From 07b182d598fd3c41067e3bb989d8016046b13622 Mon Sep 17 00:00:00 2001
From: Jialin Ma <marlin@inventati.org>
Date: Thu, 20 Mar 2025 07:11:45 +0800
Subject: [PATCH 01/11] feat: drop odeintr support

---
 DESCRIPTION                     |   5 +-
 NAMESPACE                       |   6 +-
 R/dxdt.R                        | 216 --------------------------------
 R/symbolic_array.R              |   7 +-
 R/symengine.R                   |   3 +-
 man/ODESystem.Rd                |  91 --------------
 man/symengine.Rd                |  19 +++
 tests/testthat/test-ODESystem.R |  25 ----
 vignettes/odesystem.Rmd         | 129 -------------------
 9 files changed, 30 insertions(+), 471 deletions(-)
 delete mode 100644 R/dxdt.R
 delete mode 100644 man/ODESystem.Rd
 delete mode 100644 tests/testthat/test-ODESystem.R
 delete mode 100644 vignettes/odesystem.Rmd

diff --git a/DESCRIPTION b/DESCRIPTION
index ed50d7c..12fe96c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -17,7 +17,6 @@ Imports:
 Suggests:
     crayon,
     pracma,
-    odeintr,
     testthat (>= 2.1.0),
     knitr,
     rmarkdown
@@ -35,12 +34,11 @@ Encoding: UTF-8
 LazyData: true
 URL: https://github.com/symengine/symengine.R
 BugReports: https://github.com/symengine/symengine.R/issues
-Additional_repositories: https://Marlin-Na.github.io/drat
 License: GPL (>= 2)
 Copyright: The R package bundles the 'SymEngine' library source and its subcomponents
     under 'src/upstream' directory. See file COPYRIGHTS for retained copyright notices
     as a relicensing and redistribution requirement.
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Collate: 
     'RcppExports.R'
     'basic-getinfo.R'
@@ -48,7 +46,6 @@ Collate:
     'basic.R'
     'codegen.R'
     'double_visitor.R'
-    'dxdt.R'
     'function_symbol.R'
     'knitr.R'
     'lambdify.R'
diff --git a/NAMESPACE b/NAMESPACE
index 8413b73..07c9fc5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,8 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method("[",symArray)
+S3method(as.data.frame,symArray)
 S3method(as.function,BasicOrVecBasic)
 S3method(as.matrix,DenseMatrix)
 S3method(cbind,SymEngineDataType)
+S3method(print,symArray)
 S3method(rbind,SymEngineDataType)
 S3method(rep,Basic)
 S3method(rep,VecBasic)
@@ -15,7 +18,6 @@ export(FunctionSymbol)
 export(GCD)
 export(LCM)
 export(Matrix)
-export(ODESystem)
 export(Real)
 export(S)
 export(Symbol)
@@ -24,7 +26,6 @@ export(Vector)
 export(as.language)
 export(codegen)
 export(dirichlet_eta)
-export(dxdt)
 export(erf)
 export(erfc)
 export(evalf)
@@ -57,7 +58,6 @@ exportMethods(choose)
 exportMethods(det)
 exportMethods(digamma)
 exportMethods(factorial)
-exportMethods(predict)
 exportMethods(psigamma)
 exportMethods(solve)
 exportMethods(t)
diff --git a/R/dxdt.R b/R/dxdt.R
deleted file mode 100644
index b20328d..0000000
--- a/R/dxdt.R
+++ /dev/null
@@ -1,216 +0,0 @@
-
-## TODO: handle dynamic parameters, i.e.
-## > VdP.sys = '
-## > dxdt[0] = x[1];
-## > dxdt[1] = mu * (1 - x[0] * x[0]) * x[1] - x[0];
-## > '
-## > compile_sys("vpol2", VdP.sys, "mu", method = "bsd")
-## > vpol2_set_params(mu = 0.5)
-
-setClass("DxdtOdeConstructor", slots = c(x="Basic"))
-setClass("DxdtOde", slots = c(x = "Basic", rhs = "Basic"))
-setClass("ODESystem", slots = c(odesys = "list", cpp_source = "character",
-                                compile_env = "environment"))
-
-#' Solve System of Ordinary Differential Equations
-#' 
-#' This is a wrapper of the `odeintr` R package using
-#' symengine objects to specify the ODE system and C code
-#' generation functionality from symengine to generate the
-#' C++ source. The `dxdt` function and defined `==` S4 method
