vendor: Update vendored sources to duckdb/duckdb@d130a01

Date: 2026-09-08 10:53:21 +0000

Track I/O operation counts alongside byte counters (https://redirect.github.com/duckdb/duckdb/pull/25409)

R-side fix:

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

r-universe read `duckdb.dev` 1.5.99.9003.1397 at 1f4b6d7 (`main-green`),
on duckdb.r-universe.dev, and one of the fifteen targets failed.

`macos-oldrel-x86_64` timed out after 3794 s:
`##[error]The action has timed out.` at 3612765 ms of the one-hour budget,
with `duckdb/ub_src_parser_peg_transformer.cpp` still compiling
(<https://duckdb.r-universe.dev/api/actions/logs/102024688950>).
Not a new target and not a new cause: this is the `MAKEFLAGS` timeout
recorded on 16fb13c for the same target, and on 59cb20f for
`macos-release-x86_64`. The log names it outright again:

    + makeflags_value='Fatal error: cannot open file '\''scripts/setup-makeflags.R'\'': No such file or directory'
    + export 'MAKEFLAGS=Fatal error: cannot open file ...'

`configure` fills `MAKEFLAGS` in from `scripts/setup-makeflags.R`,
`.Rbuildignore` lists `^scripts$`,
so `R CMD build` strips the directory
and no package installed from a tarball can read it;
`MAKEFLAGS` is exported as the error string rather than as `-jN`
and every source install from the built tarball compiles serially.
Which targets fall over is boundary noise; the cause is constant.
duckdb#2678 moves the helper to `tools/`, which `R CMD build` keeps,
and refuses a value that is not `-jN`.
It has been open as a draft since 2026-08-27 and every firing since has
paid for it; the series gets it when stage 4 ports it, never before.

This exact read was already posted as evidence on that PR by the firing
four hours earlier (duckdb#2678, comment of 2026-09-08 11:49 UTC),
so this firing added no second comment — only this record, which that
firing had no `-dev` commit to write.

The consequence is a stale published binary, not a broken one:
`mac-x86_64` still serves 1.5.99.9003.1396, built 2026-09-07.
The `rcc` gate is Linux on one R version and compiles that target
on no run, so no `each-rcc` record says anything either way.

`windows-devel-arm64`, recorded on 59cb20f as the runner's rather than
the tree's, is OK again on this build — one occurrence, not a pattern.

Author: claude

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: duckdb.dev
 Title: DBI Package for the DuckDB Database Management System
-Version: 1.5.99.9003.1398
+Version: 1.5.99.9003.1399
 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 <- "2.1.0-dev83997"
+duckdb_version <- "2.1.0-dev83999"
 
 # 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-dev83997"
+#define DUCKDB_PATCH_VERSION "0-dev83999"
 #endif
 #ifndef DUCKDB_MINOR_VERSION
 #define DUCKDB_MINOR_VERSION 1
@@ -8,10 +8,10 @@
 #define DUCKDB_MAJOR_VERSION 2
 #endif
 #ifndef DUCKDB_VERSION
-#define DUCKDB_VERSION "v2.1.0-dev83997"
+#define DUCKDB_VERSION "v2.1.0-dev83999"
 #endif
 #ifndef DUCKDB_SOURCE_ID
-#define DUCKDB_SOURCE_ID "56b103b7f7"
+#define DUCKDB_SOURCE_ID "d130a01ebc"
 #endif
 #include "duckdb/function/table/system_functions.hpp"
 #include "duckdb/main/database.hpp"

src/duckdb/src/include/duckdb/main/profiler/metrics.hpp

@@ -124,6 +124,20 @@ struct MetricIOTotalBytesWritten {
 	static constexpr const char *Unit = "bytes";
 	static constexpr const char *TypeStr = "uint64";
 };
+struct MetricIOTotalReadOperations {
+	using METRIC_TYPE = uint64_t;
+	static constexpr const char *Name = "io.total_read_operations";
+	static constexpr const char *Description = "The total number of read operations issued to storage";
+	static constexpr const char *Unit = "operations";
+	static constexpr const char *TypeStr = "uint64";
+};
+struct MetricIOTotalWriteOperations {
+	using METRIC_TYPE = uint64_t;
+	static constexpr const char *Name = "io.total_write_operations";
+	static constexpr const char *Description = "The total number of write operations issued to storage";
+	static constexpr const char *Unit = "operations";
+	static constexpr const char *TypeStr = "uint64";
+};
 
 // Storage metrics
 struct MetricStorageAttachLoadStorageLatency {

src/duckdb/src/include/duckdb/main/profiler/profiling_utils.hpp

@@ -38,7 +38,9 @@ struct QueryMetrics {
 
 	// Always-tracked byte counters (used by progress bar even when profiling is disabled)
 	atomic<idx_t> bytes_read;
+	atomic<idx_t> read_operations;
 	atomic<idx_t> bytes_written;
+	atomic<idx_t> write_operations;
 	// Thread-safe memory allocation counter (updated from allocator callbacks on any thread)
 	atomic<idx_t> total_memory_allocated;
 
