--- a/dist-files.mk	Sat Jan 26 10:19:17 2019 -0500
+++ b/dist-files.mk	Sun Jan 20 17:59:50 2019 +0100
@@ -515,6 +515,7 @@
   of-odepkg-3-deprecated.patch \
   of-odepkg.mk \
   of-optim-1-fixes.patch \
+  of-optim-2-deprecated.patch \
   of-optim.mk \
   of-optiminterp-1-dev-fixes.patch \
   of-optiminterp.mk \

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/of-optim-2-deprecated.patch	Sun Jan 20 17:59:50 2019 +0100
@@ -0,0 +1,573 @@
+# HG changeset patch
+# User Olaf Till <i7tiol@t-online.de>
+# Date 1547218871 -3600
+#      Fri Jan 11 16:01:11 2019 +0100
+# Node ID 5fcbf411d5c2a4b076e3ababeb6126125243e49d
+# Parent  158b61118c7557f549656bf76ddc144c70bd3aa5
+remove deprecated samin.cc, still available as backend to nonlin_min
+
+diff -r 158b61118c75 -r 5fcbf411d5c2 src/Makefile.in
+--- a/src/Makefile.in	Fri Jan 11 15:29:45 2019 +0100
++++ b/src/Makefile.in	Fri Jan 11 16:01:11 2019 +0100
+@@ -46,7 +46,7 @@
+ TEXIFILE := $(addsuffix .texi,$(basename $(INFOFILE)))
+ TXIFILE := $(addsuffix .txi,$(basename $(INFOFILE)))
+ HTMLDIR := ../doc/html/
+-OCTFILES := __bfgsmin.oct numgradient.oct numhessian.oct samin.oct __disna_optim__.oct
++OCTFILES := __bfgsmin.oct numgradient.oct numhessian.oct __disna_optim__.oct
+ 
+ OCTSOURCEFILES := $(addsuffix .cc,$(basename $(OCTFILES)))
+ DSFILES := $(addsuffix .docstrings,$(OCTSOURCEFILES))
+diff -r 158b61118c75 -r 5fcbf411d5c2 src/samin.cc
+--- a/src/samin.cc	Fri Jan 11 15:29:45 2019 +0100
++++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
+@@ -1,549 +0,0 @@
+-// Copyright (C) 2004, 2006 Michael Creel <michael.creel@uab.es>
+-//
+-// This program is free software; you can redistribute it and/or modify it under
+-// the terms of the GNU General Public License as published by the Free Software
+-// Foundation; either version 3 of the License, or (at your option) any later
+-// version.
+-//
+-// This program is distributed in the hope that it will be useful, but WITHOUT
+-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+-// FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+-// details.
+-//
+-// You should have received a copy of the GNU General Public License along with
+-// this program; if not, see <http://www.gnu.org/licenses/>.
+-
+-// References:
+-//
+-// The code follows the article
+-// Goffe, William L. (1996) "SIMANN: A Global Optimization Algorithm
+-//      using Simulated Annealing " Studies in Nonlinear Dynamics & Econometrics
+-//      Oct96, Vol. 1 Issue 3.
+-//
+-// The code uses the same names for control variables,
+-// for the most part. A notable difference is that the initial
+-// temperature is found automatically to ensure that the active
+-// bounds when the temperature begins to reduce cover the entire
+-// parameter space (defined as a n-dimensional
+-// rectangle that is the Cartesian product of the
+-// (lb_i, ub_i), i = 1,2,..n
+-//
+-// Also of note:
+-// Corana et. al., (1987) "Minimizing Multimodal Functions of Continuous
+-//      Variables with the "Simulated Annealing" Algorithm",
+-//      ACM Transactions on Mathematical Software, V. 13, N. 3.
+-//
+-// Goffe, et. al. (1994) "Global Optimization of Statistical Functions
+-//      with Simulated Annealing", Journal of Econometrics,
+-//      V. 60, N. 1/2.