-#' allow one to intuitively specify the ODE system with symengine
-#' objects. The `ODESystem` will generate C++ source
-#' and compile on the fly with Rcpp. Then `predict` can be used to get
-#' results.
-#' 
-#' @param x A SymEngine Basic object of type Symbol or a R object
-#'     that will be converted to `Symbol(x)`.
-#' @rdname ODESystem
-#' @return `dxdt` returns a DxdtOdeConstructor S4 object.
-#' @export
-#' @md
-#' @examples 
-#' # A differential equation specified with dxdt and ==
-#' x <- Symbol("x")
-#' eq <- dxdt(x) == 1/exp(x)
-#' print(eq)
-dxdt <- function(x) {
-    x <- Symbol(x)
-    new("DxdtOdeConstructor", x = x)
-}
-
-#' @param e1 A DxdtOdeConstructor S4 object which can be returned by `dxdt`.
-#' @param e2 A Basic object or an R object that will be converted to `S(e2)`.
-#' @return S4 method of `==` for "DxdtOdeConstructor" returns a DxdtOde S4 object.
-#' @rdname ODESystem
-setMethod("==", signature=c(e1 = "DxdtOdeConstructor", e2 = "ANY"),
-    function(e1, e2) {
-        x <- e1@x
-        rhs <- S(e2)
-        new("DxdtOde", x = x, rhs = rhs)
-    }
-)
-
-setMethod("show", signature = c(object = "DxdtOde"),
-    function(object) {
-        x <- object@x
-        rhs <- object@rhs
-        cat("Ordinary differential equation:\n")
-        x_str <- as.character(x)
-        rhs_str <- as.character(rhs)
-        cat(sprintf("d(%s)/dt == %s\n", x_str, rhs_str))
-    }
-)
-
-#' @param odesys,... DxdtOde S4 objects that can be returned with
-#'     `dxdt(x) == rhs`. Or `odesys` can be a list of DxdtOde S4 objects
-#'     when there is no dot arguments.
-#' @param method,atol,rtol Passed to `odeintr::compile_sys`.
-#' @param compile Logical, whether to compile the C++ source. Useful if
-#'     you only want to obtain the code.
-#' @return `ODESystem` returns a ODESystem S4 object.
-#' @rdname ODESystem
-#' @export
-#' @examples
-#' \dontrun{
-#' ## Lorenz system
-#' use_vars(x, y, z)
-#' sigma <- 10
-#' rho <- 28
-#' beta <- 8/3
-#' lorenz_sys <- ODESystem(
-#'     dxdt(x) == sigma * (y - x),
-#'     dxdt(y) == (rho - z) * x - y,
-#'     dxdt(z) == - beta * z + x * y
-#' )
-#' res <- predict(
-#'     lorenz_sys, init = c(x = 1, y = 1, z = 1), duration = 100, step_size = 0.001
-#' )
-#' plot(res[, c(2, 4)], type = 'l', col = "steelblue", main = "Lorenz Attractor")
-#' }
-ODESystem <- function(odesys, ..., method = "rk5_i",
-                      atol = 1e-06, rtol = 1e-06, compile = TRUE) {
-    if (!missing(...))
-        odesys <- list(odesys, ...)
-    if (is(odesys, "DxdtOde"))
-        odesys <- list(odesys)
-    
-    ## Some checks
-    check_odesys <- function(odesys) {
-        stopifnot(is.list(odesys))
-        
-        for (el in odesys)
-            stopifnot(is(el, "DxdtOde"))
-        
-        rhs_list <- lapply(odesys, function(x) x@rhs)
-        x_list <- lapply(odesys, function(x) x@x)
-        
-        check_symbol <- function(names) {
-            #if (any(grepl("^_", names)))
-            #    stop(sprintf("variable name [%s] can not start with '_'",
-            #                 names[grepl("^_", names)[1]]))
-            if (any(names == ""))
-                stop("variable name can not be empty string")
-            if (any(grepl("(\\[|\\]| )", names)))
-                stop(sprintf("variable name [%s] can not have space, '[' or ']'",
-                             names[grepl("^_", names)[1]]))
-        }
-        check_symbol(unlist(lapply(rhs_list, function(rhs) as.character(free_symbols(rhs)))))
-        check_symbol(unlist(lapply(x_list, as.character)))
-        
-        if (length(unique(Vector(x_list))) != length(x_list))
