| ... | ... |
@@ -1,10 +1,10 @@ |
| 1 | 1 |
Package: GSVA |
| 2 |
-Version: 1.33.4 |
|
| 2 |
+Version: 1.33.5 |
|
| 3 | 3 |
Title: Gene Set Variation Analysis for microarray and RNA-seq data |
| 4 | 4 |
Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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| 5 | 5 |
person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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| 6 | 6 |
person("Joan", "Fernandez", role="ctb", email="joanfernandez1331@gmail.com"))
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| 7 |
-Depends: R (>= 3.0.0) |
|
| 7 |
+Depends: R (>= 3.5.0) |
|
| 8 | 8 |
Imports: methods, BiocGenerics, Biobase, GSEABase (>= 1.17.4), |
| 9 | 9 |
geneplotter, shiny, shinythemes |
| 10 | 10 |
Suggests: limma, RColorBrewer, genefilter, |
| ... | ... |
@@ -1,3 +1,12 @@ |
| 1 |
+CHANGES IN VERSION 1.34 |
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| 2 |
+----------------------- |
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| 3 |
+ |
|
| 4 |
+BUG FIXES |
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| 5 |
+ |
|
| 6 |
+ 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). |
|
| 7 |
+ |
|
| 8 |
+ o Bugfix to handle when arguments 'method="ssgsea"' and 'tau=0'. Bug reporting thanks to Lena Morill (https://github.com/rcastelo/GSVA/issues/4). |
|
| 9 |
+ |
|
| 1 | 10 |
CHANGES IN VERSION 1.28 |
| 2 | 11 |
----------------------- |
| 3 | 12 |
|
| ... | ... |
@@ -28,9 +28,9 @@ argumentsDataInput <- function(id) {
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| 28 | 28 |
"True" = TRUE)), |
| 29 | 29 |
numericInput("minSz","min.sz:",value = 1),
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| 30 | 30 |
numericInput("maxSz","max.sz (Write 0 for infinite):",value = 0),
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| 31 |
- numericInput("parallelSz","parallel.sz:",value = 0),
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| 32 |
- selectInput("parallelType", "parallel.type:",
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| 33 |
- c("SOCK","MPI","NWS")),
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| 31 |
+ ## numericInput("parallelSz","parallel.sz:",value = 0),
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| 32 |
+ ## selectInput("parallelType", "parallel.type:",
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| 33 |
+ ## c("SOCK","MPI","NWS")),
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| 34 | 34 |
radioButtons("mxDiff", "mx.diff:",
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| 35 | 35 |
c("True" = TRUE,
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| 36 | 36 |
"False" = FALSE)), |
| ... | ... |
@@ -172,9 +172,14 @@ gsva_generation <- function(input, output, session, newY, genes,varMaxsz) {
|
| 172 | 172 |
#GSVA Generation |
| 173 | 173 |
withProgress(message = 'Runing GSVA', value = 0, {
|
| 174 | 174 |
incProgress(1, detail = "This may take a while...") |
| 175 |
- generated_gsva <<- gsva(newY, genes, method=input$method, kcdf=input$kcdf, abs.ranking=as.logical(input$absRanking), |
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| 176 |
- min.sz=input$minSz, max.sz=varMaxsz, parallel.sz=input$parallelSz, parallel.type=input$parallelType, |
|
| 177 |
- mx.diff=as.logical(input$mxDiff), tau=selectedTau, ssgsea.norm=as.logical(input$ssgseaNorm), |
|
| 175 |
+ generated_gsva <<- gsva(newY, genes, method=input$method, kcdf=input$kcdf, |
|
| 176 |
+ abs.ranking=as.logical(input$absRanking), |
|
| 177 |
+ min.sz=input$minSz, max.sz=varMaxsz, |
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| 178 |
+ ## parallel.sz=input$parallelSz, parallel.type=input$parallelType, |
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| 179 |
+ parallel.sz=1, ## disable parallelism |
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| 180 |
+ mx.diff=as.logical(input$mxDiff), |
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| 181 |
+ tau=selectedTau, |
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| 182 |
+ ssgsea.norm=as.logical(input$ssgseaNorm), |
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| 178 | 183 |
verbose=as.logical(input$verbose)) |
| 179 | 184 |
}) |
| 180 | 185 |
} |
| ... | ... |
@@ -265,4 +270,4 @@ function(input, output, session) {
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| 265 | 270 |
observeEvent(input$closeSave, {
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| 266 | 271 |
stopApp(generated_gsva) #Stops the app and returns the generated_gsva object |
| 267 | 272 |
}) |
| 268 |
-} |
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| 269 | 273 |
\ No newline at end of file |
| 274 |
+} |
