debugging

Author: inecik

.Rbuildignore

@@ -7,6 +7,7 @@
 ^CODE_OF_CONDUCT\.md$
 ^CONTRIBUTING\.md$
 ^LICENSE\.md$
-^PUBLISHING\.md$
+^publishing\.md$
 ^README\.md$
+^cran-comments\.md$
 ^cellucid-logo\.svg$

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

@@ -5,7 +5,6 @@ name: R-CMD-check
 # If this workflow is green, you are generally in good shape for:
 # - GitHub releases
 # - CRAN submission (see publishing.md for the final `--as-cran` steps)
-# - Bioconductor submission (also run the BiocCheck workflow)
 
 on:
   push:

.github/workflows/bioccheck.yaml

@@ -3,9 +3,9 @@
 # This workflow is designed for beginners:
 # - Create a GitHub Release (or run manually)
 # - Download the `.tar.gz` artifact from the workflow run
-# - Upload that exact tarball to CRAN, or attach it in your Bioconductor submission
+# - Upload that exact tarball to CRAN
 #
-# This does *not* auto-submit to CRAN/Bioconductor (those still require a human),
+# This does *not* auto-submit to CRAN (that still requires a human),
 # but it automates the parts that are easy to get wrong: reproducible building
 # and pre-flight checks.
 
@@ -43,6 +43,15 @@ jobs:
 
       - uses: r-lib/actions/setup-tinytex@v2
 
+      - name: Ensure pdflatex is available
+        run: |
+          if ! command -v pdflatex >/dev/null 2>&1; then
+            sudo apt-get update
+            sudo apt-get install -y texlive-latex-base texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
+          fi
+          pdflatex --version
+        shell: bash
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck, local::.

.github/workflows/release.yaml

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 message: "If you use this software, please cite it."
 type: software
 title: "cellucid (R): Export Single-Cell Data to the Cellucid Viewer Format"
-version: 0.99.0  # CELLUCID_VERSION
+version: 0.9.0  # CELLUCID_VERSION
 authors:
   - family-names: Inecik
     given-names: Kemal

CITATION.cff

@@ -17,7 +17,7 @@ Cellucid is split by responsibility:
 |---|---|---|
 | `cellucid` | Web app (UI + state + WebGL rendering) | are fixing UI bugs, rendering/performance, figure export, sessions, or community annotation frontend |
 | `cellucid-python` | Python package + CLI (`prepare`, `serve`, `show_anndata`, hooks) + Sphinx docs | are fixing Python/CLI bugs, data prep/export, server endpoints, Jupyter hooks, or docs on ReadTheDocs |
-| `cellucid-r` (this repo) | R package for exporting data to the Cellucid viewer format | are changing the R exporter (`cellucid_prepare()`), adding R-side tests/docs, or preparing for Bioconductor |
+| `cellucid-r` (this repo) | R package for exporting data to the Cellucid viewer format | are changing the R exporter (`cellucid_prepare()`), adding R-side tests/docs, or preparing for CRAN |
 | `cellucid-annotation` | GitHub repo template for community annotation | are changing the repo schema/validation/workflows |
 
 If you’re not sure where a bug belongs, open an issue in the repo you’re currently using and include:
@@ -48,7 +48,7 @@ If the bug is “the viewer looks wrong”, also include:
 
 Docs live in:
 - `cellucid-r/man/` (generated `.Rd` files)
-- `cellucid-r/vignettes/` (BiocStyle vignette)
+- `cellucid-r/vignettes/` (package vignette)
 - `cellucid-r/README.md`
 
 If you edit `.Rd` files directly, be aware they are usually generated from roxygen comments in `cellucid-r/R/`.
@@ -60,7 +60,7 @@ Fast workflow:
 1) Set up your R dev environment (see “Development setup”)
 2) Make a small, focused change
 3) Add/adjust tests (`testthat`)
-4) Run `devtools::check()` (and `BiocCheck::BiocCheck()` if relevant)
+4) Run `devtools::check()`
 5) Submit a PR with a clear “what/why/how to verify”
 
 ---
@@ -91,19 +91,15 @@ In R:
 install.packages(c("devtools", "roxygen2", "testthat"))
 ```
 
-For vignette builds and Bioconductor-style docs:
+For vignette builds:
 
 ```r
-if (!requireNamespace("BiocManager", quietly = TRUE)) {
-  install.packages("BiocManager")
-}
-BiocManager::install(c("BiocStyle", "knitr", "rmarkdown"))
+install.packages(c("knitr", "rmarkdown"))
 ```
 
 Optional (useful during release prep):
 