+-
+-#include <oct.h>
+-#include <octave/parse.h>
+-#include <octave/Cell.h>
+-#include <octave/lo-mappers.h>
+-#include <octave/oct-rand.h>
+-#include <float.h>
+-
+-#include "error-helpers.h"
+-
+-// define argument checks
+-static bool any_bad_argument(const octave_value_list& args)
+-{
+-
+-  // objective function name is a string?
+-  if (!args(0).is_string())
+-    {
+-      _p_error("samin: first argument must be string holding objective function name");
+-      return true;
+-    }
+-
+-  // are function arguments contained in a cell?
+-  if (!args(1).OV_ISCELL ())
+-    {
+-      _p_error("samin: second argument must cell array of function arguments");
+-      return true;
+-    }
+-
+-  // is control a cell?
+-  Cell control;
+-  bool err;
+-  SET_ERR (control =args(2).cell_value(), err);
+-  if (err)
+-    {
+-      _p_error("samin: third argument must cell array of algorithm controls");
+-      return true;
+-    }
+-
+-  // does control have proper number of elements?
+-  if (!(control.numel () == 11))
+-    {
+-      _p_error("samin: third argument must be a cell array with 11 elements");
+-      return true;
+-    }
+-
+-  // now check type of each element of control
+-  if (!(control(0).is_real_matrix()) && !(control(0).is_real_scalar()))
+-    {
+-      _p_error("samin: 1st element of controls must be LB: a vector of lower bounds");
+-      return true;
+-    }
+-
+-  if ((control(0).is_real_matrix()) && (control(0).columns() != 1))
+-    {
+-      _p_error("samin: 1st element of controls must be LB: a vector of lower bounds");
+-      return true;
+-    }
+-
+-  if (!(control(1).is_real_matrix()) && !(control(1).is_real_scalar()))
+-    {
+-      _p_error("samin: 1st element of controls must be UB: a vector of lower bounds");
+-      return true;
+-    }
+-
+-  if ((control(1).is_real_matrix()) && (control(1).columns() != 1))
+-    {
+-      _p_error("samin: 2nd element of controls must be UB: a vector of lower bounds");
+-      return true;
+-    }
+-
+-  int tmp;
+-  SET_ERR (tmp = control(2).int_value(), err);
+-  if (err || tmp < 1)
+-    {
+-      _p_error("samin: 3rd element of controls must be NT: positive integer\n\
+-loops per temperature reduction");
+-      return true;
+-    }
+-
+-  SET_ERR (tmp = control(3).int_value(), err);
+-  if (err || tmp < 1)
+-    {
+-      _p_error("samin: 4th element of controls must be NS: positive integer\n\
+-loops per stepsize adjustment");
+-      return true;
+-    }
+-
+-  double tmp2;
+-  SET_ERR (tmp2 = control(4).double_value(), err);
+-  if (err || tmp < 0)
+-    {
+-      _p_error("samin: 5th element of controls must be RT:\n\
+-temperature reduction factor, RT > 0");
+-      return true;
+-    }
+-
+-  SET_ERR (tmp2 = control(5).double_value(), err);
+-  if (err || tmp < 0)
+-    {
+-      _p_error("samin: 6th element of controls must be integer MAXEVALS > 0 ");
+-      return true;
+-    }
+-
+-  SET_ERR (tmp = control(6).int_value(), err);
+-  if (err || tmp < 0)
+-    {
+-      _p_error("samin: 7th element of controls must be NEPS: positive integer\n\
+-number of final obj. values that must be within EPS of eachother ");
+-      return true;
+-    }
+-
+-  SET_ERR (tmp2 = control(7).double_value(), err);
+-  if (err || tmp2 < 0)
+-    {
+-      _p_error("samin: 8th element of controls must must be FUNCTOL (> 0)\n\
+-used to compare the last NEPS obj values for convergence test");
+-      return true;
+-    }
+-
+-  SET_ERR (tmp2 = control(8).double_value(), err);
+-  if (err || tmp2 < 0)
+-    {
+-      _p_error("samin: 9th element of controls must must be PARAMTOL (> 0)\n\
+-used to compare the last NEPS obj values for convergence test");
+-      return true;
+-    }
+-
+-  SET_ERR (tmp = control(9).int_value(), err);
+-  if (err || tmp < 0 || tmp > 2)
+-    {
+-      _p_error("samin: 9th element of controls must be VERBOSITY (0, 1, or 2)");
+-      return true;
+-    }
+-
+-  SET_ERR (tmp = control(10).int_value(), err);
+-  if (err || tmp < 0)
+-    {
+-      _p_error("samin: 10th element of controls must be MINARG (integer)\n\
