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Fixes for R checks. (#8330)

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- Bump configure.ac version.
- Remove amalgamation to reduce the build time for a single object with the added benefit that we can use parallel build during development.
- Fix c function prototype warning.
- Remove Windows automake file generation step to make the build script easier to understand.
This commit is contained in:
Jiaming Yuan 2022-10-20 02:52:54 +08:00 committed by GitHub
parent 5bd849f1b5
commit 28a466ab51
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GPG Key ID: 4AEE18F83AFDEB23
8 changed files with 165 additions and 144 deletions
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10
Makefile
View File

@ -123,16 +123,8 @@ Rpack: clean_all
cp -r dmlc-core/include xgboost/src/dmlc-core/include
cp -r dmlc-core/src xgboost/src/dmlc-core/src
cp ./LICENSE xgboost
# Modify PKGROOT in Makevars.in
cat R-package/src/Makevars.in|sed '2s/.*/PKGROOT=./' > xgboost/src/Makevars.in
# Configure Makevars.win (Windows-specific Makevars, likely using MinGW)
cp xgboost/src/Makevars.in xgboost/src/Makevars.win
cat xgboost/src/Makevars.in| sed '3s/.*/ENABLE_STD_THREAD=0/' > xgboost/src/Makevars.win
sed -i -e 's/@OPENMP_CXXFLAGS@/$$\(SHLIB_OPENMP_CXXFLAGS\)/g' xgboost/src/Makevars.win
sed -i -e 's/-pthread/$$\(SHLIB_PTHREAD_FLAGS\)/g' xgboost/src/Makevars.win
sed -i -e 's/@ENDIAN_FLAG@/-DDMLC_CMAKE_LITTLE_ENDIAN=1/g' xgboost/src/Makevars.win
sed -i -e 's/@BACKTRACE_LIB@//g' xgboost/src/Makevars.win
sed -i -e 's/@OPENMP_LIB@//g' xgboost/src/Makevars.win
cat R-package/src/Makevars.win|sed '2s/.*/PKGROOT=./' > xgboost/src/Makevars.win
rm -f xgboost/src/Makevars.win-e # OSX sed create this extra file; remove it
bash R-package/remove_warning_suppression_pragma.sh
bash xgboost/remove_warning_suppression_pragma.sh

2
R-package/DESCRIPTION
View File

@ -2,7 +2,7 @@ Package: xgboost
Type: Package
Title: Extreme Gradient Boosting
Version: 1.7.0.1
Date: 2022-09-28
Date: 2022-10-18
Authors@R: c(
person("Tianqi", "Chen", role = c("aut"),
email = "tianqi.tchen@gmail.com"),

18
R-package/configure vendored
View File

@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.69 for xgboost 1.6-0.
# Generated by GNU Autoconf 2.69 for xgboost 1.7.0.
#
#
# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@ -576,8 +576,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='xgboost'
PACKAGE_TARNAME='xgboost'
PACKAGE_VERSION='1.6-0'
PACKAGE_STRING='xgboost 1.6-0'
PACKAGE_VERSION='1.7.0'
PACKAGE_STRING='xgboost 1.7.0'
PACKAGE_BUGREPORT=''
PACKAGE_URL=''
@ -1195,7 +1195,7 @@ 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 1.6-0 to adapt to many kinds of systems.
\`configure' configures xgboost 1.7.0 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@ -1257,7 +1257,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
short | recursive ) echo "Configuration of xgboost 1.6-0:";;
short | recursive ) echo "Configuration of xgboost 1.7.0:";;
esac
cat <<\_ACEOF
@ -1336,7 +1336,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
xgboost configure 1.6-0
xgboost configure 1.7.0
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@ -1479,7 +1479,7 @@ 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 1.6-0, which was
It was created by xgboost $as_me 1.7.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@ -3287,7 +3287,7 @@ cat >>$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 1.6-0, which was
This file was extended by xgboost $as_me 1.7.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@ -3340,7 +3340,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
xgboost config.status 1.6-0
xgboost config.status 1.7.0
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"

