[med-svn] [Git][med-team/spades][master] fix gcc-13 build issues

[vimerbf (@vimerbf-guest)]

vimerbf pushed to branch master at Debian Med / spades


Commits:
a5d75e13 by Bo YU at 2023-07-20T22:03:52+08:00
fix gcc-13 build issues

Signed-off-by: Bo YU <tsu.yubo at gmail.com>

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/fix-gcc13.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+spades (3.15.5+dfsg-3) UNRELEASED; urgency=medium
+  
+  * Team upload.
+  
+  [Bo YU]
+  * Add fix-gcc13.patch to fix gcc-13 build issues. (Closes: #1037863)
+
+ -- Bo YU <tsu.yubo at gmail.com>  Thu, 20 Jul 2023 21:38:50 +0800
+
 spades (3.15.5+dfsg-2) unstable; urgency=medium
 
   * d/control: add missing build-deps following llvm reorganization.


=====================================
debian/patches/fix-gcc13.patch
=====================================
@@ -0,0 +1,38 @@
+Description: fix gcc-13 build issue 
+Author: Bo YU <tsu.yubo at gmail.com> 
+Bug: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037863 
+Forwarded: https://github.com/ablab/spades/pull/1157 
+Last-Update: 2023-07-19
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/assembler/ext/include/llvm/Support/Signals.h
++++ b/assembler/ext/include/llvm/Support/Signals.h
+@@ -15,6 +15,7 @@
+ #define LLVM_SUPPORT_SIGNALS_H
+ 
+ #include <string>
++#include <cstdint>
+ 
+ namespace llvm {
+ class StringRef;
+--- a/assembler/src/common/pipeline/library_data.hpp
++++ b/assembler/src/common/pipeline/library_data.hpp
+@@ -8,6 +8,7 @@
+ 
+ #include <map>
+ #include <string>
++#include <cstdint>
+ 
+ // Forward decls for LLVM YAML API
+ namespace llvm { namespace yaml { class IO; template<typename T> struct MappingTraits; } }
+--- a/assembler/src/common/sequence/nucl.hpp
++++ b/assembler/src/common/sequence/nucl.hpp
+@@ -8,6 +8,8 @@
+ #ifndef NUCL_HPP_
+ #define NUCL_HPP_
+ 
++#include <cstdint>
++
+ #include "utils/verify.hpp"
+ 
+ /**


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+fix-gcc13.patch
 0002_use_debian_packaged_python-joblib.patch
 0003_accept-system-bwa.patch
 0101_cmake_ignore_removed_python-yaml.patch



View it on GitLab: https://salsa.debian.org/med-team/spades/-/commit/a5d75e136861d2a43f46e56f0bbdf4a95c774530

-- 
View it on GitLab: https://salsa.debian.org/med-team/spades/-/commit/a5d75e136861d2a43f46e56f0bbdf4a95c774530
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