[med-svn] [Git][med-team/seqan-raptor][master] 4 commits: d/patches/debian_seqan3: set patch to vendored seqan3 libraries.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Wed Jul 19 11:53:41 BST 2023
Michael R. Crusoe pushed to branch master at Debian Med / seqan-raptor
Commits:
d2e58abe by Michael R. Crusoe at 2023-07-14T14:15:13+02:00
d/patches/debian_seqan3: set patch to vendored seqan3 libraries.
- - - - -
7e9f5570 by Michael R. Crusoe at 2023-07-19T12:13:03+02:00
test in experimental with seqan3 3.3.0 RC1
- - - - -
b43d0710 by Michael R. Crusoe at 2023-07-19T12:30:36+02:00
d/patches/gcc13*: cherry-pick from upstream to fix gcc-13 build. Closes: #1037856
- - - - -
887f3410 by Michael R. Crusoe at 2023-07-19T12:52:42+02:00
release with gcc-13 fixes to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/patches/debian_seqan3
- debian/patches/debian_xxhash
- + debian/patches/gcc13-bogus-dangling
- + debian/patches/gcc13_ambiguous_name
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+seqan-raptor (3.0.0+ds-2) unstable; urgency=medium
+
+ * d/patches/debian_seqan3: set patch to vendored seqan3 libraries.
+ * d/control: build-dep on seqan3 3.3.0 release candidate.
+ * d/patches/gcc13*: cherry-pick from upstream to fix gcc-13 build.
+ Closes: #1037856
+
+ -- Michael R. Crusoe <crusoe at debian.org> Fri, 14 Jul 2023 14:15:12 +0200
+
seqan-raptor (3.0.0+ds-1) unstable; urgency=medium
* d/watch: find complete source archives.
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Michael R. Crusoe <crusoe at debian.org>
Build-Depends: debhelper-compat (= 13),
cmake,
- libseqan3-dev (>= 3.2.0+ds-7),
+ libseqan3-dev (>= 3.3.0~rc.1),
libgtest-dev,
libxxhash-dev,
libcereal-dev,
=====================================
debian/patches/debian_seqan3
=====================================
@@ -21,7 +21,7 @@ Forwarded: not-needed
# Define cmake configuration flags to configure and build external projects with the same flags as specified for
--- seqan-raptor.orig/src/CMakeLists.txt
+++ seqan-raptor/src/CMakeLists.txt
-@@ -13,9 +13,8 @@
+@@ -13,9 +13,9 @@
# Dependency: Chopper
include (FetchContent)
@@ -29,6 +29,7 @@ Forwarded: not-needed
+FetchContent_Declare (raptor_chopper_project SOURCE_DIR "${RAPTOR_SUBMODULES_DIR}/chopper")
-set (SEQAN3_SUBMODULES_DIR "${RAPTOR_SUBMODULES_DIR}")
++set (SEQAN3_SUBMODULES_DIR "/usr/include/seqan3/submodules")
set (CHOPPER_SUBMODULES_DIR
"${RAPTOR_SUBMODULES_DIR}"
CACHE STRING "Directory containing submodules."
