version 0.8.1-2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: duckdb
 Title: DBI Package for the DuckDB Database Management System
-Version: 0.8.1-1
+Version: 0.8.1-2
 Authors@R: 
     c(person(given = "Hannes",
              family = "Mühleisen",
@@ -49,7 +49,7 @@ Suggests: arrow, bit64, callr, DBItest, dplyr, dbplyr, rlang, testthat,
 Encoding: UTF-8
 RoxygenNote: 7.2.3
 NeedsCompilation: yes
-Packaged: 2023-07-17 13:01:26 UTC; hannes
+Packaged: 2023-08-25 07:12:45 UTC; kirill
 Author: Hannes Mühleisen [aut, cre] (<https://orcid.org/0000-0001-8552-0029>),
   Mark Raasveldt [aut] (<https://orcid.org/0000-0001-5005-6844>),
   Stichting DuckDB Foundation [cph],
@@ -78,4 +78,4 @@ Author: Hannes Mühleisen [aut, cre] (<https://orcid.org/0000-0001-8552-0029>),
   PCG Project contributors [cph]
 Maintainer: Hannes Mühleisen <[email protected]>
 Repository: CRAN
-Date/Publication: 2023-07-17 19:50:08 UTC
+Date/Publication: 2023-08-25 14:50:02 UTC

