Merge branch 'dmlc:master' into dev/sycl/unify_multiclass_calc

CMakeLists.txt

@@ -4,7 +4,7 @@ if(PLUGIN_SYCL)
   string(REPLACE " -isystem ${CONDA_PREFIX}/include" "" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
 endif()
 
-project(xgboost LANGUAGES CXX C VERSION 2.2.0)
+project(xgboost LANGUAGES CXX C VERSION 3.0.0)
 include(cmake/Utils.cmake)
 list(APPEND CMAKE_MODULE_PATH "${xgboost_SOURCE_DIR}/cmake/modules")
 

R-package/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: xgboost
 Type: Package
 Title: Extreme Gradient Boosting
-Version: 2.2.0.0
-Date: 2024-06-03
+Version: 3.0.0.0
+Date: 2024-11-26
 Authors@R: c(
   person("Tianqi", "Chen", role = c("aut"),
          email = "tianqi.tchen@gmail.com"),

R-package/R/utils.R

@@ -572,8 +572,6 @@ check.deprecation <- function(..., env = parent.frame()) {
       warning("'", pars_par, "' was partially matched to '", old_par, "'")
     }
     .Deprecated(new_par, old = old_par, package = 'xgboost')
-    if (new_par != 'NULL') {
-      eval(parse(text = paste(new_par, '<-', pars[[pars_par]])), envir = env)
-    }
+    stop()
   }
 }

R-package/configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for xgboost 2.2.0.
+# Generated by GNU Autoconf 2.71 for xgboost 3.0.0.
 #
 #
 # Copyright (C) 1992-1996, 1998-2017, 2020-2021 Free Software Foundation,
@@ -607,8 +607,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='xgboost'
 PACKAGE_TARNAME='xgboost'
-PACKAGE_VERSION='2.2.0'
-PACKAGE_STRING='xgboost 2.2.0'
+PACKAGE_VERSION='3.0.0'
+PACKAGE_STRING='xgboost 3.0.0'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -647,6 +647,7 @@ ac_header_cxx_list=
 ac_subst_vars='LTLIBOBJS
 LIBOBJS
 BACKTRACE_LIB
+DMLC_DEFS
 ENDIAN_FLAG
 OPENMP_LIB
 OPENMP_CXXFLAGS
@@ -1259,7 +1260,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures xgboost 2.2.0 to adapt to many kinds of systems.
+\`configure' configures xgboost 3.0.0 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1321,7 +1322,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of xgboost 2.2.0:";;
+     short | recursive ) echo "Configuration of xgboost 3.0.0:";;
    esac
   cat <<\_ACEOF
 
@@ -1404,7 +1405,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-xgboost configure 2.2.0
+xgboost configure 3.0.0
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -1504,6 +1505,68 @@ fi
 
 } # ac_fn_cxx_try_link
 
+# ac_fn_cxx_check_func LINENO FUNC VAR
+# ------------------------------------
+# Tests whether FUNC exists, setting the cache variable VAR accordingly
+ac_fn_cxx_check_func ()
+{
+  as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
+  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $2" >&5
+printf %s "checking for $2... " >&6; }
+if eval test \${$3+y}
+then :
+  printf %s "(cached) " >&6
+else $as_nop
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+/* Define $2 to an innocuous variant, in case <limits.h> declares $2.
+   For example, HP-UX 11i <limits.h> declares gettimeofday.  */
+#define $2 innocuous_$2
+
+/* System header to define __stub macros and hopefully few prototypes,
+   which can conflict with char $2 (); below.  */
+
+#include <limits.h>
+#undef $2
+
+/* Override any GCC internal prototype to avoid an error.
+   Use char because int might match the return type of a GCC
+   builtin and then its argument prototype would still apply.  */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $2 ();
+/* The GNU C library defines this for functions which it implements
+    to always fail with ENOSYS.  Some functions are actually named
+    something starting with __ and the normal name is an alias.  */
+#if defined __stub_$2 || defined __stub___$2
+choke me
+#endif
+
+int
+main (void)
+{
+return $2 ();
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"
+then :
+  eval "$3=yes"
+else $as_nop
+  eval "$3=no"
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.beam \
+    conftest$ac_exeext conftest.$ac_ext
+fi
+eval ac_res=\$$3
+	       { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
+printf "%s\n" "$ac_res" >&6; }
+  eval $as_lineno_stack; ${as_lineno_stack:+:} unset as_lineno
+
+} # ac_fn_cxx_check_func
+
 # ac_fn_cxx_try_run LINENO
 # ------------------------
 # Try to run conftest.$ac_ext, and return whether this succeeded. Assumes that
@@ -1603,7 +1666,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by xgboost $as_me 2.2.0, which was
+It was created by xgboost $as_me 3.0.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -2192,11 +2255,10 @@ ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ex
 ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
 