-            stop("lhs variables should be unique")
-    }
-    check_odesys(odesys)
-    
-    rhs_list <- lapply(odesys, function(x) x@rhs)
-    x_list <- lapply(odesys, function(x) x@x)
-    
-    x_mapping_to <- sprintf("x[%s]", seq(length(x_list)) - 1L)
-    x_mapping_to <- lapply(x_mapping_to, Symbol)
-    lhs_mapping_to <- sprintf("dxdt[%s]", seq(length(x_list)) - 1L)
-    lhs_mapping_to <- lapply(lhs_mapping_to, Symbol)
-    
-    rhs_mapping_to <- rhs_list
-    for (i in seq_along(x_list))
-        for (j in seq_along(rhs_mapping_to))
-            rhs_mapping_to[[j]] <- subs(rhs_mapping_to[[j]], x_list[[i]], x_mapping_to[[i]])
-    
-    ccode_str <- sprintf("%s = %s", codegen(Vector(lhs_mapping_to), type="ccode"),
-                                    codegen(Vector(rhs_mapping_to), type="ccode"))
-    
-    compile_sys_env <- new.env()
-    
-    if (!requireNamespace("odeintr", quietly = TRUE))
-        stop("'odeintr' package needs to be installed for this functionality")
-    
-    rcpp_code <- odeintr::compile_sys(
-        name = "predict",
-        sys = ccode_str,
-        pars = NULL,
-        const = FALSE,
-        method = method,
-        sys_dim = length(x_list),
-        atol = atol,
-        rtol = rtol,
-        compile = FALSE,
-        observer = NULL,
-        env = compile_sys_env
-    )
-    # Sanity check
-    stopifnot(length(ls(compile_sys_env, all.names = TRUE)) == 0L)
-    if (compile) {
-        res <- Rcpp::sourceCpp(
-            code = rcpp_code, env = compile_sys_env, verbose = FALSE)
-    }
-    
-    new("ODESystem", odesys = odesys,
-        cpp_source = rcpp_code, compile_env = compile_sys_env)
-}
-
-
-#' @param object A ODESystem S4 object.
-#' @param init A numeric vector specifying the initial conditions. It can
-#'     be named with the variable names or it can be unnamed but in the
-#'     same of order of equations.
-#' @param duration,step_size,start Passed to the function generated by
-#'     `odeintr::compile_sys`.
-#' @return `predict` returns a dataframe.
-#' @rdname ODESystem
-#' @export
-setMethod("predict", c(object = "ODESystem"),
-    function(object, init, duration, step_size = 1, start = 0) {
-        x_list <- lapply(object@odesys, function(x) x@x)
-        x_names <- vapply(x_list, as.character, character(1))
-        
-        stopifnot(length(init) == length(x_list))
-        
-        # Reorder 'init' if it is named
-        if (!is.null(names(init))) {
-            matching <- match(x_names, names(init))
-            if (anyDuplicated(matching) || any(is.na(matching)))
-                stop("Invalid names specified 'init'")
-            init <- init[matching]
-        }
-        
-        ans <- object@compile_env$predict(init, duration, step_size, start)
-        stopifnot(
-            identical(names(ans), c("Time", paste0("X", seq_along(x_list))))
-        )
-        names(ans)[2:length(ans)] <- x_names
-        ans
-    }
-)
-
-setMethod("show", c(object = "ODESystem"),
-    function(object) {
-        x_list <- lapply(object@odesys, function(x) x@x)
-        x_names <- vapply(x_list, as.character, character(1))
-        rhs_list <- lapply(object@odesys, function(x) x@rhs)
-        cat(sprintf('%s with variables %s:\n', class(object),
-                    paste(x_names, collapse = ", ")))
-        for (i in seq_along(x_list)) {
-            cat(sprintf("  d(%s)/dt = %s\n", x_names[i], as.character(rhs_list[[i]])))
-        }
-    }
-)
diff --git a/R/symbolic_array.R b/R/symbolic_array.R
index 972748f..b5bed14 100644
--- a/R/symbolic_array.R
+++ b/R/symbolic_array.R
@@ -10,6 +10,7 @@ symArray <- function(...) {
     ans
 }
 