+-                position of argument to minimize wrt");
+-      return true;
+-    }
+-
+-  // make sure that minarg points to an existing element
+-  if ((tmp > args(1).length ()) || (tmp < 1))
+-    {
+-      _p_error("bfgsmin: 4th argument must be a positive integer that indicates \n\
+-which of the elements of the second argument is the one minimization is over");
+-      return true;
+-    }
+-
+-  return false;
+-}
+-
+-//-------------- The annealing algorithm --------------
+-DEFUN_DLD(samin, args, , "samin: simulated annealing minimization of a function. See samin_example.m\n\
+-\n\
+-samin will be removed from a future version of the optim package.\n\
+-Equivalent functionality is now in the samin backend of nonlin_min.\n\
+-\n\
+-usage: [x, obj, convergence, details] = samin(\"f\", {args}, {control})\n\
+-\n\
+-Arguments:\n\
+-* \"f\": function name (string)\n\
+-* {args}: a cell array that holds all arguments of the function,\n\
+-* {control}: a cell array with 11 elements\n\
+-        * LB  - vector of lower bounds\n\
+-        * UB - vector of upper bounds\n\
+-        * nt - integer: # of iterations between temperature reductions\n\
+-        * ns - integer: # of iterations between bounds adjustments\n\
+-        * rt - (0 < rt <1): temperature reduction factor\n\
+-        * maxevals - integer: limit on function evaluations\n\
+-        * neps - integer:  number of values final result is compared to\n\
+-        * functol -   (> 0): the required tolerance level for function value\n\
+-                           comparisons\n\
+-        * paramtol -  (> 0): the required tolerance level for parameters\n\
+-        * verbosity - scalar: 0, 1, or 2.\n\
+-                * 0 = no screen output\n\
+-                * 1 = only final results to screen\n\
+-                * 2 = summary every temperature change\n\
+-        * minarg - integer: which of function args is minimization over?\n\
+-\n\
+-Returns:\n\
+-* x: the minimizer\n\
+-* obj: the value of f() at x\n\
+-* convergence:\n\
+-        0 if no convergence within maxevals function evaluations\n\
+-        1 if normal convergence to a point interior to the parameter space\n\
+-        2 if convergence to point very near bounds of parameter space\n\
+-          (suggest re-running with looser bounds)\n\
+-* details: a px3 matrix. p is the number of times improvements were found.\n\
+-           The columns record information at the time an improvement was found\n\
+-           * first: cumulative number of function evaluations\n\
+-           * second: temperature\n\
+-           * third: function value\n\
+-\n\
+-Example: see samin_example\n\
+-")
+-{
+-  static bool warned = false;
+-  if (! warned)
+-    {
+-      warned = true;
+-      warning_with_id ("Octave:deprecated-function",
+-                       "samin will be removed from a future version of the optim package, equivalent functionality is now in the samin backend of nonlin_min");
+-    }
+-
+-  int nargin = args.length();
+-  if (!(nargin == 3))
+-    {
+-      error("samin: you must supply 3 arguments");
+-      return octave_value_list();
+-    }
+-
+-  // check the arguments
+-  if (any_bad_argument (args))
+-    {
+-      error ("error in samin");
+-      return octave_value_list();
+-    }
+-
+-  std::string obj_fn (args(0).string_value());
+-  Cell f_args_cell = args(1).cell_value (); // args to obj fn come in as a cell to allow arbitrary number
+-  Cell control (args(2).cell_value());
+-
+-  octave_value_list f_args;
+-  octave_value_list f_return; // holder for feval returns
+-
+-  int m, i, j, k, h, n, nacc, func_evals;
+-  int nup, nrej, nnew, ndown, lnobds;
+-  int converge, test, coverage_ok;
+-
+-  // user provided controls
+-  const ColumnVector lb (control(0).column_vector_value());
+-  const ColumnVector ub (control(1).column_vector_value());
+-  const int nt (control(2).int_value());
+-  const int ns (control(3).int_value());
+-  const double rt (control(4).double_value());
+-  const int maxevals (control(5).int_value());
+-  const int neps (control(6).int_value());
