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Merged
RLumSK merged 7 commits into from
Sep 17, 2025
Merged

Upkeep to satisfy CRAN checks and requests #15

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5a0e910
Update the OS requested in the github workflow.
mcol Sep 17, 2025
26e7210
Fix notes from R CMD check.
mcol Sep 17, 2025
ab13710
Update roxygen2 documentation.
mcol Sep 17, 2025
adf03e3
Stop requiring C++11 to satisfy CRAN request.
mcol Sep 17, 2025
94c59b8
Fix compilation warnings due to the new RCppArmadillo.
mcol Sep 17, 2025
1492b31
Update some action versions.
mcol Sep 17, 2025
8000cd3
Fix error on Linux CI machines.
mcol Sep 17, 2025
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20 changes: 10 additions & 10 deletions .github/workflows/GitHub_Actions_CI.yaml
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Expand Up @@ -23,26 +23,26 @@ jobs:
fail-fast: false
matrix:
config:
- {os: macos-11, r: 'release', rspm: "https://packagemanager.rstudio.com/all/latest"}
- {os: macos-10.15, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/all/latest"}
- {os: ubuntu-20.04, r: 'devel', not_cran: 'true', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: 'release', not_cran: 'true', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: 'oldrel', not_cran: 'true', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: macos-13, r: 'release', rspm: "https://packagemanager.rstudio.com/all/latest"}
- {os: macos-13, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/all/latest"}
- {os: ubuntu-24.04, r: 'devel', not_cran: 'true', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-24.04, r: 'release', not_cran: 'true', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-24.04, r: 'oldrel', not_cran: 'true', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}

env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-r@v1
- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}

- uses: r-lib/actions/setup-pandoc@v1
- uses: r-lib/actions/setup-pandoc@v2

- name: Install remotes
run: |
Expand All @@ -52,7 +52,7 @@ jobs:

- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v2
uses: actions/cache@v4
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
Expand All @@ -64,7 +64,7 @@ jobs:
while read -r cmd
do
eval sudo $cmd
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "22.04"))')

- name: Install ghostscript (Linux)
if: runner.os == 'Linux'
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -52,7 +52,7 @@ Collate:
simulate_TL.R
translate_sequence.R
trace_ParameterStateEvolution.R
RoxygenNote: 7.1.2
RoxygenNote: 7.3.2
Encoding: UTF-8
LazyData: true
VignetteBuilder: R.rsp
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3 changes: 1 addition & 2 deletions R/RLumModel-package.R
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Expand Up @@ -8,7 +8,6 @@
#' published models.
#'
#' @name RLumModel-package
#' @docType package
#' @details **Authors**
#'
#' \tabular{ll}{
Expand Down Expand Up @@ -49,7 +48,7 @@
#' @importFrom grDevices rgb
#' @importFrom graphics axis lines mtext par rect
#' @useDynLib RLumModel, .registration = TRUE
NULL
"_PACKAGE"


#' Example data (TL curve) simulated with parameter set from Pagonis 2007
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2 changes: 0 additions & 2 deletions R/extract_pars.R
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Expand Up @@ -10,8 +10,6 @@
#'
#' @author Johannes Friedrich, University of Bayreuth (Germany),
#'
#' @references
#'
#' @seealso \code{\link{simulate_CW_OSL}},\code{\link{simulate_heating}}, \code{\link{simulate_illumination}},
#' \code{\link{simulate_irradiation}}, \code{\link{simulate_LM_OSL}}, \code{\link{simulate_pause}},
#' \code{\link{simulate_RF}}, \code{\link{simulate_TL}}
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4 changes: 2 additions & 2 deletions R/read_SEQ2R.R
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Expand Up @@ -44,9 +44,9 @@ read_SEQ2R <- function(

# Integrity tests and conversion --------------------------------------------------------------

if(class(file)!= "character")
if(!inherits(file, "character"))
stop("[read_SEQ2R()] class of file has to be a character.")

if(!file.exists(file))
stop("[read_SEQ2R()] file name doesn't seem to exist.")