+#' @export
 print.symArray <- function(x, ...) {
     ## TODO: to improve this...
     ## maybe we need to define method for format instead?
@@ -21,6 +22,7 @@ print.symArray <- function(x, ...) {
 
 ## Preserve class attributes for these functions
 
+#' @export
 `[.symArray` <- function(x,...) {
     ans <- NextMethod("[")
     class(ans) <- class(x)
@@ -29,5 +31,8 @@ print.symArray <- function(x, ...) {
 
 
 ## So that it can be used in data frame
-as.data.frame.symArray <- as.data.frame.vector
+#' @export
+as.data.frame.symArray <- function(...) {
+    as.data.frame.vector(...)
+}
 
diff --git a/R/symengine.R b/R/symengine.R
index d1d3a10..493adf7 100644
--- a/R/symengine.R
+++ b/R/symengine.R
@@ -69,10 +69,9 @@
 #' - `lambertw`, `zeta`, `dirichlet_eta`, `erf`, `erfc`
 #' - `atan2`, `kronecker_delta`, `lowergamma`, `uppergamma`, `psigamma`, `beta`
 #' 
-#' @docType package
 #' @name symengine
 #' @md
-NULL
+"_PACKAGE"
 
 #' @import methods
 #' @importFrom Rcpp cppFunction
diff --git a/man/ODESystem.Rd b/man/ODESystem.Rd
deleted file mode 100644
index d5ba8a4..0000000
--- a/man/ODESystem.Rd
+++ /dev/null
@@ -1,91 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/dxdt.R
-\name{dxdt}
-\alias{dxdt}
-\alias{==,DxdtOdeConstructor,ANY-method}
-\alias{ODESystem}
-\alias{predict,ODESystem-method}
-\title{Solve System of Ordinary Differential Equations}
-\usage{
-dxdt(x)
-
-\S4method{==}{DxdtOdeConstructor,ANY}(e1, e2)
-
-ODESystem(
-  odesys,
-  ...,
-  method = "rk5_i",
-  atol = 1e-06,
-  rtol = 1e-06,
-  compile = TRUE
-)
-
-\S4method{predict}{ODESystem}(object, init, duration, step_size = 1, start = 0)
-}
-\arguments{
-\item{x}{A SymEngine Basic object of type Symbol or a R object
-that will be converted to \code{Symbol(x)}.}
-
-\item{e1}{A DxdtOdeConstructor S4 object which can be returned by `dxdt`.}
-
-\item{e2}{A Basic object or an R object that will be converted to `S(e2)`.}
-
-\item{odesys, ...}{DxdtOde S4 objects that can be returned with
-`dxdt(x) == rhs`. Or `odesys` can be a list of DxdtOde S4 objects
-when there is no dot arguments.}
-
-\item{method, atol, rtol}{Passed to `odeintr::compile_sys`.}
-
-\item{compile}{Logical, whether to compile the C++ source. Useful if
-you only want to obtain the code.}
-
-\item{object}{A ODESystem S4 object.}
-
-\item{init}{A numeric vector specifying the initial conditions. It can
-be named with the variable names or it can be unnamed but in the
-same of order of equations.}
-
-\item{duration, step_size, start}{Passed to the function generated by
-`odeintr::compile_sys`.}
-}
-\value{
-\code{dxdt} returns a DxdtOdeConstructor S4 object.
-
-S4 method of `==` for "DxdtOdeConstructor" returns a DxdtOde S4 object.
-
-`ODESystem` returns a ODESystem S4 object.
-
-`predict` returns a dataframe.
-}
-\description{
-This is a wrapper of the \code{odeintr} R package using
-symengine objects to specify the ODE system and C code
-generation functionality from symengine to generate the
-C++ source. The \code{dxdt} function and defined \code{==} S4 method
-allow one to intuitively specify the ODE system with symengine
-objects. The \code{ODESystem} will generate C++ source
-and compile on the fly with Rcpp. Then \code{predict} can be used to get
-results.
-}
-\examples{
-# A differential equation specified with dxdt and ==
-x <- Symbol("x")
-eq <- dxdt(x) == 1/exp(x)
-print(eq)
-\dontrun{
-## Lorenz system
-use_vars(x, y, z)
-sigma <- 10
-rho <- 28
-beta <- 8/3
-lorenz_sys <- ODESystem(
-    dxdt(x) == sigma * (y - x),
-    dxdt(y) == (rho - z) * x - y,
-    dxdt(z) == - beta * z + x * y
-)
-res <- predict(
-    lorenz_sys, init = c(x = 1, y = 1, z = 1), duration = 100, step_size = 0.001
-)
-plot(res[, c(2, 4)], type = 'l', col = "steelblue", main = "Lorenz Attractor")
-}
-}
diff --git a/man/symengine.Rd b/man/symengine.Rd
index 9f2405f..c0d324a 100644
--- a/man/symengine.Rd
+++ b/man/symengine.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/symengine.R
 \docType{package}
 \name{symengine}
+\alias{symengine-package}
 \alias{symengine}
 \title{symengine: R interface to SymEngine C++ library for symbolic computation}
 \description{
@@ -83,3 +84,21 @@ objects. For example \code{S(~ sin(x) + 1)} and \code{S(quote(sin(x) + 1))}.
 }
 }
 