=====================================
debian/patches/debian_xxhash
=====================================
@@ -15,7 +15,7 @@ Forwarded: not-needed
add_custom_target (xxhash_project)
--- seqan-raptor.orig/src/CMakeLists.txt
+++ seqan-raptor/src/CMakeLists.txt
-@@ -35,14 +35,8 @@
+@@ -36,14 +36,8 @@
FetchContent_MakeAvailable (raptor_chopper_project)
# Dependency: xxHash
=====================================
debian/patches/gcc13-bogus-dangling
=====================================
@@ -0,0 +1,116 @@
+From 2d327f99780c1381b22360ce78d7ad2ee5aa7d8c Mon Sep 17 00:00:00 2001
+From: Enrico Seiler <enrico.seiler at hotmail.de>
+Date: Tue, 2 May 2023 12:25:45 +0200
+Subject: [PATCH] [FIX] GCC13 bogus dangling reference warning
+
+---
+ include/raptor/search/search_singular_ibf.hpp | 2 +-
+ src/search/search_partitioned_ibf.cpp | 4 ++--
+ test/performance/bin_influence_benchmark.cpp | 2 +-
+ util/applications/src/iScience/generate_reads.cpp | 2 +-
+ util/applications/src/iScience/generate_reads_refseq.cpp | 3 +--
+ util/applications/src/iScience/threshold_info.cpp | 2 +-
+ util/iScience/thresholding/src/random_data.cpp | 2 +-
+ 7 files changed, 8 insertions(+), 9 deletions(-)
+
+diff --git a/include/raptor/search/search_singular_ibf.hpp b/include/raptor/search/search_singular_ibf.hpp
+index d7b48f5a..9615561d 100644
+--- a/include/raptor/search/search_singular_ibf.hpp
++++ b/include/raptor/search/search_singular_ibf.hpp
+@@ -65,7 +65,7 @@ void search_singular_ibf(search_arguments const & arguments, index_t && index)
+ seqan3::window_size{arguments.window_size},
+ seqan3::seed{adjust_seed(arguments.shape_weight)});
+
+- for (auto && [id, seq] : records | seqan3::views::slice(start, end))
++ for (auto && [id, seq] : seqan3::views::slice(records, start, end))
+ {
+ result_string.clear();
+ result_string += id;
+diff --git a/src/search/search_partitioned_ibf.cpp b/src/search/search_partitioned_ibf.cpp
+index 909e213e..ebae526b 100644
+--- a/src/search/search_partitioned_ibf.cpp
++++ b/src/search/search_partitioned_ibf.cpp
+@@ -82,7 +82,7 @@ void search_partitioned_ibf(search_arguments const & arguments)
+ seqan3::window_size{arguments.window_size},
+ seqan3::seed{adjust_seed(arguments.shape_weight)});
+
+- for (auto && [id, seq] : records | seqan3::views::slice(start, end))
++ for (auto && [id, seq] : seqan3::views::slice(records, start, end))
+ {
+ auto minimiser_view = seq | hash_view | std::views::common;
+ local_compute_minimiser_timer.start();
+@@ -135,7 +135,7 @@ void search_partitioned_ibf(search_arguments const & arguments)
+ seqan3::window_size{arguments.window_size},
+ seqan3::seed{adjust_seed(arguments.shape_weight)});
+
+- for (auto && [id, seq] : records | seqan3::views::slice(start, end))
++ for (auto && [id, seq] : seqan3::views::slice(records, start, end))
+ {
+ result_string.clear();
+ result_string += id;
+diff --git a/test/performance/bin_influence_benchmark.cpp b/test/performance/bin_influence_benchmark.cpp
+index a284ae12..81384e0f 100644
+--- a/test/performance/bin_influence_benchmark.cpp
++++ b/test/performance/bin_influence_benchmark.cpp
+@@ -62,7 +62,7 @@ static std::vector<std::vector<seqan3::dna4>> const reads{
+ for (auto && read_start :
+ seqan3::test::generate_numeric_sequence<size_t>(read_count, 0, genome_size - read_size - 1, 0))
+ {
+- auto v = genome | seqan3::views::slice(read_start, read_start + read_size);
++ auto v = seqan3::views::slice(genome, read_start, read_start + read_size);
+ result[i++].assign(v.begin(), v.end());
+ }
+ return result;
+diff --git a/util/applications/src/iScience/generate_reads.cpp b/util/applications/src/iScience/generate_reads.cpp
+index 82a2f249..f27694e7 100644
+--- a/util/applications/src/iScience/generate_reads.cpp
++++ b/util/applications/src/iScience/generate_reads.cpp
