Update to 4.4.1

2018-10-28 13:14:45 -06:00 · 2018-10-28 13:14:45 -06:00 · 281df3b846
parent 65d166658d
commit 281df3b846
9 changed files with 561 additions and 80 deletions
--- a/.gitignore
+++ b/.gitignore
@ -28,3 +28,5 @@ octave-3.2.4.tar.bz2
 /octave-4.2.0.tar.lz
 /octave-4.2.1.tar.lz
 /octave-4.2.2.tar.lz
+/octave-4.4.1.tar.lz
+/octave-4.4.1-docs.tar.gz
--- a/macros.octave
+++ b/macros.octave
@ -60,9 +60,9 @@ echo "endfunction" >> %{buildroot}%{octpkgdir}/packinfo/on_uninstall.m \
 if [ -e %{_builddir}/%{buildsubdir}/build/%{octpkg}-%{version}/*.metainfo.xml ] \
 then \
  echo "Found .metainfo.xml appdata file" \
-  mkdir -p %{buildroot}/%{_datadir}/appdata \
-  cp -p %{_builddir}/%{buildsubdir}/build/%{octpkg}-%{version}/*.metainfo.xml %{buildroot}/%{_datadir}/appdata/ \
-  appstream-util validate-relax --nonet %{buildroot}/%{_datadir}/appdata/*.metainfo.xml \
+  mkdir -p %{buildroot}/%{_metainfodir} \
+  cp -p %{_builddir}/%{buildsubdir}/build/%{octpkg}-%{version}/*.metainfo.xml %{buildroot}/%{_metainfodir}/ \
+  appstream-util validate-relax --nonet %{buildroot}/%{_metainfodir}/*.metainfo.xml \
 else \
  echo "Did not find a .metainfo.xml appdata file" \
 fi \
--- a/octave-appdata.patch
+++ b/octave-appdata.patch
@ -1,9 +0,0 @@
-diff -up octave-4.2.1/etc/icons/octave.appdata.xml.in.appdata octave-4.2.1/etc/icons/octave.appdata.xml.in
--- octave-4.2.1/etc/icons/octave.appdata.xml.in.appdata	2017-02-24 20:46:50.581334701 -0700
-+++ octave-4.2.1/etc/icons/octave.appdata.xml.in	2017-02-24 20:47:29.866515768 -0700
-@@ -58,5 +58,4 @@
- 
-   <url type="homepage">http://www.octave.org</url>
-   <update_contact>maintainers@octave.org</update_contact>
-  <project_group>GNU</project_group>
- </component>
--- a/octave-crash.patch
+++ b/octave-crash.patch
@ -1,12 +1,12 @@
-diff -up octave-4.2.2/libinterp/corefcn/input.cc.crash octave-4.2.2/libinterp/corefcn/input.cc
--- octave-4.2.2/libinterp/corefcn/input.cc.crash	2018-02-28 11:41:44.000000000 -0700
-+++ octave-4.2.2/libinterp/corefcn/input.cc	2018-06-21 21:29:18.352517844 -0600
-@@ -298,7 +298,7 @@ octave_base_reader::octave_gets (bool& e
+diff -up octave-4.4.1/libinterp/corefcn/input.cc.crash octave-4.4.1/libinterp/corefcn/input.cc
+--- octave-4.4.1/libinterp/corefcn/input.cc.crash	2018-11-11 17:27:39.588037444 -0700
+++ octave-4.4.1/libinterp/corefcn/input.cc	2018-11-11 17:30:42.344208272 -0700
+@@ -255,7 +255,7 @@ namespace octave
 
-       octave_diary << retval;
+         octave_diary << retval;
 
