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From: "David Seifert" <soap@gentoo.org>
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Message-ID: <1681812277.0f6ed95b2b57ae7f9978b1a3b1620c3dcb06256e.soap@gentoo>
Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/files/, sci-biology/bedtools/
X-VCS-Repository: repo/gentoo
X-VCS-Files: sci-biology/bedtools/bedtools-2.30.0.ebuild sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch
X-VCS-Directories: sci-biology/bedtools/ sci-biology/bedtools/files/
X-VCS-Committer: soap
X-VCS-Committer-Name: David Seifert
X-VCS-Revision: 0f6ed95b2b57ae7f9978b1a3b1620c3dcb06256e
X-VCS-Branch: master
Date: Tue, 18 Apr 2023 10:04:45 +0000 (UTC)
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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 <soap@gentoo.org>
+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;
+