Merge branch 'master' into ggmatrix

* master: (45 commits) Add news use inherits over class(x) = y Display label on side in addition to facet try to fix the examples. Reduce a if logic to a single value. Fix eval on data column col try to fix ggnet logical logic More function changes similar to #305 do not use actions. too many problems use cloud repo location and statnet.common pkg use cran, but try to install sna and mvtnorm with source type remove the cran repo to try to be able to install sna and mvtnorm do not try to install sys deps when checking pass in formula to geom_smooth with y~x to avoid message. Fix other ggplot2 3.3 gtable issues white space adjustment Remove dev badges. Remove gitter link. Update ggplot2 links Fix partial arg match Update roxygen version ignore .github Use community link vs stackoverflow Create R-CMD-check.yaml Fix spacing. Use `as.factor` over `factor` ...
ggobi · Feb 10, 2020 · 329a018 · 329a018
2 parents 827bd9a + c3a75aa
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -13,7 +13,6 @@ ggmapTemp.png
 README.html
 notes/
 tests/testthat/Rplots.pdf
-revdep
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^cran-comments\.md$
@@ -30,3 +29,5 @@ ggduo_paper.txt
 ^man-roxygen
 ^\.httr-oauth$
 ^scripts/
+^revdep$
+^\.github/
diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md
@@ -1,4 +1,4 @@
-Please briefly describe your problem and what output you expect. If you have a question, please try using stackoverflow <http://stackoverflow.com> first.
+Please briefly describe your problem and what output you expect. If you have a general question, please try using [RStudio Community](https://community.rstudio.com/tags/c/general/17/ggally) first.
 
 Please include a minimal reprex. The goal of a reprex is to make it as easy as possible for me to recreate your problem so that I can fix it. If you've never heard of a reprex before, start by reading <https://github.com/jennybc/reprex#what-is-a-reprex>, and follow the advice further down the page. Do NOT include session info unless it's explicitly asked for, or you've used `reprex::reprex(..., si = TRUE)` to hide it away.
 

