From 69dc3fd2852e358ff6fca3a83f68a7e17c732bdb Mon Sep 17 00:00:00 2001
From: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@hhu.de>
Date: Fri, 22 Jun 2018 12:54:00 +0200
Subject: [PATCH] corrections for cran submission
---
DESCRIPTION | 4 +-
R/mergeReact2Modelorg.R | 2 +-
R/reactClass.R | 52 +++++++++----------
README.md | 2 +-
inst/NEWS.Rd | 12 ++++-
man/addReact.Rd | 20 ++++++--
man/modelorg-class.Rd | 88 ++++++++++++++++++++++++++++++++
man/optsol_blockedReact-class.Rd | 1 -
man/printReaction-methods.Rd | 5 ++
9 files changed, 148 insertions(+), 38 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 1ea3272..d84c1c9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: sybil
Type: Package
Title: Efficient Constrained Based Modelling in R
Version: 2.1.1
-Date: 2018-03-26
+Date: 2018-05-14
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")),
@@ -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: 2018-03-26 12:34:14 UTC; jonathan
+Packaged: 2018-05-14 12:34:14 UTC; jonathan
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut],
Rajen Piernikarczyk [ctb],
diff --git a/R/mergeReact2Modelorg.R b/R/mergeReact2Modelorg.R
index 2f4f586..0c7cb3a 100644
--- a/R/mergeReact2Modelorg.R
+++ b/R/mergeReact2Modelorg.R
@@ -35,7 +35,7 @@
#------------------------------------------------------------------------------#
-# definition of the class mergeReact2Modelorg #
+# definition of the function mergeReact2Modelorg #
#------------------------------------------------------------------------------#
diff --git a/R/reactClass.R b/R/reactClass.R
index 029bf1a..29ac5e8 100644
--- a/R/reactClass.R
+++ b/R/reactClass.R
@@ -438,36 +438,34 @@ setMethod("printReaction", signature(object = "react"),
mat <- s(object)
reaction <- character(1)
- for (j in seq(along = cind)) {
- met <- met_id(object)
- nzv <- mat
-
- ed <- nzv < 0
- pd <- nzv > 0
-
- if (sum(ed) > 0) {
- educt <- paste(paste("(", abs(nzv[ed]), ")", sep = ""),
- met[ed], collapse = " + ")
- }
- else {
- educt = ""
- }
-
- if (sum(pd) > 0) {
- product <- paste(paste("(", nzv[pd], ")", sep = ""),
- met[pd], collapse = " + ")
- }
- else {
- product = ""
- }
-
- arrow <- ifelse(react_rev(object)[cind[j]], " <==> ", " --> ")
-
- reaction[j] <- paste(react_id(check)[j],
- paste(educt, product, sep = arrow), sep = "\t")
+ met <- met_id(object)
+ nzv <- mat
+
+ ed <- nzv < 0
+ pd <- nzv > 0
+
+ if (sum(ed) > 0) {
+ educt <- paste(paste("(", abs(nzv[ed]), ")", sep = ""),
+ met[ed], collapse = " + ")
+ }
+ else {
+ educt = ""
}
+ if (sum(pd) > 0) {
+ product <- paste(paste("(", nzv[pd], ")", sep = ""),
+ met[pd], collapse = " + ")
+ }
+ else {
+ product = ""
+ }
+
+ arrow <- ifelse(react_rev(object), " <==> ", " --> ")
+
+ reaction <- paste(react_id(object),
+ paste(educt, product, sep = arrow), sep = "\t")
+
if (isTRUE(printOut)) {
cat("abbreviation\tequation", reaction, sep = "\n", ...)
}
diff --git a/README.md b/README.md
index 4ddeacb..105f078 100644
--- a/README.md
+++ b/README.md
@@ -5,4 +5,4 @@ The package sybil is a Systems Biology Library for R, implementing algorithms fo
Please consider downloading and installing the package via the R internal package management:
`install.packages("sybil")`
-Alternatively you can visit the [CRAN pakage website](http://cran.r-project.org/package=sybil).
+Alternatively you can visit the [CRAN pakage website](https://cran.r-project.org/package=sybil).
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index a841bbc..a6c0a7e 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -4,7 +4,17 @@
\title{sybil News}
\encoding{UTF-8}
-\newcommand{\CRANpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
+\newcommand{\CRANpkg}{\href{https://CRAN.R-project.org/package=#1}{\pkg{#1}}}
+
+\section{Changes in version 2.1.1 2018-07-17}{
+ \itemize{
+ \item Package sybilSBML gets rejected on CRAN, but can be downloaded
+ at \url{http://www.cs.hhu.de/en/research-groups/computational-cell-biology/software.html}.
+ \item Documentation for \code{react-class} and related methods.
+ \
+ }
+}
+% ---------------------------------------------------------------------------- %
\section{Changes in version 2.1.0 2017-07-17}{
\itemize{
diff --git a/man/addReact.Rd b/man/addReact.Rd
index 2470300..597e078 100644
--- a/man/addReact.Rd
+++ b/man/addReact.Rd
@@ -1,8 +1,12 @@
-\name{addReact}
-\alias{addReact}
-
+\name{addReact,modelorg-method}
+\docType{methods}
\encoding{utf8}
+
+\alias{addReact}
+\alias{addReact,modelorg-method}
+\alias{addReact,modelorg,ANY-method}
+
\title{
Add/Change Reactions in a Model
}
@@ -11,9 +15,15 @@
The function \code{addReact} adds one reaction to a metabolic model, or
changes one reaction in a metabolic model.
