v2.1.1 (#408)

ggobi · Mar 8, 2021 · 03b5335 · 03b5335
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -19,73 +19,66 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: macOS-latest,   r: 'devel' }
-          - { os: windows-latest, r: 'devel' }
-          - { os: macOS-latest,   r: 'release' }
-          - { os: windows-latest, r: 'release' }
-          - { os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" }
-          - { os: macOS-latest,   r: 'oldrel' }
-          - { os: windows-latest, r: 'oldrel' }
-          - { os: ubuntu-16.04,   r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" }
+          # - { os: macOS-latest,   r: 'devel',   force_suggests: "0" }
+          - { os: windows-latest, r: 'devel',   force_suggests: "1" }
+
+          - { os: macOS-latest,   r: 'release', force_suggests: "1" }
+          - { os: windows-latest, r: 'release', force_suggests: "1" }
+          - { os: ubuntu-16.04,   r: 'release', force_suggests: "1",  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" }
+
+          - { os: macOS-latest,   r: 'oldrel',  force_suggests: "1" }
+          - { os: windows-latest, r: 'oldrel',  force_suggests: "1" }
+          - { os: ubuntu-16.04,   r: 'oldrel',  force_suggests: "1" , 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 }}
-      _R_CHECK_FORCE_SUGGESTS_: 0
+      _R_CHECK_FORCE_SUGGESTS_: ${{ matrix.config.force_suggests }}
 
     steps:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@master
+        id: install-r
         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(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+      - name: Install pak and query dependencies
         shell: Rscript {0}
+        run: |
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps_tree("local::.", dependencies = TRUE), ".github/r-depends.rds")
 
       - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+        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-
+          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'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        shell: Rscript {0}
         run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
+          pak::local_system_requirements(execute = TRUE)
+          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
+          pak::pkg_system_requirements("sessioninfo", execute = TRUE)
 
       - name: Install dependencies
-        if: runner.os != 'Windows' || matrix.config.r == 'devel'
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
-      - name: Install dependencies (Windows binary)
-        if: runner.os == 'Windows' && matrix.config.r != 'devel'
         run: |
-          remotes::install_deps(dependencies = TRUE, type = "binary")
-          remotes::install_cran("rcmdcheck", type = "binary")
-        shell: Rscript {0}
+          pak::local_install_dev_deps(upgrade = TRUE)
+          pak::pkg_install(c("rcmdcheck", "sessioninfo"))
 
       - name: Session info
+        shell: Rscript {0}
         run: |
           options(width = 100)
           pkgs <- installed.packages()[, "Package"]
           sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
 
       - name: Check with printing
         env:

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -13,36 +13,54 @@ name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ${{ matrix.config.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: ubuntu-16.04,   r: 'release', force_suggests: "1",  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" }
+
     env:
+      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@master
+        id: install-r
+        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(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+      - name: Install pak and query dependencies
         shell: Rscript {0}
+        run: |
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps_tree("local::.", dependencies = TRUE), ".github/r-depends.rds")
 
       - name: Cache R packages
-        uses: actions/cache@v1
+        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-
+          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-pkgdown-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: |
+            ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-pkgdown-
+            ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
 
-      - name: Install dependencies
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        shell: Rscript {0}
         run: |
-          install.packages("remotes")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_dev("pkgdown")
+          pak::local_system_requirements(execute = TRUE)
+          pak::pkg_system_requirements("pkgdown", execute = TRUE)
+
+      - name: Install dependencies
         shell: Rscript {0}
+        run: |
+          pak::local_install_dev_deps(upgrade = TRUE)
+          pak::pkg_install("pkgdown")
 
       - name: Install package
         run: R CMD INSTALL .

