diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..32358936d0b933fa577bc062610396a386202048
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,5 @@
+# ignore pdf files
+*.pdf
+
+# ignore build r package:
+sybil_*.tar.gz
diff --git a/DESCRIPTION b/DESCRIPTION
new file mode 100644
index 0000000000000000000000000000000000000000..8321a8503b8cab429e4a5d868adcd58d0430fd43
--- /dev/null
+++ b/DESCRIPTION
@@ -0,0 +1,12 @@
+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>
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000000000000000000000000000000000000..9ec36d732677d97fb67344907a0c87860272cafc
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1,10 @@
+import(gurobi)
+importFrom("sybil", optObj)
+
+exportClass("optObj_sybilGUROBI")
+
+export(
+checkSolutionStatus,
+getReturnString,
+getStatusString
+)
diff --git a/R/compatibility.R b/R/compatibility.R
new file mode 100644
index 0000000000000000000000000000000000000000..bc604ea4be51730255cb39a7621dcbda79b4d4c2
--- /dev/null
+++ b/R/compatibility.R
@@ -0,0 +1,55 @@
+# 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)
+}
+
diff --git a/R/optObj_sybilGUROBIClass.R b/R/optObj_sybilGUROBIClass.R
new file mode 100644
index 0000000000000000000000000000000000000000..1be1a017fce6d3cec31665ece132b9ca7ef93acb
--- /dev/null
+++ b/R/optObj_sybilGUROBIClass.R
@@ -0,0 +1,659 @@
+# 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)
+ }
+)
+
+
+#------------------------------------------------------------------------------#
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/R/zzz.R b/R/zzz.R
new file mode 100644
index 0000000000000000000000000000000000000000..03405ff7292a6e44d4e7e9eb8f135aa2aeeb01e7
--- /dev/null
+++ b/R/zzz.R
@@ -0,0 +1,43 @@
+# 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"))
+# )
+
+}
+
+
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..c1eb4ba51b4bd5643aa6fff32aab627dacad8b09
--- /dev/null
+++ b/inst/NEWS.Rd
@@ -0,0 +1,51 @@
+%% 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
+ }
+}
+