-      if (retval[retval.length () - 1] != '\n')
-+      if (!retval.empty () && retval.back () != '\n')
-         octave_diary << "\n";
- 
-       do_input_echo (retval);
+-        if (retval.back () != '\n')
+        if (!retval.empty () && retval.back () != '\n')
+           octave_diary << "\n";
+       }
+     else
--- a/octave-gnulib.patch
+++ b/octave-gnulib.patch
@ -1,11 +0,0 @@
-diff -up octave-4.0.0/liboctave/cruft/Faddeeva/Faddeeva.hh.gnulib octave-4.0.0/liboctave/cruft/Faddeeva/Faddeeva.hh
--- octave-4.0.0/liboctave/cruft/Faddeeva/Faddeeva.hh.gnulib	2015-05-23 08:21:53.000000000 -0600
-+++ octave-4.0.0/liboctave/cruft/Faddeeva/Faddeeva.hh	2016-02-19 19:50:04.693811663 -0700
-@@ -27,6 +27,7 @@
- #ifndef FADDEEVA_HH
- #define FADDEEVA_HH 1
- 
-+#include <math.h>
- #include <complex>
- 
- namespace Faddeeva {
--- a/octave-qbuttongroup.patch
+++ b/octave-qbuttongroup.patch
@ -1,11 +0,0 @@
-diff -up octave-4.2.2/libgui/src/settings-dialog.cc.orig octave-4.2.2/libgui/src/settings-dialog.cc
--- octave-4.2.2/libgui/src/settings-dialog.cc.orig	2018-02-28 11:41:44.000000000 -0700
-+++ octave-4.2.2/libgui/src/settings-dialog.cc	2018-06-02 14:09:38.138706993 -0600
-@@ -36,6 +36,7 @@ along with Octave; see the file COPYING.
- #include <QHash>
- #include <QMessageBox>
- #include <QTextCodec>
-+#include <QButtonGroup>
- 
- #if defined (HAVE_QSCINTILLA)
- #  include "octave-qscintilla.h"
--- a/octave-sundials3.patch
+++ b/octave-sundials3.patch
@ -0,0 +1,504 @@
+diff -up octave-4.4.1/configure.ac.sundials3 octave-4.4.1/configure.ac
+--- octave-4.4.1/configure.ac.sundials3	2018-08-09 12:20:32.000000000 -0600
+++ octave-4.4.1/configure.ac	2018-10-28 14:06:56.907293616 -0600
+@@ -2315,15 +2315,15 @@ OCTAVE_CHECK_LIB(sundials_ida, [SUNDIALS
+   [], [don't use SUNDIALS IDA library, solvers ode15i and ode15s will be disabled],
+   [warn_sundials_ida=
+    OCTAVE_CHECK_SUNDIALS_SIZEOF_REALTYPE
+-   OCTAVE_CHECK_SUNDIALS_IDA_DENSE
+-   OCTAVE_CHECK_SUNDIALS_IDAKLU])
+   OCTAVE_CHECK_SUNDIALS_SUNLINSOL_DENSE
+   OCTAVE_CHECK_SUNDIALS_SUNLINSOL_KLU])
+ LIBS="$save_LIBS"
+ 
+ dnl Define this way instead of with an #if in oct-conf-post.h so that
+ dnl the build features script will get the correct value.
+ if test -n "$SUNDIALS_IDA_LIBS" \
+     && test -n "$SUNDIALS_NVECSERIAL_LIBS" \
+-    && test $octave_cv_sundials_ida_dense = yes \
+    && test $octave_cv_sundials_sunlinsol_dense = yes \
+     && test $octave_cv_sundials_realtype_is_double = yes; then
+   AC_DEFINE(HAVE_SUNDIALS, 1, [Define to 1 if SUNDIALS is available.])
+ fi
+diff -up octave-4.4.1/libinterp/dldfcn/__ode15__.cc.sundials3 octave-4.4.1/libinterp/dldfcn/__ode15__.cc
+--- octave-4.4.1/libinterp/dldfcn/__ode15__.cc.sundials3	2018-08-09 12:20:32.000000000 -0600
+++ octave-4.4.1/libinterp/dldfcn/__ode15__.cc	2018-10-28 14:26:11.482248630 -0600
+@@ -1,6 +1,7 @@
+ /*
+ 
+ Copyright (C) 2016-2018 Francesco Faccio <francesco.faccio@mail.polimi.it>
+Copyright (C) 2018 William Greene <w.h.greene@gmail.com>
+ 
+ This file is part of Octave.
+ 
+@@ -43,15 +44,34 @@ along with Octave; see the file COPYING.
+ #    include <ida/ida.h>
+ #  endif
+ 
+-#  if defined (HAVE_IDA_IDA_DENSE_H)
+-#    include <ida/ida_dense.h>
+#  if defined (HAVE_SUNDIALS_SUNDIALS_MATRIX_H)
+#    include <sundials/sundials_matrix.h>
+ #  endif
+ 
+-#  if defined (HAVE_IDA_IDA_KLU_H)
+-#    include <ida/ida_klu.h>
+#  if defined (HAVE_SUNDIALS_SUNDIALS_LINEARSOLVER_H)
+#    include <sundials/sundials_linearsolver.h>
+#  endif
+
+#  if defined (HAVE_SUNLINSOL_SUNLINSOL_DENSE_H)
+#    include <sunlinsol/sunlinsol_dense.h>
+#  endif
+
+#  if defined (HAVE_IDA_IDA_DIRECT_H)
+#    include <ida/ida_direct.h>
+#  endif
+
+#  if defined (HAVE_SUNDIALS_SUNDIALS_SPARSE_H)
+ #    include <sundials/sundials_sparse.h>
+ #  endif
+ 
+#  if defined (HAVE_SUNLINSOL_SUNLINSOL_KLU_H)
+#    include <sunlinsol/sunlinsol_klu.h>
+#  endif
+
+#  if defined (HAVE_SUNMATRIX_SUNMATRIX_SPARSE_H)
+#    include <sunmatrix/sunmatrix_sparse.h>
+#  endif
+
+ #  if defined (HAVE_NVECTOR_NVECTOR_SERIAL_H)
+ #    include <nvector/nvector_serial.h>
+ #  endif
+@@ -111,7 +131,8 @@ namespace octave
+         havejacsparse (false), mem (nullptr), num (), ida_fun (nullptr),