MD5

@@ -1,11 +1,11 @@
-4a621f9382e8f478266d9c67bb5b8bb5 *DESCRIPTION
+7ed633426be62ce6294fa4d4074eb1ad *DESCRIPTION
 6793c89d1af721728c4d58c99d5b9d30 *LICENSE
 e975be1b49bcc0e567737d712d3e3cc8 *NAMESPACE
-ced14ada4cfff8a89e7feb2203f589fb *R/Connection.R
+020754c4367c905a2a063f2c8a286ebf *R/Connection.R
 91c325c3a74cc6795a82cac48f471fa3 *R/Driver.R
-ffaef65bbcda5b3ba21238b82bce945e *R/Result.R
+1b19f326281b21675272963c31a52816 *R/Result.R
 d0ef7160705dbda6bfa1a4f64cdcd036 *R/Viewer.R
-fdc48d3020beeb6cd3285a54a0033bcb *R/backend-dbplyr__duckdb_connection.R
+02d714be6689e35f22b89efab32aa095 *R/backend-dbplyr__duckdb_connection.R
 2db929241b4ff8a8df57623513228184 *R/cpp11.R
 d49f39f1e48e4dedb7534852ff82d37c *R/csv.R
 dd4470c96c18d554032e42de78a4a49f *R/dbAppendTable__duckdb_connection.R
@@ -14,7 +14,7 @@ dd4470c96c18d554032e42de78a4a49f *R/dbAppendTable__duckdb_connection.R
 c8258883a4c6568425d2e855aa1907da *R/dbClearResult__duckdb_result.R
 07635ddf3e35a5cb81c94d4ca62c314f *R/dbColumnInfo__duckdb_result.R
 96da806c02ffbfcc8c7bdbc23b04d7da *R/dbCommit__duckdb_connection.R
-d22f52b957888a7734ff48f48832996f *R/dbConnect__duckdb_driver.R
+8e2ba2b5cc33da139e0543d6e47e2755 *R/dbConnect__duckdb_driver.R
 0acc42e921d89f2d65b2f53391e0b9c1 *R/dbDataType__duckdb_connection.R
 9738c730904876bffc2fedb5cf603794 *R/dbDataType__duckdb_driver.R
 0a4ffb009247ea7406b0557441152681 *R/dbDisconnect__duckdb_connection.R
@@ -48,16 +48,16 @@ e48e0f4d25ce5a055ce7df9b95f99082 *R/show__duckdb_driver.R
 8dccf29cb4095ecb8722e8f8731dbc69 *R/show__duckdb_result.R
 864c0e9b6d8b508b57234347d3d1d360 *R/sql.R
 f3ae5b73437b0149357f91f20741ee7d *R/substrait.R
-9a728d72a986d6af11a632eb0c8fcd1b *R/zzz.R
-189ce5ba8d8483c372b8961817c1bfbf *README.md
+6ef65b78d5a154855e7e7709b8a89c60 *R/zzz.R
+a9aab4bcaefc5b07326a047127c88585 *README.md
 95645911d270eeea9ebcdc773288dbed *inst/icons/duckdb.png
 e8a15f1b5781b5d2803afe6ab00d6404 *inst/include/cpp11.hpp
 ac46452ffea887725873cc0608f5025d *inst/include/cpp11/R.hpp
 d146ab6c79c037331fd3bd99d5739c4b *inst/include/cpp11/altrep.hpp
 b577ac42eb0aeaca47a811a7ed63568d *inst/include/cpp11/as.hpp
 19239fd0521865044d48fb9b53017afb *inst/include/cpp11/attribute_proxy.hpp
 dd330b4252b03edc39a35fded7420487 *inst/include/cpp11/data_frame.hpp
-f70bf6d07cf5c94ed61504a799dab0e0 *inst/include/cpp11/declarations.hpp
+14d6e0185a877260325764e51718e7ca *inst/include/cpp11/declarations.hpp
 15f3dafbd512e527a36b6264f01897a6 *inst/include/cpp11/doubles.hpp
 a675556cd67b8898f5593319a6504a16 *inst/include/cpp11/environment.hpp
 99a5723507db2ab211a44dc6c1a493f5 *inst/include/cpp11/external_pointer.hpp
@@ -68,7 +68,7 @@ db94f12cca5bf0fc32e24fe818106300 *inst/include/cpp11/list.hpp
 4b22e60584cc8ae8a3e28e018d6da5dd *inst/include/cpp11/logicals.hpp
 0be378f1d599c9fb84deb6a0f01a7358 *inst/include/cpp11/matrix.hpp
 8efb781a399a0676e1b3dbd5ea3b8d8d *inst/include/cpp11/named_arg.hpp
-f4fd2e4f609f940fe9702d12b80cf230 *inst/include/cpp11/protect.hpp
+0de15dfa3de4f9f7c20de1ba06becfa3 *inst/include/cpp11/protect.hpp
