[med-svn] [Git][med-team/sortmerna][master] 3 commits: concurrentqueue.h.patch: update concurrentqueue.h location.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / sortmerna


Commits:
60576c41 by Étienne Mollier at 2023-09-06T19:42:54+02:00
concurrentqueue.h.patch: update concurrentqueue.h location.

Closes: #1051325

- - - - -
dbd310b7 by Étienne Mollier at 2023-09-06T19:43:01+02:00
gcc-13.patch: new: fix ftbfs with gcc-13.

- - - - -
045e85aa by Étienne Mollier at 2023-09-06T19:44:57+02:00
ready to upload to unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/patches/concurrentqueue.h.patch
- + debian/patches/gcc-13.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,10 +1,13 @@
-sortmerna (4.3.6-3) UNRELEASED; urgency=medium
+sortmerna (4.3.6-3) unstable; urgency=medium
 
   * d/rules: convert example files to Unicode per lintian flag.
   * typos.patch: add; fix typos caught by lintian.
   * d/copyright: update copyright year.
+  * concurrentqueue.h.patch: update concurrentqueue.h location.
+    (Closes: #1051325)
+  * gcc-13.patch: new: fix ftbfs with gcc-13.
 
- -- Étienne Mollier <emollier at debian.org>  Sat, 07 Jan 2023 17:42:57 +0100
+ -- Étienne Mollier <emollier at debian.org>  Wed, 06 Sep 2023 19:43:10 +0200
 
 sortmerna (4.3.6-2) unstable; urgency=medium
 


=====================================
debian/patches/concurrentqueue.h.patch
=====================================
@@ -1,6 +1,9 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 31 Jan 2022 13:37:04 +0100
+Last-Update: Wed, 06 Sep 2023 19:31:43 +0200
 Description: Fix include statement for Debian packaged concurrentqueue
+Bug-Debian: https://bugs.debian.org/1051325
+Reviewed-By: Étienne Mollier <emollier at debian.org>
+Forwarded: no
 
 --- a/include/readsqueue.hpp
 +++ b/include/readsqueue.hpp
@@ -9,7 +12,7 @@ Description: Fix include statement for Debian packaged concurrentqueue
  
  #if defined(CONCURRENTQUEUE)
 -#  include "concurrentqueue.h"
-+#  include <concurrentqueue/concurrentqueue.h>
++#  include <concurrentqueue/moodycamel/concurrentqueue.h>
  #elif defined(LOCKQUEUE)
  #  include <queue>
  #endif


=====================================
debian/patches/gcc-13.patch
=====================================
@@ -0,0 +1,21 @@
+Description: fix build failure with gcc 13
+ This patch fixes occurrences of the following error with gcc 13:
+ .
+  /<<PKGBUILDDIR>>/src/sortmerna/kseq_load.cpp:53:12: error: ‘uint64_t’ has not been declared
+    53 |            uint64_t number_total_read,
+       |            ^~~~~~~~
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2023-09-06
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- sortmerna.orig/src/sortmerna/kseq_load.cpp
++++ sortmerna/src/sortmerna/kseq_load.cpp
+@@ -33,6 +33,7 @@
+  * @brief Load input reads directly into RAM (FASTA, FASTQ and compressed formats)
+  */
+ 
++#include <cstdint>
+ #include <sstream>
+ #include <iostream>
+ 


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ rapidjson.patch
 concurrentqueue.h.patch
 no_static_linking.patch
 typos.patch
+gcc-13.patch



View it on GitLab: https://salsa.debian.org/med-team/sortmerna/-/compare/376f5e91da83105dd0d817d8cc81f56ce619777d...045e85aab813bcb2a8e449159d162f3c55561b5f

-- 
View it on GitLab: https://salsa.debian.org/med-team/sortmerna/-/compare/376f5e91da83105dd0d817d8cc81f56ce619777d...045e85aab813bcb2a8e449159d162f3c55561b5f
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