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Updated documentation and NEWS file.

[rcastelo] authored on 28/10/2019 17:11:35
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 Package: GSVA
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-Version: 1.33.4
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+Version: 1.33.5
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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              person("Joan", "Fernandez", role="ctb", email="joanfernandez1331@gmail.com"))
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-Depends: R (>= 3.0.0)
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+Depends: R (>= 3.5.0)
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 Imports: methods, BiocGenerics, Biobase, GSEABase (>= 1.17.4),
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          geneplotter, shiny, shinythemes
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 Suggests: limma, RColorBrewer, genefilter,
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+CHANGES IN VERSION 1.34
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+-----------------------
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+
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+BUG FIXES
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+
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+   o Bugfix to handle when parallel::detectCores() returns NA instead of an integer number of cores, which may happen when running GSVA in a docker container. Bug reporting and pull request fix thanks to Aaron (https://github.com/rcastelo/GSVA/pull/10).
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+
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+   o Bugfix to handle when arguments 'method="ssgsea"' and 'tau=0'. Bug reporting thanks to Lena Morill (https://github.com/rcastelo/GSVA/issues/4).
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+
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 CHANGES IN VERSION 1.28
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 -----------------------
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@@ -28,9 +28,9 @@ argumentsDataInput <- function(id) {
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                          "True" = TRUE)),
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           numericInput("minSz","min.sz:",value = 1),
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           numericInput("maxSz","max.sz (Write 0 for infinite):",value = 0),
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-          numericInput("parallelSz","parallel.sz:",value = 0),
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-          selectInput("parallelType", "parallel.type:",
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-                      c("SOCK","MPI","NWS")),
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+          ## numericInput("parallelSz","parallel.sz:",value = 0),
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+          ## selectInput("parallelType", "parallel.type:",
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+          ##             c("SOCK","MPI","NWS")),
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           radioButtons("mxDiff", "mx.diff:",
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                        c("True" = TRUE,
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                          "False" = FALSE)),
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@@ -172,9 +172,14 @@ gsva_generation <- function(input, output, session, newY, genes,varMaxsz) {
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   #GSVA Generation
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   withProgress(message = 'Runing GSVA', value = 0, {
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     incProgress(1, detail = "This may take a while...")
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-    generated_gsva <<- gsva(newY, genes, method=input$method, kcdf=input$kcdf, abs.ranking=as.logical(input$absRanking),
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-                            min.sz=input$minSz, max.sz=varMaxsz, parallel.sz=input$parallelSz, parallel.type=input$parallelType,
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-                            mx.diff=as.logical(input$mxDiff), tau=selectedTau, ssgsea.norm=as.logical(input$ssgseaNorm),
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+    generated_gsva <<- gsva(newY, genes, method=input$method, kcdf=input$kcdf,
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+                            abs.ranking=as.logical(input$absRanking),
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+                            min.sz=input$minSz, max.sz=varMaxsz,
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+                            ## parallel.sz=input$parallelSz, parallel.type=input$parallelType,
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+                            parallel.sz=1, ## disable parallelism
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+                            mx.diff=as.logical(input$mxDiff),
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+                            tau=selectedTau,
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+                            ssgsea.norm=as.logical(input$ssgseaNorm),
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                             verbose=as.logical(input$verbose))
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   })
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 }
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@@ -265,4 +270,4 @@ function(input, output, session) {
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   observeEvent(input$closeSave, {
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     stopApp(generated_gsva) #Stops the app and returns the generated_gsva object
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   })
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-}
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\ No newline at end of file
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+}