Merge pull request #71 from xoopR/0.2.3

0.2.3 prep

.github/workflows/pkgdown.yml

@@ -30,11 +30,13 @@ jobs:
           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
+        run: brew install harfbuzz fribidi
+
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown")
-          remotes::install_github("mlr-org/mlr3pkgdowntemplate")
+          install.packages(c("pkgdown", "textshaping"))
         shell: Rscript {0}
 
       - name: Install package

.github/workflows/rcmdcheck.yml

@@ -4,90 +4,102 @@ on:
   schedule:
     - cron: "0 4 * * *"
 
-name: Check/Codecov/Render
+name: R-CMD-check
 
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
-    name: R CMD Check (${{ matrix.config.os }} (${{ matrix.config.r }}))
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
     strategy:
       fail-fast: false
       matrix:
         config:
-          - { os: macOS-latest, r: "release" }
-          - { os: macOS-latest, r: "3.6" }
-          - { os: macOS-latest, r: "devel" }
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/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
+      - uses: r-lib/actions/setup-r@v1
+        id: install-r
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v1
 
-      - name: Query dependencies
+      - name: Install pak and query dependencies
         run: |
-          install.packages(c("remotes", "devtools"))
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@v1
+      - 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-
+          path: |
+            ${{ env.R_LIBS_USER }}/*
+            !${{ env.R_LIBS_USER }}/pak
+          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          pak::local_system_requirements(execute = TRUE)
+          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
+        shell: Rscript {0}
 
       - name: Install dependencies
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
+          pak::local_install_dev_deps(upgrade = TRUE)
+          pak::pkg_install("rcmdcheck")
+        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_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+          _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: 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
+          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
           path: check
 
-      - name: Install covr
-        if: ${{ github.event_name == 'pull_request' && runner.os == 'macOS' }}
-        run: install.packages('covr')
-        shell: Rscript {0}
+      - 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
 
       - name: Test coverage
-        if: ${{ github.event_name == 'pull_request' && runner.os == 'macOS' }}
-        run: covr::codecov()
-        shell: Rscript {0}
-
-      - name: Render rmd
-        if: ${{ github.event_name == 'pull_request' && runner.os == 'macOS' }}
+        if: ${{ runner.os == 'Linux' && matrix.config.r == 'release'}}
         run: |
-          devtools::install()
-          rmarkdown::render('README.Rmd')
+          install.packages('covr')
+          covr::codecov()
         shell: Rscript {0}
-
-      - name: Commit changes
-        if: ${{ github.event_name == 'pull_request' && runner.os == 'macOS' }}
-        uses: EndBug/add-and-commit@v7
-        with:
-          author_name: github-actions
-          author_email: 41898282+github-actions[bot]@users.noreply.github.com
-          message: 'Update README.md'
-          add: 'README.md'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: set6
 Title: R6 Mathematical Sets Interface
-Version: 0.2.2.9000
+Version: 0.2.3
 Authors@R:
       c(person(given = "Raphael",
              family = "Sonabend",

NEWS.md

@@ -1,4 +1,4 @@
-# set6 0.2.2.9000
+# set6 0.2.3
 
 * Containedness checks for 'n' dimensional sets no longer require same length vectors if power is
 "n"
@@ -100,4 +100,4 @@
 - `set6` upgrades the `sets` package to R6. Many forms of mathematical sets are implemented, including (countably finite) sets, tuples, intervals (countably infinite or uncountable), and fuzzy variants. Wrappers extend functionality by allowing symbolic representations of complex operations on sets, including unions, (cartesian) products, exponentiation, and differences (asymmetric and symmetric).
 - See [the website](https://xoopR.github.io/set6/) for more details and the project readme
 - See [getting started vignette](https://xoopR.github.io/set6/articles/set6.html) for a short tutorial and introduction
-- `set6` is currently 'maturing', so whilst no major updates are planned they may happen. Constant minor updates should be expected.
+- `set6` is currently 'maturing', so whilst no major updates are planned they may happen. Constant minor updates should be expected.

