Fixed compiler error

bbuchfink · bbuchfink · commit 49d560baa1f5 · 2025-07-22T21:27:25.000+02:00
diff --git a/src/basic/shape_config.h b/src/basic/shape_config.h
@@ -46,7 +46,7 @@ class ShapeConfig
 		}
 	}
 
-	unsigned count() const
+	int count() const
 	{ return n_; }
 
 	const Shape& operator[](size_t i) const
diff --git a/src/cluster/external/cluster.cpp b/src/cluster/external/cluster.cpp
@@ -190,7 +190,7 @@ string cluster_bidirectional(Job& job, const vector<string>& edges, const Volume
 	if (lock.fetch_add() == 0) {
 		job.log("Computing clustering (bi-directional coverage)");
 		vector<uint32_t> degree(volumes.records(), 0);
-		for (int bucket = 0; bucket < edges.size(); ++bucket) {
+		for (int bucket = 0; bucket < (int)edges.size(); ++bucket) {
 			VolumedFile file(edges[bucket]);
 			InputBuffer<Edge> data(file);
 			job.log("Getting node degrees. Bucket=%lli/%lli Records=%s Size=%s", bucket + 1, edges.size(), format(data.size()).c_str(), format(data.byte_size()).c_str());
diff --git a/src/cluster/external/external.cpp b/src/cluster/external/external.cpp
@@ -365,7 +365,7 @@ static void build_chunks(Job& job, const VolumedFile& db, const vector<string>&
 
 string round(Job& job, const VolumedFile& volumes) {
 	::shapes = ShapeConfig(Search::shape_codes.at(config.sensitivity), 0);
-	job.log("Starting round %i sensitivity %s %i shapes\n", job.round(), to_string(config.sensitivity), ::shapes.count());
+	job.log("Starting round %i sensitivity %s %i shapes\n", job.round(), to_string(config.sensitivity).c_str(), ::shapes.count());
 	job.set_round(volumes.size(), volumes.records());
 	const std::string pair_table_base = job.base_dir() + PATH_SEPARATOR + "pair_table";
 	mkdir(pair_table_base);
diff --git a/src/cluster/external/external.h b/src/cluster/external/external.h
@@ -137,10 +137,10 @@ struct Job {
 
 	void log(const char* format, ...) {
 		char buffer[1024];
-		char* ptr = buffer + sprintf(buffer, "[%i, %lli] ", worker_id_, std::chrono::duration_cast<std::chrono::duration<long long int>>(std::chrono::system_clock::now() - start_).count());
+		char* ptr = buffer + snprintf(buffer, 1024, "[%i, %lli] ", worker_id_, std::chrono::duration_cast<std::chrono::duration<long long int>>(std::chrono::system_clock::now() - start_).count());
 		va_list args;
 		va_start(args, format);
-		int i = vsprintf(ptr, format, args);
+		int i = vsnprintf(ptr, 1024 - (ptr - buffer), format, args);
 #ifdef WIN32
 		ptr[i++] = '\r';
 #endif
diff --git a/src/cluster/external/output.cpp b/src/cluster/external/output.cpp
@@ -1,3 +1,4 @@
+#include <inttypes.h>
 #include "external.h"
 
 using std::vector;
@@ -47,11 +48,7 @@ void output(Job& job) {
 	for (int64_t i = 0; i < (int64_t)inner.size(); ++i) {
 		if (inner[i] == i)
 			++n;
-#ifdef _MSC_VER
-		fprintf(out, "%lli\t%lli\n", inner[i], i);
-#else
-		fprintf(out, "%li\t%li\n", inner[i], i);
-#endif
+		fprintf(out, PRId64 "\t" PRId64 "\n", inner[i], i);
 	}
 	fclose(out);
 	job.log("Cluster count = %lli", n);
diff --git a/src/data/index.cpp b/src/data/index.cpp
@@ -28,10 +28,10 @@ void makeindex() {
 	out.write(SEED_INDEX_VERSION);
 	out.write((uint32_t)shapes.count());
 
-	for (unsigned i = 0; i < shapes.count(); ++i)
+	for (int i = 0; i < shapes.count(); ++i)
 		out.write(index.table(i).size());
 
