vendor: Update vendored sources to duckdb/duckdb@4a0d6fd

Date: 2026-09-01 15:30:44 +0000

Validate LIST offsets before use (https://redirect.github.com/duckdb/duckdb/pull/25212)

R-side fix:

Nothing in the tree — a finding with no repair to carry,
recorded here because nothing else keeps it.

Two r-universe targets failed on the previous green,
1b37203 (`duckdb.dev` 1.5.5.9013.1395, krlmlr.r-universe.dev):
`macos-release-x86_64` at 3804 s and `windows-devel-x86_64` at 3664 s,
both `##[error]The action has timed out.` inside a one-hour action budget,
both with `src/duckdb` still compiling.

The Windows one is new, and it is the same cause as the macOS one
(d49ded3, and duckdb#2678):
`.Rbuildignore` lists `^scripts$`,
so `R CMD build` strips the directory
and `configure` / `configure.win` cannot read `scripts/setup-makeflags.R`,
which is where `MAKEFLAGS` comes from.
What differs is only how the failure shows:
this platform's `Rscript` reports the missing file on stderr,
which `2>/dev/null` swallows,
so `makeflags_value` is empty,
no `MAKEFLAGS` line is printed at all,
and the build simply compiles serially with nothing in the log to say why —
where macOS keeps the error string and prints it.
The Windows log shows one `g++` invocation at a time
from 17:31 to the timeout at 18:31, which is the same serial build.

So the target list this costs is wider than macOS:
every platform that installs from the built tarball compiles serially,
and the ones near the hour fall off the edge.

duckdb#2678 moves the helper to `tools/`, which `R CMD build` keeps,
and refuses a value that is not `-jN`; this firing added the Windows
evidence to it. It is open against `main`;
the series gets it when stage 4 ports it, never before.

The consequence is stale published binaries, not broken ones:
`mac-x86_64` and `win-x86_64` both still serve 1.5.5.9013.1373,
built earlier the same day.
The `rcc` gate is Linux on one R version and never compiles either target,
and no `each-rcc` run records the outcome either way.

Author: claude

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: duckdb.dev
 Title: DBI Package for the DuckDB Database Management System
-Version: 1.5.5.9013.1402
+Version: 1.5.5.9013.1403
 Authors@R: c(
     person("Hannes", "Mühleisen", , "hannes@cwi.nl", role = "aut",
            comment = c(ORCID = "0000-0001-8552-0029")),

R/version.R

@@ -1,7 +1,7 @@
 # Generated by rconfigure.py, do not edit by hand
 # DuckDB version information
 
-duckdb_version <- "2.0.0-dev83354"
+duckdb_version <- "2.0.0-dev83357"
 
 # Function to get DuckDB version without establishing a connection
 get_duckdb_version <- function() {

src/duckdb/src/function/table/version/pragma_version.cpp

@@ -1,5 +1,5 @@
 #ifndef DUCKDB_PATCH_VERSION
-#define DUCKDB_PATCH_VERSION "0-dev83354"
+#define DUCKDB_PATCH_VERSION "0-dev83357"
 #endif
 #ifndef DUCKDB_MINOR_VERSION
 #define DUCKDB_MINOR_VERSION 0
@@ -8,10 +8,10 @@
 #define DUCKDB_MAJOR_VERSION 2
 #endif
 #ifndef DUCKDB_VERSION
-#define DUCKDB_VERSION "v2.0.0-dev83354"
+#define DUCKDB_VERSION "v2.0.0-dev83357"
 #endif
 #ifndef DUCKDB_SOURCE_ID
-#define DUCKDB_SOURCE_ID "fb922caa6d"
+#define DUCKDB_SOURCE_ID "4a0d6fdecb"
 #endif
 #include "duckdb/function/table/system_functions.hpp"
 #include "duckdb/main/database.hpp"

src/duckdb/src/storage/table/list_column_data.cpp

@@ -1,3 +1,4 @@
+#include "duckdb/common/exception.hpp"
 #include "duckdb/common/vector/flat_vector.hpp"
 #include "duckdb/common/vector/list_vector.hpp"
 #include "duckdb/storage/table/list_column_data.hpp"
@@ -9,6 +10,28 @@
 
 namespace duckdb {
 
+[[noreturn]] static void ThrowListOffsetOutOfRange() {
+	throw DataCorruptionException("Corrupted LIST column: offset exceeds the child column count");
+}
+
+[[noreturn]] static void ThrowListOffsetsOutOfOrder() {
+	throw DataCorruptionException("Corrupted LIST column: later offset is smaller than the preceding offset");
+}
+
+static void ValidateListOffset(idx_t offset, idx_t child_count) {
+	if (offset > child_count) {
+		ThrowListOffsetOutOfRange();
+	}
+}
+
+static idx_t GetListLength(idx_t start_offset, idx_t end_offset, idx_t child_count) {
+	if (end_offset < start_offset) {
+		ThrowListOffsetsOutOfOrder();
+	}
+	ValidateListOffset(end_offset, child_count);
+	return end_offset - start_offset;
+}
+
 ListColumnData::ListColumnData(BlockManager &block_manager, DataTableInfo &info, idx_t column_index, LogicalType type_p,
                                ColumnDataType data_type, optional_ptr<ColumnData> parent)
     : ColumnData(block_manager, info, column_index, std::move(type_p), data_type, parent) {
@@ -58,14 +81,19 @@ void ListColumnData::InitializeScan(ColumnScanState &state) {
 }
 
