From b6f2184cce5a8198e0beedeea5e846859ec5dfbb Mon Sep 17 00:00:00 2001
From: George Young <A-N-Other@users.noreply.github.com>
Date: Thu, 8 Jun 2023 19:59:01 +0100
Subject: bedtools2: patching to build with gcc@13 (#38254)

* bedtools2: patching to build with gcc@13

* bedtools2: patching to build with gcc@13

* Update var/spack/repos/builtin/packages/bedtools2/package.py

Yep, sure. Makes sense.

Co-authored-by: Alec Scott <alec@bcs.sh>

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Alec Scott <alec@bcs.sh>
---
 .../packages/bedtools2/bedtools-gcc13.patch        | 25 ++++++++++++++++++++++
 .../repos/builtin/packages/bedtools2/package.py    |  2 ++
 2 files changed, 27 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/bedtools2/bedtools-gcc13.patch

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/bedtools2/bedtools-gcc13.patch b/var/spack/repos/builtin/packages/bedtools2/bedtools-gcc13.patch
new file mode 100644
index 0000000000..c63faf31c8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bedtools2/bedtools-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;
+ 
diff --git a/var/spack/repos/builtin/packages/bedtools2/package.py b/var/spack/repos/builtin/packages/bedtools2/package.py
index 74a4f584b9..5313c7bbdb 100644
--- a/var/spack/repos/builtin/packages/bedtools2/package.py
+++ b/var/spack/repos/builtin/packages/bedtools2/package.py
@@ -29,5 +29,7 @@ class Bedtools2(Package):
     depends_on("xz", when="@2.29:")
     depends_on("python", type="build")
 
+    patch("bedtools-gcc13.patch", level=1, when="@2.27:%gcc@13:")
+
     def install(self, spec, prefix):
         make("prefix=%s" % prefix, "install")
-- 
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