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| author | George Young <A-N-Other@users.noreply.github.com> | 2023-06-08 19:59:01 +0100 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-06-08 14:59:01 -0400 |
| commit | b6f2184cce5a8198e0beedeea5e846859ec5dfbb (patch) | |
| tree | 44d640b5b6f2035089d9164dc65ba8a5bc5838c7 | |
| parent | 9288067380bde9db945d2d6a93574d28ef281377 (diff) | |
| download | spack-b6f2184cce5a8198e0beedeea5e846859ec5dfbb.tar.gz spack-b6f2184cce5a8198e0beedeea5e846859ec5dfbb.tar.bz2 spack-b6f2184cce5a8198e0beedeea5e846859ec5dfbb.tar.xz spack-b6f2184cce5a8198e0beedeea5e846859ec5dfbb.zip | |
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>
| -rw-r--r-- | var/spack/repos/builtin/packages/bedtools2/bedtools-gcc13.patch | 25 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/bedtools2/package.py | 2 |
2 files changed, 27 insertions, 0 deletions
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") |