[med-svn] [Git][med-team/indelible][master] 4 commits: 0007-gcc-16.patch: new: fix build failure with gcc-16.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Aug 6 08:41:04 BST 2026
Étienne Mollier pushed to branch master at Debian Med / indelible
Commits:
a22a21cd by Étienne Mollier at 2026-08-06T09:30:05+02:00
0007-gcc-16.patch: new: fix build failure with gcc-16.
Closes: #1143661
- - - - -
73eabf11 by Étienne Mollier at 2026-08-06T09:33:52+02:00
d/u/metadata: document upstream repository and bugs database.
- - - - -
a148dd07 by Étienne Mollier at 2026-08-06T09:34:18+02:00
d/control: bump to debhelper-compat 14.
This change involves activation of dh-sequence-single-binary.
- - - - -
1f0bcbfb by Étienne Mollier at 2026-08-06T09:35:44+02:00
d/changelog: ready for upload to unstable.
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/0007-gcc-16.patch
- debian/patches/series
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,15 @@
-indelible (1.03-8) UNRELEASED; urgency=medium
+indelible (1.03-8) unstable; urgency=medium
- * Team upload.
+ [ Andreas Tille ]
* Fix DEP3 headers
- -- Andreas Tille <tille at debian.org> Sat, 23 May 2026 08:02:46 +0200
+ [ Étienne Mollier ]
+ * 0007-gcc-16.patch: new: fix build failure with gcc-16. (Closes: #1143661)
+ * d/u/metadata: document upstream repository and bugs database.
+ * d/control: bump to debhelper-compat 14.
+ This change involves activation of dh-sequence-single-binary.
+
+ -- Étienne Mollier <emollier at debian.org> Thu, 06 Aug 2026 09:35:17 +0200
indelible (1.03-7) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -3,7 +3,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Fabian Klötzl <kloetzl at evolbio.mpg.de>,
Étienne Mollier <emollier at debian.org>
Section: science
-Build-Depends: debhelper-compat (= 13)
+Build-Depends: debhelper-compat (= 14),
+ dh-sequence-single-binary
Standards-Version: 4.7.4
Vcs-Browser: https://salsa.debian.org/med-team/indelible
Vcs-Git: https://salsa.debian.org/med-team/indelible.git
=====================================
debian/patches/0007-gcc-16.patch
=====================================
@@ -0,0 +1,54 @@
+Description: fix build failure with gcc-16.
+ The function definition of "identity" now clashes with a struct from
+ ranges_cmp.h:
+ .
+ src/paml.cpp:473:20: error: reference to ‘identity’ is ambiguous
+ 473 | if (t<1e-100) { identity (P, n); return(0); }
+ | ^~~~~~~~
+ • there are 2 candidates
+ In file included from /usr/include/c++/16/bits/iterator_concepts.h:40,
+ from /usr/include/c++/16/bits/stl_iterator_base_types.h:73,
+ from /usr/include/c++/16/bits/stl_construct.h:61,
+ from /usr/include/c++/16/bits/char_traits.h:59,
+ from /usr/include/c++/16/ios:44,
+ from /usr/include/c++/16/bits/ostream.h:43,
+ from /usr/include/c++/16/ostream:42,
+ from /usr/include/c++/16/iostream:43,
+ from src/indelible.cpp:116:
+ • candidate 1: ‘struct std::identity’
+ /usr/include/c++/16/bits/ranges_cmp.h:47:10:
+ 47 | struct identity
+ | ^~~~~~~~
+ • candidate 2: ‘int identity(double*, int)’
+ src/paml.cpp:61:5:
+ 61 | int identity (double x[], int n)
+ | ^~~~~~~~
+ .
+ This change renames the function identity as identity_matrix, which
+ does not clash and is a clearer description of what it achieves.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/1143661
+Forwarded: no
+Last-Update: 2026-08-06
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- indelible.orig/src/paml.cpp
++++ indelible/src/paml.cpp
+@@ -58,7 +58,7 @@
+
+ #define FOR(i,n) for(i=0; i<n; i++)
+
+-int identity (double x[], int n)
++int identity_matrix (double x[], int n)
+ { int i,j; FOR (i,n) { FOR(j,n) x[i*n+j]=0; x[i*n+i]=1; } return (0); }
+
+ int zero (double x[], int n)
+@@ -470,7 +470,7 @@
+
+ NPMatUVRoot++;
+ if (t<-0.1) printf ("\nt = %.5f in PMatUVRoot", t);
+- if (t<1e-100) { identity (P, n); return(0); }
++ if (t<1e-100) { identity_matrix (P, n); return(0); }
+ for (k=0,zero(P,n*n); k<n; k++)
+ for (i=0,pP=P,expt=exp(t*Root[k]); i<n; i++)
+ for (j=0,uexpt=U[i*n+k]*expt; j<n; j++)
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@
0004-added-auto-tools-build-system.patch
0005-remove-unnecessary-whitespace-from-the-end-of-sequen.patch
0006-spelling.patch
+0007-gcc-16.patch
=====================================
debian/upstream/metadata
=====================================
@@ -16,3 +16,7 @@ Registry:
Entry: NA
- Name: SciCrunch
Entry: NA
+Bug-Database: https://github.com/evolbioinfo/indelible/issues
+Bug-Submit: https://github.com/evolbioinfo/indelible/issues/new
+Repository: https://github.com/evolbioinfo/indelible.git
+Repository-Browse: https://github.com/evolbioinfo/indelible
View it on GitLab: https://salsa.debian.org/med-team/indelible/-/compare/a554dc06c28573e48b5f94192fff070e41bb25d4...1f0bcbfb31092f108108af42bee3e578e96ef3c0
--
View it on GitLab: https://salsa.debian.org/med-team/indelible/-/compare/a554dc06c28573e48b5f94192fff070e41bb25d4...1f0bcbfb31092f108108af42bee3e578e96ef3c0
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