2
R-package/configure.ac
View File

@ -2,7 +2,7 @@
AC_PREREQ(2.69)
AC_INIT([xgboost],[1.6-0],[],[xgboost],[])
AC_INIT([xgboost],[1.7.0],[],[xgboost],[])
# Use this line to set CC variable to a C compiler
AC_PROG_CC

79
R-package/src/Makevars.in
View File

@ -19,7 +19,78 @@ $(foreach v, $(XGB_RFLAGS), $(warning $(v)))
PKG_CPPFLAGS= -I$(PKGROOT)/include -I$(PKGROOT)/dmlc-core/include -I$(PKGROOT)/rabit/include -I$(PKGROOT) $(XGB_RFLAGS)
PKG_CXXFLAGS= @OPENMP_CXXFLAGS@ @ENDIAN_FLAG@ -pthread $(CXX_VISIBILITY)
PKG_LIBS = @OPENMP_CXXFLAGS@ @OPENMP_LIB@ @ENDIAN_FLAG@ @BACKTRACE_LIB@ -pthread
OBJECTS= ./xgboost_R.o ./xgboost_custom.o ./xgboost_assert.o ./init.o \
$(PKGROOT)/amalgamation/xgboost-all0.o $(PKGROOT)/amalgamation/dmlc-minimum0.o \
$(PKGROOT)/rabit/src/engine.o $(PKGROOT)/rabit/src/rabit_c_api.o \
$(PKGROOT)/rabit/src/allreduce_base.o
OBJECTS= \
./xgboost_R.o \
./xgboost_custom.o \
./xgboost_assert.o \
./init.o \
$(PKGROOT)/src/metric/metric.o \
$(PKGROOT)/src/metric/elementwise_metric.o \
$(PKGROOT)/src/metric/multiclass_metric.o \
$(PKGROOT)/src/metric/rank_metric.o \
$(PKGROOT)/src/metric/auc.o \
$(PKGROOT)/src/metric/survival_metric.o \
$(PKGROOT)/src/objective/objective.o \
$(PKGROOT)/src/objective/regression_obj.o \
$(PKGROOT)/src/objective/multiclass_obj.o \
$(PKGROOT)/src/objective/rank_obj.o \
$(PKGROOT)/src/objective/hinge.o \
$(PKGROOT)/src/objective/aft_obj.o \
$(PKGROOT)/src/objective/adaptive.o \
$(PKGROOT)/src/gbm/gbm.o \
$(PKGROOT)/src/gbm/gbtree.o \
$(PKGROOT)/src/gbm/gbtree_model.o \
$(PKGROOT)/src/gbm/gblinear.o \
$(PKGROOT)/src/gbm/gblinear_model.o \
$(PKGROOT)/src/data/simple_dmatrix.o \
$(PKGROOT)/src/data/data.o \
$(PKGROOT)/src/data/sparse_page_raw_format.o \
$(PKGROOT)/src/data/ellpack_page.o \
$(PKGROOT)/src/data/gradient_index.o \
$(PKGROOT)/src/data/gradient_index_page_source.o \
$(PKGROOT)/src/data/gradient_index_format.o \
$(PKGROOT)/src/data/sparse_page_dmatrix.o \
$(PKGROOT)/src/data/proxy_dmatrix.o \
$(PKGROOT)/src/data/iterative_dmatrix.o \
$(PKGROOT)/src/predictor/predictor.o \
$(PKGROOT)/src/predictor/cpu_predictor.o \
$(PKGROOT)/src/tree/constraints.o \
$(PKGROOT)/src/tree/param.o \
$(PKGROOT)/src/tree/tree_model.o \
$(PKGROOT)/src/tree/tree_updater.o \
$(PKGROOT)/src/tree/updater_approx.o \
$(PKGROOT)/src/tree/updater_colmaker.o \
$(PKGROOT)/src/tree/updater_prune.o \
$(PKGROOT)/src/tree/updater_quantile_hist.o \
$(PKGROOT)/src/tree/updater_refresh.o \
$(PKGROOT)/src/tree/updater_sync.o \
$(PKGROOT)/src/linear/linear_updater.o \
$(PKGROOT)/src/linear/updater_coordinate.o \
$(PKGROOT)/src/linear/updater_shotgun.o \
$(PKGROOT)/src/learner.o \
$(PKGROOT)/src/logging.o \
$(PKGROOT)/src/global_config.o \
$(PKGROOT)/src/collective/communicator.o \
$(PKGROOT)/src/collective/socket.o \
$(PKGROOT)/src/common/charconv.o \
$(PKGROOT)/src/common/column_matrix.o \
$(PKGROOT)/src/common/common.o \
$(PKGROOT)/src/common/hist_util.o \
$(PKGROOT)/src/common/host_device_vector.o \
$(PKGROOT)/src/common/io.o \
$(PKGROOT)/src/common/json.o \
$(PKGROOT)/src/common/numeric.o \
$(PKGROOT)/src/common/pseudo_huber.o \
$(PKGROOT)/src/common/quantile.o \
$(PKGROOT)/src/common/random.o \
$(PKGROOT)/src/common/survival_util.o \
$(PKGROOT)/src/common/threading_utils.o \
$(PKGROOT)/src/common/timer.o \
$(PKGROOT)/src/common/version.o \
$(PKGROOT)/src/c_api/c_api.o \
$(PKGROOT)/src/c_api/c_api_error.o \
$(PKGROOT)/amalgamation/dmlc-minimum0.o \
$(PKGROOT)/rabit/src/engine.o \
$(PKGROOT)/rabit/src/rabit_c_api.o \
$(PKGROOT)/rabit/src/allreduce_base.o