 uint64_t ListColumnData::FetchListOffset(idx_t row_idx) {
+	if (row_idx >= count) {
+		throw DataCorruptionException("Corrupted database: list offset row ID is out of range");
+	}
 	auto segment = data.GetSegment(row_idx);
 	ColumnFetchState fetch_state;
 	Vector result(LogicalType::UBIGINT, 1);
 	auto index_in_segment = UnsafeNumericCast<row_t>(row_idx - segment->GetRowStart());
 	segment->GetNode().FetchRow(fetch_state, index_in_segment, result, 0U);
+	auto offset = FlatVector::GetData<uint64_t>(result)[0];
+	ValidateListOffset(offset, child_column->GetMaxEntry());
 
 	// initialize the child scan with the required offset
-	return FlatVector::GetData<uint64_t>(result)[0];
+	return offset;
 }
 
 void ListColumnData::InitializeScanWithOffset(ColumnScanState &state, idx_t row_idx) {
@@ -81,7 +109,6 @@ void ListColumnData::InitializeScanWithOffset(ColumnScanState &state, idx_t row_
 
 	// we need to read the list at position row_idx to get the correct row offset of the child
 	auto child_offset = FetchListOffset(row_idx - 1);
-	D_ASSERT(child_offset <= child_column->GetMaxEntry());
 	if (child_offset < child_column->GetMaxEntry()) {
 		child_column->InitializeScanWithOffset(state.child_states[1], child_offset);
 	}
@@ -109,21 +136,20 @@ idx_t ListColumnData::ScanCount(ColumnScanState &state, Vector &result, idx_t co
 	validity->ScanCount(state.child_states[0], result, count);
 
 	auto data = offset_vector.Values<uint64_t>();
-	auto last_entry = data[scan_count - 1].GetValueUnsafe();
-
 	// shift all offsets so they are 0 at the first entry
 	auto result_data = FlatVector::Writer<list_entry_t>(result, scan_count);
-	auto base_offset = state.last_offset;
+	auto previous_offset = state.last_offset;
 	idx_t current_offset = 0;
+	auto child_count = child_column->GetMaxEntry();
 	for (idx_t i = 0; i < scan_count; i++) {
 		auto offset = data[i].GetValueUnsafe();
-		auto length = offset - current_offset - base_offset;
+		auto length = GetListLength(previous_offset, offset, child_count);
 		result_data.WriteValue(list_entry_t(current_offset, length));
 		current_offset += length;
+		previous_offset = offset;
 	}
 
-	D_ASSERT(last_entry >= base_offset);
-	idx_t child_scan_count = last_entry - base_offset;
+	idx_t child_scan_count = current_offset;
 	ListVector::Reserve(result, child_scan_count);
 
 	if (child_scan_count > 0) {
@@ -135,7 +161,7 @@ idx_t ListColumnData::ScanCount(ColumnScanState &state, Vector &result, idx_t co
 		}
 		child_column->ScanCount(state.child_states[1], child_entry, child_scan_count);
 	}
-	state.last_offset = last_entry;
+	state.last_offset = previous_offset;
 
 	ListVector::SetListSize(result, child_scan_count);
 	return scan_count;
@@ -156,7 +182,7 @@ void ListColumnData::Skip(ColumnScanState &state, idx_t count) {
 	offset_vector.ToUnifiedFormat(offsets);
 	auto data = UnifiedVectorFormat::GetData<uint64_t>(offsets);
 	auto last_entry = data[offsets.sel->get_index(scan_count - 1)];
-	idx_t child_scan_count = last_entry - state.last_offset;
+	idx_t child_scan_count = GetListLength(state.last_offset, last_entry, child_column->GetMaxEntry());
 	if (child_scan_count == 0) {
 		return;
 	}
@@ -298,14 +324,15 @@ void ListColumnData::FetchRows(TransactionData transaction, ColumnFetchState &st
 		const auto row_id = offsets[sel.get_index(idx)];
 		auto start_offset = row_id == 0 ? 0 : FetchListOffset(row_id - 1);
 		auto end_offset = FetchListOffset(row_id);
+		auto length = GetListLength(start_offset, end_offset, child_column->GetMaxEntry());
 		auto result_idx = result_offset + idx;
 		auto &list_entry = list_data[result_idx];
 		// set the list entry offset to the size of the current list
 		list_entry.offset = ListVector::GetListSize(result);
-		list_entry.length = end_offset - start_offset;
+		list_entry.length = length;
 		if (!validity_mask.RowIsValid(result_idx)) {
 			// the list is NULL! no need to fetch the child
-			D_ASSERT(list_entry.length == 0);
+			list_entry.length = 0;
 			continue;
 		}