commit: c7ca08dc6bc40fa62cee3dae9e3b4467496a9d96 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Wed Feb 11 10:00:41 2026 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Wed Feb 11 10:00:41 2026 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c7ca08dc
sci-biology/raxml: fix C23 build issues Closes: https://bugs.gentoo.org/941996 Closes: https://bugs.gentoo.org/944195 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/raxml/files/raxml-8.2.13-c23.patch | 19 +++++++++++++++++++ sci-biology/raxml/raxml-8.2.13.ebuild | 9 ++++++--- 2 files changed, 25 insertions(+), 3 deletions(-) diff --git a/sci-biology/raxml/files/raxml-8.2.13-c23.patch b/sci-biology/raxml/files/raxml-8.2.13-c23.patch new file mode 100644 index 000000000000..b0ce95bf2ae8 --- /dev/null +++ b/sci-biology/raxml/files/raxml-8.2.13-c23.patch @@ -0,0 +1,19 @@ +--- a/rmq.h ++++ b/rmq.h +@@ -2,15 +2,12 @@ + #define _rmq_h_ + + #include <math.h> +- +-#define false 0 +-#define true 1 ++#include <stdbool.h> + + typedef int DT; // use long for 64bit-version (but take care of fast log!) + typedef unsigned int DTidx; // for indexing in arrays + typedef unsigned char DTsucc; + typedef unsigned short DTsucc2; +-typedef int bool; + DTidx query(DTidx, DTidx); + void RMQ_succinct(DT* a, DTidx n); + void RMQ_succinct_destroy(void); diff --git a/sci-biology/raxml/raxml-8.2.13.ebuild b/sci-biology/raxml/raxml-8.2.13.ebuild index 859016195389..0aa191b50785 100644 --- a/sci-biology/raxml/raxml-8.2.13.ebuild +++ b/sci-biology/raxml/raxml-8.2.13.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2024 Gentoo Authors +# Copyright 1999-2026 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -12,11 +12,14 @@ S="${WORKDIR}/standard-RAxML-${PV}" LICENSE="GPL-2" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" IUSE="cpu_flags_x86_sse3 +threads" # mpi is not supported in version 7.2.2. mpi is enabled by adding -DPARALLEL to CFLAGS -PATCHES=( "${FILESDIR}"/${P}-makefile.patch ) +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-c23.patch +) src_configure() { use cpu_flags_x86_sse3 &&
