.gitignore

@@ -14,4 +14,3 @@
 /seqan3-3.4.0-rc.2.tar.gz
 /seqan3-3.4.0-rc.3.tar.gz
 /seqan3-3.4.0.tar.gz
-/seqan3-3.4.2.tar.gz

seqan3-fix_gcc-16.patch

@@ -0,0 +1,47 @@
+From e6ddc2529cad39497f15199f9fdc4eb99672018c Mon Sep 17 00:00:00 2001
+From: Enrico Seiler <enrico.seiler@hotmail.de>
+Date: Tue, 20 Jan 2026 13:11:14 +0100
+Subject: [PATCH] fix(gcc-16): bogus warning with fedora
+
+---
+ .../alphabet/container/bitpacked_sequence.hpp | 26 +++++++++++++++++++
+ 1 file changed, 26 insertions(+)
+
+diff --git a/include/seqan3/alphabet/container/bitpacked_sequence.hpp b/include/seqan3/alphabet/container/bitpacked_sequence.hpp
+index 67abc29d22..eb353200a7 100644
+--- a/include/seqan3/alphabet/container/bitpacked_sequence.hpp
++++ b/include/seqan3/alphabet/container/bitpacked_sequence.hpp
+@@ -87,7 +87,33 @@ class bitpacked_sequence
+         //!\brief Update the sdsl-proxy.
+         constexpr void on_update() noexcept
+         {
++            // Alternative patch in the SDSL.
++            // The problem is that, in the Fedora build type, there is a warning about accessing lo_set[65],
++            // which is out of bounds (size is 64).
++            // However, during runtime, lo_set[65] is never actually accessed (bogus warning).
++            // Making `len > 64` undefined behaviour resolves the warning.
++            // Note that the SDSL uses an older C++ standard and has not `std::unreachable()` available.
++            // Also, `__builtin_unreachable()` is only valid for GCC and Clang. The SDSL also supports MSVC,
++            // where there is an equivalent but different builtin for that.
++            // The diff is for the amalgamated seqan3/contrib/sdsl-lite.hpp; but the patch should be applied upstream.
++            // ```diff
++            // diff --git a/include/seqan3/contrib/sdsl-lite.hpp b/include/seqan3/contrib/sdsl-lite.hpp
++            // index a82da4ac2..b59628a56 100644
++            // --- a/include/seqan3/contrib/sdsl-lite.hpp
++            // +++ b/include/seqan3/contrib/sdsl-lite.hpp
++            // @@ -510,6 +510,8 @@ constexpr uint32_t bits_impl<T>::sel11(uint64_t x, uint32_t i, uint32_t c)
++            //  template <typename T>
++            //  constexpr void bits_impl<T>::write_int(uint64_t * word, uint64_t x, uint8_t offset, const uint8_t len)
++            //  {
++            // +    if (len > 64)
++            // +        __builtin_unreachable();
++            //      x &= bits_impl<T>::lo_set[len];
++            //      if (offset + len < 64)
++            //      {
++            // ```
++            SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_START(-Warray-bounds)
+             internal_proxy = base_t::to_rank();
++            SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_STOP
+         }
+ 
+     public:

