diff --git a/DESCRIPTION b/DESCRIPTION index 571f34d62b479f70a9bd12f4ec7e1f4ee0e3d56e..c138f323f364b420c935397e958c25ffdbc807b1 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 b968cef0681fa0c1586d0c0aad84375903bb3593..737bebc00403fc8df1f2fa6bd54bc8212dd43a82 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 cba15730edd648b9bb5754d2a34b1f88e945f307..d716d5da1082b61923ed360f871e5ce618201b05 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 3618af1db62558e595ebff43eebf966b7133a351..65e74da6d47450a0def6e9edb8d48a437a09bf45 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 0e19868e4b10f2c4961d658287e61832b8c029bd..4ddeacb919d4d63e2363c1a50ba2997f98a59168 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 081bc5a432bed65324561d7b625ee2c6f8757059..34065f209f010aa1553d1d96358af6e54f8868ed 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"}}