declarations for no global bindings error

R/plotIntegratedPatientNetwork.R

@@ -210,6 +210,5 @@ if (plotCytoscape) {
 	)
 }
 
-
 return(out)
 }

R/plot_tSNE.R

@@ -26,6 +26,9 @@ if (all.equal(pheno$ID[idx],samps)!=TRUE) {
 }
 st <- pheno$STATUS[idx]
 
+# to eliminate the "no visible binding for global variable" problem
+y <- status <- NULL
+
 message("* Plotting")
 colnames(dat) <- c("x","y")
 dat <- as.data.frame(dat,stringsAsFactors=TRUE)

R/runQuery.R

@@ -8,8 +8,6 @@
 #' numCores*GMmemory will be used and distributed for all GM threads
 #' @param numCores (integer) number of CPU cores for parallel processing
 #' @param debugMode (logical) when TRUE runs jobs in serial instead of parallel and 
-#' prints verbose messages.
-#' @param debugMode (logical) when TRUE runs jobs in serial instead of parallel and 
 #' prints verbose messages. Also prints system Java calls.
 #' @return (char) path to GeneMANIA query result files with patient similarity
 #' rankings (*PRANK) and feature weights (*NRANK)

R/smooMutationPropagation.R

@@ -75,6 +75,8 @@ smoothMutations_LabelProp <- function(mat,net,numCores=1L) {
 	cl <- makeCluster(numCores)
 	registerDoParallel(cl)
 
+	# to address the "no visible binding for global variable" error
+	k <- NULL
   res.l <- foreach(k = 1:length(inds),
 	.packages=c("netSmooth","scater","clusterExperiment")) %dopar% {
     nS.res=netSmooth(mat[,inds[[k]]], net , alpha=0.2, verbose = 'auto', 

vignettes/Predict_CaseControl_from_CNV.Rmd

@@ -70,8 +70,8 @@ out <- buildPredictor_sparseGenetic(
       path_GRList,
 		outDir=outDir, ## absolute path
       numSplits=3L, featScoreMax=3L,
-      enrichLabels=TRUE,numPermsEnrich=20L,
-      numCores=2L,debugMode=TRUE)
+      enrichLabels=TRUE,numPermsEnrich=3L,
+      numCores=2L)
 
 # plot ROC curve. Note that the denominator only includes
 # patients with events in networks that are label-enriched
@@ -197,7 +197,7 @@ out <-
                              path_GRList,
                              outDir=outDir, ## absolute path
                              numSplits=3L, featScoreMax=3L,
-                             enrichLabels=TRUE,numPermsEnrich=20L,
+                             enrichLabels=TRUE,numPermsEnrich=3L,
                              numCores=2L)
 ```
 

vignettes/SmoothMutationsUsingInteractionNets.Rmd

@@ -12,6 +12,12 @@ vignette: >
     %\VignetteEncoding{UTF-8}
 ---
 
+```{r, include = FALSE}
+is_check <- ("CheckExEnv" %in% search()) || any(c("_R_CHECK_TIMINGS_",
+             "_R_CHECK_LICENSE_") %in% names(Sys.getenv()))
+knitr::opts_chunk$set(eval = !is_check)
+```
+
 # TL;DR
 This code block is not evaluated. Need a breakdown? Look at the following sections.
 ```{r,eval=FALSE}