+@@ -75,7 +75,7 @@ void run_program(config const & cfg)
+ ++current_read_number, ++read_counter, ++reads_per_bin_counter)
+ {
+ size_t const read_start_pos = read_start_dis(rng);
+- auto read_slice = seq | seqan3::views::slice(read_start_pos, read_start_pos + cfg.read_length);
++ auto read_slice = seqan3::views::slice(seq, read_start_pos, read_start_pos + cfg.read_length);
+ read.assign(read_slice.begin(), read_slice.end());
+
+ introduce_errors();
+diff --git a/util/applications/src/iScience/generate_reads_refseq.cpp b/util/applications/src/iScience/generate_reads_refseq.cpp
+index 9bdb2541..407ab93c 100644
+--- a/util/applications/src/iScience/generate_reads_refseq.cpp
++++ b/util/applications/src/iScience/generate_reads_refseq.cpp
+@@ -117,8 +117,7 @@ void run_program(cmd_arguments const & arguments)
+ ++current_read_number, ++read_counter, ++bin_read_counter)
+ {
+ uint64_t const read_start_pos = read_start_dis(rng);
+- auto read_slice =
+- seq | seqan3::views::slice(read_start_pos, read_start_pos + arguments.read_length);
++ auto read_slice = seqan3::views::slice(seq, read_start_pos, read_start_pos + arguments.read_length);
+ read.assign(read_slice.begin(), read_slice.end());
+
+ for (uint8_t error_count = 0; error_count < arguments.errors; ++error_count)
+diff --git a/util/applications/src/iScience/threshold_info.cpp b/util/applications/src/iScience/threshold_info.cpp
+index 9e16358a..b1e55bcf 100644
+--- a/util/applications/src/iScience/threshold_info.cpp
++++ b/util/applications/src/iScience/threshold_info.cpp
+@@ -51,7 +51,7 @@ void threshold_info(raptor::search_arguments const & arguments, std::string cons
+ seqan3::window_size{arguments.window_size},
+ seqan3::seed{raptor::adjust_seed(kmer_size)});
+
+- for (auto && [seq] : records | seqan3::views::slice(start, end))
++ for (auto && [seq] : seqan3::views::slice(records, start, end))
+ {
+ size_t const minimiser_count{static_cast<size_t>(std::ranges::distance(seq | hash_adaptor))};
+
+diff --git a/util/iScience/thresholding/src/random_data.cpp b/util/iScience/thresholding/src/random_data.cpp
+index 80ed188c..df33b87e 100644
+--- a/util/iScience/thresholding/src/random_data.cpp
++++ b/util/iScience/thresholding/src/random_data.cpp
+@@ -60,7 +60,7 @@ void run_program(std::filesystem::path const & out_directory,
+ for (size_t i = 0; i < number_of_queries; ++i)
+ {
+ size_t start = dis_pos(gen);
+- auto query_slice = reference_sequence | seqan3::views::slice(start, start + query_length);
++ auto query_slice = seqan3::views::slice(reference_sequence, start, start + query_length);
+ query_sequence.assign(query_slice.begin(), query_slice.end());
+
+ for (size_t j = 0; j < errors; ++j)
=====================================
debian/patches/gcc13_ambiguous_name
=====================================
@@ -0,0 +1,80 @@
+From 42a3db03a5c22ade5a7a2e20bcd8a720961cb42c Mon Sep 17 00:00:00 2001
+From: Enrico Seiler <enrico.seiler at hotmail.de>
+Date: Tue, 2 May 2023 12:25:58 +0200
+Subject: [PATCH] [FIX] Ambiguous type/function name
+
+---
+ .../hierarchical_interleaved_bloom_filter.hpp | 28 +++++++++----------
+ 1 file changed, 14 insertions(+), 14 deletions(-)
+
+diff --git a/include/raptor/hierarchical_interleaved_bloom_filter.hpp b/include/raptor/hierarchical_interleaved_bloom_filter.hpp
+index 84d472d7..49aeccb4 100644
+--- a/include/raptor/hierarchical_interleaved_bloom_filter.hpp
++++ b/include/raptor/hierarchical_interleaved_bloom_filter.hpp
+@@ -91,7 +91,7 @@ class hierarchical_interleaved_bloom_filter
+ class user_bins;
+
+ // Forward declaration
+- class membership_agent;
++ class membership_agent_type;
+
+ #if RAPTOR_HIBF_HAS_COUNT
+ // Forward declaration
+@@ -135,9 +135,9 @@ class hierarchical_interleaved_bloom_filter
+ user_bins user_bins;
+
+ //!\brief Returns a membership_agent to be used for counting.
