.github/workflows/rchk.yml: New.

r/ Fix rchk warnings.

Author: MLopez-Ibanez

.github/workflows/R.yml

@@ -107,32 +107,6 @@ jobs:
           name: results-${{ runner.os }}-r${{ matrix.r }}
           path: r/check
 
-  rchk:
-    if: false # Skip until https://github.com/r-lib/actions/issues/783
-    needs: R-CMD-check
-    runs-on: ubuntu-latest
-    container:
-      image: rhub/ubuntu-rchk
-      options: --user=root
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/run-rchk@v2
-        with:
-          setup-only: true
-
-      - run: ls -R /home/docker/R-svn/bin
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::rcmdcheck, local::., any::eaf
-          working-directory: r
-
-      - uses: r-lib/actions/run-rchk@v2
-        with:
-          run-only: true
-
   coverage:
     needs: R-CMD-check
     name: Coverage ${{ matrix.os }} (${{ matrix.r }})

.github/workflows/rchk.yml

@@ -0,0 +1,80 @@
+# adapted from a similar check run by {arrow}
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+name: rchk
+
+on:
+  workflow_run:
+    workflows: ['R']
+    types:
+     - completed
+    branches-ignore: [gh-pages]
+    paths:
+      - ".github/workflows/rchk.yml"
+      - "r/**"
+      - 'c/Make*'
+      - 'c/*.mk'
+      - 'c/**/*.[ch]p?p?'
+
+env:
+  R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+  _R_CHECK_FORCE_SUGGESTS_: false
+  _R_CHECK_CRAN_INCOMING_REMOTE_: false
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  rchk:
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+    runs-on: ubuntu-latest
+    name: Run rchk
+    steps:
+      - uses: actions/checkout@v4
+      - uses: r-lib/actions/setup-r@v2
+        with:
+            r-version: 'devel'
+
+      - name: Install minimal dependencies
+        run: |
+          install.packages(c("Rdpack","matrixStats"))
+        shell: Rscript {0}
+        working-directory: r
+
+      - name: Build
+        run: |
+          R CMD build --no-build-vignettes r
+          mkdir packages
+          mv moocore_*.tar.gz packages
+
+      - name: Run rchk
+        run: |
+          docker run -v `pwd`/packages:/rchk/packages kalibera/rchk:latest /rchk/packages/moocore_*.tar.gz |& tee rchk.out
+      - name: Confirm that rchk has no errors
+        # Suspicious call, [UP], and [PB] are all of the error types currently at
+        # https://github.com/kalibera/cran-checks/tree/HEAD/rchk/results
+        # though this might not be exhaustive, there does not appear to be a way to have rchk return an error code
+        # CRAN also will remove some of the outputs (especially those related to Rcpp and strptime, e.g.
+        # ERROR: too many states (abstraction error?))
+        # https://github.com/kalibera/rchk
+        run: |
+          if [ $(grep -Fc "Suspicious call" rchk.out) -gt 0 ] || [ $(grep -F "[UP]" rchk.out | grep -Fvc "results will be incomplete") -gt 0 ] || [ $(grep -Fc "[PB]" rchk.out) -gt 0 ]; then
+            echo "Found rchk errors"
+            exit 1
+          fi
+        if: always()

r/DESCRIPTION

@@ -32,7 +32,7 @@ URL: https://multi-objective.github.io/moocore/r/, https://github.com/multi-obje
 LazyLoad: true
 LazyData: true
 Encoding: UTF-8
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE,
               roclets = c("collate", "rd", "namespace",
                           "doctest::dt_roclet"))

r/src/Rcommon.h

@@ -9,19 +9,19 @@
 
 #define CHECK_ARG_IS_NUMERIC_VECTOR(A)					\
     if (!Rf_isReal(A) || !Rf_isVector(A))                               \
-	Rf_error("Argument '" #A "' is not a numeric vector");
+        Rf_error("Argument '" #A "' is not a numeric vector");
 
 #define CHECK_ARG_IS_NUMERIC_MATRIX(A)					\
     if (!Rf_isReal(A) || !Rf_isMatrix(A))                               \
-	Rf_error("Argument '" #A "' is not a numeric matrix");
+        Rf_error("Argument '" #A "' is not a numeric matrix");
 
