@@ -1,5 +1,5 @@

 Package: GSVA

-Version: 1.45.2

+Version: 1.45.3

 Title: Gene Set Variation Analysis for microarray and RNA-seq data

 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),

              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),

@@ -885,7 +885,7 @@ ssgsea <- function(X, geneSets, alpha=0.25, parallel.sz,

   colnames(es) <- colnames(X)

   if(is(X, "dgCMatrix")){

-    es <- as(es, "dgCMatrix")

+    es <- as(as(as(es, "dMatrix"), "generalMatrix"), "CsparseMatrix")

   }

   es

@@ -920,7 +920,7 @@ zscore <- function(X, geneSets, parallel.sz, verbose=TRUE,

   es <- do.call("cbind", es)

   if(is(X, "dgCMatrix")){

-    es <- as(es, "dgCMatrix")

+    es <- as(as(as(es, "dMatrix"), "generalMatrix"), "CsparseMatrix")

   }

   rownames(es) <- names(geneSets)

@@ -955,7 +955,7 @@ plage <- function(X, geneSets, parallel.sz, verbose=TRUE,

     es <- do.call(rbind, es)

-    es <- as(es, "dgCMatrix")

+    es <- as(as(as(es, "dMatrix"), "generalMatrix"), "CsparseMatrix")

   } else {

new file mode 100644

@@ -0,0 +1,3 @@

+.onLoad <- function(libname, pkgname) {

+  options(Matrix.warnDeprecatedCoerce = 2)

+}

@@ -9,7 +9,7 @@ test_sparseMethods <- function(){

   gene.sets <- list("my_list1"= paste0("gene_", 1:2),

                     "my_list2"= paste0("gene_", 3:4))

-  M <- as(m, "dgCMatrix")

+  M <- as(as(as(m, "dMatrix"), "generalMatrix"), "CsparseMatrix")

   checkEqualsNumeric(gsva(m, gene.sets), gsva(M, gene.sets))

   checkEqualsNumeric(gsva(m, gene.sets, method="plage"), gsva(M, gene.sets, method="plage"))