Updated

.Rbuildignore

@@ -0,0 +1,12 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+pkgdown/
+docs/
+index.md
+.Rhistory
+_pkgdown.yml
+NEWS.md
+.github/
+.git/
+vignettes/
+vignettes/*

.github/workflows/main.yml

@@ -0,0 +1,136 @@
+name: build
+on:
+  push:
+    branches:
+      - master
+jobs:
+  linux:
+    name: ubuntu
+    runs-on: ubuntu-18.04
+    strategy:
+      fail-fast: false
+      matrix:
+        r: [3.5]
+    steps:
+      - uses: actions/checkout@v1
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{matrix.r}}
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Install linux dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libfreetype6-dev libcurl4-openssl-dev libssl-dev libxml2-dev
+
+      - name: Check R installation
+        run: Rscript -e "print('R installation works!')"
+
+      - name: Cache R packages
+        id: cache-rp
+        uses: actions/cache@v1
+        with:
+          path: "/home/runner/work/_temp/Library"
+          key: ${{ runner.os }}-cache-rp-$(ls /home/runner/work/_temp/Library/ | sha256sum)
+
+      - name: Install R dependencies
+        if: steps.cache-rp.outputs.cache-hit != 'true'
+        run: |
+          Rscript -e "install.packages(c('remotes','covr','rcmdcheck'))"
+          Rscript -e "remotes::install_deps(pkgdir='.',dependencies=TRUE,repos='https://cran.rstudio.com/')"
+      - name: RMD check and install package
+        run: |
+          Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'warning', check_dir = 'check')"
+          R CMD INSTALL .
+
+      - name: Code coverage
+        run: Rscript -e 'covr::codecov(token="${{ secrets.CODECOV_TOKEN }}",quiet=FALSE)'
+
+  windows:
+    runs-on: windows-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        r: [3.5,3.6]
+    steps:
+      - uses: actions/checkout@v1
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{matrix.r}}
+
+      - name: Cache R packages
+        id: cache-rp
+        uses: actions/cache@v1
+        with:
+          path: "C:/R/library"
+          key: ${{ runner.os }}-cache-rp
+
+      - name: Install R dependencies
+        if: steps.cache-rp.outputs.cache-hit != 'true'
+        run: |
+          Rscript -e "install.packages(c('remotes','rcmdcheck','stringi'),lib='C:/R/library')"
+          Rscript -e "remotes::install_deps(pkgdir='.',dependencies=TRUE,repos='https://cran.rstudio.com/',lib='C:/R/library')"
+          Rscript -e "(print(.libPaths()))"
+      - name: RMD check and install package
+        run: |
+          Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'warning', check_dir = 'check')"
+          R CMD INSTALL .
+  pkgdown:
+    needs: [mac, linux, windows]
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v1
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: 3.6.2
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Install linux dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libfreetype6-dev libcurl4-openssl-dev libssl-dev libxml2-dev
+
+      - name: Check R installation
+        run: Rscript -e "print('R installation works!')"
+
+      - name: Cache R packages
+        id: cache-rp
+        uses: actions/cache@v1
+        with:
+          path: "/home/runner/work/_temp/Library"
+          key: ${{ runner.os }}-cache-rp-$(ls /home/runner/work/_temp/Library/ | sha256sum)
+
+      - name: Install R dependencies
+        if: steps.cache-rp.outputs.cache-hit != 'true'
+        run: |
+          Rscript -e "install.packages(c('remotes','rcmdcheck','pkgdown'))"
+          Rscript -e "remotes::install_deps(pkgdir='.',dependencies=TRUE,repos='https://cran.rstudio.com/')"
+
+      - name: RMD check and install package
+        run: |
+          Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'warning', check_dir = 'check')"
+          R CMD INSTALL .
+
+      - name: Render site, pull repo, copy folder, push repo
+        run: |
+          # Add git info
+          git config --global user.email "do_not_email@example.com"
+          git config --global user.name "gh_action"
+
+          # Render website
+          Rscript -e "pkgdown::build_site()"
+
+          # Clone gh-pages branch
+          git clone --single-branch --branch gh-pages "https://${{ secrets.TOKEN }}@github.com/${GITHUB_REPOSITORY}.git" tmprepo
+          cd tmprepo
+          rm -rf *
+          git add .
+          git commit -m "Old contents deleted."
+          cp -r ../docs/* .
+          echo "Folder contents at $(pwd):"
+          ls -lh
+
+          # Push changes back
+          git add .
+          git commit -m "Updated contents at $(date +%Y%m%d-%H%M%S)"
+          git push origin

DESCRIPTION

@@ -2,8 +2,8 @@ Package: pophelper
 Type: Package
 Title: Tabulate, analyse and visualise admixture proportions from STRUCTURE, TESS, BAPS, ADMIXTURE and tab-delimited q-matrices
     files
-Version: 2.3.0
-Date: 2019-08-15
+Version: 2.3.1
+Date: 2020-02-10
 Author: Roy Mathew Francis
 Authors@R: person("Roy", "Francis", email = "roy.m.francis@outlook.com",role = c("aut", "cre"))
 Maintainer: Roy Mathew Francis <roy.m.francis@outlook.com>
@@ -13,18 +13,22 @@ Description: A set of useful functions for processing admixture proportion files
     K using Evanno method, export clumpp files, export distruct files and generate barplots.
 URL: https://github.com/royfrancis/pophelper
 Depends:
-    R(>= 3.5.0),
-    ggplot2
+    R(>= 3.5.0)
 Imports:
+    ggplot2,
+    grDevices,
     grid,
     gridExtra,
     gtable,
     label.switching,
-    tidyr
+    stats,
+    tidyr,
+    utils
 Suggests:
     bookdown,
     curl,
     captioner,
+    extrafont,
     showtext,
     ggpubr,
     knitr,
@@ -33,5 +37,4 @@ Suggests:
 License: GPL-3
 Encoding: UTF-8
 BugReports: https://github.com/royfrancis/pophelper/issues
-VignetteBuilder: knitr
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2

NAMESPACE

@@ -26,8 +26,12 @@ export(splitQ)
 export(summariseQ)
 export(tabulateQ)
 export(verifyGrplab)
+import(ggplot2)
+import(grDevices)
 import(grid)
 import(gridExtra)
 import(gtable)
 import(label.switching)
+import(stats)
 import(tidyr)
+import(utils)

NEWS

@@ -1,3 +1,11 @@
+pophelper 2.3.1
+=================
+* 10-Feb-2020
+* Built on R-3.6.2. Min req R-3.5.0.
+* Error bars in first plot of Evanno method showed max/min rather than SD. Fixed to show SD.
+* Fixed dependency issues
+* Automatic CI testing added
+
 pophelper 2.3.0
 =================
 * 11-Aug-2019