 #define CHECK_ARG_IS_INT_VECTOR(A)					\
     if (!Rf_isInteger(A) || !Rf_isVector(A))                            \
-	Rf_error("Argument '" #A "' is not an integer vector");
+        Rf_error("Argument '" #A "' is not an integer vector");
 
 #define CHECK_ARG_IS_LOGICAL_VECTOR(A)					\
     if (!Rf_isLogical(A) || !Rf_isVector(A))                            \
-	Rf_error("Argument '" #A "' is not a logical vector");
+        Rf_error("Argument '" #A "' is not a logical vector");
 
 /* The C API of R is awfully ugly and unpractical (and poorly
    documented). These wrappers make it a little more bearable. */

r/src/Rmoocore.c

@@ -1,8 +1,7 @@
 #include "Rcommon.h"
 #include "eaf.h"
 
-#define DECLARE_CALL(RET_TYPE, NAME, ...)                                      \
-    extern RET_TYPE NAME(__VA_ARGS__);
+#define DECLARE_CALL(NAME, ...) extern SEXP NAME(__VA_ARGS__);
 #include "init.h"
 #undef DECLARE_CALL
 
@@ -52,8 +51,7 @@ compute_eaf_C(SEXP DATA, SEXP CUMSIZES, SEXP PERCENTILE)
     eaf_t **eaf = compute_eaf_helper(DATA, nobj, cumsizes, nruns, percentile, nlevels);
     int totalpoints = eaf_totalpoints (eaf, nlevels);
 
-    SEXP mat;
-    PROTECT(mat = Rf_allocMatrix(REALSXP, totalpoints, nobj + 1));
+    SEXP mat = PROTECT(Rf_allocMatrix(REALSXP, totalpoints, nobj + 1));
     eaf2matrix_R(REAL(mat), eaf, nobj, totalpoints, percentile, nlevels);
     eaf_free(eaf, nlevels);
     UNPROTECT(1);
@@ -271,8 +269,7 @@ R_read_datasets(SEXP FILENAME)
     const int ntotal = cumsizes[nruns - 1];
 
     /* FIXME: Is this the fastest way to transfer a matrix from C to R ? */
-    SEXP DATA;
-    PROTECT(DATA = Rf_allocMatrix(REALSXP, ntotal, nobj + 1));
+    SEXP DATA = PROTECT(Rf_allocMatrix(REALSXP, ntotal, nobj + 1));
     double *rdata = REAL(DATA);
     matrix_transpose_double (rdata, data, ntotal, nobj);
 
@@ -290,7 +287,7 @@ R_read_datasets(SEXP FILENAME)
 
 #include "nondominated.h"
 
-void
+SEXP
 normalise_C(SEXP DATA, SEXP RANGE, SEXP LBOUND, SEXP UBOUND, SEXP MAXIMISE)
 {
     int nprotected = 0;
@@ -310,6 +307,7 @@ normalise_C(SEXP DATA, SEXP RANGE, SEXP LBOUND, SEXP UBOUND, SEXP MAXIMISE)
                     lbound, ubound);
     free (maximise);
     UNPROTECT(nprotected);
+    return R_NilValue;
 }
 
 SEXP
@@ -356,15 +354,12 @@ pareto_ranking_C(SEXP DATA)
 SEXP
 hypervolume_C(SEXP DATA, SEXP REFERENCE)
 {
-    int nprotected = 0;
     /* We transpose the matrix before calling this function. */
     SEXP_2_DOUBLE_MATRIX(DATA, data, nobj, npoint);
     SEXP_2_DOUBLE_VECTOR(REFERENCE, reference, reference_len);
     assert (nobj == reference_len);
-    new_real_vector(hv, 1);
-    hv[0] = fpli_hv(data, nobj, npoint, reference);
-    UNPROTECT (nprotected);
-    return Rexp(hv);
+    double hv = fpli_hv(data, nobj, npoint, reference);
+    return Rf_ScalarReal(hv);
 }
 
