From 170918713135a6595ff3b1a77aadae996eca92a8 Mon Sep 17 00:00:00 2001
From: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@hhu.de>
Date: Tue, 17 Nov 2015 10:47:19 +0100
Subject: [PATCH] changes in namespace for cran submission
---
DESCRIPTION | 4 ++--
NAMESPACE | 4 ++++
R/fluxDistributionClass.R | 2 +-
R/optObj_cplexAPIClass.R | 2 +-
README.md | 2 +-
man/sysBiolAlg_fbaEasyConstraint-class.Rd | 1 +
6 files changed, 10 insertions(+), 5 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 571f34d..c138f32 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: sybil
Type: Package
Title: Efficient Constrained Based Modelling in R
Version: 1.3.2
-Date: 2015-10-21
+Date: 2015-11-16
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")),
@@ -53,7 +53,7 @@ Collate: generics.R validmodelorg.R validoptsol.R validreactId.R
sysBiolAlg_lmomaClass.R sysBiolAlg_momaClass.R
sysBiolAlg_mtfClass.R sysBiolAlg_mtfEasyConstraintClass.R
sysBiolAlg_roomClass.R sybilLogClass.R
-Packaged: 2014-11-19 20:39:37 UTC; gabriel
+Packaged: 2015-11-16 12:34:14 UTC; jonathan
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut],
Rajen Piernikarczyk [ctb],
diff --git a/NAMESPACE b/NAMESPACE
index b968cef..737bebc 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -4,6 +4,10 @@ import(methods)
import(Matrix)
import(lattice)
+importFrom("grDevices", "colorRampPalette", "grey")
+importFrom("graphics", "arrows", "hist", "points", "polygon", "segments")
+importFrom("utils", "combn", "edit", "read.table", "str", "write.table")
+
exportPattern("^[^\\.]")
exportClass(
diff --git a/R/fluxDistributionClass.R b/R/fluxDistributionClass.R
index cba1573..d716d5d 100644
--- a/R/fluxDistributionClass.R
+++ b/R/fluxDistributionClass.R
@@ -280,7 +280,7 @@ setMethod("plot", signature(x = "fluxDistribution", y = "missing"),
# x1 = c(2, 10, 10), y1 = c(5, 5, 1),
# default.units = "native")
- grid.points(5, 5, pch = 16, size=unit(5, "mm"))
+ grid::grid.points(5, 5, pch = 16, size=grid::unit(5, "mm"))
# default.units = "native")
panel.levelplot(...)
diff --git a/R/optObj_cplexAPIClass.R b/R/optObj_cplexAPIClass.R
index 3618af1..65e74da 100644
--- a/R/optObj_cplexAPIClass.R
+++ b/R/optObj_cplexAPIClass.R
@@ -518,7 +518,7 @@ setMethod("changeRowsBnds", signature(lp = "optObj_cplexAPI"),
if (sum(rng) > 0) {
rngv <- abs(ub[rng] - lb[rng])
- out <- chgRngValCPLEX(lp@oobj@env, lp@oobj@lp,
+ out <- cplexAPI::chgRngValCPLEX(lp@oobj@env, lp@oobj@lp,
sum(rng), i[rng]-1, rngv)
}
diff --git a/README.md b/README.md
index 0e19868..4ddeacb 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/web/packages/sybil/index.html).
+Alternatively you can visit the [CRAN pakage website](http://cran.r-project.org/package=sybil).
diff --git a/man/sysBiolAlg_fbaEasyConstraint-class.Rd b/man/sysBiolAlg_fbaEasyConstraint-class.Rd
index 081bc5a..34065f2 100644
--- a/man/sysBiolAlg_fbaEasyConstraint-class.Rd
+++ b/man/sysBiolAlg_fbaEasyConstraint-class.Rd
@@ -11,6 +11,7 @@
\alias{sysBiolAlg_mtfEasyConstraint}
\alias{mtfEasyConstraint}
\alias{fbaEasyConstraint}
+\alias{EasyConstraint}
\title{Class \code{"sysBiolAlg_fbaEasyConstraint"} and \cr Class \code{"sysBiolAlg_mtfEasyConstraint"}}
--
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