+- membership_agent membership_agent() const
++ membership_agent_type membership_agent() const
+ {
+- return typename hierarchical_interleaved_bloom_filter<data_layout_mode>::membership_agent{*this};
++ return typename hierarchical_interleaved_bloom_filter<data_layout_mode>::membership_agent_type{*this};
+ }
+
+ #if RAPTOR_HIBF_HAS_COUNT
+@@ -307,7 +307,7 @@ class hierarchical_interleaved_bloom_filter<data_layout_mode>::user_bins
+ * In contrast to the [seqan3::interleaved_bloom_filter][1], the result will consist of indices of user bins.
+ */
+ template <seqan3::data_layout data_layout_mode> // TODO: value_t as template?
+-class hierarchical_interleaved_bloom_filter<data_layout_mode>::membership_agent
++class hierarchical_interleaved_bloom_filter<data_layout_mode>::membership_agent_type
+ {
+ private:
+ //!\brief The type of the augmented hierarchical_interleaved_bloom_filter.
+@@ -351,18 +351,18 @@ class hierarchical_interleaved_bloom_filter<data_layout_mode>::membership_agent
+ /*!\name Constructors, destructor and assignment
+ * \{
+ */
+- membership_agent() = default; //!< Defaulted.
+- membership_agent(membership_agent const &) = default; //!< Defaulted.
+- membership_agent & operator=(membership_agent const &) = default; //!< Defaulted.
+- membership_agent(membership_agent &&) = default; //!< Defaulted.
+- membership_agent & operator=(membership_agent &&) = default; //!< Defaulted.
+- ~membership_agent() = default; //!< Defaulted.
+-
+- /*!\brief Construct a membership_agent for an existing hierarchical_interleaved_bloom_filter.
++ membership_agent_type() = default; //!< Defaulted.
++ membership_agent_type(membership_agent_type const &) = default; //!< Defaulted.
++ membership_agent_type & operator=(membership_agent_type const &) = default; //!< Defaulted.
++ membership_agent_type(membership_agent_type &&) = default; //!< Defaulted.
++ membership_agent_type & operator=(membership_agent_type &&) = default; //!< Defaulted.
++ ~membership_agent_type() = default; //!< Defaulted.
++
++ /*!\brief Construct a membership_agent_type for an existing hierarchical_interleaved_bloom_filter.
+ * \private
+ * \param hibf The hierarchical_interleaved_bloom_filter.
+ */
+- explicit membership_agent(hibf_t const & hibf) : hibf_ptr(std::addressof(hibf))
++ explicit membership_agent_type(hibf_t const & hibf) : hibf_ptr(std::addressof(hibf))
+ {}
+ //!\}
+
+@@ -384,7 +384,7 @@ class hierarchical_interleaved_bloom_filter<data_layout_mode>::membership_agent
+ * ### Thread safety
+ *
+ * Concurrent invocations of this function are not thread safe, please create a
+- * raptor::hierarchical_interleaved_bloom_filter::membership_agent for each thread.
++ * raptor::hierarchical_interleaved_bloom_filter::membership_agent_type for each thread.
+ */
+ template <std::ranges::forward_range value_range_t>
+ [[nodiscard]] std::vector<int64_t> const & bulk_contains(value_range_t && values, size_t const threshold) & noexcept
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,5 @@
+gcc13_ambiguous_name
+gcc13-bogus-dangling
fix_missing_lambda_capture.patch
privacy
chopper_no_test
View it on GitLab: https://salsa.debian.org/med-team/seqan-raptor/-/compare/e8e194b72726012ca8db5109199b2a1916b560d5...887f34109a71678fde0caaecb83d6849f1c96483
--
View it on GitLab: https://salsa.debian.org/med-team/seqan-raptor/-/compare/e8e194b72726012ca8db5109199b2a1916b560d5...887f34109a71678fde0caaecb83d6849f1c96483
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