Install scrapper and scater from libscran and alanocallaghan GitHub.

Use remotes for libscran/scrapper (master) and alanocallaghan/scater@devel
so CI installs compatible versions with quickRnaQc.se support.

Co-authored-by: Cursor <cursoragent@cursor.com>

Author: stemangiola

.github/workflows/rworkflows.yml

@@ -56,7 +56,7 @@ jobs:
         runner_os: ${{ runner.os }}
         run_telemetry: ${{ false }}
         force_install: ${{ true }}
-        cache_version: cache-v3-scran-scrapper-devel
+        cache_version: cache-v4-libscran-scrapper
         docker_registry: ghcr.io
 
   docker-build-and-push:

DESCRIPTION

@@ -71,8 +71,8 @@ Suggests:
     cellNexus
 VignetteBuilder: knitr
 Remotes:
-    github::bioc/scran@devel,
-    github::bioc/scrapper@devel,
+    libscran/scrapper,
+    alanocallaghan/scater@devel,
     MangiolaLaboratory/cellNexus
 URL: https://github.com/tidyomics/tidySpatialWorkshop
 BugReports: https://github.com/tidyomics/tidySpatialWorkshop/issues

Dockerfile

@@ -6,6 +6,6 @@ COPY --chown=rstudio:rstudio . /home/rstudio/
 
 RUN Rscript -e "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager'); BiocManager::install(version = 'devel', ask = FALSE)"
 
-RUN Rscript -e "if (!requireNamespace('remotes', quietly = TRUE)) install.packages('remotes'); options(repos = BiocManager::repositories()); remotes::install_github(c('bioc/scran', 'bioc/scrapper'), ref = 'devel', upgrade = 'never'); BiocManager::install(c('nnSVG', 'BiocStyle', 'BiocVersion'), ask = FALSE); remotes::install_github('MangiolaLaboratory/cellNexus', build_vignettes = FALSE, upgrade = 'never')"
+RUN Rscript -e "if (!requireNamespace('remotes', quietly = TRUE)) install.packages('remotes'); options(repos = BiocManager::repositories()); remotes::install_github('libscran/scrapper', upgrade = 'never'); remotes::install_github('alanocallaghan/scater', ref = 'devel', upgrade = 'never'); BiocManager::install(c('nnSVG', 'BiocStyle', 'BiocVersion'), ask = FALSE); remotes::install_github('MangiolaLaboratory/cellNexus', build_vignettes = FALSE, upgrade = 'never')"
 
 RUN Rscript -e "options(repos = BiocManager::repositories()); devtools::install('.', dependencies = TRUE, build_vignettes = TRUE, upgrade = FALSE)"