seqan3-fix_latest_google_benchmark.patch

@@ -0,0 +1,174 @@
+From d1d486500e842433d9203ce97b0c3323acd4ad90 Mon Sep 17 00:00:00 2001
+From: Enrico Seiler <enrico.seiler@hotmail.de>
+Date: Sun, 18 Jan 2026 18:30:43 +0100
+Subject: [PATCH] fix: latest google benchmark
+
+---
+ test/performance/range/gap_decorator_helper.hpp        | 10 +++++++++-
+ .../dream_index/interleaved_bloom_filter_benchmark.cpp | 10 +++++++++-
+ .../search/index_construction_benchmark.cpp            | 10 +++++++++-
+ .../search/views/view_kmer_hash_benchmark.cpp          | 10 +++++++++-
+ .../search/views/view_minimiser_hash_benchmark.cpp     | 10 +++++++++-
+ .../utility/bloom_filter/bloom_filter_benchmark.cpp    | 10 +++++++++-
+ 6 files changed, 54 insertions(+), 6 deletions(-)
+
+diff --git a/test/performance/range/gap_decorator_helper.hpp b/test/performance/range/gap_decorator_helper.hpp
+index 638d1b998a..6d1fada68b 100644
+--- a/test/performance/range/gap_decorator_helper.hpp
++++ b/test/performance/range/gap_decorator_helper.hpp
+@@ -16,6 +16,14 @@
+ #include <seqan3/alignment/exception.hpp>
+ #include <seqan3/alphabet/all.hpp>
+ 
++namespace benchmark
++{
++#pragma GCC diagnostic push
++#pragma GCC diagnostic ignored "-Wdeprecated-declarations"
++using Benchmark = benchmark::internal::Benchmark;
++#pragma GCC diagnostic pop
++} // namespace benchmark
++
+ #define SEQAN3_LEN_LONG 1 << 18
+ #define SEQAN3_LEN_SHORT 1 << 12
+ 
+@@ -29,7 +37,7 @@
+  *  | !SEQAN3_LONG_TESTS  |  1 << [4:2:12]   | [1, 5, 50] %
+  *  | SEQAN3_LONG_TESTS   |  1 << [4:2:18]   | [1, 5, 25, 50, 75] %
+  */
+-void custom_arguments(benchmark::internal::Benchmark * b)
++void custom_arguments(benchmark::Benchmark * b)
+ {
+     std::vector<long long int> gap_percentages{1, 5, 50};
+     long long int seq_len_max = SEQAN3_LEN_SHORT;
+diff --git a/test/performance/search/dream_index/interleaved_bloom_filter_benchmark.cpp b/test/performance/search/dream_index/interleaved_bloom_filter_benchmark.cpp
+index a4cad0a0c6..cca693982a 100644
+--- a/test/performance/search/dream_index/interleaved_bloom_filter_benchmark.cpp
++++ b/test/performance/search/dream_index/interleaved_bloom_filter_benchmark.cpp
+@@ -9,12 +9,20 @@
+ #include <seqan3/utility/range/to.hpp>
+ #include <seqan3/utility/views/zip.hpp>
+ 
++namespace benchmark
++{
++#pragma GCC diagnostic push
++#pragma GCC diagnostic ignored "-Wdeprecated-declarations"
++using Benchmark = benchmark::internal::Benchmark;
++#pragma GCC diagnostic pop
++} // namespace benchmark
++
+ inline benchmark::Counter hashes_per_second(size_t const count)
+ {
+     return benchmark::Counter(count, benchmark::Counter::kIsIterationInvariantRate, benchmark::Counter::OneK::kIs1000);
+ }
+ 
+-static void arguments(benchmark::internal::Benchmark * b)
++static void arguments(benchmark::Benchmark * b)
+ {
+     // Bins must be powers of two
+     for (int32_t bins : {64, 8192})
+diff --git a/test/performance/search/index_construction_benchmark.cpp b/test/performance/search/index_construction_benchmark.cpp
+index d83943bcd7..86ebfb48e2 100644
+--- a/test/performance/search/index_construction_benchmark.cpp
++++ b/test/performance/search/index_construction_benchmark.cpp
+@@ -17,10 +17,18 @@
+ #    include <seqan/index.h>
+ #endif
+ 
++namespace benchmark
++{
++#pragma GCC diagnostic push
++#pragma GCC diagnostic ignored "-Wdeprecated-declarations"
++using Benchmark = benchmark::internal::Benchmark;
++#pragma GCC diagnostic pop
++} // namespace benchmark
++
+ static constexpr int32_t max_length{50000};
+ static constexpr size_t seed{0x6'12'6f};
+ 
+-static void arguments(benchmark::internal::Benchmark * b)
++static void arguments(benchmark::Benchmark * b)
+ {
+ #ifndef NDEBUG
+     constexpr std::array<int32_t, 2> values{50, 5000};
+diff --git a/test/performance/search/views/view_kmer_hash_benchmark.cpp b/test/performance/search/views/view_kmer_hash_benchmark.cpp
+index 09b98d7d24..8d9a5d313a 100644
+--- a/test/performance/search/views/view_kmer_hash_benchmark.cpp
++++ b/test/performance/search/views/view_kmer_hash_benchmark.cpp
+@@ -13,6 +13,14 @@
+ #    include <seqan/index.h>
+ #endif // SEQAN3_HAS_SEQAN2
+ 
++namespace benchmark
++{
++#pragma GCC diagnostic push
++#pragma GCC diagnostic ignored "-Wdeprecated-declarations"
++using Benchmark = benchmark::internal::Benchmark;
++#pragma GCC diagnostic pop
++} // namespace benchmark
++
+ inline benchmark::Counter bp_per_second(size_t const basepairs)
+ {
+     return benchmark::Counter(basepairs,
+@@ -32,7 +40,7 @@ inline seqan3::shape make_gapped_shape(size_t const k)
+     return shape;
+ }
+ 
+-static void arguments(benchmark::internal::Benchmark * b)
++static void arguments(benchmark::Benchmark * b)
+ {
+     for (int32_t sequence_length : {1000, 50000, /*1'000'000*/})
+     {
+diff --git a/test/performance/search/views/view_minimiser_hash_benchmark.cpp b/test/performance/search/views/view_minimiser_hash_benchmark.cpp
+index 39c8c8395a..d2c012990d 100644
+--- a/test/performance/search/views/view_minimiser_hash_benchmark.cpp
++++ b/test/performance/search/views/view_minimiser_hash_benchmark.cpp
+@@ -16,6 +16,14 @@
+ #    include <seqan/index.h>
+ #endif // SEQAN3_HAS_SEQAN2
+ 
++namespace benchmark
++{
++#pragma GCC diagnostic push
++#pragma GCC diagnostic ignored "-Wdeprecated-declarations"
++using Benchmark = benchmark::internal::Benchmark;
++#pragma GCC diagnostic pop
++} // namespace benchmark
++
+ inline benchmark::Counter bp_per_second(size_t const basepairs)
+ {
+     return benchmark::Counter(basepairs,
+@@ -35,7 +43,7 @@ inline seqan3::shape make_gapped_shape(size_t const k)
+     return shape;
+ }
+ 
+-static void arguments(benchmark::internal::Benchmark * b)
++static void arguments(benchmark::Benchmark * b)
+ {
+     for (int32_t sequence_length : {50000, /*1'000'000*/})
+     {
+diff --git a/test/performance/utility/bloom_filter/bloom_filter_benchmark.cpp b/test/performance/utility/bloom_filter/bloom_filter_benchmark.cpp
+index 07f56fa4e0..71737edd9d 100644
+--- a/test/performance/utility/bloom_filter/bloom_filter_benchmark.cpp
++++ b/test/performance/utility/bloom_filter/bloom_filter_benchmark.cpp
+@@ -7,12 +7,20 @@
+ #include <seqan3/test/performance/sequence_generator.hpp>
+ #include <seqan3/utility/bloom_filter/bloom_filter.hpp>
+ 
++namespace benchmark
++{
++#pragma GCC diagnostic push
++#pragma GCC diagnostic ignored "-Wdeprecated-declarations"
++using Benchmark = benchmark::internal::Benchmark;
++#pragma GCC diagnostic pop
++} // namespace benchmark
++
+ inline benchmark::Counter hashes_per_second(size_t const count)
+ {
+     return benchmark::Counter(count, benchmark::Counter::kIsIterationInvariantRate, benchmark::Counter::OneK::kIs1000);
+ }
+ 
+-static void arguments(benchmark::internal::Benchmark * b)
++static void arguments(benchmark::Benchmark * b)
+ {
+     // Size of the IBF will be 2^bits bits
+     for (int32_t bits = 15; bits <= 20; bits += 5)

