Merge branch 'master' into misc/type-hints-basic-logging

.github/workflows/r_package.yml

@@ -181,7 +181,7 @@ jobs:
       - name: Install Git before checkout
         shell: bash
         run: |
-          apt-get update
+          apt-get update --allow-releaseinfo-change
           apt-get install --no-install-recommends -y git
       - name: Checkout repository
         uses: actions/checkout@v2.3.4
@@ -210,7 +210,7 @@ jobs:
       - name: Install Git before checkout
         shell: bash
         run: |
-          apt-get update
+          apt-get update --allow-releaseinfo-change
           apt-get install --no-install-recommends -y git
       - name: Checkout repository
         uses: actions/checkout@v2.3.4

R-package/R/lgb.Booster.R

@@ -23,11 +23,9 @@ Booster <- R6::R6Class(
     initialize = function(params = list(),
                           train_set = NULL,
                           modelfile = NULL,
-                          model_str = NULL,
-                          ...) {
+                          model_str = NULL) {
 
       # Create parameters and handle
-      params <- append(params, list(...))
       handle <- NULL
 
       # Attempts to create a handle for the dataset

R-package/R/lgb.Dataset.R

@@ -831,7 +831,7 @@ lgb.Dataset.construct <- function(dataset) {
 #' @title Dimensions of an \code{lgb.Dataset}
 #' @description Returns a vector of numbers of rows and of columns in an \code{lgb.Dataset}.
 #' @param x Object of class \code{lgb.Dataset}
-#' @param ... other parameters
+#' @param ... other parameters (ignored)
 #'
 #' @return a vector of numbers of rows and of columns
 #'
@@ -853,6 +853,16 @@ lgb.Dataset.construct <- function(dataset) {
 #' @export
 dim.lgb.Dataset <- function(x, ...) {
 
+  additional_args <- list(...)
+  if (length(additional_args) > 0L) {
+    warning(paste0(
+      "dim.lgb.Dataset: Found the following passed through '...': "
+      , paste(names(additional_args), collapse = ", ")
+      , ". These are ignored. In future releases of lightgbm, this warning will become an error. "
+      , "See ?dim.lgb.Dataset for documentation on how to call this function."
+    ))
+  }
+
   # Check if dataset is not a dataset
   if (!lgb.is.Dataset(x = x)) {
     stop("dim.lgb.Dataset: input data should be an lgb.Dataset object")
@@ -978,7 +988,7 @@ slice.lgb.Dataset <- function(dataset, idxset, ...) {
 #' @description Get one attribute of a \code{lgb.Dataset}
 #' @param dataset Object of class \code{lgb.Dataset}
 #' @param name the name of the information field to get (see details)
-#' @param ... other parameters
+#' @param ... other parameters (ignored)
 #' @return info data
 #'
 #' @details
@@ -1017,6 +1027,16 @@ getinfo <- function(dataset, ...) {
 #' @export
 getinfo.lgb.Dataset <- function(dataset, name, ...) {
 
+  additional_args <- list(...)
+  if (length(additional_args) > 0L) {
+    warning(paste0(
+      "getinfo.lgb.Dataset: Found the following passed through '...': "
+      , paste(names(additional_args), collapse = ", ")
+      , ". These are ignored. In future releases of lightgbm, this warning will become an error. "
+      , "See ?getinfo.lgb.Dataset for documentation on how to call this function."
+    ))
+  }
+
   # Check if dataset is not a dataset
   if (!lgb.is.Dataset(x = dataset)) {
     stop("getinfo.lgb.Dataset: input dataset should be an lgb.Dataset object")
@@ -1032,7 +1052,7 @@ getinfo.lgb.Dataset <- function(dataset, name, ...) {
 #' @param dataset Object of class \code{lgb.Dataset}
 #' @param name the name of the field to get
 #' @param info the specific field of information to set
-#' @param ... other parameters
+#' @param ... other parameters (ignored)
 #' @return the dataset you passed in
 #'
 #' @details
@@ -1071,6 +1091,16 @@ setinfo <- function(dataset, ...) {
 #' @export
 setinfo.lgb.Dataset <- function(dataset, name, info, ...) {
 
+  additional_args <- list(...)
+  if (length(additional_args) > 0L) {
+    warning(paste0(
+      "setinfo.lgb.Dataset: Found the following passed through '...': "
+      , paste(names(additional_args), collapse = ", ")
+      , ". These are ignored. In future releases of lightgbm, this warning will become an error. "
+      , "See ?setinfo.lgb.Dataset for documentation on how to call this function."
+    ))
+  }
+
   if (!lgb.is.Dataset(x = dataset)) {
     stop("setinfo.lgb.Dataset: input dataset should be an lgb.Dataset object")
   }

