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chore: Restore state before the CRAN release
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krlmlr committed Jan 22, 2025
1 parent b1050c0 commit f168f92
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Showing 1,412 changed files with 99,167 additions and 53,396 deletions.
2 changes: 1 addition & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: duckdb
Title: DBI Package for the DuckDB Database Management System
Version: 1.1.3-2
Version: 1.1.3.9039
Authors@R: c(
person("Hannes", "Mühleisen", , "[email protected]", role = "aut",
comment = c(ORCID = "0000-0001-8552-0029")),
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60 changes: 60 additions & 0 deletions patch/0007-Remove-stderr-for-zstd.patch
Original file line number Diff line number Diff line change
@@ -0,0 +1,60 @@
From 1e6fb864921a6314b5d4a946bbd406ed72de0e30 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <[email protected]>
Date: Fri, 20 Dec 2024 19:59:12 +0100
Subject: [PATCH] Remove stderr for zstd

---
src/duckdb/third_party/zstd/dict/cover.cpp | 3 +--
src/duckdb/third_party/zstd/dict/fastcover.cpp | 3 +--
src/duckdb/third_party/zstd/dict/zdict.cpp | 3 ++-
3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/duckdb/third_party/zstd/dict/cover.cpp b/src/duckdb/third_party/zstd/dict/cover.cpp
index 935c96609..4a80eb1c5 100644
--- a/src/duckdb/third_party/zstd/dict/cover.cpp
+++ b/src/duckdb/third_party/zstd/dict/cover.cpp
@@ -58,10 +58,9 @@
static int g_displayLevel = 0;
#endif
#undef DISPLAY
+// CRAN does not allow stderr references
#define DISPLAY(...) \
{ \
- fprintf(stderr, __VA_ARGS__); \
- fflush(stderr); \
}
#undef LOCALDISPLAYLEVEL
#define LOCALDISPLAYLEVEL(displayLevel, l, ...) \
diff --git a/src/duckdb/third_party/zstd/dict/fastcover.cpp b/src/duckdb/third_party/zstd/dict/fastcover.cpp
index b3d103125..af4556676 100644
--- a/src/duckdb/third_party/zstd/dict/fastcover.cpp
+++ b/src/duckdb/third_party/zstd/dict/fastcover.cpp
@@ -55,10 +55,9 @@ namespace duckdb_zstd {
static int g_displayLevel = 0;
#endif
#undef DISPLAY
+// CRAN does not allow stderr references
#define DISPLAY(...) \
{ \
- fprintf(stderr, __VA_ARGS__); \
- fflush(stderr); \
}
#undef LOCALDISPLAYLEVEL
#define LOCALDISPLAYLEVEL(displayLevel, l, ...) \
diff --git a/src/duckdb/third_party/zstd/dict/zdict.cpp b/src/duckdb/third_party/zstd/dict/zdict.cpp
index 7381e505d..069691d19 100644
--- a/src/duckdb/third_party/zstd/dict/zdict.cpp
+++ b/src/duckdb/third_party/zstd/dict/zdict.cpp
@@ -75,7 +75,8 @@ static const U32 g_selectivity_default = 9;
* Console display
***************************************/
#undef DISPLAY
-#define DISPLAY(...) do { fprintf(stderr, __VA_ARGS__); fflush( stderr ); } while (0)
+// CRAN does not allow stderr references
+#define DISPLAY(...) do { } while (0)
#undef DISPLAYLEVEL
#define DISPLAYLEVEL(l, ...) do { if (notificationLevel>=l) { DISPLAY(__VA_ARGS__); } } while (0) /* 0 : no display; 1: errors; 2: default; 3: details; 4: debug */

--
2.43.0

25 changes: 25 additions & 0 deletions patch/0008-Avoid-pragma-for-zstd.patch
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
From a8efb1ccf35192701564878566a22bc7f014c9c7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <[email protected]>
Date: Fri, 20 Dec 2024 20:00:18 +0100
Subject: [PATCH] Avoid pragma for zstd

---
src/duckdb/third_party/zstd/dict/divsufsort.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/duckdb/third_party/zstd/dict/divsufsort.cpp b/src/duckdb/third_party/zstd/dict/divsufsort.cpp
index b40901734..d0d00f8ca 100644
--- a/src/duckdb/third_party/zstd/dict/divsufsort.cpp
+++ b/src/duckdb/third_party/zstd/dict/divsufsort.cpp
@@ -26,7 +26,7 @@

/*- Compiler specifics -*/
#ifdef __clang__
-#pragma clang diagnostic ignored "-Wshorten-64-to-32"
+// CRAN does not allow pragmas
#endif

