[R] Fix warnings from R check --as-cran (#6374)

* Remove exit and printf.

* Fix warnings.

Makefile

@@ -141,7 +141,7 @@ Rpack: clean_all
 R ?= R
 
 Rbuild: Rpack
-	$(R) CMD build --no-build-vignettes xgboost
+	$(R) CMD build xgboost
 	rm -rf xgboost
 
 Rcheck: Rbuild

R-package/R/xgb.ggplot.R

@@ -118,8 +118,7 @@ xgb.ggplot.shap.summary <- function(data, shap_contrib = NULL, features = NULL,
   p_data <- prepare.ggplot.shap.data(data_list, normalize = TRUE)
   # Reverse factor levels so that the first level is at the top of the plot
   p_data[, "feature" := factor(feature, rev(levels(feature)))]
-
-  p <- ggplot2::ggplot(p_data, ggplot2::aes(x = feature, y = shap_value, colour = feature_value)) +
+  p <- ggplot2::ggplot(p_data, ggplot2::aes(x = feature, y = p_data$shap_value, colour = p_data$feature_value)) +
     ggplot2::geom_jitter(alpha = 0.5, width = 0.1) +
     ggplot2::scale_colour_viridis_c(limits = c(-3, 3), option = "plasma", direction = -1) +
     ggplot2::geom_abline(slope = 0, intercept = 0, colour = "darkgrey") +

R-package/R/xgb.plot.shap.R

@@ -212,6 +212,9 @@ xgb.plot.shap.summary <- function(data, shap_contrib = NULL, features = NULL, to
 #' Prepare data for SHAP plots. To be used in xgb.plot.shap, xgb.plot.shap.summary, etc.
 #' Internal utility function.
 #'
+#' @inheritParams xgb.plot.shap
+#' @keywords internal
+#'
 #' @return A list containing: 'data', a matrix containing sample observations
 #'   and their feature values; 'shap_contrib', a matrix containing the SHAP contribution
 #'   values for these observations.

R-package/man/xgb.shap.data.Rd

@@ -18,6 +18,31 @@ xgb.shap.data(
   max_observations = 1e+05
 )
 }
+\arguments{
+\item{data}{data as a \code{matrix} or \code{dgCMatrix}.}
+
+\item{shap_contrib}{a matrix of SHAP contributions that was computed earlier for the above
+\code{data}. When it is NULL, it is computed internally using \code{model} and \code{data}.}
+
+\item{features}{a vector of either column indices or of feature names to plot. When it is NULL,
+feature importance is calculated, and \code{top_n} high ranked features are taken.}
+
+\item{top_n}{when \code{features} is NULL, top_n [1, 100] most important features in a model are taken.}
+
+\item{model}{an \code{xgb.Booster} model. It has to be provided when either \code{shap_contrib}
+or \code{features} is missing.}
+
+\item{trees}{passed to \code{\link{xgb.importance}} when \code{features = NULL}.}
+
+\item{target_class}{is only relevant for multiclass models. When it is set to a 0-based class index,
+only SHAP contributions for that specific class are used.
+If it is not set, SHAP importances are averaged over all classes.}
+
+\item{approxcontrib}{passed to \code{\link{predict.xgb.Booster}} when \code{shap_contrib = NULL}.}
+
+\item{subsample}{a random fraction of data points to use for plotting. When it is NULL,
+it is set so that up to 100K data points are used.}
+}
 \value{
 A list containing: 'data', a matrix containing sample observations
   and their feature values; 'shap_contrib', a matrix containing the SHAP contribution
@@ -27,3 +52,4 @@ A list containing: 'data', a matrix containing sample observations
 Prepare data for SHAP plots. To be used in xgb.plot.shap, xgb.plot.shap.summary, etc.
 Internal utility function.
 }
+\keyword{internal}

rabit/include/rabit/internal/utils.h

@@ -69,10 +69,6 @@ inline bool StringToBool(const char* s) {
   return CompareStringsCaseInsensitive(s, "true") == 0 || atoi(s) != 0;
 }
 