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://github.com/symengine/symengine.R}
+  \item Report bugs at \url{https://github.com/symengine/symengine.R/issues}
+}
+
+}
+\author{
+\strong{Maintainer}: Jialin Ma \email{marlin@inventati.org}
+
+Authors:
+\itemize{
+  \item Isuru Fernando \email{isuruf@gmail.com}
+  \item Xin Chen \email{xinchen.tju@gmail.com}
+}
+
+}
diff --git a/tests/testthat/test-ODESystem.R b/tests/testthat/test-ODESystem.R
deleted file mode 100644
index 2e06b52..0000000
--- a/tests/testthat/test-ODESystem.R
+++ /dev/null
@@ -1,25 +0,0 @@
-
-context("ODESystem")
-
-test_that("dxdt constructor", {
-    x <- S("x")
-    rhs <- x^2L + x + 1L
-    eq <- dxdt(x) == rhs
-    expect_true(class(eq) == "DxdtOde")
-})
-
-x <- S("x")
-y <- S("y")
-rhs1 <- 1L / (x^2L + y + 1L)
-rhs2 <- 1L / (y^2L + 2L*x + 1L)
-
-test_that("ODESystem and predict works", {
-    skip_if(!requireNamespace("odeintr", quietly = TRUE))
-    eq1 <- dxdt(x) == rhs1
-    eq2 <- dxdt(y) == rhs2
-    sys <- ODESystem(eq1, eq2)
-    expect_true(class(sys) == "ODESystem")
-    res <- predict(sys, init = c(x = 1, y = 1), duration = 10)
-    expect_true(is.data.frame(res))
-    expect_true(identical(names(res), c("Time", "x", "y")))
-})
diff --git a/vignettes/odesystem.Rmd b/vignettes/odesystem.Rmd
deleted file mode 100644
index e7422fd..0000000
--- a/vignettes/odesystem.Rmd
+++ /dev/null
@@ -1,129 +0,0 @@
----
-title: "Numerical ODE Solver"
-output:
-  rmarkdown::html_vignette:
-    toc: true
-vignette: >
-  %\VignetteIndexEntry{odesystem}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-<!-- Custom styles -->
-<style>
-pre.sourceCode, code.sourceCode {
-  background-color: #e5fbe6;
-}
-body {
-  margin-left: 0px;
-}
-</style>
-
-```{r, eval=TRUE, include=FALSE}
-if (!all(sapply(c("odeintr"), requireNamespace, quietly = TRUE)))
-  knitr::opts_chunk$set(eval = FALSE)
-```
-
-[odeintr](https://github.com/thk686/odeintr) by Timothy H. Keitt is an R package for
-integrating differential equations with the
-[Boost odeint library](https://headmyshoulder.github.io/odeint-v2/).
-It allows specifying the model in C++ code and compiling it on the fly with
-Rcpp.
-
-Here we provide an interface to the `odeintr` package, but
-
-1. Use an intuitive way to specify the ODE model with symengine objects;
-2. Use symengine's code generation functionality to generate the C++ source
-   and compile with `odeintr`.
-
-However, the interface is not stable and may subject to change in future.
-This mainly serves an example of how to extend symengine and you are welcome
-to check out the
-[source code](https://github.com/symengine/symengine.R/blob/master/R/dxdt.R).
-
-```{r}
-library(symengine)
-```
-
-## Define ordinary differential equations with symengine
-
-A ordinary differential equation could be constructed with `dxdt(x) == rhs`
-where `x` and `rhs` will be converted to SymEngine's 'Basic' S4 object.
-This works by defining a S4 method of `==` for the return type of `dxdt()`.
-
-For example
-
-```{r}
-x <- Symbol("x")
-a <- 3
-eq <- dxdt(x) == a/(x + 1)
-eq
-```
-
-## Define ODE system
-
-`ODESystem` will take a list of ordinary differential equations,
-generate C++ source code and compile on the fly with Rcpp.
-The following is the Lorenz system.
-
-```{r}
-sigma <- 10
-rho <- 28
-beta <- 8/3
-use_vars(x, y, z)
-```
-
-```{r}
-lorenz_sys <- list(
-    dxdt(x) == sigma * (y - x),
-    dxdt(y) == (rho - z) * x - y,
-    dxdt(z) == - beta * z + x * y
-)
-lorenz_sys <- ODESystem(lorenz_sys, method = "rk5_i")
-```
-
-The method argument is passed to `odeintr::compile_sys`.
-
-## Get results
-
-A S4 method of `predict` is defined to run the model with given
-initial conditions, duration and step_size.
-
-```{r}
-res <- predict(lorenz_sys, init = c(x=1, y=1, z=1),
-               duration = 100, step_size = 0.001, start = 0)
-head(res)
-```
-
-```{r fig.height=5, fig.width=5}
-plot(res[, c(2, 4)], type = 'l', col = "steelblue", main = "Lorenz Attractor")
-```
-
-## Van der Pol Oscillator
-
-Example of Van der Pol oscillator from `odeintr` package.
-
-```{r}
-use_vars(x, y)
-vdp_sys <- ODESystem(
-    dxdt(x) == y,
-    dxdt(y) == 2 * (1 - x * x) * y - x,
-    method = "bsd" # Bulirsch-Stoer
-)
-res <- predict(vdp_sys, init = rep(1e-4, 2), duration = 100, step_size = 0.01)
-```
-
-```{r fig.height=5, fig.width=5}
-oldpar <- par(mfrow = c(2, 2), mar = rep(0.5, 4), oma = rep(5, 4), xpd = NA)
-make.plot <- function(xy, xlab = NA, ylab = NA)
-  plot(xy, col = "steelblue", lwd = 2, type = "l",
-       axes = FALSE, xlab = xlab, ylab = ylab)
-plot.new()
-make.plot(res[, c(3, 1)]); axis(3); axis(4)
-make.plot(res[, c(1, 2)], "Time", "X1"); axis(1); axis(2)
-make.plot(res[, c(3, 2)], "X2"); axis(1); axis(4)
-title(main = "Van der Pol Oscillator", outer = TRUE)
-par(oldpar)
-```
-
-

From 0f10c66d5fc6452893e5dd655e4898bf7ded2649 Mon Sep 17 00:00:00 2001
From: Jialin Ma <marlin@inventati.org>
Date: Thu, 20 Mar 2025 07:17:08 +0800
Subject: [PATCH 02/11] feat: bump version to 0.2.7

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 12fe96c..fb454ed 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: symengine
 Title: Interface to the 'SymEngine' Library
-Version: 0.2.6
+Version: 0.2.7
 Authors@R: c(person("Jialin", "Ma", email="marlin@inventati.org", role = c("cre", "aut")),
              person("Isuru", "Fernando", email="isuruf@gmail.com", role = c("aut")),
              person("Xin", "Chen", email="xinchen.tju@gmail.com", role = c("aut")))

From abf5983c776f431aa7eb8a41971da79a9a9687e4 Mon Sep 17 00:00:00 2001
From: Jialin Ma <marlin@inventati.org>
Date: Thu, 20 Mar 2025 21:18:12 +0900
Subject: [PATCH 03/11] feat: add cran comments

---
 tools/cran_comments/cran-comments_0.2.7.md | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 tools/cran_comments/cran-comments_0.2.7.md

diff --git a/tools/cran_comments/cran-comments_0.2.7.md b/tools/cran_comments/cran-comments_0.2.7.md
new file mode 100644
index 0000000..4696d1f
--- /dev/null
+++ b/tools/cran_comments/cran-comments_0.2.7.md
@@ -0,0 +1,3 @@
+
+This version (0.2.7) drops the dependency of odeintr and relevant functionalities,
+which should fix the issues in CRAN check results.