+         ida_jac (nullptr), dfdy (nullptr), dfdyp (nullptr), spdfdy (nullptr),
+         spdfdyp (nullptr), fun (nullptr), jacfun (nullptr), jacspfun (nullptr),
+-        jacdcell (nullptr), jacspcell (nullptr)
+        jacdcell (nullptr), jacspcell (nullptr),
+        sunJacMatrix (nullptr), sunLinearSolver (nullptr)
+     { }
+ 
+ 
+@@ -121,11 +142,17 @@ namespace octave
+         havejacsparse (false), mem (nullptr), num (), ida_fun (ida_fcn),
+         ida_jac (nullptr), dfdy (nullptr), dfdyp (nullptr), spdfdy (nullptr),
+         spdfdyp (nullptr), fun (daefun), jacfun (nullptr), jacspfun (nullptr),
+-        jacdcell (nullptr), jacspcell (nullptr)
+        jacdcell (nullptr), jacspcell (nullptr),
+        sunJacMatrix (nullptr), sunLinearSolver (nullptr)
+     { }
+ 
+ 
+-    ~IDA (void) { IDAFree (&mem); }
+    ~IDA (void)
+    {
+      IDAFree (&mem);
+      SUNLinSolFree(sunLinearSolver);
+      SUNMatDestroy(sunJacMatrix);
+    }
+ 
+     IDA&
+     set_jacobian (octave_function *jac, DAEJacFuncDense j)
+@@ -183,7 +210,7 @@ namespace octave
+     static N_Vector ColToNVec (const ColumnVector& data, long int n);
+ 
+     void
+-    set_up (void);
+    set_up (const ColumnVector& y);
+ 
+     void
+     set_tolerance (ColumnVector& abstol, realtype reltol);
+@@ -198,25 +225,24 @@ namespace octave
+     void
+     resfun_impl (realtype t, N_Vector& yy,
+                  N_Vector& yyp, N_Vector& rr);
+-
+     static int
+-    jacdense (long int Neq, realtype t,  realtype cj, N_Vector yy,
+-              N_Vector yyp, N_Vector, DlsMat JJ, void *user_data,
+    jacdense (realtype t, realtype cj, N_Vector yy,
+              N_Vector yyp, N_Vector, SUNMatrix JJ, void *user_data,
+               N_Vector, N_Vector, N_Vector)
+     {
+       IDA *self = static_cast <IDA *> (user_data);
+-      self->jacdense_impl (Neq, t, cj, yy, yyp, JJ);
+      self->jacdense_impl (t, cj, yy, yyp, JJ);
+       return 0;
+     }
+ 
+     void
+-    jacdense_impl (long int Neq, realtype t, realtype cj,
+-                   N_Vector& yy, N_Vector& yyp, DlsMat& JJ);
+    jacdense_impl (realtype t, realtype cj,
+                   N_Vector& yy, N_Vector& yyp, SUNMatrix& JJ);
+ 
+-#  if defined (HAVE_SUNDIALS_IDAKLU)
+#  if defined (HAVE_SUNDIALS_SUNLINSOL_KLU)
+     static int
+     jacsparse (realtype t, realtype cj, N_Vector yy, N_Vector yyp,
+-               N_Vector, SlsMat Jac, void *user_data, N_Vector,
+               N_Vector, SUNMatrix Jac, void *user_data, N_Vector,
+                N_Vector, N_Vector)
+     {
+       IDA *self = static_cast <IDA *> (user_data);
+@@ -226,7 +252,7 @@ namespace octave
+ 
+     void
+     jacsparse_impl (realtype t, realtype cj, N_Vector& yy,
+-                    N_Vector& yyp, SlsMat& Jac);
+                    N_Vector& yyp, SUNMatrix& Jac);
+ #endif
+ 
+     void set_maxstep (realtype maxstep);
+@@ -290,6 +316,8 @@ namespace octave
+     DAEJacFuncSparse jacspfun;
+     DAEJacCellDense jacdcell;
+     DAEJacCellSparse jacspcell;
+    SUNMatrix sunJacMatrix;
+    SUNLinearSolver sunLinearSolver;
+   };
+ 
+   int
+@@ -322,36 +350,61 @@ namespace octave
+   }
+ 
+   void
+-  IDA::set_up (void)
+  IDA::set_up (const ColumnVector& y)
+   {
+    N_Vector yy = ColToNVec(y, num);
+
+     if (havejacsparse)
+       {
+-#  if defined (HAVE_SUNDIALS_IDAKLU)
+-        if (IDAKLU (mem, num, num*num, CSC_MAT) != 0)
+-          error ("IDAKLU solver not initialized");
+#if defined (HAVE_SUNDIALS_SUNLINSOL_KLU)
+
+        sunJacMatrix = SUNSparseMatrix (num, num, num*num, CSC_MAT);
+        if (! sunJacMatrix)
+          error ("Unable to create sparse Jacobian for Sundials");
+
+        sunLinearSolver = SUNKLU (yy, sunJacMatrix);
+        if (! sunLinearSolver)
+          error ("Unable to create KLU sparse solver");
+
+        if (IDADlsSetLinearSolver (mem, sunLinearSolver, sunJacMatrix))
+          error ("Unable to set sparse linear solver");
+
+        IDADlsSetJacFn(mem, IDA::jacsparse);
+ 
+-        IDASlsSetSparseJacFn (mem, IDA::jacsparse);
+ #  else
+-        error ("IDAKLU is not available in this version of Octave");
+        error ("SUNDIALS SUNLINSOL KLU is not available in this version of Octave");
