trying to fix github actions issue

zabore · Jan 18, 2024 · 5d1d13f · 5d1d13f
1 parent e8bc9af
commit 5d1d13f
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Showing 29 changed files with 83 additions and 70 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,18 +29,21 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -17,7 +17,7 @@ Imports:
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 VignetteBuilder: knitr
 Suggests: 
     testthat,

diff --git a/R/d.R b/R/d.R
@@ -49,7 +49,7 @@ d <- function(label, M, factors, data) {
   }
 
   # Check if M is a numeric variable >=2
-  if (class(M) != "numeric" | M < 2) {
+  if (!is.numeric(M) | M < 2) {
     stop("The argument to M, the total number of subtypes, must be a numeric value >=2.")
   }
 

diff --git a/R/dstar.R b/R/dstar.R
@@ -51,7 +51,7 @@ dstar <- function(label, M, factors, data) {
   }
 
   # Check if M is a numeric variable >=2
-  if (class(M) != "numeric" | M < 2) {
+  if (!is.numeric(M) | M < 2) {
     stop("The argument to M, the total number of subtypes, must be a numeric value >=2.")
   }
 

diff --git a/R/eh_test_subtype.R b/R/eh_test_subtype.R
@@ -80,7 +80,7 @@ eh_test_subtype <- function(label, M, factors, data, digits = 2) {
   }
 
   # Check if M is a numeric variable >=2
-  if (class(M) != "numeric" | M < 2) {
+  if (!is.numeric(M) | M < 2) {
     stop("The argument to M, the total number of subtypes, must be a numeric value >=2.")
   }
 

diff --git a/R/optimal_kmeans_d.R b/R/optimal_kmeans_d.R
@@ -69,7 +69,7 @@ optimal_kmeans_d <- function(markers, M, factors, case, data,
                              nstart = 100, seed = NULL) {
 
   # Check if M is a numeric variable >=2
-  if (class(M) != "numeric" | M < 2) {
+  if (!is.numeric(M) | M < 2) {
     stop("The argument to M, the total number of subtypes, must be a numeric value >=2.")
   }
 

diff --git a/README.Rmd b/README.Rmd
@@ -5,7 +5,7 @@ output: github_document
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 [![Coverage status](https://codecov.io/gh/zabore/riskclustr/branch/master/graph/badge.svg)](https://codecov.io/github/zabore/riskclustr?branch=master)
-[![R-CMD-check](https://github.com/zabore/riskclustr/workflows/R-CMD-check/badge.svg)](https://github.com/zabore/riskclustr/actions)
+[![R-CMD-check](https://github.com/zabore/riskclustr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/zabore/riskclustr/actions/workflows/R-CMD-check.yaml)
 [![CRAN status](https://www.r-pkg.org/badges/version/riskclustr)](https://cran.r-project.org/package=riskclustr)
 [![status](https://joss.theoj.org/papers/10.21105/joss.01269/status.svg)](https://joss.theoj.org/papers/10.21105/joss.01269)
 
@@ -46,3 +46,5 @@ See [http://www.emilyzabor.com/riskclustr/reference/](http://www.emilyzabor.com/
 > Begg CB, Zabor EC, Bernstein JL, Bernstein L, Press MF, Seshan VE. A conceptual and methodological framework for investigating etiologic heterogeneity. *Stat Med.* 2013;32(29):5039-52. doi: 10.1002/sim.5902
 
 > Begg CB, Seshan VE, Zabor EC, et al. Genomic investigation of etiologic heterogeneity: methodologic challenges. *BMC Med Res Methodol.* 2014;14:138. doi: 10.1186/1471-2288-14-138
+
+> Zabor, EC. riskclustr: Functions to Study Etiologic Heterogeneity. *Journal of Open Source Software.* 2019;4(35):1269. doi:10.21105/joss.01269
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 
 [![Coverage
 status](https://codecov.io/gh/zabore/riskclustr/branch/master/graph/badge.svg)](https://codecov.io/github/zabore/riskclustr?branch=master)
-[![R-CMD-check](https://github.com/zabore/riskclustr/workflows/R-CMD-check/badge.svg)](https://github.com/zabore/riskclustr/actions)
+[![R-CMD-check](https://github.com/zabore/riskclustr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/zabore/riskclustr/actions/workflows/R-CMD-check.yaml)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/riskclustr)](https://cran.r-project.org/package=riskclustr)
 [![status](https://joss.theoj.org/papers/10.21105/joss.01269/status.svg)](https://joss.theoj.org/papers/10.21105/joss.01269)
@@ -64,3 +64,7 @@ function documentation.
 > Begg CB, Seshan VE, Zabor EC, et al. Genomic investigation of
 > etiologic heterogeneity: methodologic challenges. *BMC Med Res
 > Methodol.* 2014;14:138. doi: 10.1186/1471-2288-14-138
+
+> Zabor, EC. riskclustr: Functions to Study Etiologic Heterogeneity.
+> *Journal of Open Source Software.* 2019;4(35):1269.
+> <doi:10.21105/joss.01269>
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/calculate_d.html b/docs/articles/calculate_d.html
diff --git a/docs/articles/contribute.html b/docs/articles/contribute.html
diff --git a/docs/articles/eh_test.html b/docs/articles/eh_test.html
diff --git a/docs/articles/factor_pvalue.html b/docs/articles/factor_pvalue.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/optimal_d.html b/docs/articles/optimal_d.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,13 +1,13 @@
-pandoc: '2.18'
-pkgdown: 2.0.6
+pandoc: 3.1.1
+pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   calculate_d: calculate_d.html
   contribute: contribute.html
   eh_test: eh_test.html
   factor_pvalue: factor_pvalue.html
   optimal_d: optimal_d.html
-last_built: 2022-10-20T14:48Z
+last_built: 2024-01-18T16:24Z
 urls:
   reference: http://www.emilyzabor.com/riskclustr/reference
   article: http://www.emilyzabor.com/riskclustr/articles

diff --git a/docs/reference/d.html b/docs/reference/d.html
diff --git a/docs/reference/dstar.html b/docs/reference/dstar.html
diff --git a/docs/reference/eh_test_marker.html b/docs/reference/eh_test_marker.html
diff --git a/docs/reference/eh_test_subtype.html b/docs/reference/eh_test_subtype.html