Merge pull request #20 from SciomeLLC/nlopt-update

LLVM-clang incompatibiltiy fix. Disabled OpenMP temporarily

.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 }}

CHANGELOG.md

@@ -1,4 +1,8 @@
 # Changes
+## Version 23.10.1.3
+## The following cumulative fixes are in version 23.10.1.3
+- Modify nlopt to avoid issues with LLVM-clang incompatibilities
+- Disable OpenMP temporarily to get approved for CRAN 
 ## Version 23.10.1.2.4 
 ## The following cumulative fixes are in version 23.10.1.2.4
 - Add the ability to set a seed for nlopt and GSL to allow for consistent results

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ToxicR
 Type: Package
 Title: Analyzing Toxicology Dose-Response Data
-Version: 24.1.1.2.4
+Version: 24.1.1.4
 Date: 2024-08-24
 Authors@R: 
     c(
@@ -80,9 +80,9 @@ LinkingTo: Rcpp, RcppEigen, RcppGSL
 RoxygenNote: 7.3.2
 Encoding: UTF-8
 VignetteBuilder: knitr
-Suggests: plotly (>= 4.9.2.1), rmarkdown, actuar (>= 3.2-0),ggpubr (>=
+Suggests: plotly (>= 4.9.2.1), rmarkdown, ggpubr (>=
         0.4.0), testthat (>= 3.1.0),gridExtra (>= 2.3), VIM (>= 6.1.1),
-        knitr (>= 1.36), modules
+        knitr (>= 1.36), modules, actuar (>= 3.2-0)
 NeedsCompilation: yes
 Packaged: 2024-04-12 20:00:54 UTC; shail.choksi
 Author: Matt Wheeler [aut, cre] (<https://orcid.org/0000-0002-8242-2391>),

R/RcppExports.R

@@ -1,47 +1,47 @@
-# Generated by using Rcpp::compileAttributes() -> do not edit by hand
-# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
-
-.owenst_fn <- function(x, fx) {
-    .Call(`_ToxicR_owenst_fn`, x, fx)
-}
-
-.run_single_dichotomous <- function(model, data, pr, options1, options2, seed) {
-    .Call(`_ToxicR_run_single_dichotomous`, model, data, pr, options1, options2, seed)
-}
-
-.run_continuous_single <- function(model, Y, X, prior, options, dist_type, seed) {
-    .Call(`_ToxicR_run_continuous_single`, model, Y, X, prior, options, dist_type, seed)
-}
-
-.run_continuous_ma_laplace <- function(model_priors, model_type, dist_type, Y, X, options, seed) {
-    .Call(`_ToxicR_run_continuous_ma_laplace`, model_priors, model_type, dist_type, Y, X, options, seed)
-}
-
-.run_continuous_ma_mcmc <- function(model_priors, model_type, dist_type, Y, X, options, seed) {
-    .Call(`_ToxicR_run_continuous_ma_mcmc`, model_priors, model_type, dist_type, Y, X, options, seed)
-}
-
-.run_ma_dichotomous <- function(data, priors, models, model_p, is_MCMC, options1, options2, seed) {
-    .Call(`_ToxicR_run_ma_dichotomous`, data, priors, models, model_p, is_MCMC, options1, options2, seed)
-}
-
-.run_dichotomous_single_mcmc <- function(model, Y, D, pr, options, seed) {
-    .Call(`_ToxicR_run_dichotomous_single_mcmc`, model, Y, D, pr, options, seed)
-}
-
-.run_continuous_single_mcmc <- function(model, Y, D, priors, options, is_logNormal, suff_stat, seed) {
-    .Call(`_ToxicR_run_continuous_single_mcmc`, model, Y, D, priors, options, is_logNormal, suff_stat, seed)
-}
-
-.polykCPP <- function(dose, tumor, daysOnStudy) {
-    .Call(`_ToxicR_polyk`, dose, tumor, daysOnStudy)
-}
-
-.setseedGSL <- function(s) {
-    invisible(.Call(`_ToxicR_setseedGSL`, s))
-}
-
-.set_threads <- function(num_threads) {
-    .Call(`_ToxicR_set_threads`, num_threads)
-}
-
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+.owenst_fn <- function(x, fx) {
+    .Call(`_ToxicR_owenst_fn`, x, fx)
+}
+
+.run_single_dichotomous <- function(model, data, pr, options1, options2, seed) {
+    .Call(`_ToxicR_run_single_dichotomous`, model, data, pr, options1, options2, seed)
+}
+
+.run_continuous_single <- function(model, Y, X, prior, options, dist_type, seed) {
+    .Call(`_ToxicR_run_continuous_single`, model, Y, X, prior, options, dist_type, seed)
+}
+
+.run_continuous_ma_laplace <- function(model_priors, model_type, dist_type, Y, X, options, seed) {
+    .Call(`_ToxicR_run_continuous_ma_laplace`, model_priors, model_type, dist_type, Y, X, options, seed)
+}
+
+.run_continuous_ma_mcmc <- function(model_priors, model_type, dist_type, Y, X, options, seed) {
+    .Call(`_ToxicR_run_continuous_ma_mcmc`, model_priors, model_type, dist_type, Y, X, options, seed)
+}
+
+.run_ma_dichotomous <- function(data, priors, models, model_p, is_MCMC, options1, options2, seed) {
+    .Call(`_ToxicR_run_ma_dichotomous`, data, priors, models, model_p, is_MCMC, options1, options2, seed)
+}
+
+.run_dichotomous_single_mcmc <- function(model, Y, D, pr, options, seed) {
+    .Call(`_ToxicR_run_dichotomous_single_mcmc`, model, Y, D, pr, options, seed)
+}
+
+.run_continuous_single_mcmc <- function(model, Y, D, priors, options, is_logNormal, suff_stat, seed) {
+    .Call(`_ToxicR_run_continuous_single_mcmc`, model, Y, D, priors, options, is_logNormal, suff_stat, seed)
+}
+
+.polykCPP <- function(dose, tumor, daysOnStudy) {
+    .Call(`_ToxicR_polyk`, dose, tumor, daysOnStudy)
+}
+
+.setseedGSL <- function(s) {
+    invisible(.Call(`_ToxicR_setseedGSL`, s))
+}
+
+.set_threads <- function(num_threads) {
+    .Call(`_ToxicR_set_threads`, num_threads)
+}
+