@@ -53,10 +55,12 @@ struct QueryMetrics {
 
 	void UpdateBytesRead(idx_t n) {
 		bytes_read += n;
+		read_operations++;
 	}
 
 	void UpdateBytesWritten(idx_t n) {
 		bytes_written += n;
+		write_operations++;
 	}
 
 	void UpdateTotalMemoryAllocated(idx_t n) {
@@ -83,10 +87,18 @@ struct QueryMetrics {
 		return bytes_read.load();
 	}
 
+	idx_t GetReadOperations() const {
+		return read_operations.load();
+	}
+
 	idx_t GetBytesWritten() const {
 		return bytes_written.load();
 	}
 
+	idx_t GetWriteOperations() const {
+		return write_operations.load();
+	}
+
 	idx_t GetTotalMemoryAllocated() const {
 		return total_memory_allocated.load();
 	}
@@ -104,7 +116,9 @@ struct QueryMetrics {
 		string_timings.clear();
 		string_counters.clear();
 		bytes_read = 0;
+		read_operations = 0;
 		bytes_written = 0;
+		write_operations = 0;
 		total_memory_allocated = 0;
 
 		query_sql = "";
@@ -125,7 +139,9 @@ struct QueryMetrics {
 			string_counters[entry.first] += entry.second;
 		}
 		bytes_read += other.bytes_read.load();
+		read_operations += other.read_operations.load();
 		bytes_written += other.bytes_written.load();
+		write_operations += other.write_operations.load();
 		total_memory_allocated += other.total_memory_allocated.load();
 	}
 

src/duckdb/src/main/profiler/metrics_manager.cpp

@@ -41,6 +41,8 @@ static const MetricDescriptor internal_metrics[] = {
 	DUCKDB_METRIC(MetricSystemTotalMemoryAllocated),
 	DUCKDB_METRIC(MetricIOTotalBytesRead),
 	DUCKDB_METRIC(MetricIOTotalBytesWritten),
+	DUCKDB_METRIC(MetricIOTotalReadOperations),
+	DUCKDB_METRIC(MetricIOTotalWriteOperations),
 	DUCKDB_METRIC(MetricStorageAttachLoadStorageLatency),
 	DUCKDB_METRIC(MetricStorageAttachReplayWALLatency),
 	DUCKDB_METRIC(MetricStorageCheckpointLatency),

src/duckdb/src/main/profiler/profiling_utils.cpp

@@ -12,15 +12,18 @@ void QueryMetrics::FinalizeMetrics(GatheredMetrics &info) {
 		info.SetMetric(key, count);
 	}
 	info.SetMetric<MetricIOTotalBytesRead>(GetBytesRead());
+	info.SetMetric<MetricIOTotalReadOperations>(GetReadOperations());
 	info.SetMetric<MetricIOTotalBytesWritten>(GetBytesWritten());
+	info.SetMetric<MetricIOTotalWriteOperations>(GetWriteOperations());
 	info.SetMetric<MetricSystemBlockedThreadTime>(blocked_thread_time);
 	info.SetMetric<MetricSystemPeakBufferMemory>(system_peak_buffer_memory);
 	info.SetMetric<MetricSystemPeakStreamingBufferSize>(system_peak_streaming_buffer_size);
 	info.SetMetric<MetricSystemPeakTempDirSize>(system_peak_temp_dir_size);
 	info.SetMetric<MetricSystemTotalMemoryAllocated>(GetTotalMemoryAllocated());
 }
 
-QueryMetrics::QueryMetrics() : bytes_read(0), bytes_written(0), total_memory_allocated(0) {
+QueryMetrics::QueryMetrics()
+    : bytes_read(0), read_operations(0), bytes_written(0), write_operations(0), total_memory_allocated(0) {
 	Reset();
 }
 

src/duckdb/src/main/query_profiler.cpp

@@ -939,7 +939,9 @@ unique_ptr<QueryProfileResult> QueryProfiler::ToLegacyResultTree() const {
 
 	emit("total_memory_allocated", "system.total_memory_allocated");
 	emit("total_bytes_written", "io.total_bytes_written");
+	emit("total_write_operations", "io.total_write_operations");
 	emit("total_bytes_read", "io.total_bytes_read");
+	emit("total_read_operations", "io.total_read_operations");
 	emit("system_peak_temp_dir_size", "system.peak_temp_dir_size");
 	emit("system_peak_buffer_memory", "system.peak_buffer_memory");
 	emit("system_peak_streaming_buffer_size", "system.peak_streaming_buffer_size");