From ede39bcaffb72aedb6cde76ad099fd1953e8ce4f Mon Sep 17 00:00:00 2001
From: Jialin Ma <marlin@inventati.org>
Date: Thu, 20 Mar 2025 21:19:03 +0900
Subject: [PATCH 04/11] chore: bump version to 0.2.8

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index fb454ed..27a0751 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: symengine
 Title: Interface to the 'SymEngine' Library
-Version: 0.2.7
+Version: 0.2.8
 Authors@R: c(person("Jialin", "Ma", email="marlin@inventati.org", role = c("cre", "aut")),
              person("Isuru", "Fernando", email="isuruf@gmail.com", role = c("aut")),
              person("Xin", "Chen", email="xinchen.tju@gmail.com", role = c("aut")))

From 2d9f902982168fb5ec1cd020a9a39aec7e13812a Mon Sep 17 00:00:00 2001
From: Jialin Ma <marlin@inventati.org>
Date: Thu, 20 Mar 2025 21:19:26 +0900
Subject: [PATCH 05/11] feat: replace IS_S4_OBJECT with Rf_isObject and Rf_isS4

---
 src/rbinding.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/rbinding.cpp b/src/rbinding.cpp
index 5a9e688..f429eed 100644
--- a/src/rbinding.cpp
+++ b/src/rbinding.cpp
@@ -173,7 +173,7 @@ typedef Rcpp::XPtr<CDenseMatrix, Rcpp::PreserveStorage, dense_matrix_free, true>
 //// Determine the pointer type by check the tag value
 
 inline s4binding_t s4binding_typeof(SEXP x) {
-    if (IS_S4_OBJECT(x) && R_has_slot(x, Rf_install("ptr"))) {
+    if (Rf_isObject(x) && Rf_isS4(x) && R_has_slot(x, Rf_install("ptr"))) {
         SEXP p = R_do_slot(x, Rf_install("ptr"));
         s4binding_t type = (s4binding_t) RAW(R_ExternalPtrTag(p))[0];
         return type;

From 3ba2311bb1d84d7921e0e007f3693d73f0af3a3e Mon Sep 17 00:00:00 2001
From: Jialin Ma <marlin@inventati.org>
Date: Thu, 3 Apr 2025 20:59:00 +0800
Subject: [PATCH 06/11] fix: cran warning in mp_class.h

---
 tools/symengine_patch.diff | 39 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/tools/symengine_patch.diff b/tools/symengine_patch.diff
index 62d69e2..fabcec2 100644
--- a/tools/symengine_patch.diff
+++ b/tools/symengine_patch.diff
@@ -31,3 +31,42 @@
      set(CMAKE_CXX_FLAGS_RELEASE_INIT "${common} -O3 -funroll-loops")
      set(CMAKE_CXX_FLAGS_DEBUG_INIT   "${common} -g -ggdb")
  elseif (CMAKE_CXX_COMPILER_ID STREQUAL "PGI")
+diff --git src/upstream/symengine/mp_class.h src/upstream/symengine/mp_class.h
+index c42d368..12d103e 100644
+--- src/upstream/symengine/mp_class.h
++++ src/upstream/symengine/mp_class.h
+@@ -74,12 +74,12 @@ typedef mpq_class rational_class;
+ inline namespace literals
+ {
+ //! Literal for creating multiple precision integers
+-inline integer_class operator"" _z(const char *str)
++inline integer_class operator""_z(const char *str)
+ {
+     return integer_class(str);
+ }
+ 
+-inline rational_class operator"" _q(const char *str)
++inline rational_class operator""_q(const char *str)
+ {
+     return rational_class(integer_class(str));
+ }
+@@ -1222,6 +1222,9 @@ inline int mp_cmpabs(const integer_class &a, const integer_class &b)
+     return mpz_cmpabs(get_mpz_t(a), get_mpz_t(b));
+ }
+ 
++// from Rmath.h
++extern "C" double unif_rand(void);
++
+ class mp_randstate
+ {
+ public:
+@@ -1241,7 +1244,8 @@ public:
+     mp_randstate()
+     {
+         gmp_randinit_default(_state);
+-        gmp_randseed_ui(_state, std::rand());
++        unsigned long int randres =  (int)(unif_rand() * (RAND_MAX - 1.0));
++        gmp_randseed_ui(_state, randres);
+     }
+ 
+     ~mp_randstate()

From 580dac341d6a695b9a1951d3ba8d3ceafe400676 Mon Sep 17 00:00:00 2001
From: Jialin Ma <marlin@inventati.org>
Date: Thu, 3 Apr 2025 21:27:06 +0800
Subject: [PATCH 07/11] feat: fix cmake_minimum_required version

