Browse code

2.17.2: if with logical length > 1 fixed

ramon diaz-uriarte (at Phelsuma) authored on 17/12/2019 11:25:52
Showing6 changed files

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@@ -1,8 +1,8 @@
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 Package: OncoSimulR
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 Type: Package
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 Title: Forward Genetic Simulation of Cancer Progression with Epistasis 
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-Version: 2.17.1
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-Date: 2019-11-24
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+Version: 2.17.2
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+Date: 2019-12-17
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 Authors@R: c(person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
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 		     email = "rdiaz02@gmail.com"),
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 	      person("Mark", "Taylor", role = "ctb", email = "ningkiling@gmail.com"))
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@@ -1058,9 +1058,11 @@ plot.oncosimul <- function(x,
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     colauto <- FALSE
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-    if(col == "auto" && (type == "line") && (show == "drivers"))
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+    if((length(col) ==1) && (col == "auto") &&
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+       (type == "line") && (show == "drivers"))
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         col <- c(8, "orange", 6:1)
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-    if(col == "auto" && (show == "genotypes")) {
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+    if((length(col) ==1) && (col == "auto") &&
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+       (show == "genotypes")) {
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         ## For categorical data, I find Dark2, Paired, or Set1 to work best.
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         col <- colorRampPalette(brewer.pal(8, "Dark2"))(ncol(x$pops.by.time) - 1)
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         colauto <- TRUE
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@@ -542,8 +542,9 @@ allFitnessORMutatorEffects <- function(rT = NULL,
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         gnum <- seq_along(noIntGenes) + mg
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         if(!is.null(names(noIntGenes))) {
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             ng <- names(noIntGenes)
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-            if( grepl(",", ng, fixed = TRUE) || grepl(">", ng, fixed = TRUE)
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-                || grepl(":", ng, fixed = TRUE))
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+            if( any(grepl(",", ng, fixed = TRUE)) ||
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+                any(grepl(">", ng, fixed = TRUE)) ||
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+                any(grepl(":", ng, fixed = TRUE))   )
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                 stop("The name of some noIntGenes contain a ',' or a '>' or a ':'")
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             if(any(ng %in% geneModule[, "Gene"] ))
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                 stop("A gene in noIntGenes also present in the other terms")
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@@ -1,3 +1,6 @@
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+Changes in version 2.17.2 (2019-12-17):
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+	- Fixed error "length(x) = 5 > 1' in coercion to 'logical(1)'"
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+	
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 Changes in version 2.17.1 (2019-11-24):
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 	- rfitness: clarified log=TRUE and truncate_at_0 after log.
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 	- Magellan_stats: really return a vector.
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@@ -218,7 +218,7 @@ test_that("LOD, strict, same as would be obtained from full structure, with init
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         loda <- OncoSimulR:::LOD.oncosimul2_pre_2.9.2(s7b, strict = FALSE)
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         ## we need this because o.w. the old output it ain't an igraph
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         ## object with names
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-        if(!grepl("_is_end", lods) && !grepl("No_descendants", lods)) {
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+        if(!any(grepl("_is_end", lods)) && !any(grepl("No_descendants", lods))) {
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             ## lods should be among the loda
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             if(!is.null(s7$pops.by.time)) {
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                 expect_true(any(
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@@ -230,7 +230,7 @@ test_that("LOD, strict, same as would be obtained from full structure, with init
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                                           lods))
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                 }
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             }
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-        } else if (grepl("No_descendants", lods)) {
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+        } else if (any(grepl("No_descendants", lods))) {
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             expect_true(identical(loda$lod_single,
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                                   lods)) 
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         } else {
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@@ -1,15 +1,15 @@
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 \usepackage[%
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-		shash={a8b5dae},
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-		lhash={a8b5dae811213fc49041804915277838c2c56f19},
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-		authname={Ramon Diaz-Uriarte},
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-		authemail={rdiaz02@users.noreply.github.com},
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-		authsdate={2019-11-25},
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-		authidate={2019-11-25 05:33:16 +0100},
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-		authudate={1574656396},
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-		commname={Ramon Diaz-Uriarte},
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-		commemail={rdiaz02@users.noreply.github.com},
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-		commsdate={2019-11-25},
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-		commidate={2019-11-25 05:33:16 +0100},
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-		commudate={1574656396},
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-		refnames={ (HEAD, origin/master, origin/HEAD)}
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+		shash={8a06478},
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+		lhash={8a064788fa0871be4bd6d6fe8be79c0b4f1cd3f7},
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+		authname={ramon diaz-uriarte (at Phelsuma)},
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+		authemail={rdiaz02@gmail.com},
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+		authsdate={2019-11-28},
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+		authidate={2019-11-28 20:43:07 +0100},
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+		authudate={1574970187},
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+		commname={ramon diaz-uriarte (at Phelsuma)},
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+		commemail={rdiaz02@gmail.com},
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+		commsdate={2019-11-28},
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+		commidate={2019-11-28 20:43:07 +0100},
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+		commudate={1574970187},
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+		refnames={ (HEAD -> master, origin/master, origin/HEAD)}
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 	]{gitsetinfo}
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\ No newline at end of file