R-package/R/lgb.cv.R

@@ -52,6 +52,7 @@ CVBooster <- R6::R6Class(
 #'                             not the number of threads (most CPU using hyper-threading to generate 2 threads
 #'                             per CPU core).}
 #'            }
+#'            NOTE: As of v3.3.0, use of \code{...} is deprecated. Add parameters to \code{params} directly.
 #' @inheritSection lgb_shared_params Early Stopping
 #' @return a trained model \code{lgb.CVBooster}.
 #'
@@ -108,13 +109,23 @@ lgb.cv <- function(params = list()
   }
 
   # Setup temporary variables
-  params <- append(params, list(...))
+  additional_params <- list(...)
+  params <- append(params, additional_params)
   params$verbose <- verbose
   params <- lgb.check.obj(params = params, obj = obj)
   params <- lgb.check.eval(params = params, eval = eval)
   fobj <- NULL
   eval_functions <- list(NULL)
 
+  if (length(additional_params) > 0L) {
+    warning(paste0(
+      "lgb.cv: Found the following passed through '...': "
+      , paste(names(additional_params), collapse = ", ")
+      , ". These will be used, but in future releases of lightgbm, this warning will become an error. "
+      , "Add these to 'params' instead. See ?lgb.cv for documentation on how to call this function."
+    ))
+  }
+
   # set some parameters, resolving the way they were passed in with other parameters
   # in `params`.
   # this ensures that the model stored with Booster$save() correctly represents

R-package/R/lgb.train.R

@@ -24,6 +24,7 @@
 #'                             not the number of threads (most CPU using hyper-threading to generate 2 threads
 #'                             per CPU core).}
 #'            }
+#'            NOTE: As of v3.3.0, use of \code{...} is deprecated. Add parameters to \code{params} directly.
 #' @inheritSection lgb_shared_params Early Stopping
 #' @return a trained booster model \code{lgb.Booster}.
 #'
@@ -91,6 +92,15 @@ lgb.train <- function(params = list(),
   fobj <- NULL
   eval_functions <- list(NULL)
 
+  if (length(additional_params) > 0L) {
+    warning(paste0(
+      "lgb.train: Found the following passed through '...': "
+      , paste(names(additional_params), collapse = ", ")
+      , ". These will be used, but in future releases of lightgbm, this warning will become an error. "
+      , "Add these to 'params' instead. See ?lgb.train for documentation on how to call this function."
+    ))
+  }
+
   # set some parameters, resolving the way they were passed in with other parameters
   # in `params`.
   # this ensures that the model stored with Booster$save() correctly represents

R-package/configure

@@ -1694,7 +1694,17 @@ if test -z "${R_HOME}"; then
     exit 1
 fi
 CC=`"${R_HOME}/bin/R" CMD config CC`
-CXX=`"${R_HOME}/bin/R" CMD config CXX11`
+CXX11=`"${R_HOME}/bin/R" CMD config CXX11`
+CXX11STD=`"${R_HOME}/bin/R" CMD config CXX11STD`
+CXX="${CXX11} ${CXX11STD}"
+CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
+CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXX11FLAGS`
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
 
 # LightGBM-specific flags
 LGB_CPPFLAGS=""
@@ -1712,12 +1722,6 @@ LGB_CPPFLAGS="${LGB_CPPFLAGS} -DEIGEN_MPL2_ONLY"
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether MM_PREFETCH works" >&5
 $as_echo_n "checking whether MM_PREFETCH works... " >&6; }
 ac_mmprefetch=no
-ac_ext=cpp
-ac_cpp='$CXXCPP $CPPFLAGS'
-ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-
 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
 
@@ -1739,7 +1743,7 @@ main ()
 
 
 _ACEOF
-${CXX} -o conftest conftest.cpp 2>/dev/null && ./conftest && ac_mmprefetch=yes
+${CXX} ${CPPFLAGS} ${CXXFLAGS} -o conftest conftest.cpp 2>/dev/null && ./conftest && ac_mmprefetch=yes
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${ac_mmprefetch}" >&5
 $as_echo "${ac_mmprefetch}" >&6; }
 if test "${ac_mmprefetch}" = yes; then
@@ -1753,12 +1757,6 @@ fi
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether MM_MALLOC works" >&5
 $as_echo_n "checking whether MM_MALLOC works... " >&6; }
 ac_mm_malloc=no
-ac_ext=cpp
-ac_cpp='$CXXCPP $CPPFLAGS'
-ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-
 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
 
@@ -1780,7 +1778,7 @@ main ()
 
 
 _ACEOF
-${CXX} -o conftest conftest.cpp 2>/dev/null && ./conftest && ac_mm_malloc=yes
+${CXX} ${CPPFLAGS} ${CXXFLAGS} -o conftest conftest.cpp 2>/dev/null && ./conftest && ac_mm_malloc=yes
 { $as_echo "$as_me:${as_lineno-$LINENO}: result: ${ac_mm_malloc}" >&5
 $as_echo "${ac_mm_malloc}" >&6; }
 if test "${ac_mm_malloc}" = yes; then

