fix: Fix format strings for rdevel (#93)

* fix binary atomics * more fixes * more errors * cran comments * also clang-format * add to build ignore
paleolimbot · Nov 30, 2023 · 1025240 · 1025240
1 parent 17f2f9e
commit 1025240
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Showing 19 changed files with 1,247 additions and 1,352 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -14,3 +14,4 @@
 ^CRAN-RELEASE$
 ^\.vscode$
 ^CRAN-SUBMISSION$
+^\.clang-format$
diff --git a/.clang-format b/.clang-format
@@ -0,0 +1,5 @@
+---
+BasedOnStyle: Google
+ColumnLimit: 90
+DerivePointerAlignment: false
+IncludeBlocks: Preserve
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,5 +1,5 @@
 
-This release fixes new warnings from the M1Mac check.
+This release fixes new warnings as shown on the package check page.
 
 ## R CMD check results
 

diff --git a/src/geoarrow-imports.h b/src/geoarrow-imports.h
@@ -55,4 +55,4 @@ class Handler {
   virtual ~Handler() {}
 };
 
-}
+}  // namespace util
diff --git a/src/geos-basic-strtree.c b/src/geos-basic-strtree.c
@@ -2,23 +2,24 @@
 #include <R.h>
 #include <Rinternals.h>
 
-#include "libgeos.h"
 #include "geos-common.h"
+#include "libgeos.h"
 
-#include <stdint.h>
 #include <limits.h>
+#include <stdint.h>
 
 SEXP geos_c_basic_strtree_create(SEXP node_capacity_sexp) {
   int node_capacity = INTEGER(node_capacity_sexp)[0];
   GEOS_INIT();
   GEOSSTRtree* tree = GEOSSTRtree_create_r(handle, node_capacity);
   if (tree == NULL) {
-    GEOS_ERROR("%s", "Failed to create GEOSSTRtree*()"); // # nocov
+    GEOS_ERROR("%s", "Failed to create GEOSSTRtree*()");  // # nocov
   }
 
   SEXP tree_size_sexp = PROTECT(Rf_ScalarInteger(0));
   SEXP tree_is_finalized = PROTECT(Rf_ScalarInteger(0));
-  SEXP tree_xptr = PROTECT(geos_common_tree_xptr(tree, tree_size_sexp, tree_is_finalized));
+  SEXP tree_xptr =
+      PROTECT(geos_common_tree_xptr(tree, tree_size_sexp, tree_is_finalized));
   UNPROTECT(3);
   return tree_xptr;
 }
@@ -33,9 +34,8 @@ SEXP geos_c_basic_strtree_finalized(SEXP tree_xptr) {
   return Rf_ScalarLogical(is_finalized);
 }
 
-GEOSGeometry* dummy_geometry_from_extent(GEOSContextHandle_t handle,
-                                         double xmin, double ymin,
-                                         double xmax, double ymax) {
+GEOSGeometry* dummy_geometry_from_extent(GEOSContextHandle_t handle, double xmin,
+                                         double ymin, double xmax, double ymax) {
   GEOSCoordSequence* seq = GEOSCoordSeq_create_r(handle, 2, 2);
   if (seq == NULL) {
     Rf_error("error creating GEOSCoordSequence");
@@ -71,7 +71,7 @@ SEXP geos_c_basic_strtree_insert_rect(SEXP tree_xptr, SEXP xmin_sexp, SEXP ymin_
 
   GEOS_INIT();
 
-  GEOSSTRtree* tree = (GEOSSTRtree*) R_ExternalPtrAddr(tree_xptr);
+  GEOSSTRtree* tree = (GEOSSTRtree*)R_ExternalPtrAddr(tree_xptr);
   if (tree == NULL) {
     Rf_error("External pointer (GEOSSTRtree) is not valid");
   }
@@ -92,17 +92,13 @@ SEXP geos_c_basic_strtree_insert_rect(SEXP tree_xptr, SEXP xmin_sexp, SEXP ymin_
       R_CheckUserInterrupt();
     }
 
