diff --git a/DESCRIPTION b/DESCRIPTION index bc9378415e2a4755981a70877eb2d2f264014e2c..bc7a4d2cf6e6ef3da728e4f944db641d2809569d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ 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], diff --git a/R/generateWT.R b/R/generateWT.R index 52811193a2e350977bf663f2863b411183958e2c..b63f54e62ba9242cdeac585d1fc5b4eb4a72ed87 100644 --- a/R/generateWT.R +++ b/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, diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd index 69f03dd906a17cee7b2801898d84310f34375cdd..620fda7b99bb7570c3023c66807944a182c6c2e9 100644 --- a/inst/NEWS.Rd +++ b/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.