-### Check whether backtrace() is part of libc or the external lib libexecinfo
-{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking Backtrace lib" >&5
-printf %s "checking Backtrace lib... " >&6; }
-{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: " >&5
-printf "%s\n" "" >&6; }
+DMLC_DEFS=""
+
+{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: Checking if/where backtrace is available" >&5
+printf "%s\n" "$as_me: Checking if/where backtrace is available" >&6;}
 
 
 
@@ -2869,8 +2931,31 @@ else $as_nop
   BACKTRACE_LIB=''
 fi
 
+if test -z "${BACKTRACE_LIB}"
+then :
+        ac_fn_cxx_check_func "$LINENO" "backtrace" "ac_cv_func_backtrace"
+if test "x$ac_cv_func_backtrace" = xyes
+then :
+
+else $as_nop
+  DMLC_DEFS="$DMLC_DEFS -DDMLC_LOG_STACK_TRACE=0"
+fi
 
-### Endian detection
+fi
+
+{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: Checking whether fopen64 is available" >&5
+printf "%s\n" "$as_me: Checking whether fopen64 is available" >&6;}
+ac_fn_cxx_check_func "$LINENO" "fopen64" "ac_cv_func_fopen64"
+if test "x$ac_cv_func_fopen64" = xyes
+then :
+
+else $as_nop
+  DMLC_DEFS="$DMLC_DEFS -DDMLC_USE_FOPEN64=0"
+fi
+
+
+{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: Endian detection" >&5
+printf "%s\n" "$as_me: Endian detection" >&6;}
 
 ac_header= ac_cache=
 for ac_item in $ac_header_cxx_list
@@ -2906,8 +2991,6 @@ then :
 
   { printf "%s\n" "$as_me:${as_lineno-$LINENO}: Checking system endianness as USE_LITTLE_ENDIAN is unset" >&5
 printf "%s\n" "$as_me: Checking system endianness as USE_LITTLE_ENDIAN is unset" >&6;}
-  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking system endianness" >&5
-printf %s "checking system endianness... " >&6; }
    { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking whether byte ordering is bigendian" >&5
 printf %s "checking whether byte ordering is bigendian... " >&6; }
 if test ${ac_cv_c_bigendian+y}
@@ -3205,6 +3288,7 @@ fi
 
 
 
+
 ac_config_files="$ac_config_files src/Makevars"
 
 ac_config_headers="$ac_config_headers config.h"
@@ -3709,7 +3793,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by xgboost $as_me 2.2.0, which was
+This file was extended by xgboost $as_me 3.0.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -3773,7 +3857,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-xgboost config.status 2.2.0
+xgboost config.status 3.0.0
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 

R-package/configure.ac

@@ -2,7 +2,7 @@
 
 AC_PREREQ(2.69)
 
-AC_INIT([xgboost],[2.2.0],[],[xgboost],[])
+AC_INIT([xgboost],[3.0.0],[],[xgboost],[])
 
 : ${R_HOME=`R RHOME`}
 if test -z "${R_HOME}"; then
@@ -22,16 +22,21 @@ CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
 LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
 AC_LANG(C++)
 
-### Check whether backtrace() is part of libc or the external lib libexecinfo
-AC_MSG_CHECKING([Backtrace lib])
-AC_MSG_RESULT([])
+DMLC_DEFS=""
+
+AC_MSG_NOTICE([Checking if/where backtrace is available])
 AC_CHECK_LIB([execinfo], [backtrace], [BACKTRACE_LIB=-lexecinfo], [BACKTRACE_LIB=''])
+AS_IF([test -z "${BACKTRACE_LIB}"],
+      dnl backtrace() might be unavailable (e.g., in musl libc)
+      [AC_CHECK_FUNC(backtrace, [], [DMLC_DEFS="$DMLC_DEFS -DDMLC_LOG_STACK_TRACE=0"])])
+
+AC_MSG_NOTICE([Checking whether fopen64 is available])
+AC_CHECK_FUNC(fopen64, [], [DMLC_DEFS="$DMLC_DEFS -DDMLC_USE_FOPEN64=0"])
 
-### Endian detection
+AC_MSG_NOTICE([Endian detection])
 AC_ARG_VAR(USE_LITTLE_ENDIAN, "Whether to build with little endian (checks at compile time if unset)")
 AS_IF([test -z "${USE_LITTLE_ENDIAN+x}"], [
   AC_MSG_NOTICE([Checking system endianness as USE_LITTLE_ENDIAN is unset])
-  AC_MSG_CHECKING([system endianness])
   AC_C_BIGENDIAN(
     [AC_MSG_RESULT([using big endian])
      ENDIAN_FLAG="-DDMLC_CMAKE_LITTLE_ENDIAN=0"],
@@ -82,6 +87,7 @@ fi
 AC_SUBST(OPENMP_CXXFLAGS)
 AC_SUBST(OPENMP_LIB)
 AC_SUBST(ENDIAN_FLAG)
+AC_SUBST(DMLC_DEFS)
 AC_SUBST(BACKTRACE_LIB)
 AC_CONFIG_FILES([src/Makevars])
 AC_CONFIG_HEADERS([config.h])