 e3711a64328f128b523e72b1cb1dda57 *inst/include/cpp11/r_bool.hpp
 e43bc609629e112a12443ecdfb196223 *inst/include/cpp11/r_string.hpp
 e1315e2cbc06e18314e40161e9057110 *inst/include/cpp11/r_vector.hpp
@@ -2574,13 +2574,13 @@ bb87e7725e015e2a819b931e6b016e4c *src/duckdb/ub_src_transaction.cpp
 c5b82a8a7752d56fe8f8b680cb7c6739 *src/include/rapi.hpp
 bfab5b7ebf664cfa9be8b9e23637cde6 *src/include/reltoaltrep.hpp
 ad38f5bba84a80f446bb280673dc237f *src/include/typesr.hpp
-7fb4b61602795fd02ac2dd7905229fb2 *src/register.cpp
-2f3291ac253e9400e34b38559565e477 *src/relational.cpp
-fb21581a23e55322399543f4a8988a40 *src/reltoaltrep.cpp
+368e7be49467a6409c1aaca0950c89ef *src/register.cpp
+67d6f1c97b7f9e0fb337e6e8fd1fb068 *src/relational.cpp
+cf10fa41c6993e787c1cf2ef439c23a4 *src/reltoaltrep.cpp
 d15a20201fdbed81487c64a0dbb689b1 *src/scan.cpp
 88f6f21f6578739bd4f4894a82d3b67e *src/statement.cpp
 e9aca686f387592f8c699e2f5a85fd55 *src/transform.cpp
-62d774991cae5c1d23ddceb875c38aee *src/types.cpp
+042a848f7cc328a4780ca05be49e1721 *src/types.cpp
 02f8c7789e450b229e5c7bf9ac1742f2 *src/utils.cpp
 78ca03523e01aa272eeb2f0bd5a53011 *tests/testthat.R
 96ce833955091e793c1265569d5063ab *tests/testthat/_snaps/backend-dbplyr__duckdb_connection.md
@@ -2590,9 +2590,11 @@ b685427653b6f6080c558a8386e7b5c4 *tests/testthat/_snaps/multi_statement.md
 dabf0e452e677b9c7afaca658ac8371b *tests/testthat/data/binary_string.parquet
 2f67292983870c49f4ee50330c4f7b7f *tests/testthat/data/userdata1.parquet
 389e9753304e62c280e1b5eafbfc2cbd *tests/testthat/helper-DBItest.R
+c5cf38e3b1ceb04719b174f0791b301c *tests/testthat/helper-arrow.R
 da441e8ef9a6b41b9d166500608413af *tests/testthat/test-DBItest.R
 416307e283e6ab4d585f42ae1479f73b *tests/testthat/test-dbQuoteIdentifier__duckdb_connection.R
 2f2914ae28fe3864659d945414650dd5 *tests/testthat/test-rel_api.R
+057e655ecc463501f146bdf4e6b54d9b *tests/testthat/test-shutdown.R
 bf47c0f3a0781587def97c78490cf625 *tests/testthat/test_ambiguous_prepare.R
 c3f90eb02a950bdd18a9cf5afe70d6de *tests/testthat/test_arrow.R
 5ad34cfb89166055e124f96647314361 *tests/testthat/test_arrow_recordbatchreader.py
@@ -2618,9 +2620,10 @@ c6b302ba389c7cedd5aae6bb7fa3731a *tests/testthat/test_parquet.R
 a3ce818c4cb2c7c4dd435207fb19c747 *tests/testthat/test_register.R
 60434301f7c5e98861b7620cd7035091 *tests/testthat/test_register_arrow.R
 891908e0804e2315fa13285f1005a689 *tests/testthat/test_register_readonly.R
-1628b8687408ce019baec5acae74918b *tests/testthat/test_relational.R
+c9ddbd8f771cc4330f1906ae1b64001b *tests/testthat/test_relational.R
 1439bba03df63e03d87acfe916b5e62f *tests/testthat/test_struct.R
 ff31415409c10783fc36512cc6ef7920 *tests/testthat/test_tbl__duckdb_connection.R
-6f39a7ff5f8d75716824165d951473e4 *tests/testthat/test_timezone.R
+b3d7eab44a600a5c4df348969b4a2a85 *tests/testthat/test_timestamp.R
+3458bc88f78f37e7b3ce9d0b5756ddb3 *tests/testthat/test_timezone.R
 0d70b43b41ce312eb3cb0c418ca2840f *tests/testthat/test_types.R
 f61a2bf9f4e00271fc78209a04c0fa07 *tests/testthat/test_viewer.R