-	for (unsigned i = 0; i < shapes.count(); ++i) {
+	for (int i = 0; i < shapes.count(); ++i) {
 		out.write(index.table(i).data(), index.table(i).size() + HashedSeedSet::Table::PADDING);
 	}
 
diff --git a/src/data/seed_histogram.cpp b/src/data/seed_histogram.cpp
@@ -39,7 +39,7 @@ size_t SeedHistogram::max_chunk_size(const int index_chunks) const
 {
 	size_t max = 0;
 	::Partition<int> p(seedp(), index_chunks);
-	for (unsigned shape = 0; shape < shapes.count(); ++shape)
+	for (int shape = 0; shape < shapes.count(); ++shape)
 		for (int chunk = 0; chunk < p.parts; ++chunk)
 			max = std::max(max, hst_size(data_[shape], SeedPartitionRange(p.begin(chunk), p.end(chunk))));
 	return max;
@@ -54,7 +54,7 @@ SeedHistogram::SeedHistogram(Block& seqs, bool serial, const Filter* filter, Enu
 		Callback(size_t seqp, int seedp_bits, vector<ShapeHistogram>& data):
 			seedp_mask(::seedp_mask(seedp_bits))
 		{
-			for (unsigned s = 0; s < shapes.count(); ++s)
+			for (int s = 0; s < shapes.count(); ++s)
 				ptr.push_back(data[s][seqp].data());
 		}
 		bool operator()(PackedSeed seed, uint64_t pos, uint32_t block_id, size_t shape)
@@ -74,7 +74,7 @@ SeedHistogram::SeedHistogram(Block& seqs, bool serial, const Filter* filter, Enu
 		cb.push_back(new Callback(i, seedp_bits, data_));
 	enum_cfg.partition = &p_;
 	if (serial)
-		for (unsigned s = 0; s < shapes.count(); ++s) {
+		for (int s = 0; s < shapes.count(); ++s) {
 			enum_cfg.shape_begin = s;
 			enum_cfg.shape_end = s + 1;
 			enum_seeds(seqs, cb, filter, enum_cfg);
diff --git a/src/data/seed_set.cpp b/src/data/seed_set.cpp
@@ -132,7 +132,7 @@ HashedSeedSet::HashedSeedSet(const string& index_file):
 	const size_t* size_ptr = (const size_t*)(buf + SEED_INDEX_HEADER_SIZE);
 	uint8_t* data_ptr = (uint8_t*)(buf + SEED_INDEX_HEADER_SIZE + sizeof(size_t) * shape_count);
 
-	for (unsigned i = 0; i < shapes.count(); ++i) {
+	for (int i = 0; i < shapes.count(); ++i) {
 		data_.push_back(new Table(data_ptr, *size_ptr));
 		log_stream << "MMAPED Shape=" << i << " Hash_table_size=" << data_[i].size() << " load=" << (double)data_[i].load() / data_[i].size() << endl;
 		data_ptr += *size_ptr + Table::PADDING;
diff --git a/src/lib/Eigen/src/Core/util/Meta.h b/src/lib/Eigen/src/Core/util/Meta.h
@@ -11,6 +11,8 @@
 #ifndef EIGEN_META_H
 #define EIGEN_META_H
 
+#include <utility>
+
 #if defined(__CUDA_ARCH__)
 #include <cfloat>
 #include <math_constants.h>
@@ -315,12 +317,19 @@ class noncopyable
   * upcoming next STL generation (using a templated result member).
   * If none of these members is provided, then the type of the first argument is returned. FIXME, that behavior is a pretty bad hack.
   */
-#if EIGEN_HAS_STD_RESULT_OF
-template<typename T> struct result_of {
-  typedef typename std::result_of<T>::type type1;
+//#if EIGEN_HAS_STD_RESULT_OF
+template <typename T>
+struct result_of;
+
+template<typename T, typename... Args> struct result_of<T(Args...)> {
+#if __cplusplus >= 201703L
+    using type1 = typename std::invoke_result<T, Args...>::type;
+#else
+  typedef typename std::result_of<T(Args...)>::type type1;
+#endif
   typedef typename remove_all<type1>::type type;
 };
-#else
+/*#else
 template<typename T> struct result_of { };
 
 struct has_none {int a[1];};
@@ -396,7 +405,7 @@ struct result_of<Func(ArgType0,ArgType1,ArgType2)> {
     enum {FunctorType = sizeof(testFunctor(static_cast<Func*>(0)))};
     typedef typename ternary_result_of_select<Func, ArgType0, ArgType1, ArgType2, FunctorType>::type type;
 };
-#endif
+#endif*/
 
 struct meta_yes { char a[1]; };
 struct meta_no  { char a[2]; };
diff --git a/src/lib/blast/blastn_score.cpp b/src/lib/blast/blastn_score.cpp
@@ -437,10 +437,10 @@ BlastScoreBlkProteinMatrixRead(BlastScoreBlk* sbp, FILE *fp)
 
