Merge pull request #43 from mmollina/add_hidecan

Add hidecan

.github/workflows/R-CMD-chek.yaml

@@ -0,0 +1,58 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, add_hidecan]
+  pull_request:
+    branches: [main, add_hidecan]
+
+name: R-CMD-check
+
+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-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: rcmdcheck curl vdiffr
+
+      - uses: r-lib/actions/check-r-package@v2
+
+      - 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

.github/workflows/test-coverage.yaml

@@ -0,0 +1,43 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: covr webshot curl
+
+
+      - name: Install dependencies
+        run: |
+          webshot::install_phantomjs()
+          webdriver::run_phantomjs(timeout = 15000)
+        shell: Rscript {0}
+
+      - name: Install viewpoly
+        shell: bash
+        run: R CMD INSTALL --preclean .
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

.gitignore

@@ -4,6 +4,7 @@
 
 # Session Data files
 .RData
+data/*.RData
 
 # User-specific files
 .Ruserdata
@@ -19,7 +20,6 @@
 
 # RStudio files
 .Rproj.user/
-.github/
 
 # produced vignettes
 vignettes/*.html

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: viewpoly
 Title: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species
-Version: 0.4.0
+Version: 0.4.1
 Authors@R: c(
            person(given = "Cristiane",
                   family = "Taniguti",
@@ -72,7 +72,7 @@ URL: https://github.com/mmollina/viewpoly
 BugReports: https://github.com/mmollina/viewpoly/issues
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Suggests: 
     testthat (>= 3.0.0),
     shinytest,

NAMESPACE

@@ -10,6 +10,7 @@ import(purrr)
 import(shiny)
 import(shinyWidgets)
 import(shinydashboard)
+import(tidyr)
 import(vroom)
 importFrom(JBrowseR,JBrowseR)
 importFrom(JBrowseR,JBrowseROutput)
@@ -33,6 +34,7 @@ importFrom(grDevices,col2rgb)
 importFrom(grDevices,hcl)
 importFrom(grDevices,hsv)
 importFrom(grDevices,rgb2hsv)
+importFrom(graphics,legend)
 importFrom(hidecan,CAN_data)
 importFrom(hidecan,DE_data)
 importFrom(hidecan,GWAS_data)