From 107c64a74dd30e1ba63e04693c3be737d5c91d16 Mon Sep 17 00:00:00 2001
From: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@hhu.de>
Date: Mon, 26 Mar 2018 14:16:15 +0200
Subject: [PATCH] replaced rBind and cBind with rbind and cbind
---
DESCRIPTION | 8 ++++----
R/addReact.R | 14 +++++++-------
R/doubleReact.R | 2 +-
R/sysBiolAlg_lmomaClass.R | 2 +-
4 files changed, 13 insertions(+), 13 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 9aa324e..1ea3272 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 915a5af..0478d7a 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 69b6c54..fbf56ab 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 cba013b..7d6944b 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"
}
--
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