diff --git a/DESCRIPTION b/DESCRIPTION
index 5c434284fd9ec74697cd5c77a25ccb41db2e7d9e..112c110518cd7fa748330debbb03b4ccb360962e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: sybil
Type: Package
Title: Efficient Constrained Based Modelling
-Version: 2.1.5
-Date: 2019-03-07
+Version: 2.2.0
+Date: 2021-05-31
Authors@R: c(
person("Mayo", "Roettger", role = c("cre"), email = "mayo.roettger@hhu.de"),
person("Gabriel", "Gelius-Dietrich", role = "aut"),
@@ -18,7 +18,7 @@ Imports: methods
Suggests: glpkAPI (>= 1.2.8), cplexAPI (>= 1.2.4), clpAPI (>= 1.2.4),
lpSolveAPI (>= 5.5.2.0), parallel, grid
URL:
- http://www.cs.hhu.de/lehrstuehle-und-arbeitsgruppen/computational-cell-biology/software/sybil.html
+ https://www.cs.hhu.de/lehrstuehle-und-arbeitsgruppen/computational-cell-biology/software-contributions/sybil
Description: This Systems Biology Package (Gelius-Dietrich et. al. (2012) <doi:10.1186/1752-0509-7-125>) implements algorithms for constraint based analyses of metabolic networks, e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis. The package is easily extendable for additional algorithms. Most of the current LP/MILP solvers are supported via additional packages.
LazyLoad: yes
License: GPL-3 | file LICENSE
@@ -56,7 +56,7 @@ 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: 2019-03-07 10:20:00 UTC; mayo
+Packaged: 2021-05-31 10:32:00 UTC; mayo
Author: Mayo Roettger [cre],
Gabriel Gelius-Dietrich [aut],
C. Jonathan Fritzemeier [ctb],
diff --git a/R/modelorg2ExPA.R b/R/modelorg2ExPA.R
index 53f0c6b22709425c6b5180ca9da401ba979293e9..9afaf6892b55592f29e758c6bde7ba5b16ce16c3 100644
--- a/R/modelorg2ExPA.R
+++ b/R/modelorg2ExPA.R
@@ -37,8 +37,6 @@ modelorg2ExPA <- function(model,
filepath = ".",
suffix = "expa",
tol = SYBIL_SETTINGS("TOLERANCE")) {
-
- on.exit( closeAllConnections() )
if (!is(model, "modelorg")) {
stop("needs an object of class modelorg!")
@@ -57,8 +55,9 @@ modelorg2ExPA <- function(model,
fh <- try(file(tofile, "wt"), silent = TRUE)
if (is(fh, "try-error")) {
- warning("cannot write ExPA file!")
- fh <- FALSE
+ stop("cannot write ExPA file ", sQuote(fh))
+ } else {
+ on.exit(close(fh))
}
# exclude reactions
@@ -171,12 +170,6 @@ modelorg2ExPA <- function(model,
}
- # ------------------------------------------------------------------------ #
-
- if (is(fh, "file")) {
- close(fh)
- }
-
#--------------------------------------------------------------------------#
# end
#--------------------------------------------------------------------------#
diff --git a/R/modelorg2tsv.R b/R/modelorg2tsv.R
index e266531b0ee13367f5e40e55799e73c4705af5fa..cc4e11251b2d42b0cb9eaf8f2f25cb4e9bff5dc4 100644
--- a/R/modelorg2tsv.R
+++ b/R/modelorg2tsv.R
@@ -36,7 +36,6 @@ modelorg2tsv <- function(model, prefix, suffix, extMetFlag = "b",
fpath = SYBIL_SETTINGS("PATH_TO_MODEL"),
...) {
- ## on.exit( closeAllConnections() )
if (!is(model, "modelorg")) {
stop("needs an object of class modelorg!")
diff --git a/R/optObj_clpAPIClass.R b/R/optObj_clpAPIClass.R
index be6050b2be0c2578b0740799a996b8c2bac646b0..0561d0f42638756331f12946adeffc8c9532537f 100644
--- a/R/optObj_clpAPIClass.R
+++ b/R/optObj_clpAPIClass.R
@@ -107,25 +107,45 @@ setMethod("backupProb", signature(lp = "optObj_clpAPI"),
setMethod("setSolverParm", signature(lp = "optObj_clpAPI"),
function(lp, solverParm) {
+ # at the moment, only parameters 'numberIterations', 'maximumIterations',
+ # and 'maximumSeconds' can be set by this function. In clpAPI,
+ # these are actually set by three individual functions. In order to
+ # stay similar to e.g. cplexAPI, we also use the setSolverParm method
+ # for clpAPI in sybil.
