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try 64 bit khint_t
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pandas/_libs/new_vector.cpp

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@@ -662,7 +662,7 @@ template <typename T, bool IsMasked> class PandasHashTable {
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return;
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}
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klib::KHashMap<T, size_t, PandasHashFunction<T>, PandasHashEquality<T>>
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klib::KHashMap<T, size_t, PandasHashFunction<T>, PandasHashEquality<T>, size_t>
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hash_map_;
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Py_ssize_t na_position_ = -1;
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};

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