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -11,36 +11,53 @@ name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ${{ matrix.config.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: ubuntu-16.04,   r: 'release', force_suggests: "1",  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" }
     env:
+      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@master
+        id: install-r
+        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(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+      - name: Install pak and query dependencies
         shell: Rscript {0}
+        run: |
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps_tree("local::.", dependencies = TRUE), ".github/r-depends.rds")
 
       - name: Cache R packages
-        uses: actions/cache@v1
+        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-
+          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-testing-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: |
+            ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-testing-
+            ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
 
-      - name: Install dependencies
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        shell: Rscript {0}
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
+          pak::local_system_requirements(execute = TRUE)
+          pak::pkg_system_requirements("covr", execute = TRUE)
+
+      - name: Install dependencies
         shell: Rscript {0}
+        run: |
+          pak::local_install_dev_deps(upgrade = TRUE)
+          pak::pkg_install("covr")
 
       - name: Test coverage
         env:

diff --git a/.gitignore b/.gitignore
@@ -2,7 +2,6 @@
 .Rhistory
 ..Rcheck
 *ggmapTemp.png
-inst/*
 tests/testthat/Rplots.pdf
 vignettes/figure
 vignettes/docs.html

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: GGally
-Version: 2.1.0
+Version: 2.1.1
 License: GPL (>= 2.0)
 Title: Extension to 'ggplot2'
 Type: Package

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,12 @@
+# GGally 2.1.1
+
+### Bug fixes
+
+* Ignore `colour` aesthetic if all values are `NA`. (@larmarange, #404)
+* Avoid all duplicates within `stat_cross()`. (@larmarange, #402)
+* Avoid an error when tidiers do not return p-values. (@larmarange, #400)
+* Suggest `emmeans` to allow `ggcoef()` example to execute. (#407)
+
 # GGally 2.1.0
 
 ### Breaking changes

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,42 +1,38 @@
 
 ## Comments
+#### 2021-03-07
 
-#### 2021-01-04
+Have addressed the missing `emmeans` package error.
 
-New features added. Time to share them to CRAN.
-
-Please let me know if there is anything I can provide!
+Have also included other small bug fixes. No new features / functions.
 
 Thank you,
 Barret
 
+#### 2021-02-24
 
-#### 2020-12-28
-
-Sorry for the delay but would you please give me 2 more days to check the package?
-
-- Mingmei
+Dear maintainer,
 
-#### 2020-12-16
+Please see the problems shown on
+<https://cran.r-project.org/web/checks/check_results_GGally.html>.
 
-Reached out to {bootclust} maintainer Mingmei Tian <[email protected]> about not importing `sets::%>%` to avoid conflict with (possibly) many packages.
+Please correct before 2021-03-10 to safely retain your package on CRAN.
 
-Waiting until >= 2020-12-29 to submit.
+Best,
+-k
 
 
 
 ## Test environments and R CMD check results
 
-* local macOS install 10.15.7
+* local macOS install 11.2.2
   * R 4.0
-* GitHub Actions - https://github.com/ggobi/ggally/pull/397/checks
-  * macOS, windows - R devel
-  * macOS, windows, ubuntu 16 - R 4.0
-  * macOS, windows, ubuntu 16 - R 3.6
+* GitHub Actions - https://github.com/ggobi/ggally/pull/408/checks
+  * windows - R devel
+  * macOS, windows, ubuntu 16 - R release
+  * macOS, windows, ubuntu 16 - R oldrelease
 
 * win-builder
-  * oldrelease
-  * release
   * devel
 
 #### R CMD check results
@@ -46,24 +42,13 @@ Waiting until >= 2020-12-29 to submit.
 
 ## revdepcheck results
 
-We checked 113 reverse dependencies (88 from CRAN + 25 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 116 reverse dependencies (91 from CRAN + 25 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 1 new problems
+ * We saw 0 new problems
  * We failed to check 1 packages
 
 Issues with CRAN packages are summarised below.
 
-### New problems
-(This reports the first line of each new failure)
-
-* bootcluster
-  checking whether package ‘bootcluster’ can be installed ... WARNING
-
-  - Maintainer (Mingmei Tian <[email protected]>) was contacted on Dec 16th about an upcoming release of GGally.
-    * A possible patch was provided over email.
-    * Mingmei replied to the email and asked for time until Jan 1st.
-    * I have not heard an update since.
-
-### Failed to check
+### Failed to install
 
 * loon.ggplot (NA)