+ out <- NULL
+
+ if ( ! ((is.data.frame(solverParm)) || (is.list(solverParm))) ) {
+ stop(sQuote(solverParm), " must be list or data.frame")
+ }
- out <- FALSE
-
- wrong_solver_msg(lp, "setSolverParm")
-
-# if ( ! ((is.data.frame(solverParm)) || (is.list(solverParm))) ) {
-# stop(sQuote(solverParm), " must be list or data.frame")
-# }
-#
-# if (any(is.na(solverParm))) {
-# stop(sQuote(solverParm), " contains NA values")
-# }
+ if (any(is.na(solverParm))) {
+ stop(sQuote(solverParm), " contains NA values")
+ }
- # no parameters in COIN-OR CLP yet.
- # lp@oobj <- clpAPI::initProbCLP()
- # clpAPI::setLogLevelCLP(lp@oobj, 0)
+ numericParm <- sapply(solverParm, is.numeric)
+ num <- solverParm[numericParm]
+ if (length(num) != length(solverParm)) {
+ stop(sQuote(solverParm), " contains non numeric values")
+ }
+
+ if (length(num) > 0) {
+ # get parameter names:
+ numericp <- names(num)
+
+ for (i in seq(along = num)) {
+ if (numericp[i] == "numberIterations") {
+ out <- clpAPI::setNumberIterationsCLP(lp@oobj, num[["numberIterations"]])
+ } else if (numericp[i] == "maximumIterations") {
+ out <- clpAPI::setMaximumIterationsCLP(lp@oobj, num[["maximumIterations"]])
+ } else if (numericp[i] == "maximumSeconds") {
+ out <- clpAPI::setMaximumSecondsCLP(lp@oobj, num[["maximumSeconds"]])
+ } else {
+ stop(sQuote("solverParm"), " contains unknown parameter ", sQuote(numericp))
+ }
+ }
+ }
return(out)
-
}
)
@@ -138,9 +158,14 @@ setMethod("getSolverParm", signature(lp = "optObj_clpAPI"),
out <- FALSE
- wrong_solver_msg(lp, "getSolverParm")
-
+ out <- list(
+ "hitMaximumIterations" = clpAPI::getHitMaximumIterationsCLP(lp@oobj),
+ "maximumIterations" = clpAPI::getMaximumIterationsCLP(lp@oobj),
+ "maximumSeconds" = clpAPI::getMaximumSecondsCLP(lp@oobj)
+ )
+
return(out)
+
}
)
diff --git a/R/optObj_cplexAPIClass.R b/R/optObj_cplexAPIClass.R
index 4a0a22ba26fc7ef6104722298ed01feaa5634aae..f596696c921bd8768e6f8f4ac9864a78b533fbe5 100644
--- a/R/optObj_cplexAPIClass.R
+++ b/R/optObj_cplexAPIClass.R
@@ -124,8 +124,11 @@ setMethod("setSolverParm", signature(lp = "optObj_cplexAPI"),
intdbl <- sapply(solverParm, is.integer)
strparm <- sapply(solverParm, is.numeric)
+ # parameters of type integer:
int <- solverParm[intdbl]
+ # parameters of type double:
dbl <- solverParm[intdbl == FALSE & strparm == TRUE]
+ # parameters of type character:
char <- solverParm[strparm == FALSE]
if (length(int) > 0) {
@@ -137,6 +140,7 @@ setMethod("setSolverParm", signature(lp = "optObj_cplexAPI"),
}
if (length(dbl) > 0) {
+ # get
dblp <- sapply(names(dbl), function(x) eval(parse(text = x)))
dblv <- unlist(dbl)
for (i in seq(along = dbl)) {
diff --git a/R/parseBoolean.R b/R/parseBoolean.R
index 4546b26b778bcd49ff2c08ff4d31cb58a54af7bd..09a9658564d4e5ecbd20c3280d6f535df484682f 100644
--- a/R/parseBoolean.R
+++ b/R/parseBoolean.R
@@ -84,13 +84,17 @@
# number of entries
num_genes <- length(genes)
-
+
+
+ # vector with unique gene numbers like "x[1]", "x[2]", "x[1]", ...
