Set up auto update docker [docker]

Author: gvegayon

.github/workflows/update-docker.yml

@@ -0,0 +1,45 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+#
+# See https://github.com/r-lib/actions/tree/master/examples#readme for
+# additional example workflows available for the R community.
+
+name: DockerHub aphylo
+
+on:
+  push:
+  schedule:
+    cron: '0 0 * * MON'
+
+env:
+  REPO: uscbiostats/aphylo
+
+
+jobs:
+  build:
+    runs-on: Ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+        if: ${{ contains(github.event.head_commit.message, '[docker]') }}
+      
+      - name: Login to Docker Hub
+        if: ${{ contains(github.event.head_commit.message, '[docker]') }}
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKER_USER }}
+          password: ${{ secrets.DOCKER_TOKEN }}
+
+      - name: Build container
+        if: ${{ contains(github.event.head_commit.message, '[docker]') }}
+        run: |
+          cd docker
+          make build
+          
+      - name: Upload
+        if: ${{ contains(github.event.head_commit.message, '[docker]') }}
+        run: |
+          cd docker
+          make push

src/RcppExports.cpp

@@ -5,6 +5,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // new_aphylo_pruner
 SEXP new_aphylo_pruner(const std::vector< std::vector< unsigned int > >& edgelist, const std::vector< std::vector< unsigned int > >& A, const std::vector< unsigned int >& types, unsigned int nannotated);
 RcppExport SEXP _aphylo_new_aphylo_pruner(SEXP edgelistSEXP, SEXP ASEXP, SEXP typesSEXP, SEXP nannotatedSEXP) {

vignettes/example.Rmd

@@ -4,7 +4,7 @@ author: "George G. Vega Yon"
 date: "August 18, 2021"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Vignette Title}
+  %\VignetteIndexEntry{Simulation and Inference}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---