initial commit of version 1.0.4

.gitignore

+# ignore pdf files
+*.pdf
+
+# ignore build r package:
+sybil_*.tar.gz

DESCRIPTION

+Package: sybilGUROBI
+Type: Package
+Title: Gurobi support for sybil
+Version: 1.0.4
+Date: 2013-07-23
+Authors@R: c(person("Gabriel", "Gelius-Dietrich", role = c("aut", "cre"), email = "geliudie@uni-duesseldorf.de"))
+Depends: R (>= 2.14.2), sybil (>= 1.2.2), gurobi, Matrix, methods
+Description: Gurobi support for sybil
+License: GPL-3
+Packaged: 2013-07-23 14:16:44 UTC; gabriel
+Author: Gabriel Gelius-Dietrich [aut, cre]
+Maintainer: Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>

NAMESPACE

+import(gurobi)
+importFrom("sybil", optObj)
+
+exportClass("optObj_sybilGUROBI")
+
+export(
+checkSolutionStatus,
+getReturnString,
+getStatusString
+)

R/compatibility.R

+#  compatibility.R
+#  Gurobi support for sybil.
+#
+#  Copyright (C) 2010-2013 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
+#  Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
+#  All right reserved.
+#  Email: geliudie@uni-duesseldorf.de
+#
+#  This file is part of sybilGUROBI.
+#
+#  SybilGUROBI is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  SybilGUROBI is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with sybilGUROBI.  If not, see <http://www.gnu.org/licenses/>.
+
+
+GRB_STATUS <- list(
+    "LOADED"          = 1,
+    "OPTIMAL"         = 2,
+    "INFEASIBLE"      = 3,
+    "INF_OR_UNBD"     = 4,
+    "UNBOUNDED"       = 5,
+    "CUTOFF"          = 6,
+    "ITERATION_LIMIT" = 7,
+    "NODE_LIMIT"      = 8,
+    "TIME_LIMIT"      = 9,
+    "SOLUTION_LIMIT"  = 10,
+    "INTERRUPTED"     = 11,
+    "NUMERIC"         = 12,
+    "SUBOPTIMAL"      = 13
+)
+
+checkSolutionStatus <- function(stat) {
+    out <- which(stat != 2)
+    return(out)
+}
+
+getReturnString <- function(code) {
+    out <- ifelse(code == 0, "ok", "not ok")
+    return(out)
+}
+
+getStatusString <- function(code) {
+    out <- names(GRB_STATUS)[code]
+    return(out)
+}
+