+
# a unique vector with all genes
gene_uniq <- unique(genes)
-
+
newTok <- match(genes, gene_uniq)
newTok <- sapply(newTok, function(x) paste("x[", x, "]", sep = ""))
+
# rule <-
#bla <- rbind(genes, newTok)
@@ -98,8 +102,9 @@
#rule <- apply(bla, 2, function(x) gsub(x[1], x[2], rule, fixed = TRUE))
#apply(bla, 1, function(x) print(x[1]))
- for (i in 1:num_genes) {
+ # replace gene names in rule by their newTok string (which is x[gene_number]):
+ for (i in 1:num_genes) {
rule <- sub(genes[i], newTok[i], rule, fixed = TRUE)
#start <- gregexpr(genes[i], gpr, fixed = TRUE)
#start <- start[[1]]
@@ -208,6 +213,8 @@
# gene = "bla"
# rule = "blubber"
+
+ # return vector with unique gene names and the rule where numbers correspond to unique gene names
return(list(gene = gene_uniq, rule = rule))
}
diff --git a/R/promptSysBiolAlg.R b/R/promptSysBiolAlg.R
index cb4b9f77578acfe1d97fc003acc642bc3ee75194..cbc589800f092e65ff7344e4f89c4d60e6a5a3d8 100644
--- a/R/promptSysBiolAlg.R
+++ b/R/promptSysBiolAlg.R
@@ -36,8 +36,6 @@ promptSysBiolAlg <- function(algorithm,
...) {
stopifnot(is(algorithm, "character"))
-
- on.exit( closeAllConnections() )
# classname
cname <- paste(prefix, algorithm, sep = sep)
@@ -52,6 +50,8 @@ promptSysBiolAlg <- function(algorithm,
if (is(sbfh, "try-error")) {
stop("can not write to file ", sQuote(sbfh))
+ } else {
+ on.exit(close(sbfh))
}
#--------------------------------------------------------------------------#
@@ -168,10 +168,6 @@ promptSysBiolAlg <- function(algorithm,
# end
#--------------------------------------------------------------------------#
- if ( (is(sbfh, "file")) && (isOpen(sbfh)) ) {
- close(sbfh)
- }
-
message("created file ", sQuote(sbfile))
return(invisible(NULL))
diff --git a/inst/CITATION b/inst/CITATION
index ca690fab8d65938f6d5b3562cc45eeea79deaf45..ee480b838a180262d5364b99cf980b21a5f2c77b 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -13,7 +13,7 @@ citEntry(
year = "2013",
number = "1",
pages = "125",
- url = "http://www.biomedcentral.com/1752-0509/7/125",
+ url = "https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-7-125",
doi = "10.1186/1752-0509-7-125",
issn = "1752-0509",
textVersion = "Gelius-Dietrich, G. et al. (2013) sybil - Efficient constraint-based modelling in R. BMC Syst Biol 7(1):125"
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 5c3f25db53dc30de4eebb3e5f0ae6b4908b92ceb..d561fa06bea48c25dcbff9a5d637e77cb2baed6e 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -7,6 +7,24 @@
\newcommand{\CRANpkg}{\href{https://CRAN.R-project.org/package=#1}{\pkg{#1}}}
% ---------------------------------------------------------------------------- %
+\section{Changes in version 2.2.0 2021-05-31}{
+ \itemize{
+ \item Changes to functions \code{modelorg2ExPA} and \code{promptSysBiolAlg},
+ where \code{closeAllConnections} was called \code{on.exit} of the function.
