generateWT.R bug fix

DESCRIPTION

 Package: sybil
 Type: Package
 Title: Efficient Constrained Based Modelling in R
-Version: 1.3.4
-Date: 2015-04-18
+Version: 2.0.3
+Date: 2017-04-20
 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")),
@@ -52,8 +52,8 @@ Collate: generics.R validmodelorg.R validoptsol.R validreactId.R
         sysBiolAlg_fbaEasyConstraintClass.R sysBiolAlg_fvClass.R
         sysBiolAlg_lmomaClass.R sysBiolAlg_momaClass.R
         sysBiolAlg_mtfClass.R sysBiolAlg_mtfEasyConstraintClass.R
-        sysBiolAlg_roomClass.R sybilLogClass.R
-Packaged: 2016-01-27 12:34:14 UTC; jonathan
+        sysBiolAlg_roomClass.R sybilLogClass.R upgradeModelorg.R
+Packaged: 2017-04-20 12:34:14 UTC; jonathan
 Author: C. Jonathan Fritzemeier [cre, ctb],
   Gabriel Gelius-Dietrich [aut],
   Rajen Piernikarczyk [ctb],

R/generateWT.R

@@ -52,30 +52,30 @@
 	
 	# setting ... parameters into list
 	ca <- list(...)
-	if(is.null(ca$solver)){
-		ca$solver <- SYBIL_SETTINGS("SOLVER")
+	if(is.null(ca[["solver"]])){
+		ca[["solver"]] <- SYBIL_SETTINGS("SOLVER")
 	}
 
-    me <- checkDefaultMethod(solver = ca$solver,
+    me <- checkDefaultMethod(solver = ca[["solver"]],
                              method = "NA",
                              probType = "lp",
                              loadPackage = FALSE)
     
-    ca$solver <- me[["sol"]]
-    ca$method <- me[["met"]]
-    ca$solverParm <- as.data.frame(NA)
+    ca[["solver"]] <- me[["sol"]]
+    ca[["method"]] <- me[["met"]]
+    ca[["solverParm"]] <- as.data.frame(NA)
     
-    ca$object <- model
-    if(is.null(ca$algorithm)) ca$algorithm <- "fba"
-    ca$react <- react
-    ca$ub <- ub
-    ca$lb <- lb
+    ca[["object"]] <- model
+    if(is.null(ca[["algorithm"]])) ca[["algorithm"]] <- "fba"
+    ca[["react"]] <- react
+    ca[["ub"]] <- ub
+    ca[["lb"]] <- lb
 
     if (is(react, "list")) {
         message("calculating fba solutions ... ", appendLF = FALSE)
         suppressMessages({
-        	ca$lpdir <- rep("max", length(react))
-        	ca$verboseMode <- 0
+        	ca[["lpdir"]] <- rep("max", length(react))
+        	ca[["verboseMode"]] <- 0
         	
         	tmp <- do.call(optimizer, ca)
 #            tmp <- optimizer(model, algorithm = algorithm,
@@ -87,8 +87,8 @@
         message("OK")
     }
     else {
-    	ca$retOptSol <- FALSE
-    	ca$lpdir <- "max"
+    	ca[["retOptSol"]] <- FALSE
+    	ca[["lpdir"]] <- "max"
     	tmp <- do.call("optimizeProb", ca)
 #        tmp <- optimizeProb(model,
 #                            react = react, lb = lb, ub = ub,

inst/NEWS.Rd

@@ -6,7 +6,40 @@
 
 \newcommand{\CRANpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
 
+\section{Changes in version 2.0.3 2017-04-20}{
+  \itemize{
+  	\item The function \code{genrateWT} caused a problem when setting only \code{solverParm} and no solver.
+  }
+}
+% ---------------------------------------------------------------------------- %
 
+\section{Changes in version 2.0.2 2017-03-24}{
+  \itemize{
+  	\item The function \code{mod2irrev} crashed when using models with just one gene.
+  }
+}
+% ---------------------------------------------------------------------------- %
+\section{Changes in version 2.0.1 2016-07-05}{
+  \itemize{
+  	\item After \code{rmReact} the columns of \code{rxnGeneMat} and 
+  		\code{allGenes}-slot did not match.
+  	\item \code{upgradeModelorg} was not working correctly, when all gprRules
+  	are empty.
+  }
+}
+% ---------------------------------------------------------------------------- %
+\section{Changes in version 2.0.0 2016-05-17}{
+  \itemize{
+  	\item \code{modelorg}-class has changed and thus a slot \code{version} was introduced.
+  	the method \code{upgradeModelorg} can convert from earlier instances of this
+  	 class. This method is only needed if \code{modelorg}-Objects were loaded 
+  	 with \code{load} from disk. 
+    \item \code{gprRules} were stored in an impractical format. This lead to bugs
+    in \code{rmReact} and further \code{geneDel}.
+    \item updated the manual of various files.
+  }
+}
+% ---------------------------------------------------------------------------- %
 \section{Changes in version 1.3.4 2016-04-18}{
   \itemize{
     \item \code{doubleGeneDel} messed up the order of deletions when using exlicit gene lists.