CI testing branch only, do not merge

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

@@ -1,16 +1,10 @@
-# 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
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
-      - develop
+    branches: [main, master, develop]
   pull_request:
-    branches:
-      - main
-      - master
-      - develop
+    branches: [main, master, develop]
 
 name: R-CMD-check
 
@@ -24,73 +18,61 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: '3.6'}
-          - {os: macOS-latest,   r: 'release'}
-          - {os: ubuntu-20.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: 'devel',   rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: 'oldrel',   rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,   r: '4.0.4', pandoc-version: '2.11.4'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v1
+      - name: Setup statsrv pandoc
+        if: ${{ matrix.config.r == '4.0.4' }}
+        uses: r-lib/actions/setup-pandoc@v2
         with:
-          r-version: ${{ matrix.config.r }}
+          pandoc-version: ${{ matrix.config.pandoc-version }}
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - name: Setup default pandoc
+        if: ${{ matrix.config.r != '4.0.4' }}
+        uses: r-lib/actions/setup-pandoc@v2
 
-      - 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: Set up tinytex
+        uses: r-lib/actions/setup-tinytex@v2
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        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: Preinstall required latex packages
+        run: >
+          tlmgr install
+          lastpage morefloats parskip pdflscape textpos multirow lipsum
+          fancyhdr colortbl soul setspace relsize makecell threeparttable
+          threeparttablex environ trimspaces
 
-      - 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", "20.04"))')
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - name: Install dependencies
+      - name: Install statsrv packages
+        if: ${{ matrix.config.r == '4.0.4' }}
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("covr")
-          install.packages("tinytex")
-          library(tinytex)
-          install_tinytex()
-        shell: Rscript {0}
+          R -q -e 'utils::install.packages("remotes")'
+          R -q -e 'remotes::install_version("Hmisc", "4.5-0")'
+          R -q -e 'remotes::install_github("FredHutch/VISCfunctions", dependencies = TRUE)'
+          R -q -e 'utils::install.packages("rcmdcheck")'
 
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        if: ${{ matrix.config.r != '4.0.4' }}
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -0,0 +1,58 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+  pull_request:
+
+name: test-coverage.yaml
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
+

README.Rmd

@@ -4,7 +4,7 @@ output: github_document
 
 <!-- badges: start -->
   [![R build status](https://github.com/FredHutch/VISCfunctions/workflows/R-CMD-check/badge.svg)](https://github.com/FredHutch/VISCfunctions/actions)
-  [![Codecov test coverage](https://codecov.io/gh/FredHutch/VISCfunctions/branch/main/graph/badge.svg)](https://codecov.io/gh/FredHutch/VISCfunctions?branch=main)
+[![Codecov test coverage](https://codecov.io/gh/FredHutch/VISCfunctions/graph/badge.svg)](https://app.codecov.io/gh/FredHutch/VISCfunctions)
   [![License:MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 <!-- badges: end -->
 

README.md

@@ -4,7 +4,7 @@
 [![R build
 status](https://github.com/FredHutch/VISCfunctions/workflows/R-CMD-check/badge.svg)](https://github.com/FredHutch/VISCfunctions/actions)
 [![Codecov test
-coverage](https://codecov.io/gh/FredHutch/VISCfunctions/branch/main/graph/badge.svg)](https://codecov.io/gh/FredHutch/VISCfunctions?branch=main)
+coverage](https://codecov.io/gh/FredHutch/VISCfunctions/graph/badge.svg)](https://app.codecov.io/gh/FredHutch/VISCfunctions)
 [![License:MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 <!-- badges: end -->
 

tests/testthat/test_statistical_tests_and_estimates.R

@@ -81,20 +81,19 @@ test_that("two_samp_cont_test testing various options (no errors)", {
   # T-Test Unpaired
   #t.test(x[1:10], x[13:22], paired=F, var.equal = F)$p.value
   expect_equal(object = two_samp_cont_test(x = x, y = y, method = 't', paired = FALSE, verbose = T),
-               expected = t.test(x~factor(y), paired = F, var.equal = F)$p.value,
+               expected = t.test(x~factor(y), var.equal = F)$p.value,
                tolerance = 1e-8)
   # T-Test Paired
-  #Note the list also works: t.test(x[1:10], x[13:22], paired=T, var.equal = F)$p.value
   expect_equal(object = two_samp_cont_test(x = x[-(11:12)], y = y[-(11:12)], method = 't', paired = TRUE, verbose = T),
-               expected = t.test(x[-c(1,10:13,22)]~factor(y[-c(1,10:13,22)]), paired = T, var.equal = F)$p.value,
+               expected = t.test(x[1:10], x[13:22], paired = T, var.equal = F)$p.value,
                tolerance = 1e-8)
   #Testing var.equal = T option in T-Test Unpaired
   expect_equal(object = two_samp_cont_test(x = x, y = y, method = 't', paired = FALSE, verbose = T, var.equal = T),
-               expected = t.test(x~factor(y), paired = F, var.equal = T)$p.value,
+               expected = t.test(x~factor(y), var.equal = T)$p.value,
                tolerance = 1e-8)
   #Testing alternative param can be used
   expect_equal(object = two_samp_cont_test(x = x, y = y, method = 't', paired = FALSE, verbose = T, alternative = 'less'),
-               expected = t.test(x~factor(y), paired = F, alternative = 'less')$p.value,
+               expected = t.test(x~factor(y), alternative = 'less')$p.value,
                tolerance = 1e-8)
 
   #Testing t.test where both levels of y have a single x value

vignettes/Overview.Rmd

@@ -11,7 +11,6 @@ output:
     number_sections: true
     keep_tex: true
 header-includes:
-  - \hypersetup{colorlinks=true, linkcolor=blue}
   - \usepackage{booktabs}
   - \usepackage{longtable}
   - \usepackage{array}
@@ -32,6 +31,8 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
+\hypersetup{colorlinks=true, linkcolor=blue}
+
 \listoftables
 
 \clearpage