R/optObj_sybilGUROBIClass.R

+#  optObj_sybilGUROBIClass.R
+#  Gurobi support for sybil.
+#
+#  Copyright (C) 2010-2013 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
+#  Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
+#  All right reserved.
+#  Email: geliudie@uni-duesseldorf.de
+#
+#  This file is part of sybilGUROBI.
+#
+#  SybilGUROBI is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  SybilGUROBI is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with sybilGUROBI.  If not, see <http://www.gnu.org/licenses/>.
+
+
+#------------------------------------------------------------------------------#
+#               definition of the class optObj_sybilGUROBI                     #
+#------------------------------------------------------------------------------#
+
+setClass(Class = "optObj_sybilGUROBI",
+         representation(grb = "character"),
+         contains = "optObj")
+
+
+#------------------------------------------------------------------------------#
+#                                  methods                                     #
+#------------------------------------------------------------------------------#
+
+setMethod("delProb", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, ...) {
+
+        .GRBenv[[lp@grb]] <- NULL
+
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("initProb", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, to = FALSE, nrows = 0, ncols = 0) {
+
+        prob        <- vector(mode = "list", length = 8)
+        names(prob) <- c("A", "obj", "sense", "rhs", "lb", "ub",
+                         "modelsense", "modelname")
+
+        repeat{
+            pn <- paste(sample(letters, 7), collapse = "")
+            if ( (is.null(.GRBenv)) || (! pn %in% ls(.GRBenv)) ) {
+                break
+            }
+        }
+        
+        lp@grb <- pn
+
+        if (isTRUE(to)) {
+            toflag <- 1
+        }
+        else {
+            toflag <- 0
+        }
+
+        .GRBenv[[lp@grb]] <- list(lp   = prob,
+                                  parm = list(OutputFlag = toflag),
+                                  sol  = vector(mode = "list", length = 0))
+
+        .GRBenv[[lp@grb]][["lp"]][["A"]]           <- Matrix(0,
+                                                             nrow = nrows,
+                                                             ncol = ncols,
+                                                             sparse = TRUE)
+        .GRBenv[[lp@grb]][["lp"]][["obj"]]         <- numeric(ncols)
+        .GRBenv[[lp@grb]][["lp"]][["sense"]]       <- rep("=", nrows)
+        .GRBenv[[lp@grb]][["lp"]][["rhs"]]         <- numeric(nrows)
+        .GRBenv[[lp@grb]][["lp"]][["lb"]]          <- numeric(ncols)
+        .GRBenv[[lp@grb]][["lp"]][["ub"]]          <- numeric(ncols)
+        .GRBenv[[lp@grb]][["lp"]][["modelsense"]]  <- "min"
+        .GRBenv[[lp@grb]][["lp"]][["modelname"]]   <- lp@grb
+
+        return(lp)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("backupProb", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp) {
+
+        repeat{
+            pn <- paste(sample(letters, 7), collapse = "")
+            if ( (is.null(.GRBenv)) || (! pn %in% ls(.GRBenv)) ) {
+                break
+            }
+        }
+
+        out <- new("optObj_sybilGUROBI", lp@solver, lp@method, lp@probType)
+
+        out@grb <- pn
+
+        .GRBenv[[out@grb]] <- .GRBenv[[lp@grb]]
+
+        return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+
+setMethod("setSolverParm", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, solverParm) {
+
+        if ( ! ((is.data.frame(solverParm)) || (is.list(solverParm))) ) {
+            stop(sQuote(solverParm), " must be list or data.frame")
+        }
+
+        if (any(is.na(solverParm))) {
+            stop(sQuote(solverParm), " contains NA values")
+        }
+
+        pn <- names(solverParm)
+        for (i in seq(along = solverParm)) {
+            .GRBenv[[lp@grb]][["parm"]][[pn[i]]] <- solverParm[[pn[i]]]
+        }
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("getSolverParm", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp) {
+
+        out <- .GRBenv[[lp@grb]][["parm"]]
+
+        return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("setObjDir", signature(lp = "optObj_sybilGUROBI",
+                                 lpdir = "character"),
+
+    function(lp, lpdir) {
+
+        .GRBenv[[lp@grb]][["lp"]][["modelsense"]] <- ifelse(lpdir == "max",
+                                                               "max", "min")
+
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("getObjDir", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp) {
+
+        out <- .GRBenv[[lp@grb]][["lp"]][["modelsense"]]
+
+        return(out)
+
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("getNumRows", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp) {
+
+        out <- nrow(.GRBenv[[lp@grb]][["lp"]][["A"]])
+
+        return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("getNumCols", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp) {
