name[i], p->y[i]); + prof_eso(); + + prof_sso("easting"); + for (i = 0; i < NUM_DIRS; i++) +- prof_dbl(dirname[i], p->e[i]); ++ prof_dbl(direction_name[i], p->e[i]); + prof_eso(); + + prof_sso("northing"); + for (i = 0; i < NUM_DIRS; i++) +- prof_dbl(dirname[i], p->n[i]); ++ prof_dbl(direction_name[i], p->n[i]); + prof_eso(); + } + diff --git a/sci-geosciences/grass/grass-8.4.1-r2.ebuild b/sci-geosciences/grass/grass-8.4.1-r2.ebuild new file mode 100644 index 000000000000..843bacb202cc --- /dev/null +++ b/sci-geosciences/grass/grass-8.4.1-r2.ebuild @@ -0,0 +1,295 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{11..13} ) +PYTHON_REQ_USE="sqlite" # bug 572440 + +inherit desktop flag-o-matic python-single-r1 toolchain-funcs xdg + +DESCRIPTION="Free GIS with raster and vector functionality, as well as 3D vizualization" +HOMEPAGE="https://grass.osgeo.org/"; + +LICENSE="GPL-2" + +if [[ ${PV} == *9999* ]]; then + SLOT="0/8.4" +else + SLOT="0/$(ver_cut 1-2 ${PV})" +fi + +GVERSION=${SLOT#*/} +MY_PM="${PN}${GVERSION}" +MY_PM="${MY_PM/.}" + +if [[ ${PV} == *9999* ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/OSGeo/grass.git"; +else + MY_P="${P/_rc/RC}" + SRC_URI="https://grass.osgeo.org/${MY_PM}/source/${MY_P}.tar.gz"; + if [[ ${PV} != *_rc* ]] ; then + KEYWORDS="~amd64 ~ppc ~x86" + fi + + S="${WORKDIR}/${MY_P}" +fi + +IUSE="blas bzip2 cxx fftw geos lapack mysql netcdf nls odbc opencl opengl openmp pdal png postgres readline sqlite svm threads tiff truetype X zstd" +REQUIRED_USE=" + ${PYTHON_REQUIRED_USE} + opengl? ( X ) + pdal? ( cxx )" + +RDEPEND=" + ${PYTHON_DEPS} + >=app-admin/eselect-1.2 + $(python_gen_cond_dep ' + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/ply[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + ') + sci-libs/gdal:= + sys-libs/gdbm:= + sys-libs/ncurses:= + sci-libs/proj:= + virtual/zlib:= + media-libs/libglvnd + media-libs/glu + blas? ( + virtual/cblas[eselect-ldso(+)] + virtual/blas[eselect-ldso(+)] + ) + bzip2? ( app-arch/bzip2:= ) + fftw? ( sci-libs/fftw:3.0= ) + geos? ( sci-libs/geos:= ) + lapack? ( virtual/lapack[eselect-ldso(+)] ) + mysql? ( dev-db/mysql-connector-c:= ) + netcdf? ( sci-libs/netcdf:= ) + odbc? ( dev-db/unixODBC ) + opencl? ( virtual/opencl ) + opengl? ( virtual/opengl ) + pdal? ( >=sci-libs/pdal-2.0.0:= ) + png? ( media-libs/libpng:= ) + postgres? ( >=dev-db/postgresql-8.4:= ) + readline? ( sys-libs/readline:= ) + sqlite? ( dev-db/sqlite:3 ) + svm? ( sci-libs/libsvm:= ) + tiff? ( media-libs/tiff:= ) + truetype? ( media-libs/freetype:2 ) + X? ( + $(python_gen_cond_dep ' + >=dev-python/matplotlib-1.2[wxwidgets,${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + >=dev-python/wxpython-4.1:4.0[${PYTHON_USEDEP}] + ') + x11-libs/cairo[X] + x11-libs/libICE + x11-libs/libSM + x11-libs/libX11 + x11-libs/libXext + x11-libs/libXt + ) + zstd? ( app-arch/zstd:= )" +DEPEND="${RDEPEND} + X? ( x11-base/xorg-proto )" +BDEPEND=" + app-alternatives/yacc + app-alternatives/lex + sys-devel/gettext + virtual/pkgconfig + X? ( dev-lang/swig )" + +PATCHES=( + # bug 746590 + "${FILESDIR}/${PN}-flock.patch" + "${FILESDIR}"/grass-8.4.1-gdal-include.patch + "${FILESDIR}"/grass-8.4.1-fix-segfault.patch +) + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp + + if use lapack; then + local mylapack=$(eselect lapack show) + if [[ -z "${mylapack/.*reference.*/}" ]] && \ + [[ -z "${mylapack/.*atlas.*/}" ]]; then + ewarn "You need to set lapack to atlas or reference. Do:" + ewarn " eselect lapack set <impl>" + ewarn "where <impl> is atlas, threaded-atlas or reference" + die "setup failed" + fi + fi + + if use blas; then + local myblas=$(eselect blas show) + if [[ -z "${myblas/.*reference.*/}" ]] && \ + [[ -z "${myblas/.*atlas.