#if defined(_MSC_VER)
--
2.43.0

33 changes: 33 additions & 0 deletions patch/0009-Remove-stderr-for-zstd.patch
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
From 4b2b14d6197ba4dbb9de0afeb974e92f42aa561f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <[email protected]>
Date: Fri, 20 Dec 2024 20:40:37 +0100
Subject: [PATCH] Remove stderr for zstd

---
src/duckdb/third_party/zstd/dict/zdict.cpp | 8 +-------
1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/src/duckdb/third_party/zstd/dict/zdict.cpp b/src/duckdb/third_party/zstd/dict/zdict.cpp
index 069691d19..8529e9442 100644
--- a/src/duckdb/third_party/zstd/dict/zdict.cpp
+++ b/src/duckdb/third_party/zstd/dict/zdict.cpp
@@ -479,15 +479,9 @@ static size_t ZDICT_trainBuffer_legacy(dictItem* dictList, U32 dictListSize,
clock_t const refreshRate = CLOCKS_PER_SEC * 3 / 10;

# undef DISPLAYUPDATE
+// CRAN does not allow stderr references
# define DISPLAYUPDATE(l, ...) \
do { \
- if (notificationLevel>=l) { \
- if (ZDICT_clockSpan(displayClock) > refreshRate) { \
- displayClock = clock(); \
- DISPLAY(__VA_ARGS__); \
- } \
- if (notificationLevel>=4) fflush(stderr); \
- } \
} while (0)

/* init */
--
2.43.0

2 changes: 1 addition & 1 deletion rconfigure.py
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
import subprocess
import platform

extensions = ['parquet']
extensions = ['parquet','core_functions']

# check if there are any additional extensions being requested
if 'DUCKDB_R_EXTENSIONS' in os.environ:
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2 changes: 1 addition & 1 deletion src/Makevars
Original file line number Diff line number Diff line change
Expand Up @@ -16,5 +16,5 @@ include include/sources.mk
include Makevars.duckdb

CXX_STD = CXX17
PKG_CPPFLAGS = -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -DBROTLI_ENCODER_CLEANUP_ON_OOM -Iduckdb/src/include -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/fast_float -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/httplib -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/third_party/libpg_query -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/lz4 -Iduckdb/third_party/brotli/include -Iduckdb/third_party/brotli/common -Iduckdb/third_party/brotli/dec -Iduckdb/third_party/brotli/enc -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/miniz -Iduckdb/third_party/pcg -Iduckdb/third_party/re2 -Iduckdb/third_party/skiplist -Iduckdb/third_party/tdigest -Iduckdb/third_party/utf8proc -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/yyjson/include -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/lz4 -Iduckdb/third_party/brotli/include -Iduckdb/third_party/brotli/common -Iduckdb/third_party/brotli/dec -Iduckdb/third_party/brotli/enc -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY
PKG_CPPFLAGS = -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -DBROTLI_ENCODER_CLEANUP_ON_OOM -Iduckdb/src/include -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/fast_float -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/httplib -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/third_party/libpg_query -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/lz4 -Iduckdb/third_party/brotli/include -Iduckdb/third_party/brotli/common -Iduckdb/third_party/brotli/dec -Iduckdb/third_party/brotli/enc -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/miniz -Iduckdb/third_party/pcg -Iduckdb/third_party/re2 -Iduckdb/third_party/skiplist -Iduckdb/third_party/tdigest -Iduckdb/third_party/utf8proc -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/yyjson/include -Iduckdb/third_party/zstd/include -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/lz4 -Iduckdb/third_party/brotli/include -Iduckdb/third_party/brotli/common -Iduckdb/third_party/brotli/dec -Iduckdb/third_party/brotli/enc -Iduckdb/third_party/snappy -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/zstd/include -Iduckdb/extension/core_functions/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -DDUCKDB_EXTENSION_CORE_FUNCTIONS_LINKED -DDUCKDB_BUILD_LIBRARY
OBJECTS=rfuns.o database.o connection.o statement.o register.o relational.o scan.o signal.o transform.o utils.o reltoaltrep.o types.o cpp11.o $(SOURCES)
2 changes: 1 addition & 1 deletion src/Makevars.win
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,6 @@ include include/sources.mk
include Makevars.duckdb

