Update headers to 6.1.1 and add testing action

.Rbuildignore

@@ -6,3 +6,4 @@ cran-comments.md
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

DESCRIPTION

@@ -17,7 +17,7 @@ Imports:
     Rcpp (>= 0.12.5)
 LinkingTo:
     Rcpp, RcppArmadillo
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Suggests: 
     knitr,
     rmarkdown,

README.md

@@ -5,7 +5,7 @@
 [![Build status](https://ci.appveyor.com/api/projects/status/3mp1p26lpqp16t3d?svg=true)](https://ci.appveyor.com/project/sn248/sundialr)    [![Travis-CI Build Status](https://travis-ci.org/sn248/sundialr.svg?branch=master)](https://travis-ci.org/sn248/sundialr)   [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/sundialr)](https://cran.r-project.org/package=sundialr) 
 [![](https://cranlogs.r-pkg.org/badges/grand-total/sundialr)]( https://CRAN.R-project.org/package=sundialr)
 [![DOI](https://zenodo.org/badge/60889710.svg)](https://zenodo.org/badge/latestdoi/60889710)
-
+[![R-CMD-check](https://github.com/sn248/sundialr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sn248/sundialr/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 ## sundialr

inst/include/cvode/cvode.h

@@ -3,7 +3,7 @@
  *                and Dan Shumaker @ LLNL
  * -----------------------------------------------------------------
  * SUNDIALS Copyright Start
- * Copyright (c) 2002-2021, Lawrence Livermore National Security
+ * Copyright (c) 2002-2022, Lawrence Livermore National Security
  * and Southern Methodist University.
  * All rights reserved.
  *
@@ -19,6 +19,7 @@
 #define _CVODE_H
 
 #include <stdio.h>
+#include <sundials/sundials_context.h>
 #include <sundials/sundials_nvector.h>
 #include <sundials/sundials_nonlinearsolver.h>
 #include <cvode/cvode_ls.h>
@@ -81,6 +82,8 @@ extern "C" {
 #define CV_PROJFUNC_FAIL        -30
 #define CV_REPTD_PROJFUNC_ERR   -31
 
+#define CV_CONTEXT_ERR          -32
+
 #define CV_UNRECOGNIZED_ERR     -99
 
 
@@ -107,7 +110,7 @@ typedef int (*CVMonitorFn)(void *cvode_mem, void *user_data);
  * ------------------- */
 
 /* Initialization functions */
-SUNDIALS_EXPORT void *CVodeCreate(int lmm);
+SUNDIALS_EXPORT void *CVodeCreate(int lmm, SUNContext sunctx);
 
 SUNDIALS_EXPORT int CVodeInit(void *cvode_mem, CVRhsFn f, realtype t0,
                               N_Vector y0);
@@ -121,30 +124,29 @@ SUNDIALS_EXPORT int CVodeSVtolerances(void *cvode_mem, realtype reltol,
 SUNDIALS_EXPORT int CVodeWFtolerances(void *cvode_mem, CVEwtFn efun);
 
