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 <[email protected]> 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 <[email protected]> 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 <[email protected]. Uploaders: Fabian Klötzl <[email protected]>, Étienne Mollier <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org. 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