Installation#

Audience: everyone
Time: 5–15 minutes (depending on your setup)
Goal: install Cellucid for R, verify version 0.9.7, and choose the correct source for current registry availability

Note

Active package version: 0.9.7. Version 0.9.7 is the CRAN submission release. The CRAN package index is authoritative for registry availability. Use the CRAN command below when the index lists cellucid 0.9.7; otherwise install the active source from the official GitHub repository.

Requirements#

  • R: cellucid targets R ≥ 4.1.0 (checked on R 4.1, 4.2, 4.3, oldrel, release and devel).

  • Hard dependencies: jsonlite, and for the viewer httpuv, later and curl

  • Optional: Matrix (sparse expression matrices and neighbour graphs; recommended), SeuratObject and SingleCellExperiment / SummarizedExperiment (each only to read its own objects), DelayedArray (assays kept on disk, such as HDF5Array), BPCells (matrices kept on disk; from https://bnprks.r-universe.dev, not CRAN)

  • Source builds: Rtools on Windows, the Xcode Command Line Tools on macOS, or a C toolchain plus the R and zlib development headers on Linux (for example r-base-dev, which brings zlib1g-dev, on Debian and Ubuntu)

Note

cellucid-r does not require Seurat or SingleCellExperiment: it reads their objects when they are installed, and works from matrices and data frames when they are not.

Install Cellucid#

From CRAN when version 0.9.7 is listed#

When the CRAN package index lists cellucid 0.9.7, install it with: 

install.packages("cellucid")

If the index does not list version 0.9.7 yet, use the official source installation below.

From the official source repository#

These routes compile Cellucid’s small C routines (the CRC-32 of the .zarr.zip writer, the SHA-256 that checks the downloaded web app, the latent-space outlier quantiles, one-pass matrix checks, and the decoders of a saved session, linked against zlib) and therefore require the source-build toolchain listed above. A platform CRAN binary, when available, does not require a local compiler.

Option A: remotes (simple, common)#

install.packages("remotes")
remotes::install_github("theislab/cellucid-r")

Option B: pak (often faster, better resolver)#

install.packages("pak")
pak::pak("theislab/cellucid-r")

Verify the installation#

library(cellucid)
packageVersion("cellucid")

You should see:

  • No error on library(cellucid)

  • Version 0.9.7 from packageVersion

Troubleshooting installation#

Symptom: “package ‘jsonlite’ is not available”#

Likely causes

  • You are using an R environment without CRAN configured.

  • You are offline or behind a restrictive proxy.

How to confirm

  • Run getOption("repos") and verify you have a CRAN mirror set.

Fix

options(repos = c(CRAN = "https://cloud.r-project.org"))
install.packages("jsonlite")

Symptom: GitHub install fails (“HTTP error 401/403”, “rate limit”)#

Likely causes

  • Corporate proxy / blocked GitHub

  • GitHub API rate limiting

Fix options

  • Try pak (often more resilient).

  • If needed, configure a GitHub PAT:

    • Sys.setenv(GITHUB_PAT = "...")

Symptom: “there is no package called ‘Matrix’”#

Fix

install.packages("Matrix")

Symptom: you installed but library(cellucid) loads the wrong version#

How to confirm

find.package("cellucid")
packageVersion("cellucid")

Fix

  • Restart R (RStudio: Session → Restart R).

  • Reinstall with:

    remotes::install_github("theislab/cellucid-r", force = TRUE)

Next steps#