+ The two functions now only close the connections that they have opened.
+ \item It is now possible to use the functions \code{setSolverParm} and
+ \code{getSolverParm} in combination with package \code{clpAPI} to set the
+ number of iterations, to set or get the maximum number of iterations or
+ maximum number of seconds and to check, if the maximum number of iterations
+ (or time) was hit. See also \code{setSolverParm-methods} and
+ \code{getSolverParm-methods} in the manual.
+ \item Updated URLs in DESCRIPTION, inst/CITATION and inst/NEWS.Rd and
+ corrected keyword definition for CRAN submission.
+ \
+ }
+}
+% ---------------------------------------------------------------------------- %
+
\section{Changes in version 2.1.5 2019-03-07}{
\itemize{
\item Minor changes removing invalid URLs for CRAN submission.
@@ -43,7 +61,7 @@
\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}.
+ at \url{https://www.cs.hhu.de/en/research-groups/computational-cell-biology/software.html}.
\item Documentation for \code{react-class} and related methods.
\
}
diff --git a/man/getSolverParm-methods.Rd b/man/getSolverParm-methods.Rd
index 1ac106f1c5145f8a060172a4b930ef0f95a1a5e8..7a2ebe4358d5b8a0c7bff7ce70a3753fa1ddfcbb 100644
--- a/man/getSolverParm-methods.Rd
+++ b/man/getSolverParm-methods.Rd
@@ -30,9 +30,13 @@
\section{Methods}{
\describe{
\item{\code{signature(lp = "optObj_clpAPI")}}{
- method to use with package \pkg{optObj_clpAPI}. This method is currently
- unused. It is not possible to provide parameters for package \pkg{clpAPI}.
- Always \code{FALSE} will be returned.
+ method to use with package \pkg{optObj_clpAPI}. This method calls
+ functions \code{clpAPI::getHitMaximumIterationsCLP},
+ \code{clpAPI::getMaximumIterationsCLP} and \code{clpAPI::getMaximumSecondsCLP}
+ and returns a list containing \code{hitMaximumIterations},
+ \code{maximumIterations} and \code{maximumSeconds} respectively.
+ \code{hitMaximumIterations} should be TRUE, if maximum number of
+ iteration (or time) bound was hit.
}
\item{\code{signature(lp = "optObj_cplexAPI")}}{
method to use with package \pkg{optObj_cplexAPI}. This method writes
diff --git a/man/setSolverParm-methods.Rd b/man/setSolverParm-methods.Rd
index a2b03d54d4fb501fae99cc8bd58c2ad6d23c4d6f..2c4cdd4ff634028c67adba6c8bc46dd702d16e4a 100644
--- a/man/setSolverParm-methods.Rd
+++ b/man/setSolverParm-methods.Rd
@@ -34,9 +34,11 @@
\section{Methods}{
\describe{
\item{\code{signature(lp = "optObj_clpAPI")}}{
- method to use with package \pkg{optObj_clpAPI}. This method is currently
- unused. It is not possible to provide parameters for package \pkg{clpAPI}.
- Always \code{FALSE} will be returned.
+ method to use with package \pkg{optObj_clpAPI}. It is possible
+ to set \code{numberIterations}, \code{maximumIterations} and
+ \code{maximumSeconds}, which call the respective functions
+ \code{setNumberIterationsCLP}, \code{setMaximumIterationsCLP} and
+ \code{setMaximumSecondsCLP} in clpAPI.
}
\item{\code{signature(lp = "optObj_cplexAPI")}}{
method to use with package \pkg{optObj_cplexAPI}. In order to set
diff --git a/man/upgradeModelorg.Rd b/man/upgradeModelorg.Rd
index 4109f58983ef1c0699b8bf357994cb372ab6d2e2..1b21640511ed9341963a2803e50e6e0ab219f8cf 100644
--- a/man/upgradeModelorg.Rd
+++ b/man/upgradeModelorg.Rd
@@ -44,5 +44,6 @@
upgradeModelorg(Ec_core)
}
-\keyword{upgrade, version}
+\keyword{upgrade}
+\keyword{version}