R/Connection.R

@@ -5,7 +5,12 @@
 #' @aliases duckdb_driver
 #' @keywords internal
 #' @export
-setClass("duckdb_driver", contains = "DBIDriver", slots = list(database_ref = "externalptr", dbdir = "character", read_only = "logical", bigint = "character"))
+setClass("duckdb_driver", contains = "DBIDriver", slots = list(
+  database_ref = "externalptr",
+  dbdir = "character",
+  read_only = "logical",
+  bigint = "character"
+))
 
 #' DuckDB connection class
 #'
@@ -14,17 +19,14 @@ setClass("duckdb_driver", contains = "DBIDriver", slots = list(database_ref = "e
 #' @aliases duckdb_connection
 #' @keywords internal
 #' @export
-setClass("duckdb_connection",
-  contains = "DBIConnection",
-  slots = list(
-    conn_ref = "externalptr",
-    driver = "duckdb_driver",
-    debug = "logical",
-    timezone_out = "character",
-    tz_out_convert = "character",
-    reserved_words = "character"
-  )
-)
+setClass("duckdb_connection", contains = "DBIConnection", slots = list(
+  conn_ref = "externalptr",
+  driver = "duckdb_driver",
+  debug = "logical",
+  timezone_out = "character",
+  tz_out_convert = "character",
+  reserved_words = "character"
+))
 