---
 tools/symengine_patch.diff | 48 +++++++++++++++++++++++++++++++++-----
 1 file changed, 42 insertions(+), 6 deletions(-)

diff --git a/tools/symengine_patch.diff b/tools/symengine_patch.diff
index fabcec2..b401b57 100644
--- a/tools/symengine_patch.diff
+++ b/tools/symengine_patch.diff
@@ -1,6 +1,14 @@
---- src/upstream/CMakeLists.txt	2019-11-13 15:14:25.000000000 -0500
-+++ src/upstream/CMakeLists.txt.new	2019-11-19 01:51:57.000000000 -0500
-@@ -535,10 +535,6 @@
+diff --git src/upstream/CMakeLists.txt src/upstream/CMakeLists.txt
+index c9f4b8b..43b6394 100644
+--- src/upstream/CMakeLists.txt
++++ src/upstream/CMakeLists.txt
+@@ -1,4 +1,4 @@
+-cmake_minimum_required(VERSION 2.8.12)
++cmake_minimum_required(VERSION 3.5..4.0)
+ 
+ if (POLICY CMP0074)
+   cmake_policy(SET CMP0074 NEW)
+@@ -539,10 +539,6 @@ if (WITH_OPENMP)
          set(WITH_SYMENGINE_THREAD_SAFE yes)
      endif()
  elseif (CMAKE_CXX_COMPILER_ID MATCHES Clang|GNU)
@@ -11,8 +19,23 @@
  endif()
  
  if (CMAKE_BUILD_TYPE STREQUAL "Debug")
---- src/upstream/cmake/UserOverride.cmake	2019-11-13 15:14:25.000000000 -0500
-+++ src/upstream/cmake/UserOverride.cmake.new	2019-11-19 01:53:01.000000000 -0500
+diff --git src/upstream/cmake/SymEngineConfig.cmake.in src/upstream/cmake/SymEngineConfig.cmake.in
+index dbfc80b..8f4ef85 100644
+--- src/upstream/cmake/SymEngineConfig.cmake.in
++++ src/upstream/cmake/SymEngineConfig.cmake.in
+@@ -31,7 +31,7 @@
+ # target_link_libraries(example ${SYMENGINE_LIBRARIES})
+ #
+ 
+-cmake_minimum_required(VERSION 2.8.12)
++cmake_minimum_required(VERSION 3.5..4.0)
+ 
+ if (POLICY CMP0074)
+   cmake_policy(SET CMP0074 NEW)
+diff --git src/upstream/cmake/UserOverride.cmake src/upstream/cmake/UserOverride.cmake
+index 523ce49..3e27a3f 100644
+--- src/upstream/cmake/UserOverride.cmake
++++ src/upstream/cmake/UserOverride.cmake
 @@ -8,7 +8,7 @@
  
  if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
@@ -22,7 +45,7 @@
      set(CMAKE_CXX_FLAGS_RELEASE_INIT "${common} -O3 -funroll-loops")
      set(CMAKE_CXX_FLAGS_DEBUG_INIT   "${common} -g -ggdb")
  elseif (CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-@@ -18,7 +18,7 @@
+@@ -18,7 +18,7 @@ elseif (CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
      set(CMAKE_CXX_FLAGS_DEBUG_INIT   "${common} -g -O0")
  elseif (CMAKE_CXX_COMPILER_ID MATCHES Clang)
      # clang
@@ -31,6 +54,19 @@
      set(CMAKE_CXX_FLAGS_RELEASE_INIT "${common} -O3 -funroll-loops")
      set(CMAKE_CXX_FLAGS_DEBUG_INIT   "${common} -g -ggdb")
  elseif (CMAKE_CXX_COMPILER_ID STREQUAL "PGI")
+diff --git src/upstream/cmake/cotire.cmake src/upstream/cmake/cotire.cmake
+index 741d690..e29c180 100644
+--- src/upstream/cmake/cotire.cmake
++++ src/upstream/cmake/cotire.cmake
+@@ -37,7 +37,7 @@ set(__COTIRE_INCLUDED TRUE)
+ if (NOT CMAKE_SCRIPT_MODE_FILE)
+ 	cmake_policy(PUSH)
+ endif()
+-cmake_minimum_required(VERSION 2.8.12)
++cmake_minimum_required(VERSION 3.5..4.0)
+ if (NOT CMAKE_SCRIPT_MODE_FILE)
+ 	cmake_policy(POP)
+ endif()
 diff --git src/upstream/symengine/mp_class.h src/upstream/symengine/mp_class.h
 index c42d368..12d103e 100644
 --- src/upstream/symengine/mp_class.h

From 750f56a70ce136dd67c65a5424e0474594d2cbd9 Mon Sep 17 00:00:00 2001
From: Jialin Ma <marlin@inventati.org>
Date: Thu, 3 Apr 2025 21:49:59 +0800
Subject: [PATCH 08/11] feat: bump version to 0.2.9

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 27a0751..5e8ec70 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: symengine
 Title: Interface to the 'SymEngine' Library
-Version: 0.2.8
+Version: 0.2.9
 Authors@R: c(person("Jialin", "Ma", email="marlin@inventati.org", role = c("cre", "aut")),
              person("Isuru", "Fernando", email="isuruf@gmail.com", role = c("aut")),
              person("Xin", "Chen", email="xinchen.tju@gmail.com", role = c("aut")))