seqan3.spec

@@ -24,7 +24,7 @@ ExclusiveArch: %{power64} x86_64 aarch64
 
 Name:      seqan3
 Summary:   The modern C++ library for sequence analysis
-Version:   3.4.2
+Version:   3.4.0
 Release:   %autorelease
 License:   BSD-3-Clause
 URL:       https://www.seqan.de/
@@ -57,10 +57,19 @@ BuildRequires: gtest-devel >= 1.10.0
 BuildRequires: texlive-newunicodechar
 BuildRequires: doxygen >= 1.9.4
 %endif
+
 # Use Fedora's CMake only
 Patch1: %{name}-3.4.0-disable_CPM.patch
+
 # Include missing header files
 Patch2: %{name}-fix_GCC15.patch
+
+# Fix (gcc-16) bogus warning
+Patch3: %{name}-fix_gcc-16.patch
+
+# Fix google benchmark
+Patch4: %{name}-fix_latest_google_benchmark.patch
+
 %description
 SeqAn3 is the new version of the popular SeqAn template
 library for the analysis of biological sequences.
@@ -83,8 +92,10 @@ Requires: sdsl-lite-devel%{?_isa} >= 3.0.1
 Requires: zlib-devel%{?_isa} >= 1.2
 Requires: bzip2-devel%{?_isa} >= 1.0
 Requires: range-v3-devel%{?_isa} >= 0.11.0
+
 Provides: bundled(bzip2stream)
 Provides: bundled(zipstream)
+
 %description devel
 C++ headers files of SeqAn3, including CMake configuration files.
 
@@ -99,6 +110,8 @@ SeqAn3 documentation.
 
 %patch 1 -p1 -b .backup
 %patch 2 -p1 -b .backup
+%patch 3 -p1 -b .backup
+%patch 4 -p1 -b .backup
 
 # Unbundle libraries already available in Fedora
 rm -rf submodules/cereal

sources

@@ -1 +1 @@
-SHA512 (seqan3-3.4.2.tar.gz) = 6337bb3d49406e89e277ab4b9e751f6b2a0524c32c7aecf2093b795863870c2337bb1df1c798791aee82325cb3f0b19ecb57e109d73db847e6fe6a2a033bbaae
+SHA512 (seqan3-3.4.0.tar.gz) = c8541ac8166c70f521c2613d7c3ad7760ae3025ed5f196740176789c2f0400cecfd4aea2c500a1c0a2f801e35a5ab4df4dfc7c3d116518ab08b30da7cf69df06