@@ -1,8 +1,8 @@

 Package: OncoSimulR

 Type: Package

 Title: Forward Genetic Simulation of Cancer Progression with Epistasis 

-Version: 2.17.1

-Date: 2019-11-24

+Version: 2.17.2

+Date: 2019-12-17

 Authors@R: c(person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),

 		     email = "rdiaz02@gmail.com"),

 	      person("Mark", "Taylor", role = "ctb", email = "ningkiling@gmail.com"))

@@ -1058,9 +1058,11 @@ plot.oncosimul <- function(x,

     colauto <- FALSE

-    if(col == "auto" && (type == "line") && (show == "drivers"))

+    if((length(col) ==1) && (col == "auto") &&

+       (type == "line") && (show == "drivers"))

         col <- c(8, "orange", 6:1)

-    if(col == "auto" && (show == "genotypes")) {

+    if((length(col) ==1) && (col == "auto") &&

+       (show == "genotypes")) {

         ## For categorical data, I find Dark2, Paired, or Set1 to work best.

         col <- colorRampPalette(brewer.pal(8, "Dark2"))(ncol(x$pops.by.time) - 1)

         colauto <- TRUE

@@ -542,8 +542,9 @@ allFitnessORMutatorEffects <- function(rT = NULL,

         gnum <- seq_along(noIntGenes) + mg

         if(!is.null(names(noIntGenes))) {

             ng <- names(noIntGenes)

-            if( grepl(",", ng, fixed = TRUE) || grepl(">", ng, fixed = TRUE)

-                || grepl(":", ng, fixed = TRUE))

+            if( any(grepl(",", ng, fixed = TRUE)) ||

+                any(grepl(">", ng, fixed = TRUE)) ||

+                any(grepl(":", ng, fixed = TRUE))   )

                 stop("The name of some noIntGenes contain a ',' or a '>' or a ':'")

             if(any(ng %in% geneModule[, "Gene"] ))

                 stop("A gene in noIntGenes also present in the other terms")

@@ -1,3 +1,6 @@

+Changes in version 2.17.2 (2019-12-17):

+	- Fixed error "length(x) = 5 > 1' in coercion to 'logical(1)'"

+	

 Changes in version 2.17.1 (2019-11-24):

 	- rfitness: clarified log=TRUE and truncate_at_0 after log.

 	- Magellan_stats: really return a vector.

@@ -218,7 +218,7 @@ test_that("LOD, strict, same as would be obtained from full structure, with init

         loda <- OncoSimulR:::LOD.oncosimul2_pre_2.9.2(s7b, strict = FALSE)

         ## we need this because o.w. the old output it ain't an igraph

         ## object with names

-        if(!grepl("_is_end", lods) && !grepl("No_descendants", lods)) {

+        if(!any(grepl("_is_end", lods)) && !any(grepl("No_descendants", lods))) {

             ## lods should be among the loda

             if(!is.null(s7$pops.by.time)) {

                 expect_true(any(

@@ -230,7 +230,7 @@ test_that("LOD, strict, same as would be obtained from full structure, with init

                                           lods))

                 }

             }

-        } else if (grepl("No_descendants", lods)) {

+        } else if (any(grepl("No_descendants", lods))) {

             expect_true(identical(loda$lod_single,

                                   lods)) 

         } else {

@@ -1,15 +1,15 @@

 \usepackage[%

-		shash={a8b5dae},

-		lhash={a8b5dae811213fc49041804915277838c2c56f19},

-		authname={Ramon Diaz-Uriarte},

-		authemail={rdiaz02@users.noreply.github.com},

-		authsdate={2019-11-25},

-		authidate={2019-11-25 05:33:16 +0100},

-		authudate={1574656396},

-		commname={Ramon Diaz-Uriarte},

-		commemail={rdiaz02@users.noreply.github.com},

-		commsdate={2019-11-25},

-		commidate={2019-11-25 05:33:16 +0100},

-		commudate={1574656396},

-		refnames={ (HEAD, origin/master, origin/HEAD)}

+		shash={8a06478},

+		lhash={8a064788fa0871be4bd6d6fe8be79c0b4f1cd3f7},

+		authname={ramon diaz-uriarte (at Phelsuma)},

+		authemail={rdiaz02@gmail.com},

+		authsdate={2019-11-28},

+		authidate={2019-11-28 20:43:07 +0100},

+		authudate={1574970187},

+		commname={ramon diaz-uriarte (at Phelsuma)},

+		commemail={rdiaz02@gmail.com},

+		commsdate={2019-11-28},

+		commidate={2019-11-28 20:43:07 +0100},

+		commudate={1574970187},

+		refnames={ (HEAD -> master, origin/master, origin/HEAD)}

 	]{gitsetinfo}

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