Version 2.2.0. Fixed two functions calling closeAllConnection. Added...

Version 2.2.0. Fixed two functions calling closeAllConnection. Added functionality of setSolverParm and getSolverParm methods for clpAPI. Updated URLs and corrected keyword definition.

DESCRIPTION

 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],

R/modelorg2ExPA.R

@@ -38,8 +38,6 @@ modelorg2ExPA <- function(model,
                           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
     #--------------------------------------------------------------------------#

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!")

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
 
-        out <- FALSE
+        if ( ! ((is.data.frame(solverParm)) || (is.list(solverParm))) ) {
+            stop(sQuote(solverParm), " must be list or data.frame")
+        }
 
-        wrong_solver_msg(lp, "setSolverParm")
+        if (any(is.na(solverParm))) {
+            stop(sQuote(solverParm), " contains NA values")
+        }
 
-#        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")
-#        }
+        numericParm <- sapply(solverParm, is.numeric)
+        num <- solverParm[numericParm]
+        if (length(num) != length(solverParm)) {
+            stop(sQuote(solverParm), " contains non numeric values")
+        }
         
-        # no parameters in COIN-OR CLP yet.
-        #    lp@oobj <- clpAPI::initProbCLP()
-        #    clpAPI::setLogLevelCLP(lp@oobj, 0)
+        if (length(num) > 0) {
+            # get parameter names:
+            numericp <- names(num)
             
-        return(out)
+            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)
+        
     }
 )
 

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)) {

R/parseBoolean.R

@@ -85,12 +85,16 @@
   # 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))
 
 }

R/promptSysBiolAlg.R

@@ -37,8 +37,6 @@ 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))

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"

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.
   	\
   }

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

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

man/upgradeModelorg.Rd

@@ -44,5 +44,6 @@
 	upgradeModelorg(Ec_core)
 }
 
-\keyword{upgrade, version}
+\keyword{upgrade}
+\keyword{version}