diff --git a/.github/workflows/R-CMD-check-CRAN.yaml b/.github/workflows/R-CMD-check-CRAN.yaml deleted file mode 100644 index d4dcf143c..000000000 --- a/.github/workflows/R-CMD-check-CRAN.yaml +++ /dev/null @@ -1,147 +0,0 @@ -# NOTE: This workflow is overkill for most R packages -# check-standard.yaml is likely a better choice -# usethis::use_github_action("check-standard") will install it. -# -# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. -# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions -on: - push: - branches: - - main - pull_request: - branches: - - main - -name: R-CMD-check-CRAN - -jobs: - R-CMD-check: - runs-on: ${{ matrix.config.os }} - - name: ${{ matrix.config.os }} (${{ matrix.config.r }}) - - strategy: - fail-fast: false - matrix: - config: - - {os: macOS-latest, r: 'release'} - - {os: windows-latest, r: 'release'} - - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" } - - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - _R_CHECK_FORCE_SUGGESTS_: false - - steps: - - name: Set git to use LF - run: | - git config --global core.autocrlf false - - - name: Install X11 dependencies on MacOS - if: runner.os == 'macOS' - run: brew install --cask xquartz - shell: bash - - - name: Install deps on MacOS - if: runner.os == 'macOS' - run: | - brew install cairo - brew install libgit2 - brew install udunits - shell: bash - - - name: Link gfortran on MacOS - if: runner.os == 'macOS' - run: | - sudo ln -s /usr/local/bin/gfortran-10 /usr/local/bin/gfortran - sudo mkdir /usr/local/gfortran - sudo ln -s /usr/local/gfortran-10 /usr/local/gfortran - shell: bash - - - name: Create Makevars for Fortran linking options on macOS - if: runner.os == 'macOS' - run: | - try(dir.create("~/.R")) - writeLines(c("GCCBASE:=$(shell brew --prefix gcc)","FLIBS=-L$(GCCBASE)/lib/gcc/10/lib -lm",""),"~/.R/Makevars") - shell: Rscript {0} - - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@v1 - with: - r-version: ${{ matrix.config.r }} - http-user-agent: ${{ matrix.config.http-user-agent }} - - - uses: r-lib/actions/setup-pandoc@v1 - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Install Symengine from source for MacOS - if: runner.os == 'macOS' - run: install.packages("symengine", type="source") - shell: Rscript {0} - - - name: Cache R packages - if: runner.os != 'Windows' - uses: actions/cache@v1 - with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install system dependencies - if: runner.os == 'Linux' - run: | - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') - - - name: Install development nlmixr2data - run: remotes::install_cran("nlmixr2data") - shell: Rscript {0} - - - name: Install development lotri - run: remotes::install_cran("nlmixr2/lotri") - shell: Rscript {0} - - - name: Install development rxode2 - run: remotes::install_cran("nlmixr2/rxode2") - shell: Rscript {0} - - - name: Install dependencies - run: remotes::install_deps(dependencies = TRUE) - shell: Rscript {0} - - - name: Session info - run: | - options(width = 100) - pkgs <- installed.packages()[, "Package"] - sessioninfo::session_info(pkgs, include_base = TRUE) - shell: Rscript {0} - - - name: Check - env: - _R_CHECK_CRAN_INCOMING_: false - run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") - shell: Rscript {0} - - - name: Show testthat output - if: always() - run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true - shell: bash - - - name: Upload check results - if: failure() - uses: actions/upload-artifact@main - with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check diff --git a/R/utils.R b/R/utils.R index b7a51fee0..1397860f6 100644 --- a/R/utils.R +++ b/R/utils.R @@ -264,7 +264,12 @@ cholSE <- function(matrix, tol = (.Machine$double.eps)^(1 / 3)) { #' @return a list of ... #' @export nmsimplex <- function(start, fr, rho = NULL, control = list()) { - if (is.null(rho)) rho <- environment(fr) + if (!is.environment(rho)) { + if (!is.null(rho)) { + warning("improper argument for 'rho'", call.=FALSE) + } + rho <- environment(fr) + } step <- -.2 * start con <- list(maxeval = 999, reltol = 1e-6, rcoeff = 1., ecoeff = 2., ccoeff = .5, trace = FALSE) diff --git a/src/RcppExportMod.cpp b/src/RcppExportMod.cpp index 9c7015717..091e82be7 100644 --- a/src/RcppExportMod.cpp +++ b/src/RcppExportMod.cpp @@ -26,36 +26,35 @@ neldermead_wrap(SEXP fcallSEXP, SEXP rhoSEXP, SEXP nparSEXP, SEXP startSEXP, SEX SEXP iprintSEXP) { BEGIN_RCPP - - ev = new Rcpp::EvalStandard(fcallSEXP, rhoSEXP); // assign R function and environment - int i, Iconv, Itnum, Nfcall, Itmax, iprint; - double ftol_rel, rcoef, ecoef, ccoef; - double Start[99], Xmin[99], Ynewlo, Step[99]; - - NPAR = INTEGER(nparSEXP)[0]; - for (i=0; igetNbEvals() <getNbEvals() <