+ #  endif
+
+       }
+     else
+       {
+-        if (IDADense (mem, num) != 0)
+-          error ("IDADense solver not initialized");
+ 
+-        if (havejac && IDADlsSetDenseJacFn (mem, IDA::jacdense) != 0)
+-          error ("Dense Jacobian not set");
+        sunJacMatrix = SUNDenseMatrix (num, num);
+        if (! sunJacMatrix)
+          error ("Unable to create dense Jacobian for Sundials");
+
+        sunLinearSolver = SUNDenseLinearSolver(yy, sunJacMatrix);
+        if (! sunLinearSolver)
+          error ("Unable to create dense linear solver");
+
+        if (IDADlsSetLinearSolver (mem, sunLinearSolver, sunJacMatrix))
+          error ("Unable to set dense linear solver");
+
+        if (havejac && IDADlsSetJacFn (mem, IDA::jacdense) != 0)
+          error("Unable to set dense Jacobian function");
+
+       }
+   }
+ 
+   void
+-  IDA::jacdense_impl (long int Neq, realtype t, realtype cj,
+-                      N_Vector& yy, N_Vector& yyp, DlsMat& JJ)
+  IDA::jacdense_impl (realtype t, realtype cj,
+                      N_Vector& yy, N_Vector& yyp, SUNMatrix& JJ)
+ 
+   {
+     BEGIN_INTERRUPT_WITH_EXCEPTIONS;
+ 
+    long int Neq = NV_LENGTH_S(yy);
+
+     ColumnVector y = NVecToCol (yy, Neq);
+ 
+     ColumnVector yp = NVecToCol (yyp, Neq);
+@@ -365,15 +418,15 @@ namespace octave
+ 
+     std::copy (jac.fortran_vec (),
+                jac.fortran_vec () + jac.numel (),
+-               JJ->data);
+      SUNDenseMatrix_Data(JJ));
+ 
+     END_INTERRUPT_WITH_EXCEPTIONS;
+   }
+ 
+-#  if defined (HAVE_SUNDIALS_IDAKLU)
+#  if defined (HAVE_SUNDIALS_SUNLINSOL_KLU)
+   void
+   IDA::jacsparse_impl (realtype t, realtype cj, N_Vector& yy, N_Vector& yyp,
+-                       SlsMat& Jac)
+                       SUNMatrix& Jac)
+ 
+   {
+     BEGIN_INTERRUPT_WITH_EXCEPTIONS;
+@@ -389,17 +442,18 @@ namespace octave
+     else
+       jac = (*jacspcell) (spdfdy, spdfdyp, cj);
+ 
+-    SparseSetMatToZero (Jac);
+-    int *colptrs = *(Jac->colptrs);
+-    int *rowvals = *(Jac->rowvals);
+    SUNMatZero_Sparse (Jac);
+    sunindextype *colptrs = SUNSparseMatrix_IndexPointers (Jac);
+    sunindextype *rowvals = SUNSparseMatrix_IndexValues (Jac);
+ 
+     for (int i = 0; i < num + 1; i++)
+       colptrs[i] = jac.cidx(i);
+ 
+    double *d = SUNSparseMatrix_Data (Jac);
+     for (int i = 0; i < jac.nnz (); i++)
+       {
+         rowvals[i] = jac.ridx(i);
+-        Jac->data[i] = jac.data(i);
+        d[i] = jac.data(i);
+       }
+ 
+     END_INTERRUPT_WITH_EXCEPTIONS;
+@@ -566,7 +620,7 @@ namespace octave
+ 
+         //main loop
+         while (((posdirection == 1 && tsol < tend)
+-                || (posdirection == 0 && tsol > tend))
+               || (posdirection == 0 && tsol > tend))
+                && status == 0)
+           {
+             if (IDASolve (mem, tend, &tsol, yy, yyp, IDA_ONE_STEP) != 0)
+@@ -691,7 +745,7 @@ namespace octave
+             // Linear interpolation
+             ie(0) = index(0);
+             te(0) = tsol - val (index(0)) * (tsol - told)
+-                    / (val (index(0)) - oldval (index(0)));
+              / (val (index(0)) - oldval (index(0)));
+ 
+             ColumnVector ytemp
+               = y - ((tsol - te(0)) * (y - yold) / (tsol - told));
+@@ -716,7 +770,7 @@ namespace octave
+                 // Linear interpolation
+                 ie(temp+i) = index(i);
+                 te(temp+i) = tsol - val(index(i)) * (tsol - told)
+-                             / (val(index(i)) - oldval(index(i)));
+                  / (val(index(i)) - oldval(index(i)));
+ 
+                 ColumnVector ytemp
+                   = y - (tsol - te (temp + i)) * (y - yold) / (tsol - told);
+@@ -1095,7 +1149,7 @@ namespace octave
+       event_fcn = options.getfield("Events").function_value ();
+ 
+     // Set up linear solver
+-    dae.set_up ();
+    dae.set_up (y0);
+ 
+     // Integrate
+     retval = dae.integrate (numt, tspan, y0, yp0, refine,
+diff -up octave-4.4.1/m4/acinclude.m4.sundials3 octave-4.4.1/m4/acinclude.m4
+--- octave-4.4.1/m4/acinclude.m4.sundials3	2018-08-09 12:20:32.000000000 -0600
+++ octave-4.4.1/m4/acinclude.m4	2018-10-28 14:06:56.909293633 -0600