 SEXP
@@ -385,20 +380,16 @@ hv_contributions_C(SEXP DATA, SEXP REFERENCE)
 SEXP
 rect_weighted_hv2d_C(SEXP DATA, SEXP RECTANGLES)
 {
-    int nprotected = 0;
     /* We transpose the matrix before calling this function. */
     SEXP_2_DOUBLE_MATRIX(DATA, data, nobj, npoint);
     SEXP_2_DOUBLE_MATRIX(RECTANGLES, rectangles, unused, rectangles_nrow);
-    new_real_vector(hv, 1);
-    hv[0] = rect_weighted_hv2d(data, npoint, rectangles, rectangles_nrow);
-    UNPROTECT (nprotected);
-    return Rexp(hv);
+    double hv = rect_weighted_hv2d(data, npoint, rectangles, rectangles_nrow);
+    return Rf_ScalarReal(hv);
 }
 
 SEXP
 preprocess_rectangles_C(SEXP RECTANGLES, SEXP REFERENCE)
 {
-    int nprotected = 0;
     /* We transpose the matrix before calling this function. */
     SEXP_2_DOUBLE_MATRIX(RECTANGLES, rectangles, ncol, nrow);
     SEXP_2_DOUBLE_VECTOR(REFERENCE, reference, reference_len);
@@ -411,7 +402,7 @@ preprocess_rectangles_C(SEXP RECTANGLES, SEXP REFERENCE)
         rectangles[k * ncol + 3] = MIN(rectangles[k * ncol + 3], reference[1]);
     }
     int skip_nrow = 0;
-    int * skip = (int *) malloc(nrow * sizeof(int));
+    int * skip = (int *) R_alloc(nrow, sizeof(int));
     for (int k = 0; k < nrow; k++) {
         bool empty = (rectangles[k * ncol + 0] == rectangles[k * ncol + 2]
                       || rectangles[k * ncol + 1] == rectangles[k * ncol + 3]);
@@ -420,8 +411,6 @@ preprocess_rectangles_C(SEXP RECTANGLES, SEXP REFERENCE)
     }
 
     if (skip_nrow == 0) {
-        free(skip);
-        UNPROTECT(nprotected);
         return RECTANGLES;
     }
     int new_nrow = nrow - skip_nrow;
@@ -440,8 +429,7 @@ preprocess_rectangles_C(SEXP RECTANGLES, SEXP REFERENCE)
             k = skip[s] + 1;
         }
     }
-    free(skip);
-    UNPROTECT(nprotected + 1);
+    UNPROTECT(1);
     return R_dest;
 }
 
@@ -450,7 +438,6 @@ preprocess_rectangles_C(SEXP RECTANGLES, SEXP REFERENCE)
 SEXP
 whv_hype_C(SEXP DATA, SEXP IDEAL, SEXP REFERENCE, SEXP NSAMPLES, SEXP DIST, SEXP SEED, SEXP MU)
 {
-    int nprotected = 0;
     SEXP_2_DOUBLE_MATRIX(DATA, data, nobj, npoints);
     SEXP_2_DOUBLE_VECTOR(IDEAL, ideal, ideal_len);
     SEXP_2_DOUBLE_VECTOR(REFERENCE, reference, reference_len);
@@ -460,20 +447,19 @@ whv_hype_C(SEXP DATA, SEXP IDEAL, SEXP REFERENCE, SEXP NSAMPLES, SEXP DIST, SEXP
     SEXP_2_STRING(DIST, dist_type);
     SEXP_2_UINT32(SEED, seed);
 
-    new_real_vector(hv, 1);
+    double hv;
     if (0 == strcmp(dist_type, "uniform")) {
-        hv[0] = whv_hype_unif(data, npoints, ideal, reference, nsamples, seed);
+        hv = whv_hype_unif(data, npoints, ideal, reference, nsamples, seed);
     } else if (0 == strcmp(dist_type, "exponential")) {
         const double * mu = REAL(MU);
-        hv[0] = whv_hype_expo(data, npoints, ideal, reference, nsamples, seed, mu[0]);
+        hv = whv_hype_expo(data, npoints, ideal, reference, nsamples, seed, mu[0]);
     } else if (0 == strcmp(dist_type, "point")) {
         const double * mu = REAL(MU);
-        hv[0] = whv_hype_gaus(data, npoints, ideal, reference, nsamples, seed, mu);
+        hv = whv_hype_gaus(data, npoints, ideal, reference, nsamples, seed, mu);
     } else {
         Rf_error("unknown 'dist' value: %s", dist_type);
     }
-    UNPROTECT (nprotected);
-    return Rexp(hv);
+    return Rf_ScalarReal(hv);
 }
 