+-  const double functol (control(7).double_value());
+-  const double paramtol (control(8).double_value());
+-  const int verbosity (control(9).int_value());
+-  const int minarg (control(10).int_value());
+-
+-  // type checking for minimization parameter done here, since we don't know minarg
+-  // until now
+-  if (!(f_args_cell(minarg - 1).is_real_matrix() || (f_args_cell(minarg - 1).is_real_scalar())))
+-    {
+-      error("samin: minimization must be with respect to a column vector");
+-      return octave_value_list();
+-    }
+-  if ((f_args_cell(minarg - 1).is_real_matrix()) && (f_args_cell(minarg - 1).columns() != 1))
+-    {
+-      error("samin: minimization must be with respect to a column vector");
+-      return octave_value_list();
+-    }
+-
+-  double f, fp, p, fopt, rand_draw, ratio, t;
+-
+-  Matrix details(1,3); // record function evaluations, temperatures and function values
+-  RowVector info(3);
+-
+-  // copy cell contents over to octave_value_list to use feval()
+-  k = f_args_cell.numel ();
+-  f_args(k); // resize only once
+-  for (i = 0; i<k; i++) f_args(i) = f_args_cell(i);
+-
+-  ColumnVector x  = f_args(minarg - 1).column_vector_value();
+-  ColumnVector bounds = ub - lb;
+-  n = x.rows();
+-  ColumnVector xopt = x;
+-  ColumnVector xp(n);
+-  ColumnVector nacp(n);
+-
+-  //  Set initial values
+-  nacc = 0; // total accepted trials
+-  t = 1000.0; // temperature - will initially rise or fall to cover parameter space. Then it will fall
+-  converge = 0; // convergence indicator 0 (failure), 1 (normal success), or 2 (convergence but near bounds)
+-  coverage_ok = 0; // has parameter space been covered? When turns to 1, temperature starts to fall
+-  // most recent values, to compare to when checking convergend
+-  ColumnVector fstar(neps,1);
+-  fstar.fill(DBL_MAX);
+-  octave_rand::distribution("uniform");  // we'll be using draws from U(0,1)
+-
+-  // check for out-of-bounds starting values
+-  for(i = 0; i < n; i++)
+-    {
+-      if(( x(i) > ub(i)) || (x(i) < lb(i)))
+-        {
+-          error("samin: initial parameter %d out of bounds", i+1);
+-          return octave_value_list();
+-        }
+-    }
+-
+-  // Initial obj_value
+-  f_return = OCTAVE__FEVAL (obj_fn, f_args);
+-  f = f_return(0).double_value();
+-  fopt = f; // give it something to compare to
+-  func_evals = 0; // total function evaluations (limited by maxeval)
+-  details(0,0) = func_evals;
+-  details(0,1) = t;
+-  details(0,2) = fopt;
+-
+-  // main loop, first increase temperature until parameter space covered, then reduce until convergence
+-  while(converge==0)
+-    {
+-      // statistics to report at each temp change, set back to zero
+-      nup = 0;
+-      nrej = 0;
+-      nnew = 0;
+-      ndown = 0;
+-      lnobds = 0;
+-
+-      // repeat nt times then adjust temperature
+-      for(m = 0;m < nt;m++)
+-        {
+-          // repeat ns times, then adjust bounds
+-          for(j = 0;j < ns;j++)
+-            {
+-              // generate new point by taking last and adding a random value
+-              // to each of elements, in turn
+-              for(h = 0;h < n;h++)
+-                {
+-                  // new Sept 2011, if bounds are same, skip the search for that vbl. Allows restrictions without complicated programming
+-                  if (lb(h) != ub(h))
+-                    {
+-                      xp = x;
+-                      rand_draw = octave_rand::scalar();
+-                      xp(h) = x(h) + (2.0 * rand_draw - 1.0) * bounds(h);
+-                      if ((xp(h) < lb(h)) || (xp(h) > ub(h)))
+-                        {
+-                          rand_draw = octave_rand::scalar(); // change 07-Nov-2007: avoid correlation with hitting bounds
+-                          xp(h) = lb(h) + (ub(h) - lb(h)) * rand_draw;
+-                          lnobds = lnobds + 1;
+-                        }
+-                      // Evaluate function at new point
+-                      f_args(minarg - 1) = xp;
+-                      f_return = OCTAVE__FEVAL (obj_fn, f_args);
+-                      fp = f_return(0).double_value();