+@@ -2174,14 +2174,11 @@ dnl Check whether SUNDIALS IDA library i
+ dnl precision realtype.
+ dnl
+ AC_DEFUN([OCTAVE_CHECK_SUNDIALS_SIZEOF_REALTYPE], [
+-  AC_CHECK_HEADERS([ida/ida.h ida.h])
+   AC_CACHE_CHECK([whether SUNDIALS IDA is configured with double precision realtype],
+     [octave_cv_sundials_realtype_is_double],
+     [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
+         #if defined (HAVE_IDA_IDA_H)
+         #include <ida/ida.h>
+-        #else
+-        #include <ida.h>
+         #endif
+         #include <assert.h>
+         ]], [[
+@@ -2197,61 +2194,72 @@ AC_DEFUN([OCTAVE_CHECK_SUNDIALS_SIZEOF_R
+   fi
+ ])
+ dnl
+-dnl Check whether SUNDIALS IDA library is configured with IDAKLU
+dnl Check whether SUNDIALS IDA library is configured with SUNLINSOL_KLU
+ dnl enabled.
+ dnl
+-AC_DEFUN([OCTAVE_CHECK_SUNDIALS_IDAKLU], [
+-  AC_CHECK_HEADERS([ida/ida_klu.h ida_klu.h])
+-  AC_CACHE_CHECK([whether SUNDIALS IDA is configured with IDAKLU enabled],
+-    [octave_cv_sundials_idaklu],
+AC_DEFUN([OCTAVE_CHECK_SUNDIALS_SUNLINSOL_KLU], [
+  AC_CHECK_HEADERS([sundials/sundials_sparse.h sunlinsol/sunlinsol_klu.h sunmatrix/sunmatrix_sparse.h])
+  AC_CACHE_CHECK([whether SUNDIALS IDA is configured with SUNLINSOL_KLU enabled],
+    [octave_cv_sundials_sunlinsol_klu],
+     [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
+-         #if defined (HAVE_IDA_IDA_KLU_H)
+-         #include <ida/ida_klu.h>
+-         #else
+-         #include <ida_klu.h>
+         #if defined (HAVE_IDA_IDA_H)
+         #include <ida/ida.h>
+         #endif
+         #if defined (HAVE_SUNDIALS_SUNDIALS_SPARSE_H)
+         #include <sundials/sundials_sparse.h>
+         #endif
+         #if defined (HAVE_SUNLINSOL_SUNLINSOL_KLU_H)
+         #include <sunlinsol/sunlinsol_klu.h>
+          #endif
+          ]], [[
+-         IDAKLU (0, 0, 0, 0);
+         SUNKLU (0, 0);
+       ]])],
+-      octave_cv_sundials_idaklu=yes,
+-      octave_cv_sundials_idaklu=no)
+      octave_cv_sundials_sunlinsol_klu=yes,
+      octave_cv_sundials_sunlinsol_klu=no)
+     ])
+-  if test $octave_cv_sundials_idaklu = yes; then
+-    AC_DEFINE(HAVE_SUNDIALS_IDAKLU, 1,
+-      [Define to 1 if SUNDIALS IDA is configured with IDAKLU enabled.])
+  if test $octave_cv_sundials_sunlinsol_klu = yes; then
+    AC_DEFINE(HAVE_SUNDIALS_SUNLINSOL_KLU, 1,
+      [Define to 1 if SUNDIALS IDA is configured with SUNLINSOL_KLU enabled.])
+   else
+-    warn_sundials_idaklu="SUNDIALS IDA library not configured with IDAKLU, ode15i and ode15s will not support the sparse Jacobian feature"
+-    OCTAVE_CONFIGURE_WARNING([warn_sundials_idaklu])
+    warn_sundials_idaklu="SUNDIALS IDA library not configured with SUNLINSOL_KLU, ode15i and ode15s will not support the sparse Jacobian feature"
+    OCTAVE_CONFIGURE_WARNING([warn_sundials_sunlinsol_klu])
+   fi
+ ])
+ dnl
+-dnl Check whether SUNDIALS IDA library has the IDADENSE linear solver.
+dnl Check whether SUNDIALS IDA library has the SUNLINSOL_DENSE linear solver.
+ dnl The IDADENSE API was removed in SUNDIALS version 3.0.0.
+ dnl
+-AC_DEFUN([OCTAVE_CHECK_SUNDIALS_IDA_DENSE], [
+-  AC_CHECK_HEADERS([ida/ida_dense.h ida_dense.h])
+-  AC_CACHE_CHECK([whether SUNDIALS IDA includes the IDADENSE linear solver],
+-    [octave_cv_sundials_ida_dense],
+AC_DEFUN([OCTAVE_CHECK_SUNDIALS_SUNLINSOL_DENSE], [
+  AC_CHECK_HEADERS([sunlinsol/sunlinsol_dense.h sundials/sundials_matrix.h sundials/sundials_linearsolver.h ida/ida_direct.h])
+  AC_CACHE_CHECK([whether SUNDIALS IDA includes the SUNLINSOL_DENSE linear solver],
+    [octave_cv_sundials_sunlinsol_dense],
+     [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
+-         #if defined (HAVE_IDA_IDA_DENSE_H)
+-         #include <ida/ida_dense.h>
+-         #else
+-         #include <ida_dense.h>
+         #if defined (HAVE_IDA_IDA_H)
+         #include <ida/ida.h>
+         #endif
+         #if defined (HAVE_SUNDIALS_SUNDIALS_MATRIX_H)
+         #include <sundials/sundials_matrix.h>
+         #endif
+         #if defined (HAVE_SUNDIALS_SUNDIALS_LINEARSOLVER_H)
+         #include <sundials/sundials_linearsolver.h>
+          #endif
+         #if defined (HAVE_IDA_IDA_DIRECT_H)