+
+        out <- ncol(.GRBenv[[lp@grb]][["lp"]][["A"]])
+
+        return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("addRowsToProb", signature(lp = "optObj_sybilGUROBI"),
+
+    # i: vector containing the new row indices (must be ascending)
+    # cind: list, containing the column indices of the new nz elements
+    # nzval: list, containing the new nz elements
+    #
+    # i, type, lb, ub, cind and nzval must have the same length
+    #
+    # type can be one of the following:
+    # "F" = free variable                -INF <  x <  INF
+    # "L" = variable with lower bound      lb <= x <  INF
+    # "U" = variable with upper bound    -INF <  x <= ub
+    # "D" = double-bounded variable        lb <= x <= ub
+    # "E" = fixed variable                 lb  = x  = ub
+
+    function(lp, i, type, lb, ub, cind, nzval, rnames = NULL) {
+
+        stopifnot(length(lb) == length(ub))
+        ubc      <- type == "U"
+        clb      <- lb
+        clb[ubc] <- ub[ubc]
+        
+        nc  <- ncol(.GRBenv[[lp@grb]][["lp"]][["A"]])
+        nr  <- nrow(.GRBenv[[lp@grb]][["lp"]][["A"]])
+        mat <- Matrix(0, nrow = length(i), ncol = nc)
+        
+        .GRBenv[[lp@grb]][["lp"]][["A"]] <- rBind(
+                                       .GRBenv[[lp@grb]][["lp"]][["A"]], mat)
+
+        .GRBenv[[lp@grb]][["lp"]][["rhs"]] <- append(
+                      .GRBenv[[lp@grb]][["lp"]][["rhs"]], numeric(length(i)))
+
+        .GRBenv[[lp@grb]][["lp"]][["sense"]] <- append(
+                   .GRBenv[[lp@grb]][["lp"]][["sense"]], rep("=", length(i)))
+
+        
+        for (k in seq(along = i)) {
+            ltype <- switch(type[k],
+                            "L" = { ">=" },
+                            "U" = { "<=" },
+                            "E" = { "=" },
+                                  { "=" }
+            )
+
+            .GRBenv[[lp@grb]][["lp"]][["A"]][(nr+k), cind[[k]]] <- nzval[[k]]
+    
+            .GRBenv[[lp@grb]][["lp"]][["rhs"]][(nr+k)] <- clb[k]
+    
+            .GRBenv[[lp@grb]][["lp"]][["sense"]][(nr+k)] <- ltype
+        }
+
+
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("changeColsBnds", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, j, lb, ub) {
+
+        .GRBenv[[lp@grb]][["lp"]][["lb"]][j] <- lb
+        .GRBenv[[lp@grb]][["lp"]][["ub"]][j] <- ub
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("changeColsBndsObjCoefs", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, j, lb, ub, obj_coef) {
+
+        .GRBenv[[lp@grb]][["lp"]][["lb"]][j]  <- lb
+        .GRBenv[[lp@grb]][["lp"]][["ub"]][j]  <- ub
+        .GRBenv[[lp@grb]][["lp"]][["obj"]][j] <- obj_coef
+
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("getColsLowBnds", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, j) {
+
+        out <- .GRBenv[[lp@grb]][["lp"]][["lb"]][j]
+
+        return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("getColsUppBnds", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, j) {
+
+        out <- .GRBenv[[lp@grb]][["lp"]][["ub"]][j]
+
+        return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("changeRowsBnds", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, i, lb, ub) {
+
+        ubc      <- .GRBenv[[lp@grb]][["lp"]][["sense"]][i] == "<="
+        clb      <- lb
+        clb[ubc] <- ub[ubc]
+
+        .GRBenv[[lp@grb]][["lp"]][["rhs"]][i] <- clb
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("setRhsZero", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp) {
+
+        nr  <- nrow(.GRBenv[[lp@grb]][["lp"]][["A"]])
+        .GRBenv[[lp@grb]][["lp"]][["rhs"]]   <- rep(0, nr)
+        .GRBenv[[lp@grb]][["lp"]][["sense"]] <- rep("=", nr)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("changeObjCoefs", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, j, obj_coef) {
+
+        .GRBenv[[lp@grb]][["lp"]][["obj"]][j] <- obj_coef
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("getObjCoefs", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, j) {
+
+        out <- .GRBenv[[lp@grb]][["lp"]][["obj"]][j]
+
+        return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("changeMatrixRow", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, i, j, val) {
+
+        .GRBenv[[lp@grb]][["lp"]][["A"]][i, j] <- val
+
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("loadLPprob", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, nCols, nRows, mat, ub, lb, obj, rlb, rtype,
+             lpdir = "max", rub = NULL, ctype = NULL,
+             cnames = NULL, rnames = NULL, pname = NULL) {
+
+        stopifnot(is(mat, "Matrix"))
+
+        crtype <- sapply(rtype,
+                         function(x) switch(x,
+                                            "L" = { ">=" },
+                                            "U" = { "<=" },
+                                            "E" = { "="  },
+                                                  { "="  }))
+
+        # optimization direction
