Fix documentation

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

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -29,7 +30,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v5
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,10 +40,6 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: actions/setup-python@v4
-        with:
-          python-version: '3.10'
-
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
@@ -57,3 +54,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SCORPIUS
 Type: Package
 Title: Inferring Developmental Chronologies from Single-Cell RNA Sequencing Data
-Version: 1.0.9
+Version: 1.0.10
 Description: An accurate and easy tool for performing linear trajectory inference on
   single cells using single-cell RNA sequencing data. In addition, 'SCORPIUS'
   provides functions for discovering the most important genes with respect to
@@ -12,13 +12,13 @@ Authors@R: c(
       "Robrecht", "Cannoodt", 
       email = "rcannood@gmail.com", 
       role = c("aut", "cre"),
-      comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood")
+      comment = c(ORCID = "0000-0003-3641-729X")
     ),
     person(
       "Wouter", "Saelens", 
       email = "wouter.saelens@ugent.be", 
       role = c("ctb"), 
-      comment = c(ORCID = "0000-0002-7114-6248", github = "zouter")
+      comment = c(ORCID = "0000-0002-7114-6248")
     )
   )
 License: GPL-3
@@ -28,7 +28,7 @@ URL: https://github.com/rcannood/SCORPIUS,
     http://rcannood.github.io/SCORPIUS/
 BugReports: https://github.com/rcannood/SCORPIUS/issues
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.3
 VignetteBuilder: 
   knitr
 Depends:

NEWS.md

@@ -1,3 +1,7 @@
+# SCORPIUS 1.0.10
+
+* Fix documentation issues (PR #47).
+
 # SCORPIUS 1.0.9
 
 * Resubmission after babelwhale was removed from CRAN.

R/dimensionality_reduction.R

@@ -5,7 +5,7 @@
 #'
 #' @param x a numeric matrix
 #' @param dist the distance metric to be used; can be any of the metrics listed in [dynutils::calculate_distance()].
-#' @param ndim the maximum dimension of the space which the data are to be represented in; must be in {1, 2, \ldots, n-1}.
+#' @param ndim the maximum dimension of the space which the data are to be represented in; must be in \eqn{[1, n - 1]}, with \eqn{n} the number of samples (rows) in \code{x}.
 #' @param num_landmarks the number of landmarks to be selected.
 #'
 #' @return A matrix containing the coordinates of each sample, represented in an \code{ndim}-dimensional space.

R/package.R

@@ -3,7 +3,6 @@
 #' SCORPIUS orders single cells with regard to an implicit timeline,
 #' such as cellular development or progression over time.
 #'
-#' @docType package
 #' @name SCORPIUS-package
 #' @aliases SCORPIUS-package SCORPIUS
 #'
@@ -43,4 +42,4 @@
 #'   path = traj$path,
 #'   progression_group = ginhoux$sample_info$group_name
 #' )
-NULL
+"_PACKAGE"

README.Rmd

@@ -20,7 +20,6 @@ library(tidyverse)
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/rcannood/SCORPIUS/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rcannood/SCORPIUS/actions/workflows/R-CMD-check.yaml)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/SCORPIUS)](https://cran.r-project.org/package=SCORPIUS)
-[![Codecov test coverage](https://codecov.io/gh/rcannood/SCORPIUS/branch/master/graph/badge.svg)](https://app.codecov.io/gh/rcannood/SCORPIUS?branch=master)
 <!-- badges: end -->
 
 SCORPIUS an unsupervised approach for inferring linear developmental chronologies from single-cell

README.md

@@ -5,8 +5,6 @@
 
 [![R-CMD-check](https://github.com/rcannood/SCORPIUS/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rcannood/SCORPIUS/actions/workflows/R-CMD-check.yaml)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/SCORPIUS)](https://cran.r-project.org/package=SCORPIUS)
-[![Codecov test
-coverage](https://codecov.io/gh/rcannood/SCORPIUS/branch/master/graph/badge.svg)](https://app.codecov.io/gh/rcannood/SCORPIUS?branch=master)
 <!-- badges: end -->
 
 SCORPIUS an unsupervised approach for inferring linear developmental

cran-comments.md

@@ -1,19 +1,18 @@
-# SCORPIUS 1.0.9
+# SCORPIUS 1.0.10
 
-* Resubmission after babelwhale was removed from CRAN.
+* Fix documentation issues (PR #47).
 
-* DOCUMENTATION: Add vignette for working with AnnData objects.
-
-* DOCUMENTATION: Add vignette for working with SingleCellExperiment objects.
-
-* DOCUMENTATION: Create pkgdown site.
+# Checks
 
-* DOCUMENTATION: Update citEntry to bibentry.
+## R CMD check results
 
-* DOCUMENTATION: Reduce execution time of examples by downscaling the example dataset.
+    * checking whether package ‘SCORPIUS’ can be installed ... WARNING
+    Warning: Found the following significant warnings:
+      Warning: `invoke()` was deprecated in purrr 1.0.0.
+    See ‘/home/runner/work/SCORPIUS/SCORPIUS/check/SCORPIUS.Rcheck/00install.out’ for details.
 
-# Checks
+    0 errors ✔ | 1 warning ✖ | 0 notes ✔
 
-## R CMD check results
+This is a WARNING caused by dynwrap <= 1.2.4.
 
-0 errors | 0 warnings | 0 notes
+dynwrap 1.2.5 has been accepted for release on CRAN, some warnings may still appear until all builds are available on CRAN.

vignettes/seurat.Rmd

@@ -43,7 +43,7 @@ srt <- NormalizeData(srt)
 
 Fetch the expression data from the Seurat object as follows.
 ```{r fetchdata}
-expression <- t(srt@assays$RNA@data)
+expression <- t(as.matrix(LayerData(srt, assay = "RNA", layer = "data")))
 ```
 
 Also fetch some metadata from the Seurat object. Change `group_name` to whatever column in `srt@meta.data` you are interested in.