R-package/src/Makevars.in

@@ -6,6 +6,7 @@ ENABLE_STD_THREAD=1
 CXX_STD = CXX17
 
 XGB_RFLAGS = \
+    @DMLC_DEFS@ \
     -DXGBOOST_STRICT_R_MODE=1 \
     -DDMLC_LOG_BEFORE_THROW=0 \
     -DDMLC_ENABLE_STD_THREAD=$(ENABLE_STD_THREAD) \

R-package/tests/testthat/test_helpers.R

@@ -537,14 +537,12 @@ test_that("check.deprecation works", {
   }
   res <- ttt(a = 1, DUMMY = 2, z = 3)
   expect_equal(res, list(a = 1, DUMMY = 2))
-  expect_warning(
-    res <- ttt(a = 1, dummy = 22, z = 3)
-  , "\'dummy\' is deprecated")
-  expect_equal(res, list(a = 1, DUMMY = 22))
-  expect_warning(
-    res <- ttt(a = 1, dumm = 22, z = 3)
-  , "\'dumm\' was partially matched to \'dummy\'")
-  expect_equal(res, list(a = 1, DUMMY = 22))
+  expect_error(
+    res <- ttt(a = 1, dummy = 22, z = 3),
+  )
+  expect_error(
+    res <- ttt(a = 1, dumm = 22, z = 3),
+  )
 })
 
 test_that('convert.labels works', {

include/xgboost/version_config.h

@@ -4,8 +4,8 @@
 #ifndef XGBOOST_VERSION_CONFIG_H_
 #define XGBOOST_VERSION_CONFIG_H_
 
-#define XGBOOST_VER_MAJOR 2  /* NOLINT */
-#define XGBOOST_VER_MINOR 2  /* NOLINT */
+#define XGBOOST_VER_MAJOR 3  /* NOLINT */
+#define XGBOOST_VER_MINOR 0  /* NOLINT */
 #define XGBOOST_VER_PATCH 0  /* NOLINT */
 
 #endif  // XGBOOST_VERSION_CONFIG_H_

jvm-packages/pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>ml.dmlc</groupId>
     <artifactId>xgboost-jvm_2.12</artifactId>
-    <version>2.2.0-SNAPSHOT</version>
+    <version>3.0.0-SNAPSHOT</version>
     <packaging>pom</packaging>
     <name>XGBoost JVM Package</name>
     <description>JVM Package for XGBoost</description>

jvm-packages/xgboost4j-example/pom.xml

@@ -6,11 +6,11 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm_2.12</artifactId>
-        <version>2.2.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
     </parent>
     <name>xgboost4j-example</name>
     <artifactId>xgboost4j-example_2.12</artifactId>
-    <version>2.2.0-SNAPSHOT</version>
+    <version>3.0.0-SNAPSHOT</version>
     <packaging>jar</packaging>
     <build>
         <plugins>

jvm-packages/xgboost4j-flink/pom.xml

@@ -6,12 +6,12 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm_2.12</artifactId>
-        <version>2.2.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
     </parent>
 
     <name>xgboost4j-flink</name>
     <artifactId>xgboost4j-flink_2.12</artifactId>
-    <version>2.2.0-SNAPSHOT</version>
+    <version>3.0.0-SNAPSHOT</version>
     <properties>
       <flink-ml.version>2.2.0</flink-ml.version>
     </properties>

jvm-packages/xgboost4j-spark-gpu/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm_2.12</artifactId>
-        <version>2.2.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
     </parent>
     <name>xgboost4j-spark-gpu</name>
     <artifactId>xgboost4j-spark-gpu_2.12</artifactId>

jvm-packages/xgboost4j-spark/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm_2.12</artifactId>
-        <version>2.2.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
     </parent>
     <name>xgboost4j-spark</name>
     <artifactId>xgboost4j-spark_2.12</artifactId>

jvm-packages/xgboost4j/pom.xml

@@ -6,11 +6,11 @@
     <parent>
         <groupId>ml.dmlc</groupId>
         <artifactId>xgboost-jvm_2.12</artifactId>
-        <version>2.2.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
     </parent>
     <name>xgboost4j</name>
     <artifactId>xgboost4j_2.12</artifactId>
-    <version>2.2.0-SNAPSHOT</version>
+    <version>3.0.0-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <dependencies>