+         #include <ida/ida_direct.h>
+         #endif         
+          ]], [[
+          void *mem = 0;
+          long int num = 0;
+          IDADense (mem, num);
+       ]])],
+-      octave_cv_sundials_ida_dense=yes,
+-      octave_cv_sundials_ida_dense=no)
+      octave_cv_sundials_sunlinsol_dense=yes,
+      octave_cv_sundials_sunlinsol_dense=no)
+     ])
+-  if test $octave_cv_sundials_ida_dense = yes; then
+-    AC_DEFINE(HAVE_SUNDIALS_IDADENSE, 1,
+-      [Define to 1 if SUNDIALS IDA includes the IDADENSE linear solver.])
+  if test $octave_cv_sundials_sunlinsol_dense = yes; then
+    AC_DEFINE(HAVE_SUNDIALS_SUNLINSOL_DENSE, 1,
+      [Define to 1 if SUNDIALS IDA includes the SUNLINSOL_DENSE linear solver.])
+   else
+-    warn_sundials_ida_dense="SUNDIALS IDA library does not include the IDADENSE linear solver, ode15i and ode15s will be disabled"
+-    OCTAVE_CONFIGURE_WARNING([warn_sundials_ida_dense])
+    warn_sundials_ida_dense="SUNDIALS IDA library does not include the SUNLINSOL_DENSE linear solver, ode15i and ode15s will be disabled"
+    OCTAVE_CONFIGURE_WARNING([warn_sundials_sunlinsol_dense])
+   fi
+ ])
+ dnl
+diff -up octave-4.4.1/scripts/ode/ode15i.m.sundials3 octave-4.4.1/scripts/ode/ode15i.m
+--- octave-4.4.1/scripts/ode/ode15i.m.sundials3	2018-08-09 12:20:32.000000000 -0600
+++ octave-4.4.1/scripts/ode/ode15i.m	2018-10-28 14:06:56.909293633 -0600
+@@ -452,7 +452,7 @@ endfunction
+ %! assert ([t(end), y(end,:)], fref, 1e-3);
+ 
+ ## Jacobian fun sparse
+-%!testif HAVE_SUNDIALS_IDAKLU
+%!testif HAVE_SUNDIALS_SUNLINSOL_KLU
+ %! opt = odeset ("Jacobian", @jacfunsparse, "AbsTol", 1e-7, "RelTol", 1e-7);
+ %! [t, y] = ode15i (@rob, [0, 100], [1; 0; 0], [-1e-4; 1e-4; 0], opt);
+ %! assert ([t(end), y(end,:)], fref, 1e-3);
+@@ -545,7 +545,7 @@ endfunction
+ %!       "invalid value assigned to field 'Jacobian'");
+ 
+ ## Jacobian cell sparse wrong dimension
+-%!testif HAVE_SUNDIALS_IDAKLU
+%!testif HAVE_SUNDIALS_SUNLINSOL_KLU
+ %! DFDY = sparse ([-0.04, 1;
+ %!                  0.04, 1]);
+ %! DFDYP = sparse ([-1,  0, 0;
+diff -up octave-4.4.1/scripts/ode/ode15s.m.sundials3 octave-4.4.1/scripts/ode/ode15s.m
+--- octave-4.4.1/scripts/ode/ode15s.m.sundials3	2018-08-09 12:20:32.000000000 -0600
+++ octave-4.4.1/scripts/ode/ode15s.m	2018-10-28 14:06:56.910293641 -0600
+@@ -545,21 +545,21 @@ endfunction
+ %! [t, y] = ode15s (@rob, [0, 100], [1; 0; 0], opt);
+ %! assert ([t(end), y(end,:)], frefrob, 1e-3);
+ 
+-%!testif HAVE_SUNDIALS_IDAKLU
+%!testif HAVE_SUNDIALS_SUNLINSOL_KLU
+ %! opt = odeset ("MStateDependence", "none",
+ %!               "Mass", [1, 0, 0; 0, 1, 0; 0, 0, 0],
+ %!               "Jacobian", @jacfunsparse);
+ %! [t, y] = ode15s (@rob, [0, 100], [1; 0; 0], opt);
+ %! assert ([t(end), y(end,:)], frefrob, 1e-3);
+ 
+-%!testif HAVE_SUNDIALS_IDAKLU
+%!testif HAVE_SUNDIALS_SUNLINSOL_KLU
+ %! opt = odeset ("MStateDependence", "none",
+ %!               "Mass", sparse ([1, 0, 0; 0, 1, 0; 0, 0, 0]),
+ %!               "Jacobian", @jacfunsparse);
+ %! [t, y] = ode15s (@rob, [0, 100], [1; 0; 0], opt);
+ %! assert ([t(end), y(end,:)], frefrob, 1e-3);
+ 
+-%!testif HAVE_SUNDIALS_IDAKLU
+%!testif HAVE_SUNDIALS_SUNLINSOL_KLU
+ %! warning ("off", "ode15s:mass_state_dependent_provided", "local");
+ %! opt = odeset ("MStateDependence", "none",
+ %!               "Mass", @massdensefunstate,
+@@ -575,14 +575,14 @@ endfunction
+ %! [t, y] = ode15s (@rob, [0, 100], [1; 0; 0], opt);
+ %! assert ([t(end), y(end,:)], frefrob, 1e-3);
+ 
+-%!testif HAVE_SUNDIALS_IDAKLU
+%!testif HAVE_SUNDIALS_SUNLINSOL_KLU
+ %! opt = odeset ("MStateDependence", "none",
+ %!               "Mass", @massdensefuntime,
+ %!               "Jacobian", @jacfunsparse);
+ %! [t, y] = ode15s (@rob, [0, 100], [1; 0; 0], opt);
+ %! assert ([t(end), y(end,:)], frefrob, 1e-3);
+ 
+-%!testif HAVE_SUNDIALS_IDAKLU
+%!testif HAVE_SUNDIALS_SUNLINSOL_KLU
+ %! opt = odeset ("MStateDependence", "none",
+ %!               "Mass", @masssparsefuntime,
+ %!               "Jacobian", @jacfunsparse);
--- a/octave.spec
+++ b/octave.spec
@ -1,5 +1,5 @@
 # From src/version.h:#define OCTAVE_API_VERSION
-%global octave_api api-v51
+%global octave_api api-v52