 /* Optional input functions */
-SUNDIALS_EXPORT int CVodeSetErrHandlerFn(void *cvode_mem, CVErrHandlerFn ehfun,
-                                         void *eh_data);
+
+SUNDIALS_EXPORT int CVodeSetConstraints(void *cvode_mem, N_Vector constraints);
 SUNDIALS_EXPORT int CVodeSetErrFile(void *cvode_mem, FILE *errfp);
-SUNDIALS_EXPORT int CVodeSetUserData(void *cvode_mem, void *user_data);
-SUNDIALS_EXPORT int CVodeSetMonitorFn(void *cvode_mem, CVMonitorFn fn);
-SUNDIALS_EXPORT int CVodeSetMonitorFrequency(void *cvode_mem, long int nst);
-SUNDIALS_EXPORT int CVodeSetMaxOrd(void *cvode_mem, int maxord);
-SUNDIALS_EXPORT int CVodeSetMaxNumSteps(void *cvode_mem, long int mxsteps);
-SUNDIALS_EXPORT int CVodeSetMaxHnilWarns(void *cvode_mem, int mxhnil);
-SUNDIALS_EXPORT int CVodeSetStabLimDet(void *cvode_mem, booleantype stldet);
+SUNDIALS_EXPORT int CVodeSetErrHandlerFn(void *cvode_mem, CVErrHandlerFn ehfun, void *eh_data);
 SUNDIALS_EXPORT int CVodeSetInitStep(void *cvode_mem, realtype hin);
-SUNDIALS_EXPORT int CVodeSetMinStep(void *cvode_mem, realtype hmin);
-SUNDIALS_EXPORT int CVodeSetMaxStep(void *cvode_mem, realtype hmax);
-SUNDIALS_EXPORT int CVodeSetStopTime(void *cvode_mem, realtype tstop);
+SUNDIALS_EXPORT int CVodeSetLSetupFrequency(void *cvode_mem, long int msbp);
+SUNDIALS_EXPORT int CVodeSetMaxConvFails(void *cvode_mem, int maxncf);
 SUNDIALS_EXPORT int CVodeSetMaxErrTestFails(void *cvode_mem, int maxnef);
+SUNDIALS_EXPORT int CVodeSetMaxHnilWarns(void *cvode_mem, int mxhnil);
 SUNDIALS_EXPORT int CVodeSetMaxNonlinIters(void *cvode_mem, int maxcor);
-SUNDIALS_EXPORT int CVodeSetMaxConvFails(void *cvode_mem, int maxncf);
-SUNDIALS_EXPORT int CVodeSetNonlinConvCoef(void *cvode_mem, realtype nlscoef);
-SUNDIALS_EXPORT int CVodeSetLSetupFrequency(void *cvode_mem, long int msbp);
-SUNDIALS_EXPORT int CVodeSetConstraints(void *cvode_mem, N_Vector constraints);
-SUNDIALS_EXPORT int CVodeSetNonlinearSolver(void *cvode_mem,
-                                            SUNNonlinearSolver NLS);
+SUNDIALS_EXPORT int CVodeSetMaxNumSteps(void *cvode_mem, long int mxsteps);
+SUNDIALS_EXPORT int CVodeSetMaxOrd(void *cvode_mem, int maxord);
+SUNDIALS_EXPORT int CVodeSetMaxStep(void *cvode_mem, realtype hmax);
+SUNDIALS_EXPORT int CVodeSetMinStep(void *cvode_mem, realtype hmin);
+SUNDIALS_EXPORT int CVodeSetMonitorFn(void *cvode_mem, CVMonitorFn fn);
+SUNDIALS_EXPORT int CVodeSetMonitorFrequency(void *cvode_mem, long int nst);
 SUNDIALS_EXPORT int CVodeSetNlsRhsFn(void *cvode_mem, CVRhsFn f);
+SUNDIALS_EXPORT int CVodeSetNonlinConvCoef(void *cvode_mem, realtype nlscoef);
+SUNDIALS_EXPORT int CVodeSetNonlinearSolver(void *cvode_mem, SUNNonlinearSolver NLS);
+SUNDIALS_EXPORT int CVodeSetStabLimDet(void *cvode_mem, booleantype stldet);
+SUNDIALS_EXPORT int CVodeSetStopTime(void *cvode_mem, realtype tstop);
 SUNDIALS_EXPORT int CVodeSetUseIntegratorFusedKernels(void *cvode_mem, booleantype onoff);
+SUNDIALS_EXPORT int CVodeSetUserData(void *cvode_mem, void *user_data);
 
 /* Rootfinding initialization function */
 SUNDIALS_EXPORT int CVodeRootInit(void *cvode_mem, int nrtfn, CVRootFn g);

inst/include/cvode/cvode_bandpre.h

@@ -3,7 +3,7 @@
  *                Alan C. Hindmarsh and Radu Serban @ LLNL
  * -----------------------------------------------------------------
  * SUNDIALS Copyright Start
- * Copyright (c) 2002-2021, Lawrence Livermore National Security
+ * Copyright (c) 2002-2022, Lawrence Livermore National Security
  * and Southern Methodist University.
  * All rights reserved.
  *

inst/include/cvode/cvode_bbdpre.h

@@ -4,7 +4,7 @@
  *                Radu Serban @ LLNL
  * -----------------------------------------------------------------
  * SUNDIALS Copyright Start
- * Copyright (c) 2002-2021, Lawrence Livermore National Security
+ * Copyright (c) 2002-2022, Lawrence Livermore National Security
  * and Southern Methodist University.
  * All rights reserved.
  *