97
R-package/src/Makevars.win
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@ -1,20 +1,8 @@
# package root
PKGROOT=./
PKGROOT=../../
ENABLE_STD_THREAD=0
# _*_ mode: Makefile; _*_
# This file is only used for Windows compilation from GitHub
# It will be replaced with Makevars.in for the CRAN version
.PHONY: all xgblib
all: $(SHLIB)
$(SHLIB): xgblib
xgblib:
cp -r ../../src .
cp -r ../../rabit .
cp -r ../../dmlc-core .
cp -r ../../include .
cp -r ../../amalgamation .
CXX_STD = CXX14
XGB_RFLAGS = -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0\
@ -29,11 +17,80 @@ endif
$(foreach v, $(XGB_RFLAGS), $(warning $(v)))
PKG_CPPFLAGS= -I$(PKGROOT)/include -I$(PKGROOT)/dmlc-core/include -I$(PKGROOT)/rabit/include -I$(PKGROOT) $(XGB_RFLAGS)
PKG_CXXFLAGS= $(SHLIB_OPENMP_CXXFLAGS) $(SHLIB_PTHREAD_FLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(SHLIB_PTHREAD_FLAGS) -lwsock32 -lws2_32
OBJECTS= ./xgboost_R.o ./xgboost_custom.o ./xgboost_assert.o ./init.o \
$(PKGROOT)/amalgamation/xgboost-all0.o $(PKGROOT)/amalgamation/dmlc-minimum0.o \
$(PKGROOT)/rabit/src/engine.o $(PKGROOT)/rabit/src/rabit_c_api.o \
$(PKGROOT)/rabit/src/allreduce_base.o
PKG_CXXFLAGS= $(SHLIB_OPENMP_CXXFLAGS) -DDMLC_CMAKE_LITTLE_ENDIAN=1 $(SHLIB_PTHREAD_FLAGS) $(CXX_VISIBILITY)
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) -DDMLC_CMAKE_LITTLE_ENDIAN=1 $(SHLIB_PTHREAD_FLAGS) -lwsock32 -lws2_32
$(OBJECTS) : xgblib
OBJECTS= \
./xgboost_R.o \
./xgboost_custom.o \
./xgboost_assert.o \
./init.o \
$(PKGROOT)/src/metric/metric.o \
$(PKGROOT)/src/metric/elementwise_metric.o \
$(PKGROOT)/src/metric/multiclass_metric.o \
$(PKGROOT)/src/metric/rank_metric.o \
$(PKGROOT)/src/metric/auc.o \
$(PKGROOT)/src/metric/survival_metric.o \
$(PKGROOT)/src/objective/objective.o \
$(PKGROOT)/src/objective/regression_obj.o \
$(PKGROOT)/src/objective/multiclass_obj.o \
$(PKGROOT)/src/objective/rank_obj.o \
$(PKGROOT)/src/objective/hinge.o \
$(PKGROOT)/src/objective/aft_obj.o \
$(PKGROOT)/src/objective/adaptive.o \
$(PKGROOT)/src/gbm/gbm.o \
