gentoo auto-resync : 18:04:2023 - 11:55:01

4 files changed, 28 insertions, 1 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index fc09f9eec99e..76d2671f3099 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index b3725dee19bf..b982e0eec460 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1,5 +1,6 @@
 AUX bedtools-2.29.2-buildsystem.patch 2002 BLAKE2B 7925c788858515ec4454ece3823680e99053790aeb30b2dcab06a52f6827c3cca85543c899fbabcc75ac5872cdfe632c9c5bf8b5dc24146c50a00dbd4ea56a1d SHA512 a76ec350aedfce4926f8fbaed742a992f81b2280727383f7aefd7f3629f7e04f300f9d3d9cce2a98c6fe2767cb6d2261074bd6242d6d5ae26a5095730c054a85
 AUX bedtools-2.29.2-python.patch 1235 BLAKE2B 34381a33be915f983b2c93f04954486e7611f56b1bc3259887e5ac3aa54107e3392a784980779948136f97424485a31a53959f2f76b573cb44b7d83023c69005 SHA512 8c22230e3bc1eaeb7d85379eab402eb1e95443f88f60a9c04f628cd38a96b91d138149a1a46d941189a8cd6097e075a8bde8d4ad883757ec7b2c129268cdb37f
+AUX bedtools-2.30.0-gcc13.patch 684 BLAKE2B 4c3a338887b5c71be1b096389e6c967aaf55de518663c4c3b5c37f80e6d651c6f8cf07c507064f8fe0f7bada66191d56dc136e71a5cb4254570c24ad8d8a1801 SHA512 a68f224a5b04f1b0949f8bd064c6847c0f5da900ac462fbfa2fe473688ce4e6c904ae94581599ecc0fe0a3baf0038effc8346c39dd4ecf7e068c449482594711
 DIST bedtools-2.30.0.tar.gz 20648577 BLAKE2B 042bc31e846455cb1c20199f7a27a3850851f7c256a45b1e674c7aa48ecedc211b0fdfc5e25f915b588f21447e757ebff2bba16a65905bb10d3c88e4b17b1db1 SHA512 3993243cc3db12d194d6220aeae200e6af843d6d32d4e5a9a82d04c9d119f8ed47e618e87241edfa82cfac081bc9a40ada18f097d21b0cafc5f912ae012701c9
-EBUILD bedtools-2.30.0.ebuild 1187 BLAKE2B 85947706157a36e021a405d5cd4308ca19874135b4ae73e715d1bde48e4808402415ebc5ab62717830bd8c9375dda87af0089dc5de9856e24bc940f5e0caf2ed SHA512 f1eb77cfcc39ed502ca011590a98092763d8a80c40825d95500447b20eaf64bf028193e32d6e49791104867d683de14a4e3ac422505e34e2155cb9f820ae7857
+EBUILD bedtools-2.30.0.ebuild 1227 BLAKE2B f54a0f5f84ade175cd07634d657b970a05b864606c76b80fac8dc3d037398c9611a5fc4c5fd7514e329e8375aa59522fd094e70c9d151af318708fc1c8bd7bbe SHA512 c3318eff7f9363f5a803b85d5d092d085b9e4198051d79d314c390d7200398989127b9a501459185497859f57352e4416fb5210f6d647ea76793a395c69f223f
 MISC metadata.xml 407 BLAKE2B f3c2890ef1648dcfc7ae92c56fec8c111de2cb82ba4c8f7402756fa9db6f2ee43fa3ccb9a75db5d1e2ca7893ed3041efc22452814944e0e56f1a589353b47774 SHA512 925406053fd5c1aecb5ef26c522b3f410c6f9a639dc1ab7790a4124513c870af5b818adc53875c93ab19a36d444b8fb23c5ef10cc11ed50080785bbe60d1eb98
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;
+