README.Rmd

@@ -20,7 +20,7 @@ set.seed(42)
 [![Lifecycle Badge](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://img.shields.io/badge/lifecycle-stable-brightgreen)
 
 [![CRAN Status Badge](https://www.r-pkg.org/badges/version-ago/set6)](https://cran.r-project.org/package=set6)
-[![CRAN Checks](https://cranchecks.info/badges/summary/set6)](https://cran.r-project.org/web/checks/check_results_set6.html)
+[![CRAN Checks](https://cranchecks.info/badges/worst/set6)](https://cran.r-project.org/web/checks/check_results_set6.html)
 [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/grand-total/set6)](https://cran.r-project.org/package=set6)
 
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.02598/status.svg)](https://doi.org/10.21105/joss.02598)

README.md

@@ -17,7 +17,7 @@ Badge](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://i
 [![CRAN Status
 Badge](https://www.r-pkg.org/badges/version-ago/set6)](https://cran.r-project.org/package=set6)
 [![CRAN
-Checks](https://cranchecks.info/badges/summary/set6)](https://cran.r-project.org/web/checks/check_results_set6.html)
+Checks](https://cranchecks.info/badges/worst/set6)](https://cran.r-project.org/web/checks/check_results_set6.html)
 [![CRAN
 Downloads](https://cranlogs.r-pkg.org/badges/grand-total/set6)](https://cran.r-project.org/package=set6)
 
@@ -31,15 +31,15 @@ chat](https://badges.gitter.im/xoopR/set6.png)](https://gitter.im/xoopR/set6)
 
 `set6` is an R6 upgrade to the `sets` package in R that includes:
 
-  - Multi-dimensional sets
-  - Tuples
-  - Finite and infinite intervals
-  - Fuzzy sets and tuples
-  - Set operations including union, intersect, (asymmetric and
+-   Multi-dimensional sets
+-   Tuples
+-   Finite and infinite intervals
+-   Fuzzy sets and tuples
+-   Set operations including union, intersect, (asymmetric and
     symmetric) difference, and product
-  - Symbolic representation of infinite sets including common special
+-   Symbolic representation of infinite sets including common special
     sets such as the Reals and Integers
-  - ConditionalSets for defining sets according to logical conditions
+-   ConditionalSets for defining sets according to logical conditions
 
 ## Installation
 
@@ -202,31 +202,31 @@ occur. There are a few features and refactoring we plan on implementing
 before we consider the package to be in its first complete version.
 These mainly include
 
-  - Finalising all methods and fields - some are missing or possibly
+-   Finalising all methods and fields - some are missing or possibly
     inaccurate for some wrappers. For example the cardinality of
     `ComplementSet`s is imprecise at the moment.
-  - We are considering adding a `simplify` method to wrappers to reduce
+-   We are considering adding a `simplify` method to wrappers to reduce
     classes inheriting from `SetWrapper` to simpler sets. This allows
     users to perform operations with `simplify = FALSE` and then to
     change their mind.
-  - There are known bottlenecks that need to be fixed to massively
+-   There are known bottlenecks that need to be fixed to massively
     improve speed and efficiency.
-  - Adding more tutorials to make the interface easier for beginners,
+-   Adding more tutorials to make the interface easier for beginners,
     especially people new to R6
 
 At a later stage we may consider adding Venn diagrams for visualisation
 of sets and intervals, but this is very low priority.
 
 ## Similar Packages
 
-  - [sets](https://CRAN.R-project.org/package=sets) - The **sets**
+-   [sets](https://CRAN.R-project.org/package=sets) - The **sets**
     package uses S3 to define some symbolic representaton of
     mathematical sets, tuple, intervals, and fuzzy variants. However the
     symbolic representation is not consistent throughout the package,
     does not allow for clear inspection of set/interval elements, and
     there is no support for multi-dimensional sets.
 
-  - [BaseSet](https://github.com/ropensci/BaseSet) - The **BaseSet**
+-   [BaseSet](https://github.com/ropensci/BaseSet) - The **BaseSet**
     package focuses on storing and analysing sets in a ‘tidy’ way, with
     more options for data storage in long and wide formats. The primary
     usage is neat and efficient inspection of finite sets, there is no

cran-comments.md

@@ -1,16 +1,16 @@
 ## Comments
 
-Early submission due to errors in R-devel.
+Early submission due to bug in downstream dependency.
 
 ## Test Environments
 
 On GitHub actions:
 
 * windows-latest (R release)
-* windows-latest (R devel)
-* windows-latest (R 3.6)
 * macOS-latest (R release)
 * ubuntu-latest (R release)
+* ubuntu-latest (R oldrel)
+* ubuntu-latest (R devel)
 
 ## R CMD check results