diff --git a/DESCRIPTION b/DESCRIPTION index be7ca6b87212fcff4299e5b3f179543bb0bef44c..e83260ccff9825f98bd0b617dbcf640237cbf981 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,22 +1,22 @@ Package: sybilSBML Type: Package -Title: SBML Integration in Package Sybil -Version: 2.0.9 -Date: 2015-07-03 +Title: SBML Integration in Package 'Sybil' +Version: 2.0.11 +Date: 2016-06-06 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")), + person("Gabriel", "Gelius-Dietrich", role = c("aut", "ctb")), person("Deya", "Alzoubi", role = "ctb")) -Maintainer: Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de> -Depends: R (>= 2.14.2), Matrix, sybil (>= 1.2.4) +Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de> +Depends: R (>= 2.14.2), Matrix, sybil (>= 2.0.0) Imports: methods -Description: SBML (Systems Biology Markup Language) integration in sybil. Many constraint based metabolic models are published in SBML format (*.xml). Herewith is the ability to read and check SBML files in sybil provided. +Description: 'SBML' (Systems Biology Markup Language) integration in 'sybil'. Many constraint based metabolic models are published in 'SBML' format ('*.xml'). Herewith is the ability to read and check 'SBML' files in 'sybil' provided. License: GPL-3 | file LICENSE LazyLoad: yes Collate: generics.R sbmlPtrClass.R sbmlErrorClass.R sybilSBML.R uglyHack.R readSBMLmod.R zzz.R -Packaged: 2014-05-21 07:11:55 UTC; gabriel +Packaged: 2015-06-06 07:11:55 UTC; jonathan Author: C. Jonathan Fritzemeier [cre, ctb], - Gabriel Gelius-Dietrich [aut], + Gabriel Gelius-Dietrich [aut, ctb], Deya Alzoubi [ctb] NeedsCompilation: yes Repository: CRAN diff --git a/R/readSBMLmod.R b/R/readSBMLmod.R index e55f7e8c07e2759e14f30444077f963d099ebc87..fe1ebba72355814d7400f3cca3c6660803526007 100644 --- a/R/readSBMLmod.R +++ b/R/readSBMLmod.R @@ -897,13 +897,14 @@ else { if ( (length(genes[[i]] == 1)) && (genes[[i]] != "") ) { geneInd <- match(genes[[i]], allGenes) rxnGeneMat[i, geneInd] <- TRUE - - for (j in 1 : length(geneInd)) { - pat <- paste("x(", j, ")", sep = "") - repl <- paste("x[", geneInd[j], "]", sep = "") - - rules[i] <- gsub(pat, repl, rules[i], fixed = TRUE) - } + + # no use because new gprRule format +# for (j in 1 : length(geneInd)) { +# pat <- paste("x(", j, ")", sep = "") +# repl <- paste("x[", geneInd[j], "]", sep = "") +# +# rules[i] <- gsub(pat, repl, rules[i], fixed = TRUE) +# } } } diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd index 719fe82c674cbc6e5029696ed37fd7adcd7769f0..6f08e633b3cc7acf365879f5cd7a815bfa64fadf 100644 --- a/inst/NEWS.Rd +++ b/inst/NEWS.Rd @@ -6,6 +6,14 @@ \newcommand{\CRANpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}} +% ---------------------------------------------------------------------------- % +\section{Changes in version 2.0.11 2015-07-03}{ + \itemize{ + \item \code{gprRules}-Slot in \code{modelorg} has changed. Thus + \code{readSBMLmod} had to be updated. + } +} + % ---------------------------------------------------------------------------- % \section{Changes in version 2.0.9 2015-07-03}{ \itemize{