From 458aa6ed92ef9366fd1bfd2db3b1d6bcbe8da00e Mon Sep 17 00:00:00 2001
From: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@hhu.de>
Date: Tue, 20 Jun 2017 09:27:30 +0200
Subject: [PATCH] generateWT.R bug fix
---
DESCRIPTION | 8 ++++----
R/generateWT.R | 30 +++++++++++++++---------------
inst/NEWS.Rd | 33 +++++++++++++++++++++++++++++++++
3 files changed, 52 insertions(+), 19 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index bc93784..bc7a4d2 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 5281119..b63f54e 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 69f03dd..620fda7 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.
--
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