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Sebastian Luque
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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
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‎.Rbuildignore‎

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EXAMPLES.*
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^TODO$
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^.AppleDouble$
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^.lintr$
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^vignettes/auto$
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^src/\.clang-format$
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man-roxygen

‎.github/workflows/build_check.yml‎

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

‎.github/workflows/rhub.yaml‎

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

‎DESCRIPTION‎

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

‎NEWS‎

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

‎R/calibrate.R‎

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

‎man/calibrateDepth.Rd‎

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‎man/labDive-internal.Rd‎

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

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