Fixing function %||% not being found

.Rhistory

@@ -0,0 +1,2 @@
+setwd("C:/Users/Konstantin/Programmierung/harmony")
+roxygen2::roxygenise()

NAMESPACE

@@ -14,4 +14,5 @@ importFrom(methods,as)
 importFrom(methods,is)
 importFrom(methods,new)
 importFrom(rlang,.data)
+importFrom(rlang,`%||%`)
 useDynLib(harmony)

R/RunHarmony.R

@@ -44,6 +44,7 @@
 #'
 #'
 #' @rdname RunHarmony
+#' @importFrom rlang `%||%`
 #' @export
 RunHarmony <- function(object, group.by.vars, ...) {
     UseMethod("RunHarmony")
@@ -57,6 +58,7 @@ RunHarmony <- function(object, group.by.vars, ...) {
 #' @return Seurat (version 3) object. Harmony dimensions placed into
 #' dimensional reduction object harmony. For downstream Seurat analyses,
 #' use reduction='harmony'.
+#' @importFrom rlang `%||%`
 #' @export
 RunHarmony.Seurat <- function(
   object,
@@ -81,7 +83,7 @@ RunHarmony.Seurat <- function(
   project.dim = TRUE,
   ...
 ) {
-  assay.use <- assay.use %||% DefaultAssay(object)
+  assay.use <- assay.use %||% Seurat::DefaultAssay(object)
   if (reduction == "pca") {
     tryCatch(
       embedding <- Seurat::Embeddings(object, reduction = "pca"),

src/RcppExports.cpp

@@ -7,6 +7,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // compute_Y
 MATTYPE compute_Y(const MATTYPE& Z_cos, const MATTYPE& R);
 RcppExport SEXP _harmony_compute_Y(SEXP Z_cosSEXP, SEXP RSEXP) {