commit: dd4ee9b222cf98145af87c7ca36dc3d0e40cd8c0 Author: Horea Christian <chr <AT> chymera <DOT> eu> AuthorDate: Mon Jan 22 17:59:43 2024 +0000 Commit: Horea Christian <horea.christ <AT> gmail <DOT> com> CommitDate: Mon Jan 22 17:59:43 2024 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=dd4ee9b2
sci-biology/SPAdes: keyword 3.15.5 for ~amd64 Signed-off-by: Horea Christian <chr <AT> chymera.eu> sci-biology/SPAdes/SPAdes-3.15.5.ebuild | 8 ++-- sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch | 49 ++++++++++++++++++++++ 2 files changed, 54 insertions(+), 3 deletions(-) diff --git a/sci-biology/SPAdes/SPAdes-3.15.5.ebuild b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild index b6d344c37..4485619e3 100644 --- a/sci-biology/SPAdes/SPAdes-3.15.5.ebuild +++ b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild @@ -17,9 +17,7 @@ SRC_URI=" LICENSE="GPL-2" SLOT="0" -KEYWORDS="" -# Fails to build: -# https://github.com/ablab/spades/issues/1238 +KEYWORDS="~amd64" REQUIRED_USE="${PYTHON_REQUIRED_USE}" DEPEND=" @@ -31,6 +29,10 @@ DEPEND=" RDEPEND="${DEPEND}" BDEPEND="dev-build/cmake" +PATCHES=( + "${FILESDIR}/${P}-gcc13.patch" +) + src_install(){ einstalldocs # WORKAROUND: This script does both compile and install in one go diff --git a/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch new file mode 100644 index 000000000..3dd3f8c02 --- /dev/null +++ b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch @@ -0,0 +1,49 @@ +From 3e802fa51d156fc958c36e25d607f20bf756f0bf Mon Sep 17 00:00:00 2001 +From: Bo YU <tsu.y...@gmail.com> +Date: Wed, 19 Jul 2023 18:42:04 +0800 +Subject: [PATCH] fix build issues due to gcc-13 + +Signed-off-by: Bo YU <tsu.y...@gmail.com> +--- + ext/include/llvm/Support/Signals.h | 1 + + src/common/pipeline/library_data.hpp | 1 + + src/common/sequence/nucl.hpp | 2 ++ + 3 files changed, 4 insertions(+) + +diff --git a/assembler/ext/include/llvm/Support/Signals.h b/assembler/ext/include/llvm/Support/Signals.h +index e0a18e72f..148216b8f 100644 +--- a/ext/include/llvm/Support/Signals.h ++++ b/ext/include/llvm/Support/Signals.h +@@ -14,6 +14,7 @@ + #ifndef LLVM_SUPPORT_SIGNALS_H + #define LLVM_SUPPORT_SIGNALS_H + ++#include <cstdint> + #include <string> + + namespace llvm { +diff --git a/assembler/src/common/pipeline/library_data.hpp b/assembler/src/common/pipeline/library_data.hpp +index 3cbaf0adb..1ffaa7b37 100644 +--- a/src/common/pipeline/library_data.hpp ++++ b/src/common/pipeline/library_data.hpp +@@ -8,6 +8,7 @@ + + #include <map> + #include <string> ++#include <cstdint> + + // Forward decls for LLVM YAML API + namespace llvm { namespace yaml { class IO; template<typename T> struct MappingTraits; } } +diff --git a/assembler/src/common/sequence/nucl.hpp b/assembler/src/common/sequence/nucl.hpp +index 9c7d6de13..e10e7f583 100755 +--- a/src/common/sequence/nucl.hpp ++++ b/src/common/sequence/nucl.hpp +@@ -8,6 +8,8 @@ + #ifndef NUCL_HPP_ + #define NUCL_HPP_ + ++#include <cstdint> ++ + #include "utils/verify.hpp" + + /**
