changes in namespace for cran submission

DESCRIPTION

@@ -2,7 +2,7 @@ Package: sybil
 Type: Package
 Title: Efficient Constrained Based Modelling in R
 Version: 1.3.2
-Date: 2015-10-21
+Date: 2015-11-16
 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")),
@@ -53,7 +53,7 @@ Collate: generics.R validmodelorg.R validoptsol.R validreactId.R
         sysBiolAlg_lmomaClass.R sysBiolAlg_momaClass.R
         sysBiolAlg_mtfClass.R sysBiolAlg_mtfEasyConstraintClass.R
         sysBiolAlg_roomClass.R sybilLogClass.R
-Packaged: 2014-11-19 20:39:37 UTC; gabriel
+Packaged: 2015-11-16 12:34:14 UTC; jonathan
 Author: C. Jonathan Fritzemeier [cre, ctb],
   Gabriel Gelius-Dietrich [aut],
   Rajen Piernikarczyk [ctb],

NAMESPACE

@@ -4,6 +4,10 @@ import(methods)
 import(Matrix)
 import(lattice)
 
+importFrom("grDevices", "colorRampPalette", "grey")
+importFrom("graphics", "arrows", "hist", "points", "polygon", "segments")
+importFrom("utils", "combn", "edit", "read.table", "str", "write.table")
+
 exportPattern("^[^\\.]")
 
 exportClass(

R/fluxDistributionClass.R

@@ -280,7 +280,7 @@ setMethod("plot", signature(x = "fluxDistribution", y = "missing"),
 #                                          x1 = c(2, 10, 10), y1 = c(5, 5, 1),
 #                                          default.units = "native")
                             
-                            grid.points(5, 5, pch = 16, size=unit(5, "mm"))
+                            grid::grid.points(5, 5, pch = 16, size=grid::unit(5, "mm"))
 #                            default.units = "native")
                             
                             panel.levelplot(...)

R/optObj_cplexAPIClass.R

@@ -518,7 +518,7 @@ setMethod("changeRowsBnds", signature(lp = "optObj_cplexAPI"),
 
         if (sum(rng) > 0) {
             rngv <- abs(ub[rng] - lb[rng])
-            out  <- chgRngValCPLEX(lp@oobj@env, lp@oobj@lp,
+            out  <- cplexAPI::chgRngValCPLEX(lp@oobj@env, lp@oobj@lp,
                                    sum(rng), i[rng]-1, rngv)
         }
         

README.md

@@ -5,4 +5,4 @@ The package sybil is a Systems Biology Library for R, implementing algorithms fo
 Please consider downloading and installing the package via the R internal package management:
 `install.packages("sybil")`
 
-Alternatively you can visit the [CRAN pakage website](http://cran.r-project.org/web/packages/sybil/index.html).
+Alternatively you can visit the [CRAN pakage website](http://cran.r-project.org/package=sybil).

man/sysBiolAlg_fbaEasyConstraint-class.Rd

@@ -11,6 +11,7 @@
 \alias{sysBiolAlg_mtfEasyConstraint}
 \alias{mtfEasyConstraint}
 \alias{fbaEasyConstraint}
+\alias{EasyConstraint}
 
 \title{Class \code{"sysBiolAlg_fbaEasyConstraint"} and \cr Class \code{"sysBiolAlg_mtfEasyConstraint"}}