R-package/configure.ac

@@ -21,7 +21,12 @@ if test -z "${R_HOME}"; then
     exit 1
 fi
 CC=`"${R_HOME}/bin/R" CMD config CC`
-CXX=`"${R_HOME}/bin/R" CMD config CXX11`
+CXX11=`"${R_HOME}/bin/R" CMD config CXX11`
+CXX11STD=`"${R_HOME}/bin/R" CMD config CXX11STD`
+CXX="${CXX11} ${CXX11STD}"
+CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
+CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXX11FLAGS`
+AC_LANG(C++)
 
 # LightGBM-specific flags
 LGB_CPPFLAGS=""
@@ -38,7 +43,6 @@ LGB_CPPFLAGS="${LGB_CPPFLAGS} -DEIGEN_MPL2_ONLY"
 
 AC_MSG_CHECKING([whether MM_PREFETCH works])
 ac_mmprefetch=no
-AC_LANG(C++)
 AC_LANG_CONFTEST(
     [
         AC_LANG_PROGRAM(
@@ -53,7 +57,7 @@ AC_LANG_CONFTEST(
         )
     ]
 )
-${CXX} -o conftest conftest.cpp 2>/dev/null && ./conftest && ac_mmprefetch=yes
+${CXX} ${CPPFLAGS} ${CXXFLAGS} -o conftest conftest.cpp 2>/dev/null && ./conftest && ac_mmprefetch=yes
 AC_MSG_RESULT([${ac_mmprefetch}])
 if test "${ac_mmprefetch}" = yes; then
     LGB_CPPFLAGS+=" -DMM_PREFETCH=1"
@@ -65,7 +69,6 @@ fi
 
 AC_MSG_CHECKING([whether MM_MALLOC works])
 ac_mm_malloc=no
-AC_LANG(C++)
 AC_LANG_CONFTEST(
     [
         AC_LANG_PROGRAM(
@@ -80,7 +83,7 @@ AC_LANG_CONFTEST(
         )
     ]
 )
-${CXX} -o conftest conftest.cpp 2>/dev/null && ./conftest && ac_mm_malloc=yes
+${CXX} ${CPPFLAGS} ${CXXFLAGS} -o conftest conftest.cpp 2>/dev/null && ./conftest && ac_mm_malloc=yes
 AC_MSG_RESULT([${ac_mm_malloc}])
 if test "${ac_mm_malloc}" = yes; then
     LGB_CPPFLAGS+=" -DMM_MALLOC=1"

docs/Installation-Guide.rst

@@ -129,6 +129,8 @@ On Linux LightGBM can be built using **CMake** and **gcc** or **Clang**.
 
 **Note**: glibc >= 2.14 is required.
 
+**Note**: In some rare cases you may need to install OpenMP runtime library separately (use your package manager and search for ``lib[g|i]omp`` for doing this).
+
 Also, you may want to read `gcc Tips <./gcc-Tips.rst>`__.
 
 macOS
@@ -437,6 +439,8 @@ On Linux an MPI version of LightGBM can be built using **Open MPI**, **CMake** a
 
 **Note**: glibc >= 2.14 is required.
 
+**Note**: In some rare cases you may need to install OpenMP runtime library separately (use your package manager and search for ``lib[g|i]omp`` for doing this).
+
 macOS
 ^^^^^
 
@@ -544,6 +548,10 @@ To build LightGBM GPU version, run the following commands:
   # cmake -DUSE_GPU=1 -DOpenCL_LIBRARY=/usr/local/cuda/lib64/libOpenCL.so -DOpenCL_INCLUDE_DIR=/usr/local/cuda/include/ ..
   make -j4
 
+**Note**: glibc >= 2.14 is required.
+
+**Note**: In some rare cases you may need to install OpenMP runtime library separately (use your package manager and search for ``lib[g|i]omp`` for doing this).
+
 Windows
 ^^^^^^^
 
@@ -626,6 +634,10 @@ To build LightGBM CUDA version, run the following commands:
   cmake -DUSE_CUDA=1 ..
   make -j4
 
+**Note**: glibc >= 2.14 is required.
+
+**Note**: In some rare cases you may need to install OpenMP runtime library separately (use your package manager and search for ``lib[g|i]omp`` for doing this).
+
 Build HDFS Version
 ~~~~~~~~~~~~~~~~~~
 
@@ -655,6 +667,10 @@ On Linux a HDFS version of LightGBM can be built using **CMake** and **gcc**.
      #   ..
      make -j4
 
+**Note**: glibc >= 2.14 is required.
+
+**Note**: In some rare cases you may need to install OpenMP runtime library separately (use your package manager and search for ``lib[g|i]omp`` for doing this).
+
 Build Java Wrapper
 ~~~~~~~~~~~~~~~~~~
 
@@ -730,6 +746,10 @@ On Linux a Java wrapper of LightGBM can be built using **Java**, **SWIG**, **CMa
      cmake -DUSE_SWIG=ON ..
      make -j4
 
+**Note**: glibc >= 2.14 is required.
+
+**Note**: In some rare cases you may need to install OpenMP runtime library separately (use your package manager and search for ``lib[g|i]omp`` for doing this).
+
 macOS
 ^^^^^