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2 changes: 1 addition & 1 deletion R/simulate_CW_OSL.R
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Expand Up @@ -80,7 +80,7 @@
}

##check if n is a RLum object
if(class(n) != "RLum.Results"){
if(!inherits(n, "RLum.Results")){
n <- n
} else {
n <- n$n
Expand Down
4 changes: 1 addition & 3 deletions R/simulate_LM_OSL.R
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Expand Up @@ -28,8 +28,6 @@
#'
#' @author Johannes Friedrich, University of Bayreuth (Germany),
#'
#' @references
#'
#' @seealso \code{\link{plot}}
#'
#' @examples
Expand Down Expand Up @@ -70,7 +68,7 @@
}

##check if object is of class RLum.Data.Curve
if(class(n) != "RLum.Results"){
if(!inherits(n, "RLum.Results")){
n <- n
} else {
n <- n$n
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2 changes: 1 addition & 1 deletion R/simulate_RF.R
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Expand Up @@ -82,7 +82,7 @@
}

##check if n is a RLum object
if(class(n) != "RLum.Results"){
if(!inherits(n, "RLum.Results")){
n <- n
} else {
n <- n$n
Expand Down
2 changes: 1 addition & 1 deletion R/simulate_RF_and_heating.R
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Expand Up @@ -73,7 +73,7 @@
}

##check if object is of class RLum.Results
if(class(n) != "RLum.Results"){
if(!inherits(n, "RLum.Results")){
n <- n
} else {
n <- n$n
Expand Down
2 changes: 1 addition & 1 deletion R/simulate_TL.R
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Expand Up @@ -65,7 +65,7 @@
}

##check if object is of class RLum.Results
if(class(n) != "RLum.Results"){
if(!inherits(n, "RLum.Results")){
n <- n
} else {
n <- n$n
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2 changes: 1 addition & 1 deletion R/simulate_heating.R
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Expand Up @@ -57,7 +57,7 @@
}

##check if object is of class RLum.Results
if(class(n) != "RLum.Results"){
if(!inherits(n, "RLum.Results")){
n <- n
} else {
n <- n$n
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4 changes: 1 addition & 3 deletions R/simulate_illumination.R
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Expand Up @@ -22,8 +22,6 @@
#'
#' @author Johannes Friedrich, University of Bayreuth (Germany),
#'
#' @references
#'
#' @seealso \code{\link{plot}}
#'
#' @examples
Expand Down Expand Up @@ -56,7 +54,7 @@
}

##check if n is a RLum object
if(class(n) != "RLum.Results"){
if(!inherits(n, "RLum.Results")){
n <- n
} else {
n <- n$n
Expand Down
2 changes: 1 addition & 1 deletion R/simulate_pause.R
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Expand Up @@ -59,7 +59,7 @@
}

##check if object is of class RLum.Data.Curve
if(class(n) != "RLum.Results"){
if(!inherits(n, "RLum.Results")){
n <- n
} else {
n <- n$n
Expand Down
2 changes: 0 additions & 2 deletions R/translate_sequence.R
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Expand Up @@ -28,8 +28,6 @@
#'
#' @author Johannes Friedrich, University of Bayreuth (Germany),
#'
#' @references
#'
#' @seealso \code{\link{model_LuminescenceSignals}}, \code{\linkS4class{RLum}}
#'
#' @examples
Expand Down
19 changes: 19 additions & 0 deletions man/RLumModel-package.Rd
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2 changes: 1 addition & 1 deletion src/Makevars
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@@ -1,2 +1,2 @@
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
CXX_STD = CXX11
PKG_CPPFLAGS = -DARMA_USE_CURRENT
2 changes: 1 addition & 1 deletion src/Makevars.win
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@@ -1,2 +1,2 @@
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
CXX_STD = CXX11
PKG_CPPFLAGS = -DARMA_USE_CURRENT
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