+-                      func_evals = func_evals + 1;
+-                      //  Accept the new point if the function value decreases
+-                      if(fp <= f)
+-                        {
+-                          x = xp;
+-                          f = fp;
+-                          nacc = nacc + 1; // total number of acceptances
+-                          nacp(h) = nacp(h) + 1; // acceptances for this parameter
+-                          nup = nup + 1;
+-                          //  If lower than any other point, record as new optimum
+-                          if(fp < fopt)
+-                            {
+-                              xopt = xp;
+-                              fopt = fp;
+-                              nnew = nnew + 1;
+-                              info(0) = func_evals;
+-                              info(1) = t;
+-                              info(2) = fp;
+-                              details = details.stack(info);
+-                            }
+-                        }
+-                      // If the point is higher, use the Metropolis criteria to decide on
+-                      // acceptance or rejection.
+-                      else
+-                        {
+-                          p = exp(-(fp - f) / t);
+-                          rand_draw = octave_rand::scalar();
+-                          if(rand_draw < p)
+-                            {
+-                              x = xp;
+-                              f = fp;
+-                              nacc = nacc + 1;
+-                              nacp(h) = nacp(h) + 1;
+-                              ndown = ndown + 1;
+-                            }
+-                          else nrej = nrej + 1;
+-                        }
+-                    }
+-                  // If maxevals exceeded, terminate the algorithm
+-                  if (func_evals >= maxevals)
+-                    {
+-                      if (verbosity >= 1)
+-                        {
+-                          printf("\n================================================\n");
+-                          printf("SAMIN results\n");
+-                          printf("NO CONVERGENCE: MAXEVALS exceeded\n");
+-                          printf("================================================\n");
+-                          printf("Convergence tolerances: Func. tol. %e	Param. tol. %e\n", functol, paramtol);
+-                          printf("Obj. fn. value %f\n\n", fopt);
+-                          printf("	   parameter	    search width\n");
+-                          for(i = 0; i < n; i++) printf("%20f%20f\n", xopt(i), bounds(i));
+-                        }
+-                      f_return(3) = details;
+-                      f_return(2) = 0;
+-                      f_return(1) = fopt;
+-                      f_return(0) = xopt;
+-                      return octave_value_list(f_return);
+-                    }
+-                }
+-            }
+-          //  Adjust bounds so that approximately half of all evaluations are accepted
+-          test = 0;
+-          for(i = 0;i < n;i++)
+-            {
+-              if (lb(i) != ub(i))
+-                {
+-                  ratio = nacp(i) / ns;
+-                  if(ratio > 0.6) bounds(i) = bounds(i) * (1.0 + 2.0 * (ratio - 0.6) / 0.4);
+-                  else if (ratio < .4)
+-                    bounds(i) = bounds(i) / (1.0 + 2.0 * ((0.4 - ratio) / 0.4));
+-                  // keep within initial bounds
+-                  if(bounds(i) >= (ub(i) - lb(i)))
+-                    {
+-                      bounds(i) = ub(i) - lb(i);
+-                      test = test + 1;
+-                    }
+-                }
+-              else
+-                test = test + 1; // make sure coverage check passes for the fixed parameters
+-            }
+-          nacp.fill(0.0);
+-          // check if we cover parameter space. if we have yet to do so
+-          if (!coverage_ok) coverage_ok = (test == n);
+-        }
+-      // intermediate output, if desired
