[med-svn] [Git][med-team/mmseqs2][master] fix gcc-13 build issue

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / mmseqs2


Commits:
620f7dfe by Bo YU at 2023-07-28T23:59:04+05:30
fix gcc-13 build issue

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

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/fix-gcc-13.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+mmseqs2 (14-7e284+ds-2) unstable; urgency=medium
+
+  * Team upload.
+  * Add fix-gcc-13.patch to fix gcc-13 build issue. (Closes: #1037779)
+
+ -- Bo YU <tsu.yubo at gmail.com>  Fri, 28 Jul 2023 10:31:23 +0800
+
 mmseqs2 (14-7e284+ds-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/fix-gcc-13.patch
=====================================
@@ -0,0 +1,47 @@
+Description: fix gcc-13 build
+ upstream has fixed the issue:
+ https://github.com/soedinglab/MMseqs2/commit/3e436173321a2d0365a08bfb3b281108ed9ad414
+Bug: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037779
+Last-Update: 2023-07-28
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/src/commons/Debug.h
++++ b/src/commons/Debug.h
+@@ -8,6 +8,7 @@
+ #include <unistd.h>
+ #include <stdlib.h>
+ #include <cstddef>
++#include <cstdint>
+ #include <sys/stat.h>
+ 
+ class TtyCheck {
+--- a/src/commons/Parameters.h
++++ b/src/commons/Parameters.h
+@@ -9,6 +9,7 @@
+ #include <map>
+ #include <typeinfo>
+ #include <cstddef>
++#include <cstdint>
+ #include <utility>
+ 
+ #include "Command.h"
+--- a/src/commons/Util.h
++++ b/src/commons/Util.h
+@@ -3,6 +3,7 @@
+ 
+ #include <string>
+ #include <cstddef>
++#include <cstdint>
+ #include <cstring>
+ #include <vector>
+ #include <limits>
+--- a/src/prefiltering/Indexer.h
++++ b/src/prefiltering/Indexer.h
+@@ -7,6 +7,7 @@
+ //
+ 
+ 
++#include <cstdint>
+ #include <string>
+ #include <iostream>
+ 


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 fix_tests.patch
 fix_util_installation.patch
 use_system_gzstream.patch
+fix-gcc-13.patch



View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/-/commit/620f7dfe48d3aefd8b81aeb00c1570dc65577a66

-- 
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/-/commit/620f7dfe48d3aefd8b81aeb00c1570dc65577a66
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