commit: 0f6ed95b2b57ae7f9978b1a3b1620c3dcb06256e Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Tue Apr 18 10:04:37 2023 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Tue Apr 18 10:04:37 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0f6ed95b
sci-biology/bedtools: fix gcc 13 build Closes: https://bugs.gentoo.org/895860 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/bedtools/bedtools-2.30.0.ebuild | 1 + .../bedtools/files/bedtools-2.30.0-gcc13.patch | 25 ++++++++++++++++++++++ 2 files changed, 26 insertions(+) diff --git a/sci-biology/bedtools/bedtools-2.30.0.ebuild b/sci-biology/bedtools/bedtools-2.30.0.ebuild index 5a8174fbdfe0..b86b87e72dc4 100644 --- a/sci-biology/bedtools/bedtools-2.30.0.ebuild +++ b/sci-biology/bedtools/bedtools-2.30.0.ebuild @@ -34,6 +34,7 @@ BDEPEND=" PATCHES=( "${FILESDIR}"/${PN}-2.29.2-buildsystem.patch "${FILESDIR}"/${PN}-2.29.2-python.patch + "${FILESDIR}"/${PN}-2.30.0-gcc13.patch ) src_configure() { diff --git a/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch b/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch new file mode 100644 index 000000000000..c63faf31c851 --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch @@ -0,0 +1,25 @@ +https://github.com/arq5x/bedtools2/pull/1045 + +From 7d7fb513b9b05b7a0512a83520e9f60036e5ff9a Mon Sep 17 00:00:00 2001 +From: David Seifert <[email protected]> +Date: Tue, 18 Apr 2023 11:59:58 +0200 +Subject: [PATCH] Add missing <cstdint> include + +* breaks build with GCC 13: + https://bugs.gentoo.org/895860 +--- + src/utils/general/ParseTools.h | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/src/utils/general/ParseTools.h b/src/utils/general/ParseTools.h +index e056c149..3418eff1 100644 +--- a/src/utils/general/ParseTools.h ++++ b/src/utils/general/ParseTools.h +@@ -16,6 +16,7 @@ + #include "string.h" + #include <cstdio> + #include <cstdlib> ++#include <cstdint> + + using namespace std; +
