Feature/131 Enable R-CMD-check on Git-Hub Actions

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,129 @@
+on:
+  push:
+    branches:
+      - release
+      - master
+      - develop
+
+  pull_request:
+    branches:
+      - release
+      - master
+      - develop
+
+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: windows-latest, r: 'devel'}
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest,   r: 'release'}
+          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps("./hyperSpec", dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@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-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('./hyperSpec/DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps("./hyperSpec", dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+          remotes::install_cran("devtools")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Roxygenize
+        run: |
+          devtools::document(
+            "./hyperSpec",
+            roclets = c('rd', 'collate', 'namespace', 'vignette')
+          )
+        shell: Rscript {0}
+
+      - name: Check
+        if: matrix.config.r != 'devel'
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: |
+          rcmdcheck::rcmdcheck(
+            "./hyperSpec",
+            args = c("--no-manual", "--as-cran"),
+            error_on = "warning",
+            check_dir = "check"
+          )
+        shell: Rscript {0}
+
+      - name: Check (R-devel)
+        if: matrix.config.r == 'devel'
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: |
+          rcmdcheck::rcmdcheck(
+            "./hyperSpec",
+            args = c("--no-manual", "--as-cran"),
+            error_on = "error",
+            check_dir = "check"
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+        working-directory: ./hyperSpec
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.gitignore

@@ -14,35 +14,6 @@
 *.idx
 *.ind
 
-hyperSpec/NAMESPACE
-hyperSpec/data/*.rda
-hyperSpec/R/sysdata.rda
-hyperSpec/vignettes/*.Rnw
-hyperSpec/vignettes/vignettes.defs
-hyperSpec/vignettes/read.txt.PerkinElmer.R
-hyperSpec/vignettes/fig-3D.png
-hyperSpec/vignettes/hyperspec.bib
-hyperSpec/vignettes/functions.RData
-hyperSpec/vignettes/rawdata
-hyperSpec/inst/doc/*.pdf
-hyperSpec/inst/doc/vignettes.defs
-hyperSpec/inst/doc/rawdata
-hyperSpec/vignettes/rawdata
-hyperSpec/vignettes/strukturhyperspec.pdf
-hyperSpec/man/*.Rd
-Vignettes/*/*.pdf
-Vignettes/*/*.png
-Vignettes/*/vignettes.defs
-Vignettes/chondro/rawdata/
-Vignettes/flu/read.txt.PerkinElmer.R
-Vignettes/fileio/wdf.Renishaw/WdfAccess
-Vignettes/flu/rawdata/flu*.txt
-Vignettes/plotting/plotting-pkg.bib
-Vignettes/laser/rawdata/*
-hyperSpec/vignettes/chondro.pdf*
-hyperSpec/vignettes/fileio.pdf*
-
-
 hyperSpec_*.tar.gz
 *.Rcheck
 
@@ -65,11 +36,19 @@ hyperSpec_*.tar.gz
 .Rproj.user
 *.Rproj
 
+# Rnw vignettes
 Vignettes/*/*-pkg.bib
+Vignettes/*/*.pdf
+Vignettes/*/*.png
+Vignettes/*/vignettes.defs
 Vignettes/chondro/chondro-internal.rda
+Vignettes/chondro/rawdata/
 Vignettes/fileio/barbiturates.rda
 Vignettes/fileio/paracetamol.rda
+Vignettes/fileio/wdf.Renishaw/WdfAccess
 Vignettes/flu/flu.rda
+Vignettes/flu/rawdata/flu*.txt
+Vignettes/flu/read.txt.PerkinElmer.R
 Vignettes/laser/laser.rda
-hyperSpec/tests/testthat/Rplots.pdf
-hyperSpec/tests/testthat/fileio
+Vignettes/laser/rawdata/*
+Vignettes/plotting/plotting-pkg.bib

README.md

@@ -1,8 +1,12 @@
 # hyperSpec
 
+<!-- badges: start -->
 [![CRAN status](https://www.r-pkg.org/badges/version/hyperSpec)](https://cran.r-project.org/package=hyperSpec)
+[![R build status](https://github.com/cbeleites/hyperSpec/workflows/R-CMD-check/badge.svg)](https://github.com/cbeleites/hyperSpec/actions)
+<!-- badges: end -->
 
-This is the new home for R package hyperSpec.
+
+This is the new home for R package **hyperSpec**.
 
 Issues and feature requests should go [here](https://github.com/cbeleites/hyperSpec/issues)!
 

hyperSpec/.Rbuildignore

@@ -2,4 +2,10 @@
 ^\.Rproj\.user$
 Makefile
 tests/testthat/fileio
-Rplots.pdf
+Rplots.pdf
+^CONTRIBUTING\.md$
+^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^data-raw$

hyperSpec/.gitignore

@@ -0,0 +1,31 @@
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# Example code in package build process
+*-Ex.R
+
+# Mac directory files
+*.DS_Store
+
+# RStudio files
+.Rproj.user
+*.Rproj
+
+# Local pkgdown files
+docs
+
+# Unit tests
+tests/testthat/Rplots.pdf
+tests/testthat/fileio
+
+# Vignettes
+vignettes/*-pkg.bib
+vignettes/resources/*.bib
+
+# Documentation
+man/*.Rd
+NAMESPACE

hyperSpec/R/chondro.R

@@ -1,11 +1,12 @@
-.make.chondro <- function() {
-  new("hyperSpec",
-    spc = (tcrossprod(.chondro.scores, .chondro.loadings) +
-      rep(.chondro.center, each = nrow(.chondro.scores))),
-    wavelength = .chondro.wl,
-    data = .chondro.extra, labels = .chondro.labels
-  )
-}
+# .make.chondro <- function() {
+#   new("hyperSpec",
+#     spc = (tcrossprod(.chondro.scores, .chondro.loadings) +
+#       rep(.chondro.center, each = nrow(.chondro.scores))),
+#     wavelength = .chondro.wl,
+#     data = .chondro.extra, labels = .chondro.labels
+#   )
+# }
+# delayedAssign("chondro", .make.chondro())
 
 ##' Raman spectra of 2 Chondrocytes in Cartilage
 ##' A Raman-map (laterally resolved Raman spectra) of chondrocytes in
@@ -22,7 +23,6 @@
 ##' @author A. Bonifacio and C. Beleites
 ##' @keywords datasets
 ##' @references The raw data is available at \url{http://hyperspec.r-forge.r-project.org/blob/chondro.zip}
-##' @export chondro
 ##' @examples
 ##'
 ##'
@@ -48,4 +48,4 @@
 ##' plotmap (chondro[, , c( 728, 782, 1098, 1240, 1482, 1577)],
 ##'        col.regions = colorRampPalette (c ("white", "gold", "dark green"), space = "Lab") (20))
 ##'
-delayedAssign("chondro", .make.chondro())
+NULL