 %global macrosdir %(d=%{_rpmconfigdir}/macros.d; [ -d $d ] || d=%{_sysconfdir}/rpm; echo $d)

@ -20,8 +20,8 @@

 Name:           octave
 Epoch:          6
-Version:        4.2.2
-Release:        6%{?rcver:.rc%{rcver}}%{?dist}.1
+Version:        4.4.1
+Release:        1%{?rcver:.rc%{rcver}}%{?dist}
 Summary:        A high-level language for numerical computations
 License:        GPLv3+
 URL:            http://www.octave.org
@ -34,16 +34,14 @@ Source0:        ftp://alpha.gnu.org/gnu/octave/octave-%{version}%{rctag}.tar.lz
 # RPM macros for helping to build Octave packages
 Source1:        macros.octave
 Source2:        xorg.conf
+# Prebuilt docs from Fedora for EPEL
+Source3:        octave-4.4.1-docs.tar.gz
 # Fix crash with Ctrl-D
 # https://bugzilla.redhat.com/show_bug.cgi?id=1589460
 Patch0:         octave-crash.patch
-# Remove project_group from appdata.xml file
-# https://bugzilla.redhat.com/show_bug.cgi?id=1293561
-Patch2:         octave-appdata.patch
-# Add needed #include <math.h> to bring in gnulib
-Patch4:         octave-gnulib.patch
-# Add #include <QButtonGroup> to fix build with latest Qt
-Patch5:         octave-qbuttongroup.patch
+# SUNDIALS 3 support
+# https://savannah.gnu.org/bugs/?52475
+Patch1:         octave-sundials3.patch

 Provides:       octave(api) = %{octave_api}
 Provides:       bundled(gnulib)
@ -67,6 +65,7 @@ Provides:       bundled(slatec-fn)
 BuildRequires:  lzip

 # For autoreconf
+BuildRequires:  automake
 BuildRequires:  libtool
 # For validating desktop and appdata files
 BuildRequires:  desktop-file-utils
@ -81,6 +80,7 @@ BuildRequires:  openblas-devel
 BuildRequires:  atlas-devel
 %endif
 BuildRequires:  bison
+BuildRequires:  bzip2-devel
 BuildRequires:  curl-devel
 BuildRequires:  fftw-devel
 BuildRequires:  flex
@ -96,6 +96,9 @@ BuildRequires:  gperf
 BuildRequires:  GraphicsMagick-c++-devel
 BuildRequires:  hdf5-devel
 BuildRequires:  java-devel
+%if 0%{?fedora}
+BuildRequires:  javapackages-local
+%endif
 BuildRequires:  less
 BuildRequires:  libsndfile-devel
 BuildRequires:  libX11-devel
@ -111,11 +114,13 @@ BuildRequires:  qrupdate-devel
 %if %{with qt5}
 BuildRequires:  qscintilla-qt5-devel
 BuildRequires:  qt5-linguist
+BuildRequires:  qt5-qttools-devel
 %else
 BuildRequires:  qscintilla-devel
 %endif
 BuildRequires:  readline-devel
 BuildRequires:  suitesparse-devel
+BuildRequires:  sundials-devel
 BuildRequires:  tex(dvips)
 BuildRequires:  texinfo
 BuildRequires:  texinfo-tex
@ -209,30 +214,19 @@ This package contains documentation for Octave.
 %prep
 %setup -q -n %{name}-%{version}%{?rctag}
 %patch0 -p1 -b .crash
-%patch2 -p1 -b .appdata
-%patch4 -p1 -b .gnulib
-%patch5 -p1 -b .qbuttongroup
-# __osmesa_print__ test is triggering a crash in libgcc, disable it
-# https://gcc.gnu.org/bugzilla/show_bug.cgi?id=78409
-#sed -i -e '/^%!/d' libinterp/dldfcn/__osmesa_print__.cc
-# Explicitly use gnulib headers
-%if 0%{?fedora} >= 24
-#find -name \*.cc -o -name \*.h -o -name \*.yy | xargs sed -i -e 's/#include <c\(math\|stdlib\)>/#include <\1.h>/'
-%endif
-#find -name \*.h -o -name \*.cc | xargs sed -i -e 's/<config.h>/"config.h"/' -e 's/<base-list.h>/"base-list.h"/'
-
-# Check permissions
-find -name *.cc -exec chmod 644 {} \;
+# EPEL7's autoconf/automake is too old so don't do
+# unneeded patches there
+%if 0%{?fedora}
+%patch1 -p1 -b .sundials3

 # Remove unused fftpack
-sed -i -e '/fftpack/d' liboctave/cruft/module.mk
-rm -r liboctave/cruft/fftpack
-
-# libinterp/dldfcn/__osmesa_print__.cc-tst is segfaulting
-# https://gcc.gnu.org/bugzilla/show_bug.cgi?id=78409
-sed -i -e '/^%/d' libinterp/dldfcn/__osmesa_print__.cc scripts/plot/util/{__opengl_info__,__pltopt__,allchild}.m test/publish/publish.tst
+sed -i -e '/fftpack/d' liboctave/external/module.mk
+rm -r liboctave/external/fftpack

