dynverse · rcannood · Sep 1, 2025 · Sep 1, 2025 · Sep 1, 2025 · Sep 1, 2025
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -11,3 +11,4 @@
 ^vignettes/.*/.*\.png$
 ^LICENSE\.md$
 ^\.github$
+^CRAN-SUBMISSION$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,51 @@
+# 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:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - 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-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
diff --git a/.github/workflows/test_coverage.yml b/.github/workflows/test_coverage.yml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,21 +1,21 @@
 Package: dynutils
 Type: Package
 Title: Common Functionality for the 'dynverse' Packages
-Version: 1.0.11
+Version: 1.0.12
 Authors@R: c(
     person(
       "Robrecht", 
       "Cannoodt", 
       email = "[email protected]", 
       role = c("aut", "cre"),
-      comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood")
+      comment = c(ORCID = "0000-0003-3641-729X")
     ),
     person(
       "Wouter", 
       "Saelens", 
       email = "[email protected]", 
       role = c("aut"), 
-      comment = c(ORCID = "0000-0002-7114-6248", github = "zouter")
+      comment = c(ORCID = "0000-0002-7114-6248")
     )
   )
 Description: 
@@ -25,7 +25,7 @@ Description:
 License: MIT + file LICENSE
 URL: https://github.com/dynverse/dynutils
 BugReports: https://github.com/dynverse/dynutils/issues
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.2
 Depends:
   R (>= 3.0.0)
 Imports: 

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# dynutils 1.0.12
+
+* DOCUMENTATION: Fix roxygen docs (PR #36).
+
 # dynutils 1.0.11
 
 * MINOR CHANGE: Always set `use_nan` to `TRUE`. Replace NaNs with 0 for `calculate_similarity()`.

diff --git a/R/mapdf.R b/R/mapdf.R
@@ -12,7 +12,7 @@ mapdf_fun <- function(purrrfun) {
 #' Apply a function to each row of a data frame
 #'
 #' The mapdf functions transform their input by applying a function to each row of a data frame and returning a vector the same length as the input.
-#' These functions work a lot like purrr's [map()] functions.
+#' These functions work a lot like purrr's `map()` functions.
 #'
 #'  * `mapdf()` always returns a list.
 #'

diff --git a/README.Rmd b/README.Rmd
@@ -13,10 +13,10 @@ set.seed(1)
 
 # dynutils
 
-[![Build Status](https://travis-ci.org/dynverse/dynutils.svg?branch=master)](https://travis-ci.org/dynverse/dynutils)
-[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/dynverse/dynutils?branch=master&svg=true)](https://ci.appveyor.com/project/dynverse/dynutils)
+  <!-- badges: start -->
+  [![R-CMD-check](https://github.com/dynverse/dynutils/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dynverse/dynutils/actions/workflows/R-CMD-check.yaml)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/dynutils)](https://cran.r-project.org/package=dynutils)
-[![Coverage Status](https://app.codecov.io/gh/dynverse/dynutils/branch/master/graph/badge.svg)](https://app.codecov.io/gh/dynverse/dynutils?branch=master)
+  <!-- badges: end -->
 
 Provides common functionality for the dynverse packages. An overview of this functionality
 is available using the `?dynutils` command or in the [examples vignette](https://CRAN.R-project.org/package=dynutils/vignettes/functionality.html). 

diff --git a/README.md b/README.md
@@ -1,13 +1,10 @@
 
 # dynutils
 
-[![Build
-Status](https://travis-ci.org/dynverse/dynutils.svg?branch=master)](https://travis-ci.org/dynverse/dynutils)
-[![AppVeyor Build
-Status](https://ci.appveyor.com/api/projects/status/github/dynverse/dynutils?branch=master&svg=true)](https://ci.appveyor.com/project/dynverse/dynutils)
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/dynverse/dynutils/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dynverse/dynutils/actions/workflows/R-CMD-check.yaml)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/dynutils)](https://cran.r-project.org/package=dynutils)
-[![Coverage
-Status](https://app.codecov.io/gh/dynverse/dynutils/branch/master/graph/badge.svg)](https://app.codecov.io/gh/dynverse/dynutils?branch=master)
+<!-- badges: end -->
 
 Provides common functionality for the dynverse packages. An overview of
 this functionality is available using the `?dynutils` command or in the

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,9 +1,6 @@
-# dynutils 1.0.11
+# dynutils 1.0.12
 
-Apologies for the quick resubmission. This version release is a bug fix for the changes
-made in the previous release.
-
-* BUG FIX: Also pass `use_nan` from `calculate_distance()` to `calculate_similarity()`.
+Fix CRAN notes.
 
 ## Test environments
 * local Fedora installation, R release
@@ -13,33 +10,11 @@ made in the previous release.
 
 ## R CMD check results
 ```
-── R CMD check results ──────────────────────────────────── dynutils 1.0.11 ────
+── R CMD check results ──────────────────────────────────── dynutils 1.0.12 ────
 Duration: 53.4s
 
 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
 
 R CMD check succeeded
 ```
 
-## Reverse dependencies
-
-A reverse dependency check was run on all downstream dependencies.
-(Summary at [revdep/README.md](revdep/README.md)). No new problems were found.
-
-```
-> revdepcheck::revdep_check(timeout = as.difftime(600, units = "mins"), num_workers = 30)
-── CHECK ──────────────────────────────────────────────────────── 10 packages ──
-✔ dynwrap 1.2.2                          ── E: 1     | W: 0     | N: 0
-I dynfeature 1.0.0                       ── E: 1     | W: 0     | N: 0
-✔ babelwhale 1.1.0                       ── E: 1     | W: 0     | N: 0
-I SCORPIUS 1.0.8                         ── E: 1     | W: 0     | N: 0
-✔ dynparam 1.0.2                         ── E: 0     | W: 0     | N: 1
-✔ dynplot 1.1.2                          ── E: 1     | W: 0     | N: 0
-✔ lmds 0.1.0                             ── E: 0     | W: 0     | N: 2
-✔ dyngen 1.0.3                           ── E: 1     | W: 0     | N: 0
-✔ GillespieSSA2 0.2.10                   ── E: 0     | W: 0     | N: 1
-✔ dyndimred 1.0.4                        ── E: 0     | W: 0     | N: 2
-OK: 10                                                              
-BROKEN: 0
-Total time: 4 min
-```
diff --git a/man/add_class.Rd b/man/add_class.Rd
diff --git a/man/calculate_distance.Rd b/man/calculate_distance.Rd
diff --git a/man/dynutils.Rd b/man/dynutils.Rd
diff --git a/man/mapdf.Rd b/man/mapdf.Rd