Addressed latest CRAN checks with _STRICT_R_HEADERS (2024-09-23)

Compilation fails with _R_USE_STRICT_R_HEADERS_=true, which defines
STRICT_R_HEADERS to 1 which removes

- the legacy definition of PI (use POSIX's M_PI, available in R fer ever).
- the RS.h declarations for Calloc, Realloc, Free (use R_ forms i
  available since R 3.4.0).

The aim is to clean the namespace: in particular having a definition
for Free has conflicted with some packages' C++ code.

It is planned that STRICT_R_HEADERS=1 will become the default for 4.5.0,
for which it would be good if all CRAN packages compile/install ok with
the new default.

Your package is among the ones which need updating.  We would thus
really appreciate if you could provide a new version of your package as
soon as possible which checks ok with STRICT_R_HEADERS=1.

You can verify that your package checks ok with STRICT_R_HEADERS=1 via R
CMD check --as-cran using a current version of R-devel.

Please correct before 2024-10-21 to safely retain your package on CRAN.

Updated GitHub workflows

.Rbuildignore

@@ -6,6 +6,7 @@
 EXAMPLES.*
 ^TODO$
 ^.AppleDouble$
+^.lintr$
 ^vignettes/auto$
 ^src/\.clang-format$
 man-roxygen

.github/workflows/build_check.yml

@@ -25,7 +25,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup pandoc
         uses: r-lib/actions/setup-pandoc@v2
@@ -63,7 +63,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -1,11 +1,16 @@
 Package: diveMove
 Type: Package
 Title: Dive Analysis and Calibration
-Version: 1.6.2
-Depends: R (>= 3.5.0), methods, stats4
+Version: 1.6.4
+Depends: R (>= 4.4.0), methods, stats4
 Suggests: knitr, lattice, pander, rmarkdown, tinytest
 Imports: geosphere, KernSmooth, plotly, quantreg, uniReg
-Author: Sebastian P. Luque <spluque@gmail.com>
+Authors@R: person(given = c("Sebastian", "P."),
+                  family = "Luque",
+		  role = c("aut", "cre"),
+		  email = "spluque@gmail.com",
+		  comment = c(ORCID = "0000-0002-9647-3691"))
+Author: Sebastian P. Luque [aut, cre] (<https://orcid.org/0000-0002-9647-3691>)
 Maintainer: Sebastian P. Luque <spluque@gmail.com>
 Description: Utilities to represent, visualize, filter, analyse, and summarize
 	     time-depth recorder (TDR) data.  Miscellaneous functions for

NEWS

@@ -1,3 +1,7 @@
+Changes in version 1.6.4:
+
+   o The package now depends on R >= 4.4.0.
+
 Changes in version 1.6.0:
 
    o Analyses for 2- and 3-process Poisson mixtures are now fully

R/calibrate.R

@@ -242,14 +242,13 @@
 ##'     \code{\link{.detDive}}, \code{\link{plotTDR}}, and
 ##'     \code{\link{plotZOC}} to visually assess ZOC procedure. See
 ##'     \code{\link{diveModel}}, \code{\link{smooth.spline}},
-##'     \code{\link{unireg}} for dive models.
+##'     \code{\link[uniReg]{unireg}} for dive models.
 ##' @references
 ##'
-##' Koellmann, C., Ickstadt, K. and Fried, R. (2014) Beyond unimodal
-##' regression: modelling multimodality with piecewise unimodal, mixture or
-##' additive regression. Technical Report 8.
-##' \url{https://sfb876.tu-dortmund.de/FORSCHUNG/techreports.html}, SFB 876, TU
-##' Dortmund
+##' Koellmann, C., Ickstadt, K. and Fried, R. (2016) Beyond unimodal
+##' regression: modelling multimodality with piecewise unimodal or
+##' deconvolution models. Technical Report
+##' \url{https://arxiv.org/abs/1606.01666}, Technische Universität Dortmund
 ##'
 ##' Luque, S.P. and Fried, R. (2011) Recursive filtering for zero offset
 ##' correction of diving depth time series. PLoS ONE 6:e15850

man/labDive-internal.Rd

@@ -34,8 +34,9 @@
   \item{dive.model, smooth.par, knot.factor, descent.crit.q,
         ascent.crit.q}{Passed from \code{calibrateDepth}.}
 
-  \item{sigmasq, g, ordpen}{default arguments for \code{\link{unireg}}, so
-    only relevant for \code{divemodel="unimodal"}.}
+  \item{sigmasq, g, ordpen}{default arguments for
+    \code{\link[uniReg]{unireg}}, so only relevant for
+    \code{divemodel="unimodal"}.}
 
   \item{act}{factor with values to label.}
 

src/run_quantile.c

@@ -29,8 +29,6 @@
 int R_finite(double x) {
     return ((x) == (x));
 }
-#define Calloc(b, t) (t *) calloc(b, sizeof(t))
-#define Free free
 #define PRINT(x)                  \
     {                             \
         if ((x) == (x))           \
@@ -384,10 +382,10 @@ void run_quantile_lite(double *In, double *Out, const int *nIn,
         }
     } else {                  /* non-trivial case */
 	/* index will hold partially sorted index numbers of Save array */
-        idx = Calloc(m, int);
+        idx = R_Calloc(m, int);
 	/* stores all points of the current running window */
-        Win = Calloc(m, double);
-        prob = Calloc(nPrb, double);
+        Win = R_Calloc(m, double);
+        prob = R_Calloc(nPrb, double);
         for (i = 0; i < m; i++) {
             Win[i] = *(in++);	/* initialize running window */
             idx[i] = i;		/* and its index */
@@ -417,9 +415,9 @@ void run_quantile_lite(double *In, double *Out, const int *nIn,
             j = (j + 1) %
                 m; /* index goes from 0 to m-1, and back to 0 again  */
         }
-        Free(Win);
-        Free(idx);
-        Free(prob);
+        R_Free(Win);
+        R_Free(idx);
+        R_Free(prob);
     }
 }
 
@@ -447,10 +445,10 @@ void run_quantile(double *In, double *Out, const int *nIn, const int *nWin,
         run_max(In, Out, nIn, nWin);
     } else {                  /* non-trivial case */
 	/* index will hold partially sorted index numbers of Save array */
-        idx = Calloc(m, int);
+        idx = R_Calloc(m, int);
 	/* store all points of the current running window */
-        Win = Calloc(m, double);
-        prob = Calloc(nPrb, double);
+        Win = R_Calloc(m, double);
+        prob = R_Calloc(nPrb, double);
         for (i = 0; i < m; i++) idx[i] = i; /* and its index */
         for (i = 0; i < k2; i++) {
             Win[i] = *(in++);	/* initialize running window */
@@ -558,9 +556,9 @@ void run_quantile(double *In, double *Out, const int *nIn, const int *nWin,
 	    /* index goes from 0 to m-1, and back to 0 again */
             j = (j + 1) % m;
         }
-        Free(Win);
-        Free(idx);
-        Free(prob);
+        R_Free(Win);
+        R_Free(idx);
+        R_Free(prob);
     }
 }