diff --git a/.github/workflows-ignore/R-CMD-check.yaml b/.github/workflows-ignore/R-CMD-check.yaml
@@ -0,0 +1,91 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - 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: windows-latest, r: '3.6'}
+          - {os: macOS-latest, r: '3.6'}
+          - {os: macOS-latest, r: 'devel'}
+          - {os: ubuntu-16.04, r: '3.2', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04, r: '3.3', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04, r: '3.4', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04, r: '3.5', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04, r: '3.6', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      CRAN: ${{ matrix.config.cran }}
+
+    steps:
+      - uses: actions/checkout@v1
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: >
+          Rscript
+          -e "install.packages('remotes')"
+          -e "saveRDS(remotes::dev_package_deps(dependencies = TRUE), 'depends.Rds', version = 2)"
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
+
+      - name: Install system dependencies
+        if: false
+        # if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+
+      - name: Install dependencies
+        run: >
+          Rscript
+          -e "library(remotes)"
+          -e "remotes::install_cran(c('statnet.common', 'mvtnorm'), repos = c(CRAN = 'https://cloud.r-project.org/'))"
+          -e "update(readRDS('depends.Rds'))"
+          -e "remotes::install_cran('rcmdcheck')"
+
+      - name: Check
+        run: >
+          Rscript
+          -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'warning', check_dir = 'check')"
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
+
+      - name: Test coverage
+        if: matrix.config.os == 'macOS-latest' && matrix.config.r == '3.6'
+        run: >
+          Rscript
+          -e 'covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")'
diff --git a/.github/workflows-ignore/deploy.yaml b/.github/workflows-ignore/deploy.yaml
@@ -0,0 +1,65 @@
+on:
+  push:
+    branches:
+      - master
+
+name: Deploy
+
+jobs:
+  deploy:
+    runs-on: ${{ matrix.config.os }}
+
+    name: Deploy
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-16.04, r: '3.6', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      CRAN: ${{ matrix.config.cran }}
+
+    steps:
+      - uses: actions/checkout@v1
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: >
+          Rscript
+          -e "install.packages('remotes')"
+          -e "saveRDS(remotes::dev_package_deps(dependencies = TRUE), 'depends.Rds', version = 2)"
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
+
+      - name: Install dependencies
+        run: >
+          Rscript
+          -e "library(remotes)"
+          -e "update(readRDS('depends.Rds'))"
+          -e "remotes::install_cran('packagedocs')"
+
+      - name: Deploy
+        env:
+          CAN_PRINT: "TRUE"
+        run: >
+          Rscript
+          -e "packagedocs::deploy_travis(valid_branches = 'master')"
+      - name: Deploy to GitHub Pages
+        if: github.ref == 'refs/heads/master'
+        uses: maxheld83/ghpages@v0.2.0
+        env:
+          BUILD_DIR: docs
+          GH_PAT: ${{ secrets.GH_PAT }}
diff --git a/.gitignore b/.gitignore
@@ -15,10 +15,6 @@ vignettes/rd_files/
 .Rproj.user
 .RData
 .lintr_cache
-revdep/checks\.rds
-revdep/checks
-revdep/\.cache\.rds
-revdep/lib
 _gh-pages
 ggduo_paper.txt
 .httr-oauth
diff --git a/.helper_functions b/.helper_functions
@@ -41,28 +41,7 @@ knit_vignettes:
 build_win:
   devtools::build_win(version = c("R-release", "R-devel"))
 reverse_depends:
-  if (packageVersion("devtools") <= "1.13.1") devtools::install_github("hadley/devtools")
-  # devtools::revdep_check_resume()
-  # devtools::revdep_check_reset()
-  source("https://bioconductor.org/biocLite.R")
-  dir.create("revdep/lib", recursive = TRUE, showWarnings = FALSE)
-  options("Ncpus" = 4, pkgType = "source")
-  do_check <- function() {
-    devtools::revdep_check(
-      bioconductor = TRUE,
-      # ignore = c("nzelect"),
-      ignore = c(),
-      libpath = .libPaths()[1],
-      srcpath = normalizePath(file.path("revdep", "lib"))
-    )
-    devtools::revdep_check_save_summary()
-    devtools::revdep_check_print_problems()
-  }
-  install.packages("GGally")
-  do_check()
-  file.rename("revdep/problems.md", "revdep/problems-cran.md")
-  load_all()
-  do_check()
-  system("diff --ignore-space-change 'revdep/problems.md' 'revdep/problems-cran.md' > revdep/problem-diff.txt")
+  # revdepcheck::revdep_reset()
+  revdepcheck::revdep_check(num_workers = 4, timeout = as.difftime(30, units = "mins"), quiet = FALSE)
 reverse_depends_email:
   devtools:::revdep_email(date = "Nov 4th alongside ggplot2's release", version = "1.3.0", author = "Barret", draft = TRUE, only_problems = FALSE)
diff --git a/.travis.yml b/.travis.yml
@@ -3,16 +3,17 @@ language: r
 sudo: false
 cache: packages
 
-matrix:
-  fast_finish: true # http://docs.travis-ci.com/user/build-configuration/#Fast-finishing
-                    # allows the build to "pass" when the non-failure-able builds are done
-  allow_failures: # http://docs.travis-ci.com/user/build-configuration/#Rows-That-are-Allowed-To-Fail
-    - r: 3.1
-    - r: devel
-  # test on older versions and devel
-  # https://docs.travis-ci.com/user/languages/r#R-Versions
+r:
+  - oldrel
+  - release
+  - devel
+
+jobs:
   include:
-    - r: release
+    - stage: "Deploy"
+      name: "Deploy tutorials"
+      if: branch IN (master, travis) AND repo = ggobi/GGally AND type = push
+      r: release
       env:
         - LINTR_COMMENT_BOT=false
         # secret key to allow for packagedocs and travisDrat
@@ -23,23 +24,14 @@ matrix:
       r_github_packages:
         - schloerke/travisDrat
         - rstudio/crosstalk
-      after_success:
+      script:
+        - Rscript -e 'remotes::install_local()'
         - Rscript -e 'covr::codecov()'
         - CAN_PRINT=TRUE Rscript -e "packagedocs::deploy_travis(valid_branches = 'dev', push_branch = 'gh-pages-dev')"
         - CAN_PRINT=TRUE Rscript -e "packagedocs::deploy_travis(valid_branches = 'master')"
         - Rscript -e "travisDrat::deploy_drat(valid_branches = 'master', drat_repo = 'schloerke/drat')"
 