+-      if(verbosity == 2)
+-        {
+-          printf("\nsamin: intermediate results before next temperature change\n");
+-          printf("\ntemperature  %e", t);
+-          printf("\ncurrent best function value %f", fopt);
+-          printf("\ntotal evaluations so far %d", func_evals);
+-          printf("\ntotal moves since last temperature reduction  %d", nup + ndown + nrej);
+-          printf("\ndownhill  %d", nup);
+-          printf("\naccepted uphill %d", ndown);
+-          printf("\nrejected uphill %d", nrej);
+-          printf("\nout of bounds trials %d", lnobds);
+-          printf("\nnew minima this temperature %d", nnew);
+-          printf("\n\n	       parameter	search width\n");
+-          for(i = 0; i < n; i++) printf("%20f%20f\n", xopt(i), bounds(i));
+-          printf("\n");
+-        }
+-      // Check for convergence, if we have covered the parameter space
+-      if (coverage_ok)
+-        {
+-          // last value close enough to last neps values?
+-          fstar(0) = f;
+-          test = 0;
+-          for (i = 1; i < neps; i++) test = test + fabs(f - fstar(i)) > functol;
+-          test = (test > 0); // if different from zero, function conv. has failed
+-          // last value close enough to overall best?
+-          if (((fopt - f) <= functol) && (!test))
+-            {
+-              // check for bound narrow enough for parameter convergence
+-              for (i = 0;i < n;i++)
+-                {
+-                  if (bounds(i) > paramtol)
+-                    {
+-                      converge = 0; // no conv. if bounds too wide
+-                      break;
+-                    }
+-                  else
+-                    converge = 1;
+-                }
+-            }
+-          // check if optimal point is near boundary of parameter space, and change convergence message if so
+-          if (converge && lnobds > 0) converge = 2;
+-          // Like to see the final results?
+-          if (converge > 0)
+-            {
+-              if (verbosity >= 1)
+-                {
+-                  printf("\n================================================\n");
+-                  printf("SAMIN results\n\n");
+-                  if (converge == 1) printf("==> Normal convergence <==\n\n");
+-                  if (converge == 2)
+-                    {
+-                      printf("==> WARNING <==: Last point satisfies convergence criteria,\n");
+-                      printf("but is near boundary of parameter space.\n");
+-                      printf("%d out of  %d evaluations were out-of-bounds in the last round.\n", lnobds, (nup+ndown+nrej));
+-                      printf("Expand bounds and re-run, unless this is a constrained minimization.\n\n");
+-                    }
+-                  printf("Convergence tolerances:\nFunction: %e\nParameters: %e\n", functol, paramtol);
+-                  printf("\nObjective function value at minimum: %f\n\n", fopt);
+-                  printf("	   parameter	    search width\n");
+-                  for(i = 0; i < n; i++) printf("%20f%20f\n", xopt(i), bounds(i));
+-                  printf("================================================\n");
+-                }
+-              f_return(3) = details;
+-              f_return(2) = converge;
+-              f_return(1) = fopt;
+-              f_return(0) = xopt;
+-              return f_return; // this breaks out, if we get here
+-            }
+-          // Reduce temperature, record current function value in the
+-          // list of last "neps" values, and loop again
+-          t = rt * t;
+-          for(i = neps-1; i > 0; i--) fstar(i) = fstar(i-1);
+-          f = fopt;
+-          x = xopt;
+-        }
+-      else
+-        {
+-          // coverage not ok - increase temperature quickly to expand search area, to cover parameter space
+-          t = t*t;
+-          for(i = neps-1; i > 0; i--) fstar(i) = fstar(i-1);
+-          f = fopt;
+-          x = xopt;
+-        }
+-    }
+-  // silence compiler warning
+-  return octave_value_list ();
+-}