replaced all occurences of require.auto with require_auto

R/bio/bioinfo_commons.R

 #library(BiocGenerics, quietly=T, warn.conflicts=F )
 #library(Biostrings, quietly=T)
-#require.auto(BiocGenerics )x
+#require_auto(BiocGenerics )x
 
-require.auto(Biostrings)
+require_auto(Biostrings)
 
 
 read.fasta <- function(fileName){

R/bio/diffex_commons.R

@@ -217,7 +217,7 @@ DEF_DAVID_ONTOLOGIES=ontologies=c("GOTERM_CC_FAT", "GOTERM_MF_FAT", "GOTERM_BP_F
 
 davidAnnotationChart <- function( someGenes, ontologies=DEF_DAVID_ONTOLOGIES ){
 
-    require.auto(RDAVIDWebService) ## just works if installed on non-network-drive (e.g. /tmp/)
+    require_auto(RDAVIDWebService) ## just works if installed on non-network-drive (e.g. /tmp/)
 
     ## expexted to have a column with gene_id
 #    echo("processing list with", length(someGenes), "genes")

R/core_commons.R

@@ -22,8 +22,8 @@ options(gsubfn.engine = "R")
 ## automatic package installation
 
 ## @Deprecated use require_auto instead
-require.auto <-  function(x){
-    warning("require.auto is deprecated. Use require_auto instead")
+require_auto <-  function(x){
+    warning("require_auto is deprecated. Use require_auto instead")
 
     x <- as.character(substitute(x))
 

R/datatable_commons.R

-require.auto(data.table)
+require_auto(data.table)
 
 
 dt.merge <- function(dfA, dfB, by=intersect(names(dfA), names(dfB)) , ...)  {

R/ggplot/ggheatmap.R

@@ -2,8 +2,8 @@
 #library(ggplot2)
 #library(reshape2)
 
-require.auto(ggdendro)
-require.auto(grid)
+require_auto(ggdendro)
+require_auto(grid)
 
 ## Adopted from  http://cwcode.wordpress.com/2013/01/30/ggheatmap-version-2/
 
@@ -164,7 +164,7 @@ ggheatmap <- function(x, rowlabels=T, xshift=ifelse(rowlabels, 10, 0), xcompress
 
 
 if(F){ #### DEBUG
-require.auto(mvtnorm)
+require_auto(mvtnorm)
 sigma=matrix(0,10,10)
 sigma[1:4,1:4] <- 0.6
 sigma[6:10,6:10] <- 0.8

R/ggplot_commons.R

-require.auto(ggplot2)
-require.auto(scales)
-require.auto(grid)
+require_auto(ggplot2)
+require_auto(scales)
+require_auto(grid)
 
 
 scale_fill_redgreed <- function() scale_fill_manual(values = c("red","darkgreen"))
@@ -157,7 +157,7 @@ plotPDF <- function(fileBaseName, expr, ...){ pdf(paste0(fileBaseName, ".pdf"),
 ## create a custom color palette for a fixed set of values
 ## scale_fill_manual(values = create_palette(unique(csWithTopoT1$t1_type)), drop = FALSE)
 create_palette <- function(x, pal = 'Set1'){
-  require.auto(RColorBrewer)
+  require_auto(RColorBrewer)
 
   ux <- sort(unique(x))
   n <-length(ux)