-inline void HandlePrint(const char *msg) {
-  printf("%s", msg);
-}
-
 /*! \brief printf, prints messages to the console */
 inline void Printf(const char *fmt, ...) {
   std::string msg(kPrintBuffer, '\0');
@@ -80,7 +76,7 @@ inline void Printf(const char *fmt, ...) {
   va_start(args, fmt);
   vsnprintf(&msg[0], kPrintBuffer, fmt, args);
   va_end(args);
-  HandlePrint(msg.c_str());
+  LOG(CONSOLE) << msg;
 }
 
 /*! \brief assert a condition is true, use this to handle debug information */

rabit/src/allreduce_base.cc

@@ -104,9 +104,7 @@ bool AllreduceBase::Init(int argc, char* argv[]) {
     }
   }
   if (dmlc_role != "worker") {
-    fprintf(stderr, "Rabit Module currently only work with dmlc worker"\
-            ", quit this program by exit 0\n");
-    exit(0);
+    LOG(FATAL) << "Rabit Module currently only work with dmlc worker";
   }
 
   // clear the setting before start reconnection
@@ -236,10 +234,10 @@ utils::TCPSocket AllreduceBase::ConnectTracker() const {
   do {
     if (!tracker.Connect(utils::SockAddr(tracker_uri.c_str(), tracker_port))) {
       if (++retry >= connect_retry) {
-        fprintf(stderr, "connect to (failed): [%s]\n", tracker_uri.c_str());
+        LOG(WARNING) << "Connect to (failed): [" << tracker_uri << "]\n";
         utils::Socket::Error("Connect");
       } else {
-        fprintf(stderr, "retry connect to ip(retry time %d): [%s]\n", retry, tracker_uri.c_str());
+        LOG(WARNING) << "Retry connect to ip(retry time " << retry << "): [" << tracker_uri << "]\n";
 #if defined(_MSC_VER) || defined (__MINGW32__)
         Sleep(retry << 1);
 #else
@@ -295,10 +293,11 @@ bool AllreduceBase::ReConnectLinks(const char *cmd) {
            "must keep rank to same if the node already have one");
     rank = newrank;
 
-    // tracker got overwhelemed and not able to assign correct rank
-    if (rank == -1) exit(-1);
+    if (rank == -1) {
+      LOG(FATAL) << "tracker got overwhelemed and not able to assign correct rank";
+    }
 
-    fprintf(stdout, "task %s got new rank %d\n", task_id.c_str(), rank);
+    LOG(CONSOLE) << "task " << task_id << " got new rank " << rank;
 
     Assert(tracker.RecvAll(&num_neighbors, sizeof(num_neighbors)) == \
          sizeof(num_neighbors), "ReConnectLink failure 4");
@@ -424,7 +423,7 @@ bool AllreduceBase::ReConnectLinks(const char *cmd) {
         setsockopt(all_link.sock, IPPROTO_TCP,
                    TCP_NODELAY, reinterpret_cast<void *>(&tcpNoDelay), sizeof(tcpNoDelay));
 #else
-        fprintf(stderr, "tcp no delay is not implemented on non unix platforms\n");
+        LOG(WARNING) << "tcp no delay is not implemented on non unix platforms";
 #endif
       }
       if (tree_neighbors.count(all_link.rank) != 0) {
@@ -444,7 +443,7 @@ bool AllreduceBase::ReConnectLinks(const char *cmd) {
            "cannot find next ring in the link");
     return true;
   } catch (const std::exception& e) {
-    fprintf(stderr, "failed in ReconnectLink %s\n", e.what());
+    LOG(WARNING) << "failed in ReconnectLink " << e.what();
     return false;
   }
 }

rabit/src/allreduce_base.h

@@ -226,8 +226,7 @@ class AllreduceBase : public IEngine {
    */
   inline void ReportStatus() const {
     if (hadoop_mode != 0) {
-      fprintf(stderr, "reporter:status:Rabit Phase[%03d] Operation %03d\n",
-              version_number, seq_counter);
+      LOG(CONSOLE) << "reporter:status:Rabit Phase[" << version_number << "] Operation " << seq_counter << "\n";
     }
   }