@@ -15,11 +15,15 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges,

          BiocParallel, SingleCellExperiment, sparseMatrixStats, DelayedArray,

          DelayedMatrixStats, HDF5Array, BiocSingular

 <<<<<<< HEAD

+<<<<<<< HEAD

 Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer,

           org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2,

           data.table, plotly

 =======

 Suggests: BiocGenerics, RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer,

+=======

+Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer,

+>>>>>>> modified imports in igsva()

           genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table,

 <<<<<<< HEAD

           plotly, shinyjs, future, promises, shinybusy

@@ -8,40 +8,41 @@ igsva <- function() {

     stop(sprintf("Please install the following packages to use the GSVA WebApp:\n\n  %s\n",

                  paste(shinydeps[!maskshinydeps], collapse=", ")))

-  namespaceImportFrom(self=getNamespace("base"),

-                      ns=getNamespace("shiny"))

-

-  namespaceImportFrom(self=getNamespace("base"),

-                      ns=getNamespace("shinythemes"),

-                      vars="shinytheme")

-

-  namespaceImportFrom(self=getNamespace("base"),

-                      ns=getNamespace("ggplot2"),

-                      vars="ggplot")

-

-  namespaceImportFrom(self=getNamespace("base"),

-                      ns=getNamespace("data.table"))

-

-  namespaceImportFrom(self=getNamespace("base"),

-                      ns=getNamespace("plotly"),

-                      vars=c("ggplotly", "event_data", "style"))

-

-  namespaceImportFrom(self=getNamespace("base"),

-                      ns=getNamespace("future"))

-

-  namespaceImportFrom(self=getNamespace("base"),

-                      ns=getNamespace("shinyjs"))

-

-  namespaceImportFrom(self=getNamespace("base"),

-                      ns=getNamespace("shinybusy"))

-

-  namespaceImportFrom(self=getNamespace("base"),

-                      ns=getNamespace("limma"))

+  # namespaceImportFrom(self=getNamespace("base"),

+  #                     ns=getNamespace("shiny"))

+  # 

+  # namespaceImportFrom(self=getNamespace("base"),

+  #                     ns=getNamespace("shinythemes"),

+  #                     vars="shinytheme")

+  # 

+  # namespaceImportFrom(self=getNamespace("base"),

+  #                     ns=getNamespace("ggplot2"),

+  #                     vars="ggplot")

+  # 

+  # namespaceImportFrom(self=getNamespace("base"),

+  #                     ns=getNamespace("data.table"))

+  # 

+  # namespaceImportFrom(self=getNamespace("base"),

+  #                     ns=getNamespace("plotly"),

+  #                     vars=c("ggplotly", "event_data", "style"))

+  # 

+  # namespaceImportFrom(self=getNamespace("base"),

+  #                     ns=getNamespace("future"))

+  # 

+  # namespaceImportFrom(self=getNamespace("base"),

+  #                     ns=getNamespace("shinyjs"))

+  # 

+  # namespaceImportFrom(self=getNamespace("base"),

+  #                     ns=getNamespace("shinybusy"))

+  # 

+  # namespaceImportFrom(self=getNamespace("base"),

+  #                     ns=getNamespace("limma"))

   appDir <- system.file("shinyApp", package="GSVA")

   if (appDir == "")

     stop("The GSVA Shiny app cannot be found within the package.")

-  runWebApp <- get("runApp", mode="function")

-  runWebApp(appDir)

+  # runWebApp <- get("runApp", mode="function")

+  # runWebApp(appDir)

+  shiny::runApp(appDir)

 }

@@ -41,6 +41,8 @@ function(input, output, session) {

     rv$gs <- NULL

     rv$dat.t <- NULL

     rv$p <- NULL

+    rv$p2 <- NULL

+    rv$p3 <- NULL

     rv$errors.gsva = NULL

     rv$matrix <- isolate(matrix())

     rv$genesets <- isolate(genesets())