$(PKGROOT)/src/gbm/gbtree.o \
$(PKGROOT)/src/gbm/gbtree_model.o \
$(PKGROOT)/src/gbm/gblinear.o \
$(PKGROOT)/src/gbm/gblinear_model.o \
$(PKGROOT)/src/data/simple_dmatrix.o \
$(PKGROOT)/src/data/data.o \
$(PKGROOT)/src/data/sparse_page_raw_format.o \
$(PKGROOT)/src/data/ellpack_page.o \
$(PKGROOT)/src/data/gradient_index.o \
$(PKGROOT)/src/data/gradient_index_page_source.o \
$(PKGROOT)/src/data/gradient_index_format.o \
$(PKGROOT)/src/data/sparse_page_dmatrix.o \
$(PKGROOT)/src/data/proxy_dmatrix.o \
$(PKGROOT)/src/data/iterative_dmatrix.o \
$(PKGROOT)/src/predictor/predictor.o \
$(PKGROOT)/src/predictor/cpu_predictor.o \
$(PKGROOT)/src/tree/constraints.o \
$(PKGROOT)/src/tree/param.o \
$(PKGROOT)/src/tree/tree_model.o \
$(PKGROOT)/src/tree/tree_updater.o \
$(PKGROOT)/src/tree/updater_approx.o \
$(PKGROOT)/src/tree/updater_colmaker.o \
$(PKGROOT)/src/tree/updater_prune.o \
$(PKGROOT)/src/tree/updater_quantile_hist.o \
$(PKGROOT)/src/tree/updater_refresh.o \
$(PKGROOT)/src/tree/updater_sync.o \
$(PKGROOT)/src/linear/linear_updater.o \
$(PKGROOT)/src/linear/updater_coordinate.o \
$(PKGROOT)/src/linear/updater_shotgun.o \
$(PKGROOT)/src/learner.o \
$(PKGROOT)/src/logging.o \
$(PKGROOT)/src/global_config.o \
$(PKGROOT)/src/collective/communicator.o \
$(PKGROOT)/src/collective/socket.o \
$(PKGROOT)/src/common/charconv.o \
$(PKGROOT)/src/common/column_matrix.o \
$(PKGROOT)/src/common/common.o \
$(PKGROOT)/src/common/hist_util.o \
$(PKGROOT)/src/common/host_device_vector.o \
$(PKGROOT)/src/common/io.o \
$(PKGROOT)/src/common/json.o \
$(PKGROOT)/src/common/numeric.o \
$(PKGROOT)/src/common/pseudo_huber.o \
$(PKGROOT)/src/common/quantile.o \
$(PKGROOT)/src/common/random.o \
$(PKGROOT)/src/common/survival_util.o \
$(PKGROOT)/src/common/threading_utils.o \
$(PKGROOT)/src/common/timer.o \
$(PKGROOT)/src/common/version.o \
$(PKGROOT)/src/c_api/c_api.o \
$(PKGROOT)/src/c_api/c_api_error.o \
$(PKGROOT)/amalgamation/dmlc-minimum0.o \
$(PKGROOT)/rabit/src/engine.o \
$(PKGROOT)/rabit/src/rabit_c_api.o \
$(PKGROOT)/rabit/src/allreduce_base.o

