From 13b3daaaa7c47d178ee59ab116aa71b7bf2f5c9b Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 18 Nov 2022 09:12:49 +0100
Subject: Remove candidate patches that were accidentally committed

---
 custom_lsoda_call_edited.patch | 116 -----------------------------------------
 1 file changed, 116 deletions(-)
 delete mode 100644 custom_lsoda_call_edited.patch

(limited to 'custom_lsoda_call_edited.patch')

diff --git a/custom_lsoda_call_edited.patch b/custom_lsoda_call_edited.patch
deleted file mode 100644
index a79cbbcd..00000000
--- a/custom_lsoda_call_edited.patch
+++ /dev/null
@@ -1,116 +0,0 @@
---- a/R/mkinfit.R
-+++ b/R/mkinfit.R
- 
-+  # Get native symbol before iterations info for speed
-+  call_lsoda <- getNativeSymbolInfo("call_lsoda", PACKAGE = "deSolve")
-+  if (solution_type == "deSolve" & use_compiled[1] != FALSE) {
-+    mkinmod$diffs_address <- getNativeSymbolInfo("diffs",
-+      PACKAGE = mkinmod$dll_info[["name"]])$address
-+    mkinmod$initpar_address <- getNativeSymbolInfo("initpar",
-+      PACKAGE = mkinmod$dll_info[["name"]])$address
-+  }
-+
-
-@@ -610,7 +619,8 @@ mkinfit <- function(mkinmod, observed,
-                          solution_type = solution_type,
-                          use_compiled = use_compiled,
-                          method.ode = method.ode,
--                         atol = atol, rtol = rtol, ...)
-+                         atol = atol, rtol = rtol,
-+                         call_lsoda = call_lsoda, ...)
- 
---- a/R/mkinpredict.R
-+++ b/R/mkinpredict.R
-
-@@ -116,9 +114,10 @@ mkinpredict.mkinmod <- function(x,
-   outtimes = seq(0, 120, by = 0.1),
-   solution_type = "deSolve",
-   use_compiled = "auto",
--  method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, maxsteps = 20000,
-+  method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, maxsteps = 20000L,
-   map_output = TRUE,
-   na_stop = TRUE,
-+  call_lsoda = NULL,
-   ...)
- {
- 
-@@ -173,20 +172,80 @@ mkinpredict.mkinmod <- function(x,
-   if (solution_type == "deSolve") {
-     if (!is.null(x$cf) & use_compiled[1] != FALSE) {
- 
--      out <- deSolve::ode(
--        y = odeini,
--        times = outtimes,
--        func = "diffs",
--        initfunc = "initpar",
--        dllname = if (is.null(x$dll_info)) inline::getDynLib(x$cf)[["name"]]
--          else x$dll_info[["name"]],
--        parms = odeparms[x$parms], # Order matters when using compiled models
--        method = method.ode,
--        atol = atol,
--        rtol = rtol,
--        maxsteps = maxsteps,
--        ...
-+      # Prepare call to "call_lsoda"
-+      # Simplified code from deSolve::lsoda() adapted to our use case
-+      if (is.null(call_lsoda)) {
-+        call_lsoda <- getNativeSymbolInfo("call_lsoda", PACKAGE = "deSolve")
-+      }
-+      if (is.null(x$diffs_address)) {
-+        x$diffs_address <- getNativeSymbolInfo("diffs",
-+          PACKAGE = x$dll_info[["name"]])$address
-+        x$initpar_address <- getNativeSymbolInfo("initpar",
-+          PACKAGE = x$dll_info[["name"]])$address
-+      }
-+      rwork <- vector("double", 20)
-+      rwork[] <- 0.
-+      rwork[6] <- max(abs(diff(outtimes)))
-+
-+      iwork <- vector("integer", 20)
-+      iwork[] <- 0
-+      iwork[6] <- maxsteps
-+
-+      n <- length(odeini)
-+      lmat <- n^2 + 2     # from deSolve::lsoda(), for Jacobian type full, internal (2)
-+      # hard-coded default values of lsoda():
-+      maxordn <- 12L
-+      maxords <- 5L
-+      lrn <- 20 + n * (maxordn + 1) + 3 * n  # length in case non-stiff method
-+      lrs <- 20 + n * (maxords + 1) + 3 * n + lmat        # length in case stiff method
-+      lrw <- max(lrn, lrs)                       # actual length: max of both
-+      liw <- 20 + n
-+
-+      on.exit(.C("unlock_solver", PACKAGE = "deSolve"))
-+
-+      out_raw <- .Call(call_lsoda,
-+        as.double(odeini),   # y
-+        as.double(outtimes), # times
-+        x$diffs_address,     # derivfunc
-+        as.double(odeparms[x$parms]), # parms
-+        rtol, atol,
-+        NULL, NULL, # rho, tcrit
-+        NULL, # jacfunc
-+        x$initpar_address, # initfunc
-+        NULL, # eventfunc
-+        0L,   # verbose
-+        1L,   # iTask
-+        as.double(rwork), # rWork
-+        as.integer(iwork), # iWork
-+        2L,     # jT full Jacobian calculated internally
-+        0L,    # nOut
-+        as.integer(lrw), # lRw
-+        as.integer(liw), # lIw
-+        1L, # Solver
-+        NULL, # rootfunc
-+        0L, as.double(0), 0L, # nRoot, Rpar, Ipar
-+        0L, # Type
-+        list(fmat = 0L, tmat = 0L, imat = 0L, ModelForc = NULL), # flist
-+        list(), # elist
-+        list(islag = 0L) # elag
-       )
-+
-+      out <- t(out_raw)
-+      colnames(out) <- c("time", mod_vars)
-     } else {
-       mkindiff <- function(t, state, parms) {
- 
-- 
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