[med-svn] [Git][med-team/murasaki][master] 4 commits: Fix build failure with GCC 16 / C++20: std::allocator::rebind removed Closes: #1133567
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Aug 12 06:25:03 BST 2026
Andreas Tille pushed to branch master at Debian Med / murasaki
Commits:
51a92cc5 by Andreas Tille at 2026-08-12T06:56:44+02:00
Fix build failure with GCC 16 / C++20: std::allocator::rebind removed Closes: #1133567
- - - - -
20d5d4d0 by Andreas Tille at 2026-08-12T06:56:59+02:00
Standards-Version: 4.7.4 (routine-update)
- - - - -
f3ef69a4 by Andreas Tille at 2026-08-12T06:57:13+02:00
Changes made by cme
- - - - -
a5ac3efe by Andreas Tille at 2026-08-12T07:24:51+02:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/gcc16.patch
- debian/patches/series
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+murasaki (1.68.6-18) unstable; urgency=medium
+
+ * Fix build failure with GCC 16 / C++20: std::allocator::rebind removed
+ Closes: #1133567
+ * Standards-Version: 4.7.4 (routine-update)
+ * Reflow Uploaders field (cme)
+
+ -- Andreas Tille <tille at debian.org> Wed, 12 Aug 2026 07:19:33 +0200
+
murasaki (1.68.6-17) unstable; urgency=medium
* Port to boost 1.90
=====================================
debian/control
=====================================
@@ -1,26 +1,29 @@
Source: murasaki
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders:
+ Andreas Tille <tille at debian.org>,
Section: science
-Build-Depends: debhelper-compat (= 13),
- libboost-regex-dev,
- libboost-iostreams-dev,
- libboost-filesystem-dev,
- libterm-readkey-perl,
- libtext-wrapper-perl,
- libcrypto++-dev,
- libpstreams-dev,
- mpi-default-dev
-Standards-Version: 4.7.3
+Build-Depends:
+ debhelper-compat (= 14),
+ libboost-regex-dev,
+ libboost-iostreams-dev,
+ libboost-filesystem-dev,
+ libterm-readkey-perl,
+ libtext-wrapper-perl,
+ libcrypto++-dev,
+ libpstreams-dev,
+ mpi-default-dev,
Vcs-Browser: https://salsa.debian.org/med-team/murasaki
Vcs-Git: https://salsa.debian.org/med-team/murasaki.git
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/
Package: murasaki
Architecture: any
-Depends: murasaki-common,
- ${shlibs:Depends},
- ${misc:Depends}
+Depends:
+ murasaki-common,
+ ${shlibs:Depends},
+ ${misc:Depends},
Description: homology detection tool across multiple large genomes
Murasaki is a scalable and fast, language theory-based homology
detection tool across multiple large genomes. It enable whole-genome
@@ -38,9 +41,10 @@ Description: homology detection tool across multiple large genomes
Package: murasaki-mpi
Architecture: any
-Depends: murasaki-common,
- ${shlibs:Depends},
- ${misc:Depends}
+Depends:
+ murasaki-common,
+ ${shlibs:Depends},
+ ${misc:Depends},
Description: homology detection tool across multiple large genomes (MPI-version)
Murasaki is a scalable and fast, language theory-based homology
detection tool across multiple large genomes. It enable whole-genome
@@ -62,14 +66,16 @@ Description: homology detection tool across multiple large genomes (MPI-version)
Package: murasaki-common
Architecture: all
-Depends: ${misc:Depends},
- ${misc:perl},
- gnuplot-nox | gnuplot,
- libbio-perl-perl,
- r-cran-rocr,
- imagemagick
-Recommends: libterm-readkey-perl,
- libtext-wrapi18n-perl | libtext-wrapper-perl
+Depends:
+ ${misc:Depends},
+ ${misc:perl},
+ gnuplot-nox | gnuplot,
+ libbio-perl-perl,
+ r-cran-rocr,
+ imagemagick,
+Recommends:
+ libterm-readkey-perl,
+ libtext-wrapi18n-perl | libtext-wrapper-perl,
Description: homology detection tool across multiple large genomes (common files)
Murasaki is a scalable and fast, language theory-based homology
detection tool across multiple large genomes. It enable whole-genome
=====================================
debian/patches/gcc16.patch
=====================================
@@ -0,0 +1,25 @@
+Description: Fix build failure with GCC 16 / C++20: std::allocator::rebind removed
+Author: Andreas Tille <tille at debian.org>
+Bug-Debian: https://bugs.debian.org/1133567
+Last-Update: 2026-08-11
+
+--- a/src/itree.h
++++ b/src/itree.h
+@@ -392,7 +392,7 @@ namespace Itree {
+ typedef _Value value_type;
+ typedef pair<key_type,value_type> init_type;
+
+- typedef typename _Alloc::template rebind<node_type >::other
++ typedef typename std::allocator_traits<_Alloc>::template rebind_alloc<node_type>
+ _Node_allocator;
+ typedef _Alloc allocator_type;
+ typedef itree_iterator<_IntType,_Value> iterator;
+@@ -810,7 +810,7 @@ namespace Itree {
+ void
+ destroy_node(_Link_type __p)
+ {
+- alloc.destroy(__p);
++ std::allocator_traits<allocator_type>::destroy(alloc, __p);
+ _M_put_node(__p);
+ }
+
=====================================
debian/patches/series
=====================================
@@ -10,3 +10,4 @@ fix_mpi.patch
boost-1.88.patch
buildflags.patch
libboost1.90.patch
+gcc16.patch
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Name: Murasaki
+Archive: SourceForge
Reference:
Author: >
Kris Popendorf and Hachiya Tsuyoshi and Yasunori Osana and
View it on GitLab: https://salsa.debian.org/med-team/murasaki/-/compare/bc5a137c737b10e7f354ec0f6099c54f81f1a02c...a5ac3efe0293b9bd9fc2c712a386f1ab08b39a99
--
View it on GitLab: https://salsa.debian.org/med-team/murasaki/-/compare/bc5a137c737b10e7f354ec0f6099c54f81f1a02c...a5ac3efe0293b9bd9fc2c712a386f1ab08b39a99
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