High-productivity afternoon

single-cell-data · Apr 2, 2024 · 5450dfe · 5450dfe
1 parent e60a6c3
commit 5450dfe
Show file tree

Hide file tree

Showing 4 changed files with 14 additions and 18 deletions.
diff --git a/apis/r/src/RcppExports.cpp b/apis/r/src/RcppExports.cpp
@@ -12,7 +12,7 @@ Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
 #endif
 
 // soma_array_reader
-nanoarrowXPtr soma_array_reader(const std::string& uri, Rcpp::Nullable<Rcpp::CharacterVector> colnames, Rcpp::Nullable<Rcpp::XPtr<tiledb::QueryCondition>> qc, Rcpp::Nullable<Rcpp::List> dim_points, Rcpp::Nullable<Rcpp::List> dim_ranges, std::string batch_size, std::string result_order, const std::string& loglevel, Rcpp::Nullable<Rcpp::CharacterVector> config);
+SEXP soma_array_reader(const std::string& uri, Rcpp::Nullable<Rcpp::CharacterVector> colnames, Rcpp::Nullable<Rcpp::XPtr<tiledb::QueryCondition>> qc, Rcpp::Nullable<Rcpp::List> dim_points, Rcpp::Nullable<Rcpp::List> dim_ranges, std::string batch_size, std::string result_order, const std::string& loglevel, Rcpp::Nullable<Rcpp::CharacterVector> config);
 RcppExport SEXP _tiledbsoma_soma_array_reader(SEXP uriSEXP, SEXP colnamesSEXP, SEXP qcSEXP, SEXP dim_pointsSEXP, SEXP dim_rangesSEXP, SEXP batch_sizeSEXP, SEXP result_orderSEXP, SEXP loglevelSEXP, SEXP configSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
@@ -130,7 +130,7 @@ BEGIN_RCPP
 END_RCPP
 }
 // create_empty_arrow_table
-nanoarrowXPtr create_empty_arrow_table();
+SEXP create_empty_arrow_table();
 RcppExport SEXP _tiledbsoma_create_empty_arrow_table() {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
@@ -140,7 +140,7 @@ BEGIN_RCPP
 END_RCPP
 }
 // sr_next
-nanoarrowXPtr sr_next(Rcpp::XPtr<tdbs::SOMAArray> sr);
+SEXP sr_next(Rcpp::XPtr<tdbs::SOMAArray> sr);
 RcppExport SEXP _tiledbsoma_sr_next(SEXP srSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;

diff --git a/apis/r/src/rinterface.cpp b/apis/r/src/rinterface.cpp
@@ -49,15 +49,15 @@ Rcpp::XPtr<ArrowArray> array_setup_struct(Rcpp::XPtr<ArrowArray> arrxp, int64_t
 
 //' @noRd
 // [[Rcpp::export(soma_array_reader_impl)]]
-nanoarrowXPtr soma_array_reader(const std::string& uri,
-                                Rcpp::Nullable<Rcpp::CharacterVector> colnames = R_NilValue,
-                                Rcpp::Nullable<Rcpp::XPtr<tiledb::QueryCondition>> qc = R_NilValue,
-                                Rcpp::Nullable<Rcpp::List> dim_points = R_NilValue,
-                                Rcpp::Nullable<Rcpp::List> dim_ranges = R_NilValue,
-                                std::string batch_size = "auto",
-                                std::string result_order = "auto",
-                                const std::string& loglevel = "auto",
-                                Rcpp::Nullable<Rcpp::CharacterVector> config = R_NilValue) {
+SEXP soma_array_reader(const std::string& uri,
+                       Rcpp::Nullable<Rcpp::CharacterVector> colnames = R_NilValue,
+                       Rcpp::Nullable<Rcpp::XPtr<tiledb::QueryCondition>> qc = R_NilValue,
+                       Rcpp::Nullable<Rcpp::List> dim_points = R_NilValue,
+                       Rcpp::Nullable<Rcpp::List> dim_ranges = R_NilValue,
+                       std::string batch_size = "auto",
+                       std::string result_order = "auto",
+                       const std::string& loglevel = "auto",
+                       Rcpp::Nullable<Rcpp::CharacterVector> config = R_NilValue) {
 
     if (loglevel != "auto") {
         spdl::set_level(loglevel);

diff --git a/apis/r/src/riterator.cpp b/apis/r/src/riterator.cpp
@@ -168,7 +168,7 @@ bool sr_complete(Rcpp::XPtr<tdbs::SOMAArray> sr) {
 //' @noRd
 //' @import nanoarrow
 // [[Rcpp::export]]
-nanoarrowXPtr create_empty_arrow_table() {
+SEXP create_empty_arrow_table() {
     int ncol = 0;
 
     // Schema first
@@ -193,7 +193,7 @@ nanoarrowXPtr create_empty_arrow_table() {
 
 
 // [[Rcpp::export]]
-nanoarrowXPtr sr_next(Rcpp::XPtr<tdbs::SOMAArray> sr) {
+SEXP sr_next(Rcpp::XPtr<tdbs::SOMAArray> sr) {
    check_xptr_tag<tdbs::SOMAArray>(sr);
 
    if (sr_complete(sr)) {

diff --git a/apis/r/src/rutilities.h b/apis/r/src/rutilities.h
@@ -63,10 +63,6 @@ struct ContextWrapper {
 };
 typedef struct ContextWrapper ctx_wrap_t;
 
-// some lipstick on the (plain C language) pig that is a SEXP:
-// allowing the nanoarrow ArrowArray XPtr be typedef'ed
-typedef SEXP nanoarrowXPtr;
-
 inline void exitIfError(const ArrowErrorCode ec, const std::string& msg) {
     if (ec != NANOARROW_OK) Rcpp::stop(msg);
 }