 #include "epsilon.h"
@@ -492,7 +478,6 @@ static inline SEXP
 unary_metric_ref(SEXP DATA, SEXP REFERENCE, SEXP MAXIMISE,
                  enum unary_metric_t metric, SEXP EXTRA)
 {
-    int nprotected = 0;
     /* We transpose the matrix before calling this function. */
     SEXP_2_DOUBLE_MATRIX(DATA, data, nobj, npoint);
     double *ref = REAL(REFERENCE);
@@ -501,32 +486,31 @@ unary_metric_ref(SEXP DATA, SEXP REFERENCE, SEXP MAXIMISE,
     SEXP_2_LOGICAL_BOOL_VECTOR(MAXIMISE, maximise, maximise_len);
     assert (nobj == maximise_len);
 
-    new_real_vector(value, 1);
+    double value;
     switch (metric) {
       case EPSILON_ADD:
-          value[0] = epsilon_additive (data, nobj, npoint, ref, ref_size, maximise);
+          value = epsilon_additive (data, nobj, npoint, ref, ref_size, maximise);
           break;
       case EPSILON_MUL:
-          value[0] = epsilon_mult (data, nobj, npoint, ref, ref_size, maximise);
+          value = epsilon_mult (data, nobj, npoint, ref, ref_size, maximise);
           break;
       case INV_GD:
-          value[0] = IGD (data, nobj, npoint, ref, ref_size, maximise);
+          value = IGD (data, nobj, npoint, ref, ref_size, maximise);
           break;
       case INV_GDPLUS:
-          value[0] = IGD_plus (data, nobj, npoint, ref, ref_size, maximise);
+          value = IGD_plus (data, nobj, npoint, ref, ref_size, maximise);
           break;
       case AVG_HAUSDORFF: {
           SEXP_2_INT(EXTRA, p);
-          value[0] = avg_Hausdorff_dist (data, nobj, npoint, ref, ref_size, maximise, p);
+          value = avg_Hausdorff_dist (data, nobj, npoint, ref, ref_size, maximise, p);
           break;
       }
       default:
           Rf_error("unknown unary metric");
     }
 
     free (maximise);
-    UNPROTECT (nprotected);
-    return Rexp(value);
+    return Rf_ScalarReal(value);
 }
 
 SEXP

r/src/init.c

@@ -7,13 +7,13 @@
 #define VA_NARGS_IMPL(_1, _2, _3, _4, _5, _6, _7, _8, _9, _10, N, ...) N
 #define VA_NARGS(...) VA_NARGS_IMPL(__VA_ARGS__, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1)
 
-#define DECLARE_CALL(RET_TYPE, NAME, ...)                                      \
-    extern RET_TYPE NAME(__VA_ARGS__);
+#define DECLARE_CALL(NAME, ...)                                      \
+    extern SEXP NAME(__VA_ARGS__);
 #include "init.h"
 #undef DECLARE_CALL
 
 
-#define DECLARE_CALL(RET_TYPE, NAME, ...)                                      \
+#define DECLARE_CALL(NAME, ...)                                      \
     {#NAME, (DL_FUNC) &NAME, VA_NARGS(__VA_ARGS__)},
 
