[med-svn] [Git][med-team/jellyfish1][master] 2 commits: Build with gcc-16 Closes: #1143666

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / jellyfish1


Commits:
5edee2dd by Andreas Tille at 2026-08-12T16:50:33+02:00
Build with gcc-16 Closes: #1143666

- - - - -
86a95567 by Andreas Tille at 2026-08-12T16:51:04+02:00
d/watch: version=5

- - - - -


4 changed files:

- debian/changelog
- + debian/patches/gcc-16.patch
- debian/patches/series
- debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+jellyfish1 (1.1.11-11) UNRELEASED; urgency=medium
+
+  * Build with gcc-16
+    Closes: #1143666
+  * d/watch: version=5
+
+ -- Andreas Tille <tille at debian.org>  Wed, 12 Aug 2026 16:50:17 +0200
+
 jellyfish1 (1.1.11-10) unstable; urgency=medium
 
   * Fix clean target


=====================================
debian/patches/gcc-16.patch
=====================================
@@ -0,0 +1,28 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-08-12
+Description: Build with gcc-16
+Bug-Debian: https://bugs.debian.org/1143666
+
+--- a/jellyfish/query_main.cc
++++ b/jellyfish/query_main.cc
+@@ -32,16 +32,16 @@ template<typename hash_t>
+ void print_mer_counts(const hash_t &h, std::istream &in, std::ostream &out) {
+   uint_t mer_len = h.get_mer_len();
+   uint_t width = mer_len + 2;
+-  char mer[width + 1];
++  std::string mer;
+ 
+   while(true) {
+     in >> std::setw(width) >> mer;
+     if(!in.good())
+       break;
+-    if(strlen(mer) != mer_len)
+-      die << "Invalid mer " << (char*)mer;
++    if(mer.length() != mer_len)
++      die << "Invalid mer " << mer;
+ 
+-    out << mer << " " << h[mer] << "\n";
++    out << mer << " " << h[mer.c_str()] << "\n";
+   }
+ }
+ 


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ man
 arm64.patch
 mips.patch
 autoconf.patch
+gcc-16.patch


=====================================
debian/watch
=====================================
@@ -1,2 +1,4 @@
-version=4
-https://www.cbcb.umd.edu/software/jellyfish/ jellyfish-(1.+)\.tar\.gz
+Version: 5
+
+Source: https://www.cbcb.umd.edu/software/jellyfish/
+Matching-Pattern: jellyfish-(1.+)\.tar\.gz



View it on GitLab: https://salsa.debian.org/med-team/jellyfish1/-/compare/60fec21221c15c6fb91f294480c00dcd6a7fc99c...86a95567f345db3da4de69a0ae4b67952b820e48

-- 
View it on GitLab: https://salsa.debian.org/med-team/jellyfish1/-/compare/60fec21221c15c6fb91f294480c00dcd6a7fc99c...86a95567f345db3da4de69a0ae4b67952b820e48
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