Improved user messages and fixed namespace issue

rcastelo · Sep 4, 2024 · cf8b541 · cf8b541
1 parent f6e9f52
commit cf8b541
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Showing 4 changed files with 11 additions and 1 deletion.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: GSVA
-Version: 1.53.18
+Version: 1.53.19
 Title: Gene Set Variation Analysis for Microarray and RNA-Seq Data
 Authors@R: c(person("Robert", "Castelo", role=c("aut", "cre"), email="[email protected]"),
              person("Justin", "Guinney", role="aut", email="[email protected]"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -92,6 +92,7 @@ importFrom(stats,sd)
 importFrom(utils,capture.output)
 importFrom(utils,head)
 importFrom(utils,installed.packages)
+importFrom(utils,packageDescription)
 importFrom(utils,read.csv)
 importFrom(utils,setTxtProgressBar)
 importFrom(utils,tail)

diff --git a/R/gsva.R b/R/gsva.R
@@ -182,7 +182,12 @@ compute.geneset.es <- function(expr, gset.idx.list, sample.idxs, kcdf,
         } else
             kernel <- FALSE
     }
+
     if (verbose) {
+        if (sparse)
+            cli_alert_info("GSVA sparse algorithm")
+        else
+            cli_alert_info("GSVA dense (classical) algorithm")
         if (kernel) {
             if (rnaseq)
                 cli_alert_info("Row-wise ECDF estimation with Poisson kernels")

diff --git a/R/gsvaNewAPI.R b/R/gsvaNewAPI.R
@@ -121,6 +121,7 @@
 NULL
 
 #' @importFrom cli cli_alert_info
+#' @importFrom utils packageDescription
 #' @aliases gsva,plageParam-method
 #' @rdname gsva
 #' @exportMethod gsva
@@ -166,6 +167,7 @@ setMethod("gsva", signature(param="plageParam"),
 
 
 #' @importFrom cli cli_alert_info
+#' @importFrom utils packageDescription
 #' @aliases gsva,zscoreParam-method
 #' @rdname gsva
 #' @exportMethod gsva
@@ -210,6 +212,7 @@ setMethod("gsva", signature(param="zscoreParam"),
           })
 
 #' @importFrom cli cli_alert_info
+#' @importFrom utils packageDescription
 #' @aliases gsva,ssgseaParam-method
 #' @rdname gsva
 #' @exportMethod gsva
@@ -257,6 +260,7 @@ setMethod("gsva", signature(param="ssgseaParam"),
 
 #' @aliases gsva,gsvaParam-method
 #' @importFrom cli cli_alert_info cli_alert_success
+#' @importFrom utils packageDescription
 #' @rdname gsva
 #' @exportMethod gsva
 setMethod("gsva", signature(param="gsvaParam"),