Merge pull request #22 from lixun910/master

add GitHub Actions for Rcheck, Rlint, pkgdown; fix some lint issues

.Rbuildignore

@@ -13,3 +13,4 @@
 ^src/libgeoda/LICENSE
 ^src/libgeoda/README.md
 ^src/libgeoda/.git
+^\.github$

.github/.gitignore

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

.github/workflows/build-check.yml

@@ -0,0 +1,123 @@
+# NOTE: This workflow is overkill for most R packages
+# check-standard.yaml is likely a better choice
+# usethis::use_github_action("check-standard") will install it.
+#
+# 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
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+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: windows-latest, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/latest"}
+          #- {os: ubuntu-18.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          #- {os: ubuntu-18.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          #- {os: ubuntu-18.04,   r: '3.6',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          #- {os: ubuntu-18.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          #- {os: ubuntu-18.04,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@v2
+        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'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "18.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+          remotes::install_cran("testthat")
+          remotes::install_cran("devtools")
+          remotes::install_cran("spdep")
+          remotes::install_cran("sf")
+        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: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_: 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
+        run: |
+          devtools::test()
+        shell: Rscript {0}
+
+      - 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
+
+      - name: Don't use tar from old Rtools to store the cache
+        if: ${{ runner.os == 'Windows' && startsWith(steps.install-r.outputs.installed-r-version, '3.6' ) }}
+        shell: bash
+        run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH

.github/workflows/lint-project.yaml

@@ -0,0 +1,31 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: lint-project
+
+jobs:
+  lint-project:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - name: Install lintr
+        run: install.packages("lintr")
+        shell: Rscript {0}
+
+      - name: Lint root directory
+        run: lintr::lint_dir()
+        shell: Rscript {0}

.github/workflows/pkgdown.yaml

@@ -0,0 +1,52 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+    tags:
+      -'*'
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@v2
+        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 dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          install.packages("pkgdown", type = "binary")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Actions"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: rgeoda
 Type: Package
 Title: R Library for Spatial Data Analysis
-Version: 0.0.8-3
-Date: 2021-07-21
+Version: 0.0.8-4
+Date: 2021-08-04
 Authors@R: 
     c(person(given = "Xun", family = "Li", email="[email protected]", role=c("aut","cre")),
       person(given = "Luc", family = "Anselin", email="[email protected]", role="aut"))

R/clustering.R

@@ -1,6 +1,7 @@
 ############################################################
 #' @title Spatial C(K)luster Analysis by Tree Edge Removal
-#' @description SKATER forms clusters by spatially partitioning data that has similar values for features of interest.
+#' @description SKATER forms clusters by spatially partitioning data that has
+#' similar values for features of interest.
 #' @param k The number of clusters
 #' @param w An instance of Weight class
 #' @param df A data frame with selected variables only. E.g. guerry[c("Crm_prs", "Crm_prp", "Litercy")]

R/init.R

@@ -4,7 +4,7 @@
 #' @useDynLib rgeoda
 NULL
 
-.onUnload = function(libname, pkgname) {
+.onUnload <- function(libname, pkgname) {
 }
 
 # When creating weights from sf/sp object, the geoda object will be created and
@@ -26,19 +26,19 @@ getGeoDaObj <- function(sf_obj) {
 
   geoda_obj <- NULL
 
-  if (exists(gda_uid, envir=cacheEnv)) {
+  if (exists(gda_uid, envir = cacheEnv)) {
     # use it directly for weights creation
-    geoda_obj <- get(gda_uid, envir=cacheEnv)
+    geoda_obj <- get(gda_uid, envir = cacheEnv)
   } else {
     # create a geoda object from sf_obj, NOT copy table
     geoda_obj <- as.geoda(sf_obj, with_table = FALSE)
     # cache it
-    assign(gda_uid, geoda_obj, envir=cacheEnv)
+    assign(gda_uid, geoda_obj, envir = cacheEnv)
   }
 
-  if (is.null(geoda_obj) || geoda_obj$GetNumObs() <=0) {
+  if (is.null(geoda_obj) || geoda_obj$GetNumObs() <= 0) {
     stop("Failed to read sf object. Please submit a bug report to https://github.com/geodacenter/rgeoda")
   }
 
-  return (geoda_obj)
+  return(geoda_obj)
 }