-    # - r: 3.1
-    - r: devel
-
-
 notifications:
   email:
     on_success: change
     on_failure: change
-
-branches:
-  only:
-    - master
-    - dev
-    - travis
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: GGally
-Version: 1.3.2.9000
+Version: 1.4.1
 License: GPL (>= 2.0)
 Title: Extension to 'ggplot2'
 Type: Package
@@ -17,7 +17,8 @@ Authors@R: c(
     person("Moritz", "Marbach", role = "aut", email = "mmarbach@mail.uni-mannheim.de", comment = "ggnet, ggnet2"),
     person("Edwin", "Thoen", role = "aut", email = "edwinthoen@gmail.com", comment = "ggsurv"),
     person("Amos", "Elberg", role = "aut", email = "amos.elberg@gmail.com", comment = "ggnetworkmap"),
-    person("Joseph", "Larmarange", role = "aut", email = "joseph@larmarange.net", comment = "ggcoef"))
+    person("Joseph", "Larmarange", role = "aut", email = "joseph@larmarange.net", comment = "ggcoef"),
+    person("Ott", "Toomet", role = "ctb", email = "otoomet@gmail.com"))
 Description:
     The R package 'ggplot2' is a plotting system based on the grammar of graphics.
     'GGally' extends 'ggplot2' by adding several functions
@@ -26,9 +27,9 @@ Description:
     matrix, a parallel coordinates plot, a survival plot, and several functions to
     plot networks.
 Depends:
-    R (>= 3.1)
+    R (>= 3.1),
+    ggplot2 (> 2.2.0)
 Imports:
-    ggplot2 (>= 2.2.0),
     grDevices,
     grid,
     gtable (>= 0.2.0),
@@ -54,7 +55,10 @@ Suggests:
     packagedocs (>= 0.4.0),
     rmarkdown,
     roxygen2,
-    testthat
-Roxygen: list(wrap = FALSE)
-RoxygenNote: 6.0.1
+    testthat,
+    crosstalk
+Roxygen: list(markdown = FALSE)
+RoxygenNote: 7.0.2
 VignetteBuilder: packagedocs
+SystemRequirements: openssl
+Encoding: UTF-8
diff --git a/NAMESPACE b/NAMESPACE
@@ -18,6 +18,7 @@ export(add_ref_boxes)
 export(add_ref_lines)
 export(brew_colors)
 export(broomify)
+export(eval_data_col)
 export(fn_switch)
 export(getPlot)
 export(ggally_barDiag)
@@ -58,6 +59,7 @@ export(ggfacet)
 export(gglegend)
 export(ggmatrix)
 export(ggmatrix_gtable)
+export(ggmatrix_progress)
 export(ggnet)
 export(ggnet2)
 export(ggnetworkmap)
@@ -71,8 +73,12 @@ export(glyphplot)
 export(glyphs)
 export(grab_legend)
 export(is.glyphplot)
+export(is_character_column)
+export(is_horizontal)
 export(lowertriangle)
 export(mapping_color_to_fill)
+export(mapping_string)
+export(mapping_swap_x_y)
 export(max1)
 export(mean0)
 export(min0)
@@ -121,6 +127,7 @@ importFrom(stats,lm)
 importFrom(stats,mad)
 importFrom(stats,median)
 importFrom(stats,na.omit)
+importFrom(stats,pf)
 importFrom(stats,qnorm)
 importFrom(stats,quantile)
 importFrom(stats,sd)