replaced rBind and cBind with rbind and cbind

DESCRIPTION

 Package: sybil
 Type: Package
 Title: Efficient Constrained Based Modelling in R
-Version: 2.1.0
-Date: 2017-07-21
+Version: 2.1.1
+Date: 2018-03-26
 Authors@R: c(
 	     person(c("C.", "Jonathan"), "Fritzemeier", role = c("cre", "ctb"), email = "clausjonathan.fritzemeier@uni-duesseldorf.de"),
 	     person("Gabriel", "Gelius-Dietrich", role = c("aut")),
@@ -12,7 +12,7 @@ Authors@R: c(
              person("Abdelmoneim", "Desouki", role = "ctb"),
              person(c("Martin", "J."), "Lercher", role = "ctb"))
 Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
-Depends: R (>= 2.14.2), Matrix, lattice
+Depends: R (>= 3.2.0), Matrix, lattice
 Imports: methods
 Suggests: glpkAPI (>= 1.2.8), cplexAPI (>= 1.2.4), clpAPI (>= 1.2.4),
         lpSolveAPI (>= 5.5.2.0), parallel, grid
@@ -55,7 +55,7 @@ Collate: generics.R validmodelorg.R validoptsol.R validreactId.R validreact.R
         sysBiolAlg_mtfClass.R sysBiolAlg_mtfEasyConstraintClass.R
         sysBiolAlg_roomClass.R sybilLogClass.R upgradeModelorg.R
         mergeReact2Modelorg.R
-Packaged: 2017-07-21 12:34:14 UTC; jonathan
+Packaged: 2018-03-26 12:34:14 UTC; jonathan
 Author: C. Jonathan Fritzemeier [cre, ctb],
   Gabriel Gelius-Dietrich [aut],
   Rajen Piernikarczyk [ctb],

R/addReact.R

@@ -186,7 +186,7 @@ setMethod("addReact", signature(model = "modelorg"),
             newRows <- Matrix::Matrix(0,
                                       nrow = nNewRows,
                                       ncol = react_num(model))
-            newS <- Matrix::rBind(newS, newRows)
+            newS <- rbind(newS, newRows)
             
             # new met attrs
             if(ncol(newMetAttr) > 0){
@@ -220,7 +220,7 @@ setMethod("addReact", signature(model = "modelorg"),
             newobj_coef  <- append(obj_coef(model),  obj)
 
             # new column in stoichiometric matrix
-            newS <- cBind(newS, rep(0, nrow(newS)))
+            newS <- cbind(newS, rep(0, nrow(newS)))
             
             # new react Attr
             # only one new row, /bc we can only add one reaction a time.
@@ -236,23 +236,23 @@ setMethod("addReact", signature(model = "modelorg"),
             		newsubSys <- ss
             	}
             	else {
-            		newsubSys <- rBind(ss, rep(FALSE, ncol(subSys(model))))
+            		newsubSys <- rbind(ss, rep(FALSE, ncol(subSys(model))))
             	}
             }
             else {
                 if (is(subSystem, "logical")) {
-                    newsubSys <- rBind(subSys(model), subSystem)
+                    newsubSys <- rbind(subSys(model), subSystem)
                 }
                 else {
                     nSubsRow  <- colnames(subSys(model)) %in% subSystem
-                    newsubSys <- rBind(subSys(model), nSubsRow)
+                    newsubSys <- rbind(subSys(model), nSubsRow)
                 }
             }
 
 
             # gpr association
             if (ncol(rxnGeneMat(model)) > 0) {
-                newrxnGeneMat   <- rBind(rxnGeneMat(model),
+                newrxnGeneMat   <- rbind(rxnGeneMat(model),
                                          rep(FALSE, ncol(rxnGeneMat(model))))
             }
             else { #if (nrow(rxnGeneMat(model)) > 0) {
@@ -294,7 +294,7 @@ setMethod("addReact", signature(model = "modelorg"),
                     }
                     else {
                         for (i in seq(along = gene_rule[["gene"]][new_gene])) {
-	    					newrxnGeneMat <- cBind(newrxnGeneMat,
+	    					newrxnGeneMat <- cbind(newrxnGeneMat,
 		    								   rep(FALSE, nrow(newrxnGeneMat)))
 			    		}
 					}

R/doubleReact.R

@@ -123,7 +123,7 @@ doubleReact <- function(model, checkRev = TRUE, linInd = FALSE) {
 
           # Put the columns of S into a new matrix, which contain the same
           # number of metabolites
-          Stmp <- cBind(S(model)[, columns[[i]] ])
+          Stmp <- cbind(S(model)[, columns[[i]] ])
 
           # translate Stmp into a matrix with the row indices of the
           # non zero elements

R/sysBiolAlg_lmomaClass.R

@@ -154,7 +154,7 @@ setMethod(f = "initialize",
                                              sparse = TRUE)
           
                       # the final contraint matrix
-                      LHS <- rBind(LHSwt, LHS, crow)
+                      LHS <- rbind(LHSwt, LHS, crow)
           
                       subalg <- "lmoma_cobra"
                   }