CXX_STD = CXX17
PKG_CPPFLAGS = -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -DBROTLI_ENCODER_CLEANUP_ON_OOM -Iduckdb/src/include -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/fast_float -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/httplib -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/third_party/libpg_query -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/lz4 -Iduckdb/third_party/brotli/include -Iduckdb/third_party/brotli/common -Iduckdb/third_party/brotli/dec -Iduckdb/third_party/brotli/enc -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/miniz -Iduckdb/third_party/pcg -Iduckdb/third_party/re2 -Iduckdb/third_party/skiplist -Iduckdb/third_party/tdigest -Iduckdb/third_party/utf8proc -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/yyjson/include -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/lz4 -Iduckdb/third_party/brotli/include -Iduckdb/third_party/brotli/common -Iduckdb/third_party/brotli/dec -Iduckdb/third_party/brotli/enc -Iduckdb/third_party/snappy -Iduckdb/third_party/zstd/include -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -DDUCKDB_PLATFORM_RTOOLS=1
PKG_CPPFLAGS = -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -DBROTLI_ENCODER_CLEANUP_ON_OOM -Iduckdb/src/include -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/fast_float -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/httplib -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/third_party/libpg_query -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/lz4 -Iduckdb/third_party/brotli/include -Iduckdb/third_party/brotli/common -Iduckdb/third_party/brotli/dec -Iduckdb/third_party/brotli/enc -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/miniz -Iduckdb/third_party/pcg -Iduckdb/third_party/re2 -Iduckdb/third_party/skiplist -Iduckdb/third_party/tdigest -Iduckdb/third_party/utf8proc -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/yyjson/include -Iduckdb/third_party/zstd/include -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/lz4 -Iduckdb/third_party/brotli/include -Iduckdb/third_party/brotli/common -Iduckdb/third_party/brotli/dec -Iduckdb/third_party/brotli/enc -Iduckdb/third_party/snappy -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/zstd/include -Iduckdb/extension/core_functions/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -DDUCKDB_EXTENSION_CORE_FUNCTIONS_LINKED -DDUCKDB_BUILD_LIBRARY -DDUCKDB_PLATFORM_RTOOLS=1
OBJECTS=rfuns.o database.o connection.o statement.o register.o relational.o scan.o signal.o transform.o utils.o reltoaltrep.o types.o cpp11.o $(SOURCES)
PKG_LIBS=-lws2_32 -L. -lrstrtmgr
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#include "duckdb/core_functions/aggregate/algebraic_functions.hpp"
#include "duckdb/core_functions/aggregate/sum_helpers.hpp"
#include "core_functions/aggregate/algebraic_functions.hpp"
#include "core_functions/aggregate/sum_helpers.hpp"
#include "duckdb/common/types/hugeint.hpp"
#include "duckdb/common/exception.hpp"
#include "duckdb/function/function_set.hpp"
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
#include "duckdb/core_functions/aggregate/algebraic_functions.hpp"
#include "duckdb/core_functions/aggregate/algebraic/covar.hpp"
#include "duckdb/core_functions/aggregate/algebraic/stddev.hpp"
#include "duckdb/core_functions/aggregate/algebraic/corr.hpp"
#include "core_functions/aggregate/algebraic_functions.hpp"
#include "core_functions/aggregate/algebraic/covar.hpp"
#include "core_functions/aggregate/algebraic/stddev.hpp"
#include "core_functions/aggregate/algebraic/corr.hpp"
#include "duckdb/function/function_set.hpp"

namespace duckdb {
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#include "duckdb/core_functions/aggregate/algebraic_functions.hpp"
#include "core_functions/aggregate/algebraic_functions.hpp"
#include "duckdb/common/types/null_value.hpp"
#include "duckdb/core_functions/aggregate/algebraic/covar.hpp"
#include "core_functions/aggregate/algebraic/covar.hpp"

namespace duckdb {

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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
#include "duckdb/core_functions/aggregate/algebraic_functions.hpp"
#include "core_functions/aggregate/algebraic_functions.hpp"
#include "duckdb/common/vector_operations/vector_operations.hpp"
#include "duckdb/function/function_set.hpp"
#include "duckdb/core_functions/aggregate/algebraic/stddev.hpp"
#include "core_functions/aggregate/algebraic/stddev.hpp"
#include <cmath>

namespace duckdb {
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
#include "duckdb/common/exception.hpp"
#include "duckdb/common/types/hash.hpp"
#include "duckdb/common/types/hyperloglog.hpp"
#include "duckdb/core_functions/aggregate/distributive_functions.hpp"
#include "core_functions/aggregate/distributive_functions.hpp"
#include "duckdb/function/function_set.hpp"
#include "duckdb/planner/expression/bound_aggregate_expression.hpp"
#include "hyperloglog.hpp"
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