}
-
+\section{Methods}{
+ \describe{
+ \item{\code{addReact}:}{
+ \code{signature(object = "modelorg")}: adds a new reaction to a \code{modelorg} object.
+ }
+ }
+}
\usage{
- addReact(model,
+\S4method{addReact}{modelorg}(model,
id,
met,
Scoef,
diff --git a/man/modelorg-class.Rd b/man/modelorg-class.Rd
index dfeb47d..ad83d5f 100644
--- a/man/modelorg-class.Rd
+++ b/man/modelorg-class.Rd
@@ -139,6 +139,90 @@
\alias{version<-}
\alias{version}
+\alias{react-class}
+\alias{react}
+\alias{comp_attr,react-method}
+\alias{comp_attr}
+\alias{comp_attr<-,react-method}
+\alias{comp_attr<-}
+\alias{genes,react-method}
+\alias{genes}
+\alias{genes<-,react-method}
+\alias{genes<-}
+\alias{gpr,react-method}
+\alias{gpr}
+\alias{gpr<-,react-method}
+\alias{gpr<-}
+\alias{gprRule,react-method}
+\alias{gprRule}
+\alias{gprRule<-,react-method}
+\alias{gprRule<-}
+\alias{lowbnd,react-method}
+\alias{lowbnd}
+\alias{lowbnd<-,react-method}
+\alias{lowbnd<-}
+\alias{met_attr,react-method}
+\alias{met_attr}
+\alias{met_attr<-,react-method}
+\alias{met_attr<-}
+\alias{met_comp,react-method}
+\alias{met_comp}
+\alias{met_comp<-,react-method}
+\alias{met_comp<-}
+\alias{met_id,react-method}
+\alias{met_id}
+\alias{met_id<-,react-method}
+\alias{met_id<-}
+\alias{met_name,react-method}
+\alias{met_name}
+\alias{met_name<-,react-method}
+\alias{met_name<-}
+\alias{mod_attr,react-method}
+\alias{mod_attr}
+\alias{mod_attr<-,react-method}
+\alias{mod_attr<-}
+\alias{obj_coef,react-method}
+\alias{obj_coef}
+\alias{obj_coef<-,react-method}
+\alias{obj_coef<-}
+\alias{react_attr,react-method}
+\alias{react_attr}
+\alias{react_attr<-,react-method}
+\alias{react_attr<-}
+\alias{react_de,react-method}
+\alias{react_de}
+\alias{react_de<-,react-method}
+\alias{react_de<-}
+\alias{react_id,react-method}
+\alias{react_id}
+\alias{react_id<-,react-method}
+\alias{react_id<-}
+\alias{react_name,react-method}
+\alias{react_name}
+\alias{react_name<-,react-method}
+\alias{react_name<-}
+\alias{react_rev,react-method}
+\alias{react_rev}
+\alias{react_rev<-,react-method}
+\alias{react_rev<-}
+\alias{react_single,react-method}
+\alias{react_single}
+\alias{react_single<-,react-method}
+\alias{react_single<-}
+\alias{s,react-method}
+\alias{s}
+\alias{s<-,react-method}
+\alias{s<-}
+\alias{subSys,react-method}
+\alias{subSys}
+\alias{subSys<-,react-method}
+\alias{subSys<-}
+\alias{uppbnd,react-method}
+\alias{uppbnd}
+\alias{uppbnd<-,react-method}
+\alias{uppbnd<-}
+
+
\encoding{utf8}
\title{Structure of Class "modelorg"}
@@ -146,6 +230,10 @@
\description{
Structure of the class \code{"modelorg"}. Objects of that class are
returned by functions like \code{\link{readTSVmod}}.
+
+ Structure of the class \code{"react"}. This depicts a subset of a metabolic model
+ that contains only one reaction. Multiple \code{react} objects can be combined to an
+ \code{"modelorg"} object.
}
\section{Objects from the Class}{
diff --git a/man/optsol_blockedReact-class.Rd b/man/optsol_blockedReact-class.Rd
index 4f0450b..2a611e2 100644
--- a/man/optsol_blockedReact-class.Rd
+++ b/man/optsol_blockedReact-class.Rd
@@ -11,7 +11,6 @@
\alias{blocked<-}
\alias{react,optsol_blockedReact-method}
\alias{react<-,optsol_blockedReact-method}
-\alias{react}
\alias{react<-}
\alias{maxSol,optsol_blockedReact-method}
\alias{minSol,optsol_blockedReact-method}
diff --git a/man/printReaction-methods.Rd b/man/printReaction-methods.Rd
index 715779a..e4e1880 100644
--- a/man/printReaction-methods.Rd
+++ b/man/printReaction-methods.Rd
@@ -7,6 +7,7 @@
\alias{printReaction-methods}
\alias{printReaction,modelorg,ANY-method}
\alias{printReaction,summaryOptsol,modelorg-method}
+\alias{printReaction,react,ANY-method}
\title{Print Columns of the Stoichiometric Matrix}
@@ -17,6 +18,7 @@
\usage{
\S4method{printReaction}{modelorg,ANY}(object, react, printOut = TRUE, ...)
\S4method{printReaction}{summaryOptsol,modelorg}(object, mod, j, ...)
+\S4method{printReaction}{react,ANY}(object, printOut = TRUE, ...)
}
\section{Methods}{
@@ -27,6 +29,9 @@
\item{\code{signature(object = "summaryOptsol", mod = "modelorg")}}{
method to use with objects of class \code{\linkS4class{summaryOptsol}}.
}
+ \item{\code{signature(object = "react", ...)}}{
+ method to use with objects of class \code{\linkS4class{react}}.
+ }
}
}
--
GitLab