diff --git a/DESCRIPTION b/DESCRIPTION index 9aa324e719a4d579d4d39fdfac9f50ba7afc0791..1ea327271ab20571f46eef746538556cd0514256 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: sybil Type: Package Title: Efficient Constrained Based Modelling in R -Version: 2.1.0 -Date: 2017-07-21 +Version: 2.1.1 +Date: 2018-03-26 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")), @@ -12,7 +12,7 @@ Authors@R: c( person("Abdelmoneim", "Desouki", role = "ctb"), person(c("Martin", "J."), "Lercher", role = "ctb")) Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de> -Depends: R (>= 2.14.2), Matrix, lattice +Depends: R (>= 3.2.0), Matrix, lattice Imports: methods Suggests: glpkAPI (>= 1.2.8), cplexAPI (>= 1.2.4), clpAPI (>= 1.2.4), lpSolveAPI (>= 5.5.2.0), parallel, grid @@ -55,7 +55,7 @@ Collate: generics.R validmodelorg.R validoptsol.R validreactId.R validreact.R sysBiolAlg_mtfClass.R sysBiolAlg_mtfEasyConstraintClass.R sysBiolAlg_roomClass.R sybilLogClass.R upgradeModelorg.R mergeReact2Modelorg.R -Packaged: 2017-07-21 12:34:14 UTC; jonathan +Packaged: 2018-03-26 12:34:14 UTC; jonathan Author: C. Jonathan Fritzemeier [cre, ctb], Gabriel Gelius-Dietrich [aut], Rajen Piernikarczyk [ctb], diff --git a/R/addReact.R b/R/addReact.R index 915a5af624f8fa8a62d32441aa33a8aa1d4c13e6..0478d7af32613189fa777a6470d55c2dc1289cca 100644 --- a/R/addReact.R +++ b/R/addReact.R @@ -186,7 +186,7 @@ setMethod("addReact", signature(model = "modelorg"), newRows <- Matrix::Matrix(0, nrow = nNewRows, ncol = react_num(model)) - newS <- Matrix::rBind(newS, newRows) + newS <- rbind(newS, newRows) # new met attrs if(ncol(newMetAttr) > 0){ @@ -220,7 +220,7 @@ setMethod("addReact", signature(model = "modelorg"), newobj_coef <- append(obj_coef(model), obj) # new column in stoichiometric matrix - newS <- cBind(newS, rep(0, nrow(newS))) + newS <- cbind(newS, rep(0, nrow(newS))) # new react Attr # only one new row, /bc we can only add one reaction a time. @@ -236,23 +236,23 @@ setMethod("addReact", signature(model = "modelorg"), newsubSys <- ss } else { - newsubSys <- rBind(ss, rep(FALSE, ncol(subSys(model)))) + newsubSys <- rbind(ss, rep(FALSE, ncol(subSys(model)))) } } else { if (is(subSystem, "logical")) { - newsubSys <- rBind(subSys(model), subSystem) + newsubSys <- rbind(subSys(model), subSystem) } else { nSubsRow <- colnames(subSys(model)) %in% subSystem - newsubSys <- rBind(subSys(model), nSubsRow) + newsubSys <- rbind(subSys(model), nSubsRow) } } # gpr association if (ncol(rxnGeneMat(model)) > 0) { - newrxnGeneMat <- rBind(rxnGeneMat(model), + newrxnGeneMat <- rbind(rxnGeneMat(model), rep(FALSE, ncol(rxnGeneMat(model)))) } else { #if (nrow(rxnGeneMat(model)) > 0) { @@ -294,7 +294,7 @@ setMethod("addReact", signature(model = "modelorg"), } else { for (i in seq(along = gene_rule[["gene"]][new_gene])) { - newrxnGeneMat <- cBind(newrxnGeneMat, + newrxnGeneMat <- cbind(newrxnGeneMat, rep(FALSE, nrow(newrxnGeneMat))) } } diff --git a/R/doubleReact.R b/R/doubleReact.R index 69b6c5475746d00ae40b9943ebc9d0c977cb4d90..fbf56ab863d7d158ad3e4aa2cf4b2a18b90e920b 100644 --- a/R/doubleReact.R +++ b/R/doubleReact.R @@ -123,7 +123,7 @@ doubleReact <- function(model, checkRev = TRUE, linInd = FALSE) { # Put the columns of S into a new matrix, which contain the same # number of metabolites - Stmp <- cBind(S(model)[, columns[[i]] ]) + Stmp <- cbind(S(model)[, columns[[i]] ]) # translate Stmp into a matrix with the row indices of the # non zero elements diff --git a/R/sysBiolAlg_lmomaClass.R b/R/sysBiolAlg_lmomaClass.R index cba013b5e1402d942bf0ecc2028cec16840fb916..7d6944b1f809311edb07d70620344991cc56ab8c 100644 --- a/R/sysBiolAlg_lmomaClass.R +++ b/R/sysBiolAlg_lmomaClass.R @@ -154,7 +154,7 @@ setMethod(f = "initialize", sparse = TRUE) # the final contraint matrix - LHS <- rBind(LHSwt, LHS, crow) + LHS <- rbind(LHSwt, LHS, crow) subalg <- "lmoma_cobra" }