Merge pull request #14 from aberHRML/devel

v0.6.3

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

@@ -1,15 +1,10 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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
-      - master
-      - devel
+    branches: [main, master, devel]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -23,68 +18,29 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
 
+      - uses: r-lib/actions/setup-pandoc@v1
+
       - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v1
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          extra-packages: rcmdcheck
 
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+      - uses: r-lib/actions/check-r-package@v1

.github/workflows/pkgdown.yaml

@@ -0,0 +1,35 @@
+# 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, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: pkgdown
+          needs: website
+
+      - name: Deploy package
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

.github/workflows/test-coverage.yaml

@@ -0,0 +1,30 @@
+# 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, master]
+  pull_request:
+    branches: [main, master]
+
+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-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: covr
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

.gitignore

@@ -8,3 +8,4 @@ Meta
 DataSets
 /doc/
 /Meta/
+docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: metaboData
 Type: Package
 Title: Example Metabolomics Data Sets
-Version: 0.6.2
+Version: 0.6.3
 Authors@R: c(
     person("Jasen", "Finch", 
         email = "[email protected]", 
@@ -39,7 +39,7 @@ Imports:
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Suggests: 
     testthat,
     covr,

NEWS.md

@@ -1,3 +1,7 @@
+# metaboData 0.6.3
+
+* Removed malformed email addresses from the [`abr1`](https://aberhrml.github.io/metaboData/reference/abr1.html) data set documentation.
+
 # metaboData 0.6.2
 
 * Fixes to the package description for CRAN submission.

R/abr1.R

@@ -32,8 +32,7 @@
 #' containing experimental meta-data.} \item{pos}{A data frame for positive
 #' data with 120 observations and 2000 variables.} \item{neg}{A data frame for
 #' negative data with 120 observations and 2000 variables.}
-#' @author Manfred Beckmann, David Enot and Wanchang Lin \email{meb,dle,
-#' wll@@aber.ac.uk}
+#' @author Manfred Beckmann, David Enot and Wanchang Lin
 #' @keywords datasets
 #' @examples
 #' 

README.md

@@ -3,8 +3,8 @@
 
 <!-- badges: start -->
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
-[![R-CMD-check](https://github.com/jasenfinch/metaboData/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/metaboData/actions)
-[![Coverage status](https://codecov.io/gh/aberHRML/metaboData/branch/master/graph/badge.svg)](https://codecov.io/github/aberHRML/metaboData?branch=master)
+[![R-CMD-check](https://github.com/aberHRML/metaboData/workflows/R-CMD-check/badge.svg)](https://github.com/aberHRML/metaboData/actions)
+[![Codecov test coverage](https://codecov.io/gh/aberHRML/metaboData/branch/master/graph/badge.svg)](https://app.codecov.io/gh/aberHRML/metaboData?branch=master)
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://github.com/aberHRML/metaboData/blob/master/LICENSE.md)
 [![CRAN status](https://www.r-pkg.org/badges/version/metaboData)](https://CRAN.R-project.org/package=metaboData)
 [![downloads](https://cranlogs.r-pkg.org/badges/metaboData)](https://cran.r-project.org/package=metaboData)

_pkgdown.yml

@@ -1 +1,4 @@
-url: https://aberHRML.github.io/metaboData/
+url: https://aberhrml.github.io/metaboData/
+template:
+  bootstrap: 5
+

codecov.yml

@@ -6,7 +6,9 @@ coverage:
       default:
         target: auto
         threshold: 1%
+        informational: true
     patch:
       default:
         target: auto
         threshold: 1%
+        informational: true