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Port R compatibility patches from 1.0.0 release branch (#5577)

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* Don't use memset to set struct when compiling for R

* Support 32-bit Solaris target for R package
This commit is contained in:
Philip Hyunsu Cho 2020-04-21 22:51:18 -07:00 committed by GitHub
parent f27b6f9ba6
commit e4f5b6c84f
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4 changed files with 15 additions and 9 deletions
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12
R-package/tests/testthat/test_helpers.R
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@ -7,8 +7,8 @@ require(vcd, quietly = TRUE)
float_tolerance = 5e-6 float_tolerance = 5e-6
# disable some tests for Win32 # disable some tests for 32-bit environment
win32_flag = .Platform$OS.type == "windows" && .Machine$sizeof.pointer != 8 flag_32bit = .Machine$sizeof.pointer != 8
set.seed(1982) set.seed(1982)
data(Arthritis) data(Arthritis)
@ -44,7 +44,7 @@ mbst.GLM <- xgboost(data = as.matrix(iris[, -5]), label = mlabel, verbose = 0,
test_that("xgb.dump works", { test_that("xgb.dump works", {
if (!win32_flag) if (!flag_32bit)
expect_length(xgb.dump(bst.Tree), 200) expect_length(xgb.dump(bst.Tree), 200)
dump_file = file.path(tempdir(), 'xgb.model.dump') dump_file = file.path(tempdir(), 'xgb.model.dump')
expect_true(xgb.dump(bst.Tree, dump_file, with_stats = T)) expect_true(xgb.dump(bst.Tree, dump_file, with_stats = T))
@ -54,7 +54,7 @@ test_that("xgb.dump works", {
# JSON format # JSON format
dmp <- xgb.dump(bst.Tree, dump_format = "json") dmp <- xgb.dump(bst.Tree, dump_format = "json")
expect_length(dmp, 1) expect_length(dmp, 1)
if (!win32_flag) if (!flag_32bit)
expect_length(grep('nodeid', strsplit(dmp, '\n')[[1]]), 188) expect_length(grep('nodeid', strsplit(dmp, '\n')[[1]]), 188)
}) })
@ -256,7 +256,7 @@ test_that("xgb.model.dt.tree works with and without feature names", {
names.dt.trees <- c("Tree", "Node", "ID", "Feature", "Split", "Yes", "No", "Missing", "Quality", "Cover") names.dt.trees <- c("Tree", "Node", "ID", "Feature", "Split", "Yes", "No", "Missing", "Quality", "Cover")
dt.tree <- xgb.model.dt.tree(feature_names = feature.names, model = bst.Tree) dt.tree <- xgb.model.dt.tree(feature_names = feature.names, model = bst.Tree)
expect_equal(names.dt.trees, names(dt.tree)) expect_equal(names.dt.trees, names(dt.tree))
if (!win32_flag) if (!flag_32bit)
expect_equal(dim(dt.tree), c(188, 10)) expect_equal(dim(dt.tree), c(188, 10))
expect_output(str(dt.tree), 'Feature.*\\"Age\\"') expect_output(str(dt.tree), 'Feature.*\\"Age\\"')
@ -283,7 +283,7 @@ test_that("xgb.model.dt.tree throws error for gblinear", {
test_that("xgb.importance works with and without feature names", { test_that("xgb.importance works with and without feature names", {
importance.Tree <- xgb.importance(feature_names = feature.names, model = bst.Tree) importance.Tree <- xgb.importance(feature_names = feature.names, model = bst.Tree)
if (!win32_flag) if (!flag_32bit)
expect_equal(dim(importance.Tree), c(7, 4)) expect_equal(dim(importance.Tree), c(7, 4))
expect_equal(colnames(importance.Tree), c("Feature", "Gain", "Cover", "Frequency")) expect_equal(colnames(importance.Tree), c("Feature", "Gain", "Cover", "Frequency"))
expect_output(str(importance.Tree), 'Feature.*\\"Age\\"') expect_output(str(importance.Tree), 'Feature.*\\"Age\\"')

4
src/common/hist_util.cc
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@ -831,7 +831,11 @@ void GHistIndexBlockMatrix::Init(const GHistIndexMatrix& gmat,
* \brief fill a histogram by zeros in range [begin, end) * \brief fill a histogram by zeros in range [begin, end)
*/ */
void InitilizeHistByZeroes(GHistRow hist, size_t begin, size_t end) { void InitilizeHistByZeroes(GHistRow hist, size_t begin, size_t end) {
#if defined(XGBOOST_STRICT_R_MODE) && XGBOOST_STRICT_R_MODE == 1
std::fill(hist.begin() + begin, hist.begin() + end, tree::GradStats());
#else // defined(XGBOOST_STRICT_R_MODE) && XGBOOST_STRICT_R_MODE == 1
memset(hist.data() + begin, '\0', (end-begin)*sizeof(tree::GradStats)); memset(hist.data() + begin, '\0', (end-begin)*sizeof(tree::GradStats));
#endif // defined(XGBOOST_STRICT_R_MODE) && XGBOOST_STRICT_R_MODE == 1
} }
/*! /*!

4
src/common/io.cc
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@ -117,14 +117,16 @@ std::string LoadSequentialFile(std::string fname) {
size_t f_size_bytes = fs.st_size; size_t f_size_bytes = fs.st_size;
buffer.resize(f_size_bytes + 1); buffer.resize(f_size_bytes + 1);
int32_t fd = open(fname.c_str(), O_RDONLY); int32_t fd = open(fname.c_str(), O_RDONLY);
#if defined(__linux__)
posix_fadvise(fd, 0, 0, POSIX_FADV_SEQUENTIAL); posix_fadvise(fd, 0, 0, POSIX_FADV_SEQUENTIAL);
#endif // defined(__linux__)
ssize_t bytes_read = read(fd, &buffer[0], f_size_bytes); ssize_t bytes_read = read(fd, &buffer[0], f_size_bytes);
if (bytes_read < 0) { if (bytes_read < 0) {
close(fd); close(fd);
ReadErr(); ReadErr();
} }
close(fd); close(fd);
#else #else // defined(__unix__)
FILE *f = fopen(fname.c_str(), "r"); FILE *f = fopen(fname.c_str(), "r");
if (f == NULL) { if (f == NULL) {
std::string msg; std::string msg;

4
src/common/observer.h
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@ -20,11 +20,11 @@
#define OBSERVER_PRINT LOG(INFO) #define OBSERVER_PRINT LOG(INFO)
#define OBSERVER_ENDL "" #define OBSERVER_ENDL ""
#define OBSERVER_NEWLINE "" #define OBSERVER_NEWLINE ""
#else #else // defined(XGBOOST_STRICT_R_MODE) && XGBOOST_STRICT_R_MODE == 1
#define OBSERVER_PRINT std::cout << std::setprecision(17) #define OBSERVER_PRINT std::cout << std::setprecision(17)
#define OBSERVER_ENDL std::endl #define OBSERVER_ENDL std::endl
#define OBSERVER_NEWLINE "\n" #define OBSERVER_NEWLINE "\n"
#endif // defined(XGBOOST_STRICT_R_MODE) #endif // defined(XGBOOST_STRICT_R_MODE) && XGBOOST_STRICT_R_MODE == 1
namespace xgboost { namespace xgboost {
/*\brief An observer for logging internal data structures. /*\brief An observer for logging internal data structures.