 duckdb_connection <- function(duckdb_driver, debug) {
   out <- new(

R/Result.R

@@ -112,8 +112,8 @@ tz_convert <- function(x, timezone) {
 }
 
 tz_force <- function(x, timezone) {
-  # convert to character, stripping the timezone
-  ct <- as.character(x, usetz = FALSE)
+  # convert to character in ISO format, stripping the timezone
+  ct <- format(x, format = "%Y-%m-%d %H:%M:%OS", usetz = FALSE)
   # recreate the POSIXct with specified timezone
   as.POSIXct(ct, tz = timezone)
 }

R/backend-dbplyr__duckdb_connection.R

@@ -367,24 +367,6 @@ sql_escape_datetime.duckdb_connection <- function(con, x) {
   dbQLit(con, x)
 }
 
-# Customized translation for fill function
-# @param .con A \code{\link{dbConnect}} object, as returned by \code{dbConnect()}
-# @param .data Data frame
-# @param cols_to_fill Which colums to be altered
-# @param order_by_cols Defined order of variables
-# @param .direction Direction in which to fill missing values.
-# @name dbplyr_fill0
-dbplyr_fill0.duckdb_connection <- function(.con, .data, cols_to_fill, order_by_cols, .direction) {
-  dbplyr_fill0 <- pkg_method("dbplyr_fill0.SQLiteConnection", "dbplyr")
-
-  # Required because of the bug in dbplyr (con is not passed to "translate_sql(cumsum..." call)
-  # See https://github.com/tidyverse/dbplyr/pull/753
-  setcon <- pkg_method("set_current_con", "dbplyr")
-  setcon(.con)
-
-  dbplyr_fill0(.con, .data, cols_to_fill, order_by_cols, .direction)
-}
-
 # Customized handling for tbl() to allow the use of replacement scans
 # @param src .con A \code{\link{dbConnect}} object, as returned by \code{dbConnect()}
 # @param from Table or parquet/csv -files to be registered

R/dbConnect__duckdb_driver.R

@@ -53,7 +53,6 @@ dbConnect__duckdb_driver <- function(drv, dbdir = DBDIR_MEMORY, ...,
 
   # aha, a late comer. let's make a new instance.
   if (!missing_dbdir && dbdir != drv@dbdir) {
-    duckdb_shutdown(drv)
     drv <- duckdb(dbdir, read_only, bigint, config)
   }
 

R/zzz.R

@@ -2,7 +2,6 @@
   s3_register("dbplyr::dbplyr_edition", "duckdb_connection")
   s3_register("dbplyr::db_connection_describe", "duckdb_connection")
   s3_register("dbplyr::sql_translation", "duckdb_connection")
-  s3_register("dbplyr::dbplyr_fill0", "duckdb_connection")
   s3_register("dbplyr::sql_expr_matches", "duckdb_connection")
   s3_register("dbplyr::sql_escape_date", "duckdb_connection")
   s3_register("dbplyr::sql_escape_datetime", "duckdb_connection")