From 8445b616efe4c487041b200ebf847cbf813d15be Mon Sep 17 00:00:00 2001
From: Jialin Ma <marlin@inventati.org>
Date: Thu, 3 Apr 2025 21:55:34 +0800
Subject: [PATCH 09/11] feat: add cran comments

---
 tools/cran_comments/cran-comments_0.2.9.md | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 tools/cran_comments/cran-comments_0.2.9.md

diff --git a/tools/cran_comments/cran-comments_0.2.9.md b/tools/cran_comments/cran-comments_0.2.9.md
new file mode 100644
index 0000000..534c598
--- /dev/null
+++ b/tools/cran_comments/cran-comments_0.2.9.md
@@ -0,0 +1,12 @@
+
+This version (0.2.9) drops the dependency of odeintr 
+and relevant functionalities, which should fix the 
+errors in CRAN check results.
+
+In addition, it addresses several other issues on CRAN
+check:
+
+1. Replaces the usage of IS_S4_OBJECT and 'rand' in compiled code. 
+2. Fixes the -Wdeprecated-literal-operator compiler warning
+3. Fixes the package build issue when using CMake 4.0
+

From 760d4fa7890e73fe229ea9a20e95e6fb19ba53be Mon Sep 17 00:00:00 2001
From: Jialin Ma <marlin@inventati.org>
Date: Fri, 4 Apr 2025 11:41:10 +0800
Subject: [PATCH 10/11] feat: remove assert statements

---
 tools/symengine_patch.diff | 48 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/tools/symengine_patch.diff b/tools/symengine_patch.diff
index b401b57..ecf4eb7 100644
--- a/tools/symengine_patch.diff
+++ b/tools/symengine_patch.diff
@@ -106,3 +106,51 @@ index c42d368..12d103e 100644
      }
  
      ~mp_randstate()
+diff --git src/upstream/symengine/lambda_double.h src/upstream/symengine/lambda_double.h
+index bf6f00d..633605a 100644
+--- src/upstream/symengine/lambda_double.h
++++ src/upstream/symengine/lambda_double.h
+@@ -562,7 +562,6 @@ public:
+     }
+     void bvisit(const NaN &nan)
+     {
+-        assert(&nan == &(*Nan) /* singleton, or do we support NaN quiet/singaling nan with payload? */);
+         result_ = [](const double * /* x  */) {
+             return std::numeric_limits<double>::signaling_NaN();
+         };
+diff --git src/upstream/symengine/parser/parser.tab.cc src/upstream/symengine/parser/parser.tab.cc
+index 24628d0..2be7083 100644
+--- src/upstream/symengine/parser/parser.tab.cc
++++ src/upstream/symengine/parser/parser.tab.cc
+@@ -1054,7 +1054,6 @@ namespace yy {
+   case 32: // pwise: PIECEWISE '(' piecewise_list ')'
+ #line 259 "parser.yy"
+     {
+-        assert(yystack_[3].value.as < std::string > () == "Piecewise");
+         yylhs.value.as < SymEngine::RCP<const SymEngine::Basic> > () = piecewise(std::move(yystack_[1].value.as < SymEngine::PiecewiseVec > ()));
+     }
+ #line 1061 "parser.tab.cc"
+diff --git src/upstream/symengine/parser/parser.yy src/upstream/symengine/parser/parser.yy
+index 7e106d0..10909bc 100644
+--- src/upstream/symengine/parser/parser.yy
++++ src/upstream/symengine/parser/parser.yy
+@@ -256,7 +256,6 @@ piecewise_list:
+ pwise:
+     PIECEWISE '(' piecewise_list ')'
+     {
+-        assert($1 == "Piecewise");
+         $$ = piecewise(std::move($3));
+     }
+ ;
+diff --git src/upstream/symengine/utilities/matchpycpp/substitution.h src/upstream/symengine/utilities/matchpycpp/substitution.h
+index 056e52a..b6e1760 100644
+--- src/upstream/symengine/utilities/matchpycpp/substitution.h
++++ src/upstream/symengine/utilities/matchpycpp/substitution.h
+@@ -50,7 +50,6 @@ substitution_union(const SubstitutionMultiset &subst,
+     for (const SubstitutionMultiset &other : others) {
+         for (const pair<const string, multiset_basic> &p : other) {
+             int ret = try_add_variable(new_subst, p.first, p.second);
+-            assert(ret == 0);
+         }
+     }
+     return new_subst;

From 6c22371db923fbbb909b34b06fef85486f6b7e64 Mon Sep 17 00:00:00 2001
From: Jialin Ma <marlin@inventati.org>
Date: Fri, 4 Apr 2025 11:42:05 +0800
Subject: [PATCH 11/11] feat: bump version to 0.2.10

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5e8ec70..154736a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: symengine
 Title: Interface to the 'SymEngine' Library
-Version: 0.2.9
+Version: 0.2.10
 Authors@R: c(person("Jialin", "Ma", email="marlin@inventati.org", role = c("cre", "aut")),
              person("Isuru", "Fernando", email="isuruf@gmail.com", role = c("aut")),
              person("Xin", "Chen", email="xinchen.tju@gmail.com", role = c("aut")))