inst/include/cvode/cvode_diag.h

@@ -3,7 +3,7 @@
  *                Radu Serban @ LLNL
  * ---------------------------------------------------------------------
  * SUNDIALS Copyright Start
- * Copyright (c) 2002-2021, Lawrence Livermore National Security
+ * Copyright (c) 2002-2022, Lawrence Livermore National Security
  * and Southern Methodist University.
  * All rights reserved.
  *

inst/include/cvode/cvode_direct.h

@@ -2,7 +2,7 @@
  * Programmer(s): Daniel R. Reynolds @ SMU
  * -----------------------------------------------------------------
  * SUNDIALS Copyright Start
- * Copyright (c) 2002-2021, Lawrence Livermore National Security
+ * Copyright (c) 2002-2022, Lawrence Livermore National Security
  * and Southern Methodist University.
  * All rights reserved.
  *
@@ -36,21 +36,28 @@ typedef CVLsJacFn CVDlsJacFn;
   Exported Functions (wrappers for equivalent routines in cvode_ls.h)
   ===================================================================*/
 
-SUNDIALS_EXPORT int CVDlsSetLinearSolver(void *cvode_mem, SUNLinearSolver LS,
-                                         SUNMatrix A);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeSetLinearSolver instead")
+int CVDlsSetLinearSolver(void *cvode_mem, SUNLinearSolver LS,
+                         SUNMatrix A);
 
-SUNDIALS_EXPORT int CVDlsSetJacFn(void *cvode_mem, CVDlsJacFn jac);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeSetJacFn instead")
+int CVDlsSetJacFn(void *cvode_mem, CVDlsJacFn jac);
 
-SUNDIALS_EXPORT int CVDlsGetWorkSpace(void *cvode_mem, long int *lenrwLS,
-                                      long int *leniwLS);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetLinWorkSpace instead")
+int CVDlsGetWorkSpace(void *cvode_mem, long int *lenrwLS,
+                      long int *leniwLS);
 
-SUNDIALS_EXPORT int CVDlsGetNumJacEvals(void *cvode_mem, long int *njevals);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetNumJacEvals instead")
+int CVDlsGetNumJacEvals(void *cvode_mem, long int *njevals);
 
-SUNDIALS_EXPORT int CVDlsGetNumRhsEvals(void *cvode_mem, long int *nfevalsLS);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetNumLinRhsEvals instead")
+int CVDlsGetNumRhsEvals(void *cvode_mem, long int *nfevalsLS);
 
-SUNDIALS_EXPORT int CVDlsGetLastFlag(void *cvode_mem, long int *flag);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetLastLinFlag instead")
+int CVDlsGetLastFlag(void *cvode_mem, long int *flag);
 
-SUNDIALS_EXPORT char *CVDlsGetReturnFlagName(long int flag);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetLinReturnFlagName instead")
+char *CVDlsGetReturnFlagName(long int flag);
 
 
 #ifdef __cplusplus

inst/include/cvode/cvode_ls.h

@@ -4,7 +4,7 @@
  *                Radu Serban @ LLNL
  * ----------------------------------------------------------------
  * SUNDIALS Copyright Start
- * Copyright (c) 2002-2021, Lawrence Livermore National Security
+ * Copyright (c) 2002-2022, Lawrence Livermore National Security
  * and Southern Methodist University.
  * All rights reserved.
  *
@@ -135,11 +135,6 @@ SUNDIALS_EXPORT int CVodeGetLastLinFlag(void *cvode_mem,
                                         long int *flag);
 SUNDIALS_EXPORT char *CVodeGetLinReturnFlagName(long int flag);
 
-
-/* Deprecated functions */
-SUNDIALS_DEPRECATED_EXPORT
-int CVodeSetMaxStepsBetweenJac(void *cvode_mem, long int msbj);
-
 #ifdef __cplusplus
 }
 #endif

inst/include/cvode/cvode_proj.h

@@ -4,7 +4,7 @@
  * Based on CPODES by Radu Serban @ LLNL
  * -----------------------------------------------------------------------------
  * SUNDIALS Copyright Start
- * Copyright (c) 2002-2021, Lawrence Livermore National Security
+ * Copyright (c) 2002-2022, Lawrence Livermore National Security
  * and Southern Methodist University.
  * All rights reserved.
  *

inst/include/cvode/cvode_spils.h

@@ -2,7 +2,7 @@
  * Programmer(s): Daniel R. Reynolds @ SMU
  * -----------------------------------------------------------------
  * SUNDIALS Copyright Start
- * Copyright (c) 2002-2021, Lawrence Livermore National Security
+ * Copyright (c) 2002-2022, Lawrence Livermore National Security
  * and Southern Methodist University.
  * All rights reserved.
  *
@@ -39,36 +39,50 @@ typedef CVLsJacTimesVecFn CVSpilsJacTimesVecFn;
   Exported Functions (wrappers for equivalent routines in cvode_ls.h)
   ====================================================================*/
 