+        setObjDir(lp, lpdir = lpdir)
+        
+        # constraint matrix
+        .GRBenv[[lp@grb]][["lp"]][["A"]] <- as(mat, "CsparseMatrix")
+
+        # column (variable) bounds and objective function
+        .GRBenv[[lp@grb]][["lp"]][["lb"]]  <- lb
+        .GRBenv[[lp@grb]][["lp"]][["ub"]]  <- ub
+        .GRBenv[[lp@grb]][["lp"]][["obj"]] <- obj
+
+        # variable type
+        .GRBenv[[lp@grb]][["lp"]][["vtypes"]] <- ctype
+
+        # right hand side
+        if (is.null(rub)) {
+            crlb      <- rlb
+        }
+        else {
+            ubc       <- rtype == "U"
+            crlb      <- rlb
+            crlb[ubc] <- rub[ubc]
+        }
+        
+        .GRBenv[[lp@grb]][["lp"]][["sense"]] <- crtype
+        .GRBenv[[lp@grb]][["lp"]][["rhs"]]   <- crlb
+
+        # problem name
+        if (!is.null(pname)) {
+            .GRBenv[[lp@grb]][["lp"]][["modelname"]] <- pname
+        }
+
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("loadQobj", signature(lp = "optObj_sybilGUROBI", mat = "Matrix"),
+
+    function(lp, mat) {
+
+        .GRBenv[[lp@grb]][["lp"]][["Q"]] <- as(mat, "CsparseMatrix")
+
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("loadQobj", signature(lp = "optObj_sybilGUROBI", mat = "numeric"),
+
+    function(lp, mat) {
+
+        dmat <- Matrix::Diagonal(length(mat), mat)
+
+        .GRBenv[[lp@grb]][["lp"]][["Q"]] <- as(dmat, "CsparseMatrix")
+
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("scaleProb", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, opt) {
+
+        .GRBenv[[lp@grb]][["parm"]][["ScaleFlag"]] <- opt
+
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("solveLp", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp) {
+
+        if (length(.GRBenv[[lp@grb]][["parm"]]) > 0) {
+            gp <- .GRBenv[[lp@grb]][["parm"]]
+        }
+        else {
+            gp <- NULL
+        }
+
+        .GRBenv[[lp@grb]][["sol"]] <- gurobi::gurobi(.GRBenv[[lp@grb]][["lp"]],gp)
+
+        .GRBenv[[lp@grb]][["sol"]][["status"]] <- GRB_STATUS[[.GRBenv[[lp@grb]][["sol"]][["status"]]]]
+                
+        if (is.null(.GRBenv[[lp@grb]][["sol"]][["objval"]])) {
+            out <- 1
+            .GRBenv[[lp@grb]][["sol"]][["objval"]] <- 0
+        }
+        else {
+            out <- 0
+        }
+        
+#        if (!is.null(.GRBenv[[lp@grb]][["lp"]][["advStartSet"]])) {
+            if (!is.null(.GRBenv[[lp@grb]][["sol"]][["vbasis"]])) {
+                .GRBenv[[lp@grb]][["lp"]][["vbasis"]] <- .GRBenv[[lp@grb]][["sol"]][["vbasis"]]
+            }
+            if (!is.null(.GRBenv[[lp@grb]][["sol"]][["cbasis"]])) {
+                .GRBenv[[lp@grb]][["lp"]][["cbasis"]] <- .GRBenv[[lp@grb]][["sol"]][["cbasis"]]
+            }
+#            .GRBenv[[lp@grb]][["lp"]][["advStartSet"]] <- TRUE
+#        }
+
+        return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("getObjVal", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp) {
+
+        out <- .GRBenv[[lp@grb]][["sol"]][["objval"]]
+
+        return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("getRedCosts", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp) {
+
+        out <- .GRBenv[[lp@grb]][["sol"]][["rc"]]
+
+        return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("getSolStat", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp) {
+
+        out <- .GRBenv[[lp@grb]][["sol"]][["status"]]
+
+        return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("getFluxDist", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp) {
+
+        fld <- .GRBenv[[lp@grb]][["sol"]][["x"]]
+        if (is.null(fld)) {
+            out <- rep(0, getNumCols(lp))
+        }
+        else {
+            out <- fld
+        }
+
+        return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("getColPrim", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, j) {
+
+        out <- .GRBenv[[lp@grb]][["sol"]][["x"]][j]
+
+        return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("getNumNnz", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp) {
+
+        out <- nnzero(.GRBenv[[lp@grb]][["lp"]][["A"]])
+
+        return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+setMethod("writeProb", signature(lp = "optObj_sybilGUROBI"),
+
+    function(lp, fname, ff = "lp") {
+
+        if (length(.GRBenv[[lp@grb]][["parm"]]) > 0) {
+            gp <- .GRBenv[[lp@grb]][["parm"]]
+        }
+        else {
+            gp <- vector(mode = "list", length = 0)
+
+        }
+
+        if (grepl(".", fname, fixed = TRUE)) {
+            fn <- fname
+        }
+        else {
+            fn <- paste(fname, ff, sep = ".")
+        }
+
+        gp[["ResultFile"]] <- fn
+        gurobi::gurobi(.GRBenv[[lp@grb]][["lp"]], gp)
+
+
+        return(TRUE)
+
+
+        #out <- save(.GRBenv[[lp@grb]][["lp"]], file = fname)
+
+        #return(out)
+    }
+)
+
+
+#------------------------------------------------------------------------------#
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

