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kallisto: fix build with gcc 15 #522275

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Merged
mdaniels5757 merged 1 commit into from
May 23, 2026
+32 −1
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kallisto: fix build with gcc 15 #522275

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26 changes: 26 additions & 0 deletions pkgs/by-name/ka/kallisto/bifrost-fix-datastorage-sz_link-typo.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
diff --git a/ext/bifrost/src/DataStorage.hpp b/ext/bifrost/src/DataStorage.hpp
index 016775f..deb849d 100644
--- a/ext/bifrost/src/DataStorage.hpp
+++ b/ext/bifrost/src/DataStorage.hpp
@@ -67,6 +67,8 @@ class DataStorage {

inline size_t getNbColors() const { return color_names.size(); }

+ inline vector<string> const& getColorNames() const { return color_names; }
+
size_t getUnitigColorsSize(const size_t nb_threads = 1) const;

uint64_t getHash(const UnitigColorMap<U>& um) const;
diff --git a/ext/bifrost/src/DataStorage.tcc b/ext/bifrost/src/DataStorage.tcc
index 02929d9..10b844e 100644
--- a/ext/bifrost/src/DataStorage.tcc
+++ b/ext/bifrost/src/DataStorage.tcc
@@ -78,7 +78,7 @@ DataStorage<U>::DataStorage(const DataStorage& o) : color_sets(nullptr), shared_

unitig_cs_link = new atomic<uint64_t>[sz_link];

- for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load();
+ for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.unitig_cs_link[i].load();
}

if ((o.data != nullptr) && (o.sz_cs != 0)){
7 changes: 6 additions & 1 deletion pkgs/by-name/ka/kallisto/package.nix
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Expand Up @@ -18,9 +18,14 @@ stdenv.mkDerivation (finalAttrs: {
repo = "kallisto";
owner = "pachterlab";
rev = "v${finalAttrs.version}";
sha256 = "sha256-hfdeztEyHvuOnLS71oSv8sPqFe2UCX5KlANqrT/Gfx8=";
hash = "sha256-hfdeztEyHvuOnLS71oSv8sPqFe2UCX5KlANqrT/Gfx8=";
};

patches = [
# https://github.com/pmelsted/bifrost/pull/18
./bifrost-fix-datastorage-sz_link-typo.patch
];

postPatch = ''
substituteInPlace CMakeLists.txt ext/bifrost/CMakeLists.txt \
--replace-fail "cmake_minimum_required(VERSION 3.0.0)" "cmake_minimum_required(VERSION 3.10)"
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