README.md

@@ -49,3 +49,21 @@ DUCKDB_R_DEBUG=1
 ```
 
 If you do this, remember to use `--vanilla` for building release builds.
+
+### Developing with Extensions
+If you wish to build or add extensions to the R package you first need to build duckdb with the 
+`extension_static_build` flag and move the desired extension to a location where it won't be 
+modified by other build scripts. The following commands allow you to add the httpfs extension to 
+a duckdb R build. See the [extension ReadMe](https://github.com/duckdb/duckdb/tree/master/extension#readme) for more 
+information about extensions 
+```sh
+cd duckdb/
+EXTENSION_STATIC_BUILD=1 make
+mv ./build/release/extension/httpfs/httpfs.duckdb_extension {{untouched_path}}/httpfs-extension.duckdb_extension
+```
+Then in R
+```r
+library(“duckdb”)
+con <- DBI::dbConnect(duckdb(config=list(“allow_unsigned_extensions”=“true”)))
+dbExecute(con, “LOAD {{untouched_path}}/httpfs-extension.duckdb_extension")
+```

inst/include/cpp11/declarations.hpp

@@ -35,7 +35,7 @@ T& unmove(T&& t) {
   SEXP err = R_NilValue;              \
   char buf[CPP11_ERROR_BUFSIZE] = ""; \
   try {
-#define END_CPP11                                               \
+#define END_CPP11_EX(RET)                                       \
   }                                                             \
   catch (cpp11::unwind_exception & e) {                         \
     err = e.token;                                              \
@@ -51,4 +51,5 @@ T& unmove(T&& t) {
   } else if (err != R_NilValue) {                               \
     CPP11_UNWIND                                                \
   }                                                             \
-  return R_NilValue;
+  return RET;
+#define END_CPP11 END_CPP11_EX(R_NilValue)

inst/include/cpp11/protect.hpp

@@ -265,14 +265,10 @@ void stop [[noreturn]] (const std::string& fmt_arg, Args&&... args) {
   safe.noreturn(Rf_errorcall)(R_NilValue, "%s", msg.c_str());
 }
 
-template <typename... Args>
-void warning(const char* fmt_arg, Args&&... args) {
-  std::string msg = fmt::format(fmt_arg, std::forward<Args>(args)...);
-  safe[Rf_warningcall](R_NilValue, "%s", msg.c_str());
-}
+// Always making copy of string to avoid weird unwind behavior.
 
 template <typename... Args>
-void warning(const std::string& fmt_arg, Args&&... args) {
+void warning(const std::string fmt_arg, Args&&... args) {
   std::string msg = fmt::format(fmt_arg, std::forward<Args>(args)...);
   safe[Rf_warningcall](R_NilValue, "%s", msg.c_str());
 }
@@ -287,13 +283,10 @@ void stop [[noreturn]] (const std::string& fmt, Args... args) {
   safe.noreturn(Rf_errorcall)(R_NilValue, fmt.c_str(), args...);
 }
 
-template <typename... Args>
-void warning(const char* fmt, Args... args) {
-  safe[Rf_warningcall](R_NilValue, fmt, args...);
-}
+// Always making copy of string to avoid weird unwind behavior.
 
 template <typename... Args>
-void warning(const std::string& fmt, Args... args) {
+void warning(const std::string fmt, Args... args) {
   safe[Rf_warningcall](R_NilValue, fmt.c_str(), args...);
 }
 #endif

src/register.cpp

@@ -42,7 +42,7 @@ using namespace duckdb;
 	static_cast<cpp11::sexp>(conn).attr("_registered_df_" + name) = R_NilValue;
 	auto res = conn->conn->Query("DROP VIEW IF EXISTS \"" + name + "\"");
 	if (res->HasError()) {
-		cpp11::stop(res->GetError().c_str());
+		cpp11::stop("%s", res->GetError().c_str());
 	}
 }
 

src/relational.cpp

@@ -338,7 +338,7 @@ bool constant_expression_is_not_null(duckdb::expr_extptr_t expr) {
 
 static SEXP result_to_df(duckdb::unique_ptr<QueryResult> res) {
 	if (res->HasError()) {
-		stop(res->GetError());
+		stop("%s", res->GetError().c_str());
 	}
 	if (res->type == QueryResultType::STREAM_RESULT) {
 		res = ((StreamQueryResult &)*res).Materialize();
@@ -420,7 +420,7 @@ static SEXP result_to_df(duckdb::unique_ptr<QueryResult> res) {
 [[cpp11::register]] SEXP rapi_rel_sql(duckdb::rel_extptr_t rel, std::string sql) {
 	auto res = rel->rel->Query("_", sql);
 	if (res->HasError()) {
-		stop(res->GetError());
+		stop("%s", res->GetError().c_str());
 	}
 	return result_to_df(std::move(res));
 }

src/reltoaltrep.cpp

@@ -1,6 +1,7 @@
 #include "rapi.hpp"
 #include "typesr.hpp"
 #include "reltoaltrep.hpp"
+#include "cpp11/declarations.hpp"
 
 using namespace duckdb;
 
@@ -68,7 +69,7 @@ struct AltrepRelationWrapper {
 			}
 			res = rel->Execute();
 			if (res->HasError()) {
-				cpp11::stop(res->GetError().c_str());
+				cpp11::stop("Error evaluating duckdb query: %s", res->GetError().c_str());
 			}
 			D_ASSERT(res->type == QueryResultType::MATERIALIZED_RESULT);
 		}
@@ -129,16 +130,20 @@ struct AltrepVectorWrapper {
 
 Rboolean RelToAltrep::RownamesInspect(SEXP x, int pre, int deep, int pvec,
                                       void (*inspect_subtree)(SEXP, int, int, int)) {
+	BEGIN_CPP11
 	AltrepRownamesWrapper::Get(x); // make sure this is alive
 	Rprintf("DUCKDB_ALTREP_REL_ROWNAMES\n");
 	return TRUE;
+	END_CPP11_EX(FALSE)
 }
 
 Rboolean RelToAltrep::RelInspect(SEXP x, int pre, int deep, int pvec, void (*inspect_subtree)(SEXP, int, int, int)) {
+	BEGIN_CPP11
 	auto wrapper = AltrepVectorWrapper::Get(x); // make sure this is alive
 	auto &col = wrapper->rel->rel->Columns()[wrapper->column_index];
 	Rprintf("DUCKDB_ALTREP_REL_VECTOR %s (%s)\n", col.Name().c_str(), col.Type().ToString().c_str());
 	return TRUE;
+	END_CPP11_EX(FALSE)
 }
 
 // this allows us to set row names on a data frame with an int argument without calling INTPTR on it
@@ -150,31 +155,43 @@ static void install_new_attrib(SEXP vec, SEXP name, SEXP val) {
 }
 
 R_xlen_t RelToAltrep::RownamesLength(SEXP x) {
+	// The BEGIN_CPP11 isn't strictly necessary here, but should be optimized away.
+	// It will become important if we ever support row names.
+	BEGIN_CPP11
 	// row.names vector has length 2 in the "compact" case which we're using
 	// see https://stat.ethz.ch/R-manual/R-devel/library/base/html/row.names.html
 	return 2;
+	END_CPP11_EX(0)
 }
 
 void *RelToAltrep::RownamesDataptr(SEXP x, Rboolean writeable) {
+	BEGIN_CPP11
 	auto rownames_wrapper = AltrepRownamesWrapper::Get(x);
 	auto row_count = rownames_wrapper->rel->GetQueryResult()->RowCount();
 	if (row_count > (idx_t)NumericLimits<int32_t>::Maximum()) {
 		cpp11::stop("Integer overflow for row.names attribute");
 	}
 	rownames_wrapper->rowlen_data[1] = -row_count;
 	return rownames_wrapper->rowlen_data;
+	END_CPP11
 }
 
 R_xlen_t RelToAltrep::VectorLength(SEXP x) {
+	BEGIN_CPP11
 	return AltrepVectorWrapper::Get(x)->rel->GetQueryResult()->RowCount();
+	END_CPP11_EX(0)
 }
 
 void *RelToAltrep::VectorDataptr(SEXP x, Rboolean writeable) {
+	BEGIN_CPP11
 	return AltrepVectorWrapper::Get(x)->Dataptr();
+	END_CPP11
 }
 
 SEXP RelToAltrep::VectorStringElt(SEXP x, R_xlen_t i) {
+	BEGIN_CPP11
 	return STRING_ELT(AltrepVectorWrapper::Get(x)->Vector(), i);
+	END_CPP11
 }
 
 static R_altrep_class_t LogicalTypeToAltrepType(const LogicalType &type) {