+# Touching module.mk appears to trigger the need for this
 autoreconf -i
+%endif
+

 %build
 %global enable64 no
@ -254,6 +248,8 @@ libjvm=$(find /usr/lib/jvm/jre/lib -name libjvm.so -printf %h)
 export JAVA_HOME=%{java_home}
 # JIT support is still experimental, and causes a segfault on ARM.
 # --enable-float-truncate - https://savannah.gnu.org/bugs/?40560
+# sundials headers need to know where to find suitesparse headers
+export CPPFLAGS=-I%{_includedir}/suitesparse
 %configure --enable-shared --disable-static --enable-64=%enable64 \
 --enable-float-truncate \
 %{?disabledocs} \
@ -262,6 +258,7 @@ export JAVA_HOME=%{java_home}
 --with-blas="-L%{_libdir}/atlas %{atlasblaslib}" \
 --with-lapack="-L%{_libdir}/atlas %{atlaslapacklib}" \
 %endif
+ --with-java-includedir=/usr/lib/jvm/java/include \
 --with-java-libdir=$libjvm \
 --with-qrupdate \
 --with-amd --with-umfpack --with-colamd --with-ccolamd --with-cholmod \
@ -290,6 +287,9 @@ cp -a doc/refcard/*.pdf %{buildroot}%{_pkgdocdir}/
 # No info directory
 rm -f %{buildroot}%{_infodir}/dir

+# EL7's makeinfo doesn't support @sortas, so use prebuilt docs
+%{?el7:tar xvf %SOURCE3 -C %{buildroot}}
+
 # Make library links
 mkdir -p %{buildroot}%{_sysconfdir}/ld.so.conf.d
 echo "%{_libdir}/octave/%{version}%{?rctag}" > %{buildroot}%{_sysconfdir}/ld.so.conf.d/octave-%{_arch}.conf
@ -300,9 +300,11 @@ perl -pi -e "s,%{buildroot},," %{buildroot}%{_datadir}/%{name}/ls-R
 # Make sure ls-R exists
 touch %{buildroot}%{_datadir}/%{name}/ls-R

-desktop-file-validate %{buildroot}%{_datadir}/applications/www.octave.org-octave.desktop
+desktop-file-validate %{buildroot}%{_datadir}/applications/org.octave.Octave.desktop
+# RHEL7 still doesn't like the GNU project_group
+%{?el7:sed -i -e /project_group/d %{buildroot}/%{_datadir}/metainfo/org.octave.Octave.appdata.xml}
 %if 0%{?fedora} || 0%{?rhel} >= 7
-appstream-util validate-relax --nonet %{buildroot}/%{_datadir}/appdata/*.appdata.xml
+appstream-util validate-relax --nonet %{buildroot}/%{_datadir}/metainfo/org.octave.Octave.appdata.xml
 %endif

 # Create directories for add-on packages
@ -314,7 +316,7 @@ mkdir -p %{buildroot}%{_libdir}/%{name}/packages
 touch %{buildroot}%{_datadir}/%{name}/octave_packages

 # Fix multilib installs
-for include in config defaults
+for include in octave-config defaults
 do
   mv %{buildroot}%{_includedir}/%{name}-%{version}%{?rctag}/%{name}/${include}.h \
      %{buildroot}%{_includedir}/%{name}-%{version}%{?rctag}/%{name}/${include}-%{__isa_bits}.h
@ -417,10 +419,10 @@ fi
 %{_mandir}/man1/octave*.1.*
 %{_infodir}/liboctave.info*
 %{_infodir}/octave.info*
-%{_datadir}/appdata/www.octave.org-octave.appdata.xml
-%{_datadir}/applications/www.octave.org-octave.desktop
+%{_datadir}/applications/org.octave.Octave.desktop
 %{_datadir}/icons/hicolor/*/apps/octave.png
 %{_datadir}/icons/hicolor/scalable/apps/octave.svg
+%{_datadir}/metainfo/org.octave.Octave.appdata.xml
 # octave_packages is %ghost, so need to list everything else separately
 %dir %{_datadir}/octave
 %{_datadir}/octave/%{version}%{?rctag}/
@ -445,6 +447,9 @@ fi
 %{_pkgdocdir}/refcard*.pdf

 %changelog
+* Sun Nov 11 2018 Orion Poplawski <orion@nwra.com> - 6:4.4.1-1
+- Update to 4.4.1
+
 * Fri Jul 13 2018 Fedora Release Engineering <releng@fedoraproject.org> - 6:4.2.2-6.1
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild

--- a/3
+++ b/3
@ -1 +1,2 @@
-SHA512 (octave-4.2.2.tar.lz) = 694453eeda99047a216c047f0d0147ce7ec89497cba766927734bb9e82eb9f9c00a5c2ddc7f9af6796fcec8f85c8102ece20db6f8ba0a7d5e9a486bcff3ab069
+SHA512 (octave-4.4.1.tar.lz) = 8fbc6d35ae2bcd14b5cd52c30f761c87940c25ad514984fdb4baa6c99d6d371cb76e07cc50b020eb19470348674b3cd7069ed0eb20010dc3826a6e78781c0fa0
+SHA512 (octave-4.4.1-docs.tar.gz) = e970d512bb036f5954e3b8c9ac246c1624e9964fa2aeadc0f84dac01cc37af7f8fe5e93329d11ccc9ae442bfbaa1625dd2a21bc157c99d0992f5e1feada6f620