*/}" ]]; then + ewarn "You need to set blas to atlas or reference. Do:" + ewarn " eselect blas set <impl>" + ewarn "where <impl> is atlas, threaded-atlas or reference" + die "setup failed" + fi + fi + + python-single-r1_pkg_setup +} + +src_prepare() { + # Fix unversioned python calls + sed -e "s:=python3:=${EPYTHON}:" -i "${S}/lib/init/grass.sh" || die + sed -e "s:= python3:= ${EPYTHON}:" -i "${S}/include/Make/Platform.make.in" || die + + default + + # When patching the build system, avoid running autoheader here. The file + # config.in.h is maintained manually upstream. Changes to it may lead to + # undefined behavior. See bug #866554. + # AT_NOEAUTOHEADER=1 eautoreconf + + ebegin "Fixing python shebangs" + python_fix_shebang -q "${S}" + eend $? + + # For testsuite, see https://bugs.gentoo.org/show_bug.cgi?id=500580#c3 + local ati_cards mesa_cards nvidia_cards render_cards + local prev_shopt=$(shopt -p nullglob) + shopt -s nullglob + ati_cards=$(echo -n /dev/ati/card*) + for card in ${ati_cards[@]}; do + addpredict "${card}" + done + mesa_cards=$(echo -n /dev/dri/card*) + for card in ${mesa_cards[@]}; do + addpredict "${card}" + done + nvidia_cards=$(echo -n /dev/nvidia*) + for card in ${nvidia_cards[@]}; do + addpredict "${card}" + done + render_cards=$(echo -n /dev/dri/renderD128*) + for card in ${render_cards[@]}; do + addpredict "${card}" + done + addpredict /dev/nvidiactl + ${prev_shopt} +} + +src_configure() { + # -Werror=strict-aliasing + # https://bugs.gentoo.org/862579 + # https://github.com/OSGeo/grass/issues/3506 + # + # Do not trust it with LTO either + append-flags -fno-strict-aliasing + filter-lto + + addwrite /dev/dri/renderD128 + + local myeconfargs=( + --enable-shared + --disable-w11 + --without-liblas + --without-opendwg + --with-regex + --with-gdal="${EPREFIX}"/usr/bin/gdal-config + --with-proj-includes="${EPREFIX}"/usr/include/proj + --with-proj-libs="${EPREFIX}"/usr/$(get_libdir) + --with-proj-share="${EPREFIX}"/usr/share/proj/ + $(use_with cxx) + $(use_with tiff) + $(use_with png libpng "${EPREFIX}"/usr/bin/libpng-config) + $(use_with postgres) + $(use_with mysql) + $(use_with mysql mysql-includes "${EPREFIX}"/usr/include/mysql) + $(use_with sqlite) + $(use_with opengl) + $(use_with odbc) + $(use_with fftw) + $(use_with blas) + $(use_with lapack) + $(use_with X cairo) + $(use_with truetype freetype) + $(use_with truetype freetype-includes "${EPREFIX}"/usr/include/freetype2) + $(use_with nls) + $(use_with readline) + $(use_with threads pthread) + $(use_with openmp) + $(use_with opencl) + $(use_with bzip2 bzlib) + $(use_with pdal pdal "${EPREFIX}"/usr/bin/pdal-config) + $(use_with netcdf netcdf "${EPREFIX}"/usr/bin/nc-config) + $(use_with geos geos "${EPREFIX}"/usr/bin/geos-config) + $(use_with svm libsvm) + $(use_with X x) + $(use_with zstd) + ) + econf "${myeconfargs[@]}" +} + +src_compile() { + # we don't want to link against embedded mysql lib + emake CC="$(tc-getCC)" MYSQLDLIB="" +} + +src_install() { + emake DESTDIR="${ED}" \ + INST_DIR=/usr/$(get_libdir)/${MY_PM} \ + prefix=/usr/ BINDIR=/usr/bin \ + install + + pushd "${ED}"/usr/$(get_libdir)/${MY_PM} >/dev/null || die + + local HTML_DOCS=( docs/html/. ) + einstalldocs + + # translations + if use nls; then + insinto /usr/share/locale + doins -r locale/. + fi + + popd >/dev/null || die + + # link libraries in the ~standard~ place + local f file + for f in "${ED}"/usr/$(get_libdir)/${MY_PM}/lib/*; do + file="${f##*/}" + dosym ${MY_PM}/lib/${file} /usr/$(get_libdir)/${file} + done + + # link headers in the ~standard~ place + dodir /usr/include/ + dosym ../$(get_libdir)/${MY_PM}/include/grass /usr/include/grass + + # set proper python interpreter + sed -e "s:os.environ\[\"GRASS_PYTHON\"\] = \"python3\":\ +os.environ\[\"GRASS_PYTHON\"\] = \"${EPYTHON}\":" \ + -i "${ED}"/usr/bin/grass || die + + if use X; then + local GUI="--gui" + make_desktop_entry "/usr/bin/grass ${GUI}" "${PN}" "${PN}-48x48" "Science;Education" + doicon -s 48 gui/icons/${PN}-48x48.png + fi + + # install .pc file so other apps know where to look for grass + insinto /usr/$(get_libdir)/pkgconfig/ + doins grass.pc + + # fix weird +x on tcl scripts + find "${ED}" -name "*.tcl" -exec chmod +r-x '{}' \; || die +} + +pkg_postinst() { + use X && xdg_pkg_postinst +} + +pkg_postrm() { + use X && xdg_pkg_postrm +}
