Enable all compilation warnings, and fix a few of them.

These warnings are not promoted to errors are some of them might come from Rcpp and we don't have any control over that.
tatami-inc · Aug 6, 2023 · a239a0c · a239a0c
1 parent 4b8a0c4
commit a239a0c
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Showing 4 changed files with 10 additions and 15 deletions.
diff --git a/include/tatami_r/COO_SparseMatrix.hpp b/include/tatami_r/COO_SparseMatrix.hpp
@@ -20,7 +20,7 @@ Parsed<Data_, Index_> parse_COO_SparseMatrix_internal(Rcpp::RObject seed, InputO
     }
 
     const size_t nnz = temp_i.nrow();
-    if (nnz != val.size()) {
+    if (nnz != static_cast<size_t>(val.size())) {
         auto ctype = get_class_name(seed);
         throw std::runtime_error(std::string("incompatible 'nzcoo' and 'nzdata' lengths in a ") + ctype + " object"); 
     }

diff --git a/include/tatami_r/UnknownMatrix.hpp b/include/tatami_r/UnknownMatrix.hpp
@@ -95,7 +95,7 @@ class UnknownMatrix : public tatami::Matrix<Value_, Index_> {
         }
 
         cache_size = cache;
-        if (cache_size == -1) {
+        if (cache_size == static_cast<size_t>(-1)) {
             Rcpp::Function fun = delayed_env["getAutoBlockSize"];
             Rcpp::NumericVector output = fun();
             if (output.size() != 1 || output[0] < 0) {
@@ -179,8 +179,8 @@ class UnknownMatrix : public tatami::Matrix<Value_, Index_> {
 
         // We define the number of chunks in the extracted block,
         // as well as the size of the extracted block itself.
-        Index_ max_block_size_in_chunks;
-        Index_ max_block_size_in_elements;
+        size_t max_block_size_in_chunks;
+        size_t max_block_size_in_elements;
 
         // No oracle, we just go for blocks.
         Index_ primary_block_start, primary_block_len;
@@ -317,8 +317,8 @@ class UnknownMatrix : public tatami::Matrix<Value_, Index_> {
 
     template<bool byrow_, bool sparse_, bool sparse_err = sparse_>
     void check_buffered_dims(const tatami::Matrix<Value_, Index_>* parsed, const Workspace<sparse_>* work) const {
-        size_t parsed_primary = (byrow_ ? parsed->nrow() : parsed->ncol());
-        size_t parsed_secondary = (byrow_ ? parsed->ncol() : parsed->nrow());
+        Index_ parsed_primary = (byrow_ ? parsed->nrow() : parsed->ncol());
+        Index_ parsed_secondary = (byrow_ ? parsed->ncol() : parsed->nrow());
 
         if (parsed_primary != work->primary_block_len || parsed_secondary != work->secondary_len) {
             auto ctype = get_class_name(original_seed);
@@ -551,12 +551,12 @@ class UnknownMatrix : public tatami::Matrix<Value_, Index_> {
             // Need to adjust the indices.
             if (output.index) {
                 if constexpr(selection_ == tatami::DimensionSelectionType::BLOCK) {
-                    for (size_t i = 0; i < output.number; ++i) {
+                    for (Index_ i = 0; i < output.number; ++i) {
                         ibuffer[i] = output.index[i] + this->block_start;
                     }
                     output.index = ibuffer;
                 } else if constexpr(selection_ == tatami::DimensionSelectionType::INDEX) {
-                    for (size_t i = 0; i < output.number; ++i) {
+                    for (Index_ i = 0; i < output.number; ++i) {
                         ibuffer[i] = this->indices[output.index[i]];
                     }
                     output.index = ibuffer;

diff --git a/tests/src/Makevars b/tests/src/Makevars
@@ -6,4 +6,5 @@ PKG_CPPFLAGS=-I../../include \
     -Wformat \
     -Werror=format-security \
     -Wdate-time \
-    -D_FORTIFY_SOURCE=2
+    -D_FORTIFY_SOURCE=2 \
+    -Wall -Wextra -Wpedantic
diff --git a/tests/src/bindings.cpp b/tests/src/bindings.cpp
@@ -249,7 +249,6 @@ Rcpp::List sparse_rows(Rcpp::RObject parsed) {
     RatXPtr ptr(parsed);
 
     size_t nr = ptr->nrow();
-    size_t nc = ptr->ncol();
     Rcpp::List output(nr);
 
     auto wrk = ptr->sparse_row();
@@ -267,7 +266,6 @@ Rcpp::List sparse_rows_subset(Rcpp::RObject parsed, int first, int last) {
     RatXPtr ptr(parsed);
 
     size_t nr = ptr->nrow();
-    size_t len = last - first + 1;
     Rcpp::List output(nr);
 
     auto wrk = ptr->sparse_row(first - 1, last - first + 1);
@@ -284,7 +282,6 @@ Rcpp::List sparse_rows_subset(Rcpp::RObject parsed, int first, int last) {
 Rcpp::List sparse_columns(Rcpp::RObject parsed) {
     RatXPtr ptr(parsed);
 
-    size_t nr = ptr->nrow();
     size_t nc = ptr->ncol();
     Rcpp::List output(nc);
 
@@ -303,7 +300,6 @@ Rcpp::List sparse_columns_subset(Rcpp::RObject parsed, int first, int last) {
     RatXPtr ptr(parsed);
 
     size_t nc = ptr->ncol();
-    size_t len = last - first + 1;
     Rcpp::List output(nc);
 
     auto wrk = ptr->sparse_column(first - 1, last - first + 1);
@@ -410,7 +406,6 @@ Rcpp::List sparse_rows_guided(Rcpp::RObject parsed, Rcpp::IntegerVector targets)
     auto wrk = ptr->sparse_row();
     auto copy = prepare_indices(targets, wrk);
 
-    size_t nc = ptr->ncol();
     Rcpp::List output(copy.size());
     size_t counter = 0;
     for (auto r : copy) {
@@ -428,7 +423,6 @@ Rcpp::List sparse_columns_guided(Rcpp::RObject parsed, Rcpp::IntegerVector targe
     auto wrk = ptr->sparse_column();
     auto copy = prepare_indices(targets, wrk);
 
-    size_t nr = ptr->nrow();
     size_t counter = 0;
     Rcpp::List output(copy.size());
     for (auto c : copy) {