 static const R_CallMethodDef CallEntries[] = {

r/src/init.h

@@ -1,19 +1,19 @@
 /* .Call calls */
-DECLARE_CALL(SEXP, compute_eaf_C, SEXP DATA, SEXP CUMSIZES, SEXP PERCENTILE)
-DECLARE_CALL(SEXP, compute_eafdiff_C, SEXP DATA, SEXP CUMSIZES, SEXP INTERVALS)
-DECLARE_CALL(SEXP, compute_eafdiff_polygon_C, SEXP DATA, SEXP CUMSIZES, SEXP INTERVALS)
-DECLARE_CALL(SEXP, compute_eafdiff_rectangles_C, SEXP DATA, SEXP CUMSIZES, SEXP INTERVALS)
-DECLARE_CALL(SEXP, R_read_datasets, SEXP FILENAME)
-DECLARE_CALL(SEXP, hypervolume_C, SEXP DATA, SEXP REFERENCE)
-DECLARE_CALL(SEXP, hv_contributions_C, SEXP DATA, SEXP REFERENCE)
-DECLARE_CALL(void, normalise_C, SEXP DATA, SEXP RANGE, SEXP LBOUND, SEXP UBOUND, SEXP MAXIMISE)
-DECLARE_CALL(SEXP, is_nondominated_C, SEXP DATA, SEXP MAXIMISE, SEXP KEEP_WEAKLY)
-DECLARE_CALL(SEXP, pareto_ranking_C, SEXP DATA)
-DECLARE_CALL(SEXP, epsilon_mul_C, SEXP DATA, SEXP REFERENCE, SEXP MAXIMISE)
-DECLARE_CALL(SEXP, epsilon_add_C, SEXP DATA, SEXP REFERENCE, SEXP MAXIMISE)
-DECLARE_CALL(SEXP, igd_C, SEXP DATA, SEXP REFERENCE, SEXP MAXIMISE)
-DECLARE_CALL(SEXP, igd_plus_C, SEXP DATA, SEXP REFERENCE, SEXP MAXIMISE)
-DECLARE_CALL(SEXP, avg_hausdorff_dist_C, SEXP DATA, SEXP REFERENCE, SEXP MAXIMISE, SEXP P)
-DECLARE_CALL(SEXP, rect_weighted_hv2d_C, SEXP DATA, SEXP RECTANGLES)
-DECLARE_CALL(SEXP, whv_hype_C, SEXP DATA, SEXP IDEAL, SEXP REFERENCE, SEXP NSAMPLES, SEXP DIST, SEXP SEED, SEXP MU)
-DECLARE_CALL(SEXP, preprocess_rectangles_C, SEXP RECTANGLES, SEXP REFERENCE)
+DECLARE_CALL(compute_eaf_C, SEXP DATA, SEXP CUMSIZES, SEXP PERCENTILE)
+DECLARE_CALL(compute_eafdiff_C, SEXP DATA, SEXP CUMSIZES, SEXP INTERVALS)
+DECLARE_CALL(compute_eafdiff_polygon_C, SEXP DATA, SEXP CUMSIZES, SEXP INTERVALS)
+DECLARE_CALL(compute_eafdiff_rectangles_C, SEXP DATA, SEXP CUMSIZES, SEXP INTERVALS)
+DECLARE_CALL(R_read_datasets, SEXP FILENAME)
+DECLARE_CALL(hypervolume_C, SEXP DATA, SEXP REFERENCE)
+DECLARE_CALL(hv_contributions_C, SEXP DATA, SEXP REFERENCE)
+DECLARE_CALL(normalise_C, SEXP DATA, SEXP RANGE, SEXP LBOUND, SEXP UBOUND, SEXP MAXIMISE)
+DECLARE_CALL(is_nondominated_C, SEXP DATA, SEXP MAXIMISE, SEXP KEEP_WEAKLY)
+DECLARE_CALL(pareto_ranking_C, SEXP DATA)
+DECLARE_CALL(epsilon_mul_C, SEXP DATA, SEXP REFERENCE, SEXP MAXIMISE)
+DECLARE_CALL(epsilon_add_C, SEXP DATA, SEXP REFERENCE, SEXP MAXIMISE)
+DECLARE_CALL(igd_C, SEXP DATA, SEXP REFERENCE, SEXP MAXIMISE)
+DECLARE_CALL(igd_plus_C, SEXP DATA, SEXP REFERENCE, SEXP MAXIMISE)
+DECLARE_CALL(avg_hausdorff_dist_C, SEXP DATA, SEXP REFERENCE, SEXP MAXIMISE, SEXP P)
+DECLARE_CALL(rect_weighted_hv2d_C, SEXP DATA, SEXP RECTANGLES)
+DECLARE_CALL(whv_hype_C, SEXP DATA, SEXP IDEAL, SEXP REFERENCE, SEXP NSAMPLES, SEXP DIST, SEXP SEED, SEXP MU)
+DECLARE_CALL(preprocess_rectangles_C, SEXP RECTANGLES, SEXP REFERENCE)