Merge remote-tracking branch 'origin/master' into ihn/update-0.30.2

NEWS.md

@@ -2,6 +2,11 @@
 
 * This release of the R package builds against [TileDB 2.26.2](https://github.com/TileDB-Inc/TileDB/releases/tag/2.26.2), and has also been tested against earlier releases as well as the development version (#757)
 
+* [#760](https://github.com/TileDB-Inc/TileDB-R/issues/758) Fix MacOS `rpath`
+
+* [#758](https://github.com/TileDB-Inc/TileDB-R/issues/758) Fix "Can't read domain for dimensions of type UINT16"
+
+
 # tiledb 0.30.1
 
 * This release of the R package builds against [TileDB 2.26.1](https://github.com/TileDB-Inc/TileDB/releases/tag/2.26.1), and has also been tested against earlier releases as well as the development version (#757)

inst/tinytest/test_dim.R

@@ -154,7 +154,11 @@ for (dtype in dimtypes) {
                    "INT64" = as.integer64(1000),
                    1000)                    # default is 1000
 
-    domain <- tiledb_domain(tiledb_dim("row", dom, tile, dtype))
+    dimension <- tiledb_dim("row", dom, tile, dtype)
+    if (dtype != "ASCII") { # no extent for string dims
+      expect_silent(tile(dimension))
+    }
+    domain <- tiledb_domain(dimension)
     attrib <- tiledb_attr("attr", type = "INT32")
     schema <- tiledb_array_schema(domain, attrib, sparse=TRUE)
     tiledb_array_create(uri, schema)

src/Makevars.in

@@ -11,14 +11,17 @@ LIB_CON_DIR = ../inst/lib$(R_ARCH)
 LIB_CON = $(LIB_CON_DIR)/libconnection@DYLIB_EXT@
 
 all: $(OBJECTS) $(LIB_CON) $(SHLIB)
-        # if we are
-        #  - on macOS aka Darwin which needs this
-        #  - the library is present (implying non-system library use)
-        # then let us call install_name_tool
-	@if [ `uname -s` = 'Darwin' ] && [ -f ../inst/tiledb/lib/libtiledb.dylib ] && [ -f tiledb.so ]; then \
-	    install_name_tool -change libz.1.dylib @rpath/libz.1.dylib ../inst/tiledb/lib/libtiledb.dylib; \
-	    install_name_tool -add_rpath @loader_path/../tiledb/lib tiledb.so; \
-	    install_name_tool -add_rpath @loader_path/../tiledb/lib $(LIB_CON); \
+        # On macOS aka Darwin we call install_name_tool
+        # Case one: If we had a downloaded TileDB Core artifact, adjust zlib path and add to @rpath
+        # Case two: If we see the system libraries (on macOS) ensure /usr/local/lib rpath is considered
+	@if [ `uname -s` = 'Darwin' ] && [ -f tiledb.so ]; then \
+	    if [ -f ../inst/tiledb/lib/libtiledb.dylib ] ; then \
+	        install_name_tool -change libz.1.dylib @rpath/libz.1.dylib ../inst/tiledb/lib/libtiledb.dylib; \
+	        install_name_tool -add_rpath @loader_path/../tiledb/lib tiledb.so; \
+	    fi; \
+	    if [ -f /usr/local/lib/libtiledb.dylib ] ; then \
+	        install_name_tool -add_rpath /usr/local/lib tiledb.so; \
+	    fi; \
 	fi
 
 $(LIB_CON): connection/connection.o

src/libtiledb.cpp

@@ -757,7 +757,7 @@ XPtr<tiledb::Dimension> libtiledb_dim(XPtr<tiledb::Context> ctx,
             Rcpp::stop("dimension domain must be a c(lower bound, upper bound) pair");
         }
         std::array<uint16_t, 2> _domain = {static_cast<uint16_t>(domain_vec[0]), static_cast<uint16_t>(domain_vec[1])};
-        int16_t _tile_extent = Rcpp::as<int16_t>(tile_extent);
+        uint16_t _tile_extent = Rcpp::as<uint16_t>(tile_extent);
         auto dim = new tiledb::Dimension(tiledb::Dimension::create<uint16_t>(*ctx.get(), name, _domain, _tile_extent));
         auto ptr = make_xptr<tiledb::Dimension>(dim);
         return ptr;
@@ -925,7 +925,7 @@ SEXP libtiledb_dim_get_domain(XPtr<tiledb::Dimension> dim) {
                             dim->domain<DataType>().second});
     }
     case TILEDB_UINT16: {
-      using DataType = tiledb::impl::tiledb_to_type<TILEDB_INT16>::type;
+      using DataType = tiledb::impl::tiledb_to_type<TILEDB_UINT16>::type;
       return IntegerVector({dim->domain<DataType>().first,
                             dim->domain<DataType>().second});
     }
@@ -1027,7 +1027,7 @@ SEXP libtiledb_dim_get_tile_extent(XPtr<tiledb::Dimension> dim) {
       return Rcpp::wrap(static_cast<int32_t>(dim->tile_extent<DataType>()));
     }
     case TILEDB_UINT16: {
-      using DataType = tiledb::impl::tiledb_to_type<TILEDB_INT16>::type;
+      using DataType = tiledb::impl::tiledb_to_type<TILEDB_UINT16>::type;
       return Rcpp::wrap(static_cast<int32_t>(dim->tile_extent<DataType>()));
     }
     case TILEDB_INT32: {