     /* Use the C scores for U and X scores for O characters;
        if this is not done then they will never align to non-gap residues */
-    x_index = AMINOACID_TO_NCBISTDAA['X'];
-    u_index = AMINOACID_TO_NCBISTDAA['U'];
-    o_index = AMINOACID_TO_NCBISTDAA['O'];
-    c_index = AMINOACID_TO_NCBISTDAA['C'];
+    x_index = AMINOACID_TO_NCBISTDAA[(int)'X'];
+    u_index = AMINOACID_TO_NCBISTDAA[(int)'U'];
+    o_index = AMINOACID_TO_NCBISTDAA[(int)'O'];
+    c_index = AMINOACID_TO_NCBISTDAA[(int)'C'];
     for (index1 = 0; index1 < sbp->alphabet_size; index1++) {
         matrix[u_index][index1] = matrix[c_index][index1];
         matrix[index1][u_index] = matrix[index1][c_index];
@@ -924,12 +924,12 @@ const SNCBIPackedScoreMatrix* NCBISM_GetStandardMatrix(const char* name) {
         for (i = 0; i < sbp->alphabet_size; i++) {
             for (j = 0; j < sbp->alphabet_size; j++) {
                 /* skip special characters */
-                if (i == AMINOACID_TO_NCBISTDAA['U'] ||
-                    i == AMINOACID_TO_NCBISTDAA['O'] ||
-                    i == AMINOACID_TO_NCBISTDAA['-'] ||
-                    j == AMINOACID_TO_NCBISTDAA['U'] ||
-                    j == AMINOACID_TO_NCBISTDAA['O'] ||
-                    j == AMINOACID_TO_NCBISTDAA['-']) {
+                if (i == AMINOACID_TO_NCBISTDAA[(int)'U'] ||
+                    i == AMINOACID_TO_NCBISTDAA[(int)'O'] ||
+                    i == AMINOACID_TO_NCBISTDAA[(int)'-'] ||
+                    j == AMINOACID_TO_NCBISTDAA[(int)'U'] ||
+                    j == AMINOACID_TO_NCBISTDAA[(int)'O'] ||
+                    j == AMINOACID_TO_NCBISTDAA[(int)'-']) {
                     continue;
                 }
                 matrix[i][j] = NCBISM_GetScore((const SNCBIPackedScoreMatrix *) psm,
diff --git a/src/run/double_indexed.cpp b/src/run/double_indexed.cpp
@@ -178,7 +178,7 @@ static void run_ref_chunk(SequenceFile &db_file,
 			timer.finish();
 		}
         if((config.command != ::Config::blastn)){
-            for (unsigned i = 0; i < shapes.count(); ++i) {
+            for (int i = 0; i < shapes.count(); ++i) {
                 if(config.global_ranking_targets)
                     cfg.global_ranking_buffer.reset(new Config::RankingBuffer());
                 search_shape(i, cfg.current_query_block, query_iteration, query_buffer, ref_buffer, cfg, target_seeds); //index_targets(0,cfg,ref_buffer,target_seeds);
diff --git a/src/tools/greedy_vertex_cover.cpp b/src/tools/greedy_vertex_cover.cpp
@@ -147,7 +147,7 @@ void greedy_vertex_cover() {
 	log_rss();
 
 	timer.go("Making flat array");
-	FlatArray<Edge> edge_array = make_flat_array_dense(move(edges), (Int)acc2oid.size(), config.threads_, Edge::GetKey());
+	FlatArray<Edge> edge_array = make_flat_array_dense(std::move(edges), (Int)acc2oid.size(), config.threads_, Edge::GetKey());
 	timer.finish();
 	log_rss();
 
diff --git a/src/util/io/compressed_stream.h b/src/util/io/compressed_stream.h
@@ -26,9 +26,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 struct ZlibSource : public StreamEntity
 {
 	ZlibSource(InputStreamBuffer *prev);
-	virtual size_t read(char *ptr, size_t count);
-	virtual void close();
-	virtual void rewind();
+	virtual size_t read(char* ptr, size_t count) override;
+	virtual void close() override;
+	virtual void rewind() override;
 	virtual bool eof() override;
 private:
 	void init();
diff --git a/src/util/string/tokenizer_dyn.h b/src/util/string/tokenizer_dyn.h
@@ -90,7 +90,7 @@ struct CharTokenizer : public TokenizerBase {
 			++ptr_;
 		return *this;
 	}
-	virtual std::pair<bool, std::string> read_record() {
+	virtual std::pair<bool, std::string> read_record() override {
 		if (ptr_ >= end_)
 			return { false,std::string() };
 		const char* b = ptr_;
@@ -104,7 +104,7 @@ struct CharTokenizer : public TokenizerBase {
 			return { true, std::string(b, ptr_ - 1) };
 		}
 	}
-	virtual std::pair<bool, std::string> read_record(TextInputFile&) {
+	virtual std::pair<bool, std::string> read_record(TextInputFile&) override {
 		throw std::runtime_error("Invalid use of CharTokenizer");
 	}
 private:

Original file line number	Diff line number	Diff line change
`@@ -46,7 +46,7 @@ class ShapeConfig`
`46`	`46`	`}`
`47`	`47`	`}`
`48`	`48`
`49`		`- unsigned count() const`
	`49`	`+ int count() const`
`50`	`50`	`{ return n_; }`
`51`	`51`
`52`	`52`	`const Shape& operator[](size_t i) const`