-    if (xmin[i] > xmax[i] || ymin[i] > ymax[i] ||
-        R_IsNA(xmin[i]) || R_IsNA(ymin[i]) || R_IsNA(xmax[i]) || R_IsNA(ymax[i])) {
+    if (xmin[i] > xmax[i] || ymin[i] > ymax[i] || R_IsNA(xmin[i]) || R_IsNA(ymin[i]) ||
+        R_IsNA(xmax[i]) || R_IsNA(ymax[i])) {
       tree_size[0]++;
       continue;
     }
 
-    geom = dummy_geometry_from_extent(
-      handle,
-      xmin[i], ymin[i],
-      xmax[i], ymax[i]
-    );
+    geom = dummy_geometry_from_extent(handle, xmin[i], ymin[i], xmax[i], ymax[i]);
     payload = tree_size[0];
     GEOSSTRtree_insert_r(handle, tree, geom, (void*)payload);
     tree_size[0]++;
@@ -160,7 +156,7 @@ void basic_query_finalize(SEXP query_xptr) {
   }
 }
 
-static void basic_query_callback(void *item, void *userdata) {
+static void basic_query_callback(void* item, void* userdata) {
   uintptr_t item_value = (uintptr_t)item;
   struct BasicQuery* query = (struct BasicQuery*)userdata;
   if (query->has_error || query->limit <= 0) {
@@ -171,8 +167,8 @@ static void basic_query_callback(void *item, void *userdata) {
 }
 
 SEXP geos_c_basic_strtree_query_geom(SEXP tree_xptr, SEXP xmin_sexp, SEXP ymin_sexp,
-                                    SEXP xmax_sexp, SEXP ymax_sexp,
-                                    SEXP limit_sexp, SEXP fill_sexp) {
+                                     SEXP xmax_sexp, SEXP ymax_sexp, SEXP limit_sexp,
+                                     SEXP fill_sexp) {
   int limit = INTEGER(limit_sexp)[0];
   if (limit < 0) {
     limit = INT_MAX;
@@ -192,7 +188,7 @@ SEXP geos_c_basic_strtree_query_geom(SEXP tree_xptr, SEXP xmin_sexp, SEXP ymin_s
 
   GEOS_INIT();
 
-  GEOSSTRtree* tree = (GEOSSTRtree*) R_ExternalPtrAddr(tree_xptr);
+  GEOSSTRtree* tree = (GEOSSTRtree*)R_ExternalPtrAddr(tree_xptr);
   if (tree == NULL) {
     Rf_error("External pointer (GEOSSTRtree) is not valid");
   }
@@ -215,19 +211,15 @@ SEXP geos_c_basic_strtree_query_geom(SEXP tree_xptr, SEXP xmin_sexp, SEXP ymin_s
       R_CheckUserInterrupt();
     }
 
-    geom = dummy_geometry_from_extent(
-      handle,
-      xmin[i], ymin[i],
-      xmax[i], ymax[i]
-    );
+    geom = dummy_geometry_from_extent(handle, xmin[i], ymin[i], xmax[i], ymax[i]);
 
     query->ix_ = i + 1;
     query->has_error = 0;
     query->limit = limit;
     GEOSSTRtree_query_r(handle, tree, geom, &basic_query_callback, query);
     GEOSGeom_destroy_r(handle, geom);
     if (query->has_error) {
-      Rf_error("Failed to allocate container for result indices [i = %d]", i + 1);
+      Rf_error("Failed to allocate container for result indices [i = %ld]", (long)i + 1);
     }
 
     if (fill && query->limit > 0) {
-Original file line number
+Diff line change
@@ Expand Up / @@ -55,4 +55,4 @@ class Handler { @@
       virtual ~Handler() {}
     };
-    }
+    }  // namespace util