-SUNDIALS_EXPORT int CVSpilsSetLinearSolver(void *cvode_mem, SUNLinearSolver LS);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeSetLinearSolver instead")
+int CVSpilsSetLinearSolver(void *cvode_mem, SUNLinearSolver LS);
 
-SUNDIALS_EXPORT int CVSpilsSetEpsLin(void *cvode_mem, realtype eplifac);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeSetEpsLin instead")
+int CVSpilsSetEpsLin(void *cvode_mem, realtype eplifac);
 
-SUNDIALS_EXPORT int CVSpilsSetPreconditioner(void *cvode_mem, CVSpilsPrecSetupFn pset,
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeSetPreconditioner instead")
+int CVSpilsSetPreconditioner(void *cvode_mem, CVSpilsPrecSetupFn pset,
                              CVSpilsPrecSolveFn psolve);
 
-SUNDIALS_EXPORT int CVSpilsSetJacTimes(void *cvode_mem, CVSpilsJacTimesSetupFn jtsetup,
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeSetJacTimes instead")
+int CVSpilsSetJacTimes(void *cvode_mem, CVSpilsJacTimesSetupFn jtsetup,
                        CVSpilsJacTimesVecFn jtimes);
 
-SUNDIALS_EXPORT int CVSpilsGetWorkSpace(void *cvode_mem, long int *lenrwLS,
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetLinWorkSpace instead")
+int CVSpilsGetWorkSpace(void *cvode_mem, long int *lenrwLS,
                         long int *leniwLS);
 
-SUNDIALS_EXPORT int CVSpilsGetNumPrecEvals(void *cvode_mem, long int *npevals);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetNumPrecEvals instead")
+int CVSpilsGetNumPrecEvals(void *cvode_mem, long int *npevals);
 
-SUNDIALS_EXPORT int CVSpilsGetNumPrecSolves(void *cvode_mem, long int *npsolves);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetNumPrecSolves instead")
+int CVSpilsGetNumPrecSolves(void *cvode_mem, long int *npsolves);
 
-SUNDIALS_EXPORT int CVSpilsGetNumLinIters(void *cvode_mem, long int *nliters);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetNumLinIters instead")
+int CVSpilsGetNumLinIters(void *cvode_mem, long int *nliters);
 
-SUNDIALS_EXPORT int CVSpilsGetNumConvFails(void *cvode_mem, long int *nlcfails);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetNumConvFails instead")
+int CVSpilsGetNumConvFails(void *cvode_mem, long int *nlcfails);
 
-SUNDIALS_EXPORT int CVSpilsGetNumJTSetupEvals(void *cvode_mem, long int *njtsetups);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetNumJTSetupEvals instead")
+int CVSpilsGetNumJTSetupEvals(void *cvode_mem, long int *njtsetups);
 
-SUNDIALS_EXPORT int CVSpilsGetNumJtimesEvals(void *cvode_mem, long int *njvevals);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetNumJtimesEvals instead")
+int CVSpilsGetNumJtimesEvals(void *cvode_mem, long int *njvevals);
 
-SUNDIALS_EXPORT int CVSpilsGetNumRhsEvals(void *cvode_mem, long int *nfevalsLS);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetNumLinRhsEvals instead")
+int CVSpilsGetNumRhsEvals(void *cvode_mem, long int *nfevalsLS);
 
-SUNDIALS_EXPORT int CVSpilsGetLastFlag(void *cvode_mem, long int *flag);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetLastLinFlag instead")
+int CVSpilsGetLastFlag(void *cvode_mem, long int *flag);
 
-SUNDIALS_EXPORT char *CVSpilsGetReturnFlagName(long int flag);
+SUNDIALS_DEPRECATED_EXPORT_MSG("use CVodeGetLinReturnFlagName instead")
+char *CVSpilsGetReturnFlagName(long int flag);
 
 
 #ifdef __cplusplus