 ```r
-BiocManager::install("BiocCheck")
 install.packages(c("pkgdown", "covr"))
 ```
 
@@ -135,12 +131,6 @@ Run a full check (recommended before PRs):
 devtools::check()
 ```
 
-For Bioconductor submission readiness:
-
-```r
-BiocCheck::BiocCheck(".")
-```
-
 Guidelines:
 - Add tests when behavior changes (especially edge cases like missing values, mismatched dimensions, sparse matrices).
 - Prefer small synthetic inputs; avoid committing real datasets.
@@ -183,7 +173,7 @@ This package is intentionally:
 
 - **minimal-dependency** (only `jsonlite` is a hard dependency)
 - **format-first** (exports must match what the web app expects)
-- **Bioconductor-friendly** (checks, vignette style, and package structure matter)
+- **CRAN-ready** (checks, documentation, and package structure matter)
 
 If you propose adding a new dependency:
 - prefer `Suggests` over `Imports` unless strictly required
@@ -240,7 +230,7 @@ Fix:
 ### `R CMD check` fails on vignettes
 
 Common causes:
-- missing suggested packages (`BiocStyle`, `knitr`, `rmarkdown`)
+- missing suggested packages (`knitr`, `rmarkdown`)
 - missing Pandoc
 
 Fix:

CONTRIBUTING.md

@@ -1,7 +1,7 @@
 Package: cellucid
 Type: Package
 Title: Export Single-Cell Data to the Cellucid Viewer Format
-Version: 0.99.0
+Version: 0.9.0
 X-Cellucid-Version-Marker: CELLUCID_VERSION
 Authors@R: c(
     person(
@@ -21,13 +21,11 @@ Depends:
 Imports:
     jsonlite
 Suggests:
-    BiocStyle,
     knitr,
     Matrix,
     rmarkdown,
     testthat (>= 3.1.0)
 VignetteBuilder: knitr
-biocViews: SingleCell, Visualization, DataRepresentation
 Config/testthat/edition: 3
 URL: https://github.com/theislab/cellucid-r,
     https://theislab.github.io/cellucid-r/

DESCRIPTION

@@ -1,5 +1,5 @@
-# cellucid 0.99.0 <!-- CELLUCID_VERSION -->
+# cellucid 0.9.0 <!-- CELLUCID_VERSION -->
 
-- Initial Bioconductor submission version.
+- Initial CRAN submission version.
 - Adds `cellucid_prepare()` / `prepare()` to export embeddings, metadata, gene expression, and connectivity to the Cellucid viewer format.
 - Rejects duplicate gene IDs and filename-sanitization collisions (obs keys / gene IDs) to prevent silent overwrites in exports.

NEWS.md

@@ -54,13 +54,11 @@ cellucid_prepare(
 
 ## Links
 
-- Web app: https://cellucid.com
-- R package docs (installation + recipes): https://cellucid.readthedocs.io/en/latest/user_guide/r_package/index.html
-- Seurat recipe: https://cellucid.readthedocs.io/en/latest/user_guide/r_package/e_integrations_recipes/01_seurat_recipe.html
-- SingleCellExperiment recipe: https://cellucid.readthedocs.io/en/latest/user_guide/r_package/e_integrations_recipes/02_singlecellexperiment_recipe.html
-- Source: https://github.com/theislab/cellucid-r
-- Viewer: https://github.com/theislab/cellucid
-- Citation: `citation("cellucid")` (or `CITATION.cff`)
+- [Web app](https://cellucid.com)
+- [Documentation](https://cellucid.readthedocs.io/en/latest/user_guide/r_package/index.html)
+- Recipes: [Seurat](https://cellucid.readthedocs.io/en/latest/user_guide/r_package/e_integrations_recipes/01_seurat_recipe.html) · [SingleCellExperiment](https://cellucid.readthedocs.io/en/latest/user_guide/r_package/e_integrations_recipes/02_singlecellexperiment_recipe.html)
+- Source: [cellucid-r](https://github.com/theislab/cellucid-r) · [cellucid](https://github.com/theislab/cellucid)
+- Citation: `citation("cellucid")`
 
 ## License
 

README.md

@@ -0,0 +1,11 @@
+## R CMD check results
+
+0 errors | 0 warnings | 0 notes
+
+## Test environments
+
+- GitHub Actions: ubuntu-latest, windows-latest, macos-latest (R release, R devel, R oldrel-1)
+
+## Notes
+
+This is a new submission.