Merge pull request #24 from caravagn/github-actions

this is not going to work

.github/workflows/R_CMD_check.yml

@@ -3,7 +3,7 @@ on:
     branches:
       - master
       - development
-      - fix-master
+      - github-actions
   pull_request:
     branches:
       - master
@@ -36,7 +36,9 @@ jobs:
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v1
+        with:
+          pandoc-version: '2.9.2.1' # The pandoc version to download (if necessary) and use.
 
       - name: Query dependencies
         run: |
@@ -67,6 +69,26 @@ jobs:
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
+      - name: Shell GIT env
+        shell: bash
+        run: |
+          SHA=${{ github.event.pull_request.head.sha }}
+          echo "github.event.pull_request.head.sha = ${SHA}"
+          echo "GITHUB_SHA = ${GITHUB_SHA}"
+          echo "GITHUB_REF = ${GITHUB_REF}"
+          echo "BRANCH = ${GITHUB_REF#refs/heads/}"
+      - name: Declare some vars to use on other actions
+        id: vars
+        shell: bash
+        run: |
+          echo "GITHUB_SHA: ${GITHUB_SHA}"
+          echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+          echo "::set-output name=sha_short::$(git rev-parse --short HEAD)"
+
+      - name: Build and install packages
+        run: |
+          Rscript -e "remotes::install_github('caravagn/mobster', ref='${{ steps.vars.outputs.sha_short }}')"
+
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false

.travis.yml

@@ -2,6 +2,23 @@
 
 language: R
 
+warnings_are_errors: false
+
+addons:
+  apt:
+    update: true
+    packages:
+      - libmagick++-dev
+      - librsvg2-dev
+      - libwebp-dev
+      - libpoppler-cpp-dev
+      - libtesseract-dev
+      - libleptonica-dev
+      - tesseract-ocr-eng
+      - libfftw3-dev
+      - cargo
+      - gsfonts
+
 cache:
     # Main R library    
     packages: true

DESCRIPTION

@@ -45,7 +45,9 @@ Suggests: knitr,
     CNAqc,
     ggmuller,
     png,
-    plotly
+    plotly,
+    gganimate,
+    magick
 Remotes:
     caravagn/easypar,
     caravagn/pio,

vignettes/a7_Example_tumour_simulation.Rmd

@@ -37,10 +37,11 @@ We have simulated a tumour with 2 clones. The tumours starts with the ancestral
 We load the simulation object [simulationdata.Rdata](./simulationdata.Rdata).
 
 ```{r, warning=FALSE, message=FALSE}
-require(mobster)
-require(dplyr)
-require(tibble)
-require(ggplot2)
+library(mobster)
+library(dplyr)
+library(tibble)
+library(ggplot2)
+library(gganimate)
 
 # Load input data from Marc
 load('simulationdata.Rdata')