R/zzz.R

+#  zzz.R
+#  Gurobi support for sybil.
+#
+#  Copyright (C) 2010-2013 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
+#  Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
+#  All right reserved.
+#  Email: geliudie@uni-duesseldorf.de
+#
+#  This file is part of sybilGUROBI.
+#
+#  SybilGUROBI is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  SybilGUROBI is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with sybilGUROBI.  If not, see <http://www.gnu.org/licenses/>.
+
+
+.GRBenv <- new.env()
+
+.onAttach <- function(lib, pkg) {
+
+    sybil::addSolver(solver = "sybilGUROBI",
+                     method = "gurobi",
+                     probType = list(c("lp", "mip", "qp")))
+    
+#    SYBIL_SETTINGS("SOLVER_CTRL_PARM",
+#                   list(OutputFlag = 0,
+#                   # i can not get rid of the logfile completely, so I put
+#                   # it to temp; an initial logfile will still be written
+#                   # into the working directory
+#                   LogFile = tempfile(pattern = "gurobi", fileext = ".log"))
+#                   )
+    
+}
+
+

inst/NEWS.Rd

+%% sybilGUROBI Version History
+
+\name{NEWS}
+\title{sybilGUROBI News}
+\encoding{UTF-8}
+
+\newcommand{\CRANpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
+
+% ---------------------------------------------------------------------------- %
+\section{Changes in version 1.0.4 2013-07-23}{
+  \itemize{
+    \item compatibility update to sybil version 1.2.2
+    \item method \code{writeProb} makes use of paramter \code{ResultFile}
+  }
+}
+
+
+% ---------------------------------------------------------------------------- %
+\section{Changes in version 1.0.3 2013-05-31}{
+  \itemize{
+    \item compatibility update to sybil version 1.2.0
+    \item uses advanced starting point for the simplex algorithm when
+          running series of optimizations
+  }
+}
+
+
+% ---------------------------------------------------------------------------- %
+\section{Changes in version 1.0.2 2013-02-18}{
+  \itemize{
+    \item added argument \code{to} to method \code{initProb}, enabling or
+          disabling output to the terminal by Gurobi
+  }
+}
+
+
+% ---------------------------------------------------------------------------- %
+\section{Changes in version 1.0.1 2013-01-08}{
+  \itemize{
+    \item compatibility update to sybil version 1.1.10
+  }
+}
+
+
+% ---------------------------------------------------------------------------- %
+\section{Changes in version 1.0.0 2012-07-27}{
+  \itemize{
+    \item initial release
+  }
+}
+