2
R-package/src/init.c
View File

@ -50,7 +50,7 @@ extern SEXP XGDMatrixSetInfo_R(SEXP, SEXP, SEXP);
extern SEXP XGDMatrixSetStrFeatureInfo_R(SEXP, SEXP, SEXP);
extern SEXP XGDMatrixSliceDMatrix_R(SEXP, SEXP);
extern SEXP XGBSetGlobalConfig_R(SEXP);
extern SEXP XGBGetGlobalConfig_R();
extern SEXP XGBGetGlobalConfig_R(void);
extern SEXP XGBoosterFeatureScore_R(SEXP, SEXP);
static const R_CallMethodDef CallEntries[] = {

99
amalgamation/xgboost-all0.cc
View File

@ -1,99 +0,0 @@
/*!
* Copyright 2015-2022 by Contributors.
* \brief XGBoost Amalgamation.
* This offers an alternative way to compile the entire library from this single file.
*
* Example usage command.
* - $(CXX) -std=c++0x -fopenmp -o -shared libxgboost.so xgboost-all0.cc -ldmlc -lrabit
*
* \author Tianqi Chen.
*/
// metrics
#include "../src/metric/metric.cc"
#include "../src/metric/elementwise_metric.cc"
#include "../src/metric/multiclass_metric.cc"
#include "../src/metric/rank_metric.cc"
#include "../src/metric/auc.cc"
#include "../src/metric/survival_metric.cc"
// objectives
#include "../src/objective/objective.cc"
#include "../src/objective/regression_obj.cc"
#include "../src/objective/multiclass_obj.cc"
#include "../src/objective/rank_obj.cc"
#include "../src/objective/hinge.cc"
#include "../src/objective/aft_obj.cc"
#include "../src/objective/adaptive.cc"
// gbms
#include "../src/gbm/gbm.cc"
#include "../src/gbm/gbtree.cc"
#include "../src/gbm/gbtree_model.cc"
#include "../src/gbm/gblinear.cc"
#include "../src/gbm/gblinear_model.cc"
// data
#include "../src/data/simple_dmatrix.cc"
#include "../src/data/data.cc"
#include "../src/data/sparse_page_raw_format.cc"
#include "../src/data/ellpack_page.cc"
#include "../src/data/gradient_index.cc"
#include "../src/data/gradient_index_page_source.cc"
#include "../src/data/gradient_index_format.cc"
#include "../src/data/sparse_page_dmatrix.cc"
#include "../src/data/proxy_dmatrix.cc"
#include "../src/data/iterative_dmatrix.cc"
// prediction
#include "../src/predictor/predictor.cc"
#include "../src/predictor/cpu_predictor.cc"
// trees
#include "../src/tree/constraints.cc"
#include "../src/tree/param.cc"
#include "../src/tree/tree_model.cc"
#include "../src/tree/tree_updater.cc"
#include "../src/tree/updater_approx.cc"
#include "../src/tree/updater_colmaker.cc"
#include "../src/tree/updater_prune.cc"
#include "../src/tree/updater_quantile_hist.cc"
#include "../src/tree/updater_refresh.cc"
#include "../src/tree/updater_sync.cc"
// linear
#include "../src/linear/linear_updater.cc"
#include "../src/linear/updater_coordinate.cc"
#include "../src/linear/updater_shotgun.cc"
// global
#include "../src/learner.cc"
#include "../src/logging.cc"
#include "../src/global_config.cc"
// collective
#include "../src/collective/communicator.cc"
// common
#include "../src/common/charconv.cc"
#include "../src/common/column_matrix.cc"
#include "../src/common/common.cc"
#include "../src/common/hist_util.cc"
#include "../src/common/host_device_vector.cc"
#include "../src/common/io.cc"
#include "../src/common/json.cc"
#include "../src/common/numeric.cc"
#include "../src/common/pseudo_huber.cc"
#include "../src/common/quantile.cc"
#include "../src/common/random.cc"
#include "../src/common/survival_util.cc"
#include "../src/common/threading_utils.cc"
#include "../src/common/timer.cc"
#include "../src/common/version.cc"
// collective
#include "../src/collective/socket.cc"
// c_api
#include "../src/c_api/c_api.cc"
#include "../src/c_api/c_api_error.cc"