From 5a0e910f018197694d99b356e0d2f59e8e0423e5 Mon Sep 17 00:00:00 2001 From: Marco Colombo Date: Wed, 17 Sep 2025 16:04:03 +0200 Subject: [PATCH 1/7] Update the OS requested in the github workflow. This should avoid long queueing times for the old machines. --- .github/workflows/GitHub_Actions_CI.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/GitHub_Actions_CI.yaml b/.github/workflows/GitHub_Actions_CI.yaml index f94037c..d753fd1 100644 --- a/.github/workflows/GitHub_Actions_CI.yaml +++ b/.github/workflows/GitHub_Actions_CI.yaml @@ -23,11 +23,11 @@ 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 From 26e7210d4da25cad8d9d80da3c62867d7175036c Mon Sep 17 00:00:00 2001 From: Marco Colombo Date: Wed, 17 Sep 2025 16:04:39 +0200 Subject: [PATCH 2/7] Fix notes from R CMD check. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This fixes these notes: N checking R code for possible problems (4.8s) Found if() conditions comparing class() to string: File ‘RLumModel/R/read_SEQ2R.R’: if (class(file) != "character") ... File ‘RLumModel/R/simulate_CW_OSL.R’: if (class(n) != "RLum.Results") ... File ‘RLumModel/R/simulate_LM_OSL.R’: if (class(n) != "RLum.Results") ... File ‘RLumModel/R/simulate_RF.R’: if (class(n) != "RLum.Results") ... File ‘RLumModel/R/simulate_RF_and_heating.R’: if (class(n) != "RLum.Results") ... File ‘RLumModel/R/simulate_TL.R’: if (class(n) != "RLum.Results") ... File ‘RLumModel/R/simulate_heating.R’: if (class(n) != "RLum.Results") ... File ‘RLumModel/R/simulate_illumination.R’: if (class(n) != "RLum.Results") ... File ‘RLumModel/R/simulate_pause.R’: if (class(n) != "RLum.Results") ... Use inherits() (or maybe is()) instead. --- R/read_SEQ2R.R | 4 ++-- R/simulate_CW_OSL.R | 2 +- R/simulate_LM_OSL.R | 2 +- R/simulate_RF.R | 2 +- R/simulate_RF_and_heating.R | 2 +- R/simulate_TL.R | 2 +- R/simulate_heating.R | 2 +- R/simulate_illumination.R | 2 +- R/simulate_pause.R | 2 +- 9 files changed, 10 insertions(+), 10 deletions(-) diff --git a/R/read_SEQ2R.R b/R/read_SEQ2R.R index ac30961..c94be4e 100755 --- a/R/read_SEQ2R.R +++ b/R/read_SEQ2R.R @@ -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.") diff --git a/R/simulate_CW_OSL.R b/R/simulate_CW_OSL.R index d1ed015..49e3605 100755 --- a/R/simulate_CW_OSL.R +++ b/R/simulate_CW_OSL.R @@ -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$n diff --git a/R/simulate_LM_OSL.R b/R/simulate_LM_OSL.R index 78eebd5..b3c64be 100755 --- a/R/simulate_LM_OSL.R +++ b/R/simulate_LM_OSL.R @@ -70,7 +70,7 @@ } ##check if object is of class RLum.Data.Curve - if(class(n) != "RLum.Results"){ + if(!inherits(n, "RLum.Results")){ n <- n } else { n <- n$n diff --git a/R/simulate_RF.R b/R/simulate_RF.R index a0da252..375e0db 100755 --- a/R/simulate_RF.R +++ b/R/simulate_RF.R @@ -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$n diff --git a/R/simulate_RF_and_heating.R b/R/simulate_RF_and_heating.R index ccc754d..5a33565 100644 --- a/R/simulate_RF_and_heating.R +++ b/R/simulate_RF_and_heating.R @@ -73,7 +73,7 @@ } ##check if object is of class RLum.Results - if(class(n) != "RLum.Results"){ + if(!inherits(n, "RLum.Results")){ n <- n } else { n <- n$n diff --git a/R/simulate_TL.R b/R/simulate_TL.R index 9cac6d5..aa29f60 100755 --- a/R/simulate_TL.R +++ b/R/simulate_TL.R @@ -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$n diff --git a/R/simulate_heating.R b/R/simulate_heating.R index 4072b70..911c698 100755 --- a/R/simulate_heating.R +++ b/R/simulate_heating.R @@ -57,7 +57,7 @@ } ##check if object is of class RLum.Results - if(class(n) != "RLum.Results"){ + if(!inherits(n, "RLum.Results")){ n <- n } else { n <- n$n diff --git a/R/simulate_illumination.R b/R/simulate_illumination.R index aea7f41..f287f3f 100755 --- a/R/simulate_illumination.R +++ b/R/simulate_illumination.R @@ -56,7 +56,7 @@ } ##check if n is a RLum object - if(class(n) != "RLum.Results"){ + if(!inherits(n, "RLum.Results")){ n <- n } else { n <- n$n diff --git a/R/simulate_pause.R b/R/simulate_pause.R index 9d71b5c..f0db30b 100755 --- a/R/simulate_pause.R +++ b/R/simulate_pause.R @@ -59,7 +59,7 @@ } ##check if object is of class RLum.Data.Curve - if(class(n) != "RLum.Results"){ + if(!inherits(n, "RLum.Results")){ n <- n } else { n <- n$n From ab13710b5c16a2cfb752f64a7eefafaf7e8f99a5 Mon Sep 17 00:00:00 2001 From: Marco Colombo Date: Wed, 17 Sep 2025 16:08:59 +0200 Subject: [PATCH 3/7] Update roxygen2 documentation. --- DESCRIPTION | 2 +- R/RLumModel-package.R | 3 +-- R/extract_pars.R | 2 -- R/simulate_LM_OSL.R | 2 -- R/simulate_illumination.R | 2 -- R/translate_sequence.R | 2 -- man/RLumModel-package.Rd | 19 +++++++++++++++++++ 7 files changed, 21 insertions(+), 11 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index da518ab..69e5a92 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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 diff --git a/R/RLumModel-package.R b/R/RLumModel-package.R index e5d611c..7bef4cb 100755 --- a/R/RLumModel-package.R +++ b/R/RLumModel-package.R @@ -8,7 +8,6 @@ #' published models. #' #' @name RLumModel-package -#' @docType package #' @details **Authors** #' #' \tabular{ll}{ @@ -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 diff --git a/R/extract_pars.R b/R/extract_pars.R index 0358ef7..0210d5d 100755 --- a/R/extract_pars.R +++ b/R/extract_pars.R @@ -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}} diff --git a/R/simulate_LM_OSL.R b/R/simulate_LM_OSL.R index b3c64be..25cdcd4 100755 --- a/R/simulate_LM_OSL.R +++ b/R/simulate_LM_OSL.R @@ -28,8 +28,6 @@ #' #' @author Johannes Friedrich, University of Bayreuth (Germany), #' -#' @references -#' #' @seealso \code{\link{plot}} #' #' @examples diff --git a/R/simulate_illumination.R b/R/simulate_illumination.R index f287f3f..7fa6159 100755 --- a/R/simulate_illumination.R +++ b/R/simulate_illumination.R @@ -22,8 +22,6 @@ #' #' @author Johannes Friedrich, University of Bayreuth (Germany), #' -#' @references -#' #' @seealso \code{\link{plot}} #' #' @examples diff --git a/R/translate_sequence.R b/R/translate_sequence.R index c47ae3b..5c7b5cf 100755 --- a/R/translate_sequence.R +++ b/R/translate_sequence.R @@ -28,8 +28,6 @@ #' #' @author Johannes Friedrich, University of Bayreuth (Germany), #' -#' @references -#' #' @seealso \code{\link{model_LuminescenceSignals}}, \code{\linkS4class{RLum}} #' #' @examples diff --git a/man/RLumModel-package.Rd b/man/RLumModel-package.Rd index 0f8ba5b..8963a47 100644 --- a/man/RLumModel-package.Rd +++ b/man/RLumModel-package.Rd @@ -2,6 +2,7 @@ % Please edit documentation in R/RLumModel-package.R \docType{package} \name{RLumModel-package} +\alias{RLumModel} \alias{RLumModel-package} \title{Solving Ordinary Differential Equations to Understand Luminescence} \description{ @@ -47,5 +48,23 @@ Johannes Friedrich, University of Bayreuth, Germany The work of Johannes Friedrich is gratefully supported by the DFG in framework of the project 'Modelling quartz luminescence signal dynamics relevant for dating and dosimetry' (SCHM 305114-1). +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://CRAN.R-project.org/package=RLumModel} + \item Report bugs at \url{https://github.com/R-Lum/RLumModel/issues} +} + +} +\author{ +\strong{Maintainer}: Johannes Friedrich \email{johannes.friedrich@posteo.de} (\href{https://orcid.org/0000-0002-0805-9547}{ORCID}) [translator] + +Authors: +\itemize{ + \item Sebastian Kreutzer (\href{https://orcid.org/0000-0002-0734-2199}{ORCID}) [thesis advisor] + \item Christoph Schmidt (\href{https://orcid.org/0000-0002-2309-3209}{ORCID}) [thesis advisor] +} + } \keyword{package} From adf03e322c49a6ac4be30b4dc8aa0f086f88c167 Mon Sep 17 00:00:00 2001 From: Marco Colombo Date: Wed, 17 Sep 2025 16:16:13 +0200 Subject: [PATCH 4/7] Stop requiring C++11 to satisfy CRAN request. --- src/Makevars | 1 - src/Makevars.win | 1 - 2 files changed, 2 deletions(-) diff --git a/src/Makevars b/src/Makevars index 6eb107b..22ebc63 100755 --- a/src/Makevars +++ b/src/Makevars @@ -1,2 +1 @@ PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -CXX_STD = CXX11 diff --git a/src/Makevars.win b/src/Makevars.win index 6eb107b..22ebc63 100755 --- a/src/Makevars.win +++ b/src/Makevars.win @@ -1,2 +1 @@ PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -CXX_STD = CXX11 From 94c59b885d9f65b4fb21ffc0402e3907330e6e55 Mon Sep 17 00:00:00 2001 From: Marco Colombo Date: Wed, 17 Sep 2025 16:17:50 +0200 Subject: [PATCH 5/7] Fix compilation warnings due to the new RCppArmadillo. --- src/Makevars | 1 + src/Makevars.win | 1 + 2 files changed, 2 insertions(+) diff --git a/src/Makevars b/src/Makevars index 22ebc63..ceab2ce 100755 --- a/src/Makevars +++ b/src/Makevars @@ -1 +1,2 @@ PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) +PKG_CPPFLAGS = -DARMA_USE_CURRENT diff --git a/src/Makevars.win b/src/Makevars.win index 22ebc63..ceab2ce 100755 --- a/src/Makevars.win +++ b/src/Makevars.win @@ -1 +1,2 @@ PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) +PKG_CPPFLAGS = -DARMA_USE_CURRENT From 1492b31e48c397bbc2003f5dfd2a3e7e9f48acd7 Mon Sep 17 00:00:00 2001 From: Marco Colombo Date: Wed, 17 Sep 2025 16:27:05 +0200 Subject: [PATCH 6/7] Update some action versions. This should fix this error when running the github workflow: Error: This request has been automatically failed because it uses a deprecated version of `actions/cache: v2`. Please update your workflow to use v3/v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down --- .github/workflows/GitHub_Actions_CI.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/GitHub_Actions_CI.yaml b/.github/workflows/GitHub_Actions_CI.yaml index d753fd1..db4d91f 100644 --- a/.github/workflows/GitHub_Actions_CI.yaml +++ b/.github/workflows/GitHub_Actions_CI.yaml @@ -35,14 +35,14 @@ jobs: 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: | @@ -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') }} From 8000cd37ed2f056ecd773d1918a9c213c3bedb02 Mon Sep 17 00:00:00 2001 From: Marco Colombo Date: Wed, 17 Sep 2025 16:54:34 +0200 Subject: [PATCH 7/7] Fix error on Linux CI machines. This is an attempt to fix the following: Run rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/runner/work/_temp/Library/curl/libs/curl.so': libssl.so.1.1: cannot open shared object file: No such file or directory Calls: loadNamespace ... asNamespace -> loadNamespace -> library.dynam -> dyn.load --- .github/workflows/GitHub_Actions_CI.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/GitHub_Actions_CI.yaml b/.github/workflows/GitHub_Actions_CI.yaml index db4d91f..ea53c93 100644 --- a/.github/workflows/GitHub_Actions_CI.yaml +++ b/.github/workflows/GitHub_Actions_CI.yaml @@ -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'