Fix input check (#24)

* fix: #22 * try fixing CMD check * Update R-CMD-check.yaml * update * update unit tests * Update test-zcurve.R * Update R-CMD-tests.yaml
FBartos · May 28, 2024 · 7085a10 · 7085a10
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commit 7085a10
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,19 +1,15 @@
-# 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
-      - pre-release
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
-      - pre-release
+    branches: [main, master]
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -24,82 +20,32 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest,   r: 'release'}
           - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
 
     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@v3
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - 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
 
-      - 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: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@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
-          sudo apt-get install libcurl4-openssl-dev
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        if: runner.os != 'Windows'
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(
-            args        = c("--no-manual", "--as-cran", "--ignore-vignettes"),
-            build_args  = c("--no-build-vignettes"),
-            error_on    = "warning",
-            check_dir   = "check")
-        shell: Rscript {0}"
-
-      - name: Check
-        if: runner.os == 'Windows'
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(
-            args        = c("--no-manual", "--as-cran", "--ignore-vignettes"),
-            build_args  = c("--no-build-vignettes"),
-            error_on    = "warning",
-            check_dir   = "check")
-        shell: Rscript {0}
-
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/R-CMD-tests.yaml b/.github/workflows/R-CMD-tests.yaml
@@ -1,19 +1,15 @@
-# 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
-      - pre-release
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
-      - pre-release
+    branches: [main, master]
 
 name: R-CMD-tests
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -24,50 +20,36 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest,   r: 'release'}
           - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
 
     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@v3
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - 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
 
-      - 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: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@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
-
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - name: Install and test z-curve (non-Windows)
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
         run: |
+          install.packages("remotes")        
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
           install.packages("devtools")

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,61 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+permissions: read-all
+
+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
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: zcurve
 Title: An Implementation of Z-Curves
-Version: 2.4.1
+Version: 2.4.2
 Authors@R: c(
     person("František", "Bartoš", email = "[email protected]", role = c("aut", "cre")),
     person("Ulrich", "Schimmack", email = "[email protected]", role = c("aut")))

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+## version 2.4.2
+- Fixes https://github.com/FBartos/zcurve/issues/22
+
 ## version 2.4.1
 - Fixes ODR computation with censored data
 

diff --git a/R/main.R b/R/main.R
@@ -92,19 +92,23 @@ zcurve       <- function(z, z.lb, z.ub, p, p.lb, p.ub, data, method = "EM", boot
     if(missing(z) & missing(p) & missing(z.lb) & missing(p.lb))
       stop("No data input")
     if(!missing(z)){
+      if(length(z) == 0)
+        stop("An empty input was passed as z-scores.")
       if(!is.numeric(z))
         stop("Wrong z-scores input: Data are not nummeric.")
       if(!is.vector(z))
-        stop("Wrong z-scores input: Data are not a vector")
+        stop("Wrong z-scores input: Data are not a vector.")
       if(all(z <= 1 & z >= 0))
-        stop("It looks like you are entering p-values rather than z-scores. To use p-values, explicitly name your argument 'zcurve(p = [vector of p-values])'")
+        stop("It looks like you are entering p-values rather than z-scores. To use p-values, explicitly name your argument 'zcurve(p = [vector of p-values])'.")
       input_type <- c(input_type, "z")
     }
     if(!missing(p)){
+      if(length(p) == 0)
+        stop("An empty input was passed as p-values.")
       if(!is.numeric(p))
         stop("Wrong p-values input: Data are not nummeric.")
       if(!is.vector(p))
-        stop("Wrong p-values input: Data are not a vector") 
+        stop("Wrong p-values input: Data are not a vector.") 
       input_type <- c(input_type, "p")
     }
   }else if(inherits(data, "zcurve_data")){