[Bug] Tutorial Code Error

[DarioS]

I am following Medium tutorial.

> SOMAExperimentOpen("soma-exp-pbmc3k")
  Error: Group: Cannot open group; Group does not exist.
> show_package_versions()
  tiledbsoma:    2.3.99.5
  tiledb-r:      0.34.0
  tiledb core:   2.30.0
  libtiledbsoma: 2.30.0
  R:             R version 4.5.1 (2025-06-13)
  OS:            Debian GNU/Linux 13 (trixie)

[jdblischak]

Did you follow the instructions to create soma-exp-pbmc3k? If you are following the Medium tutorial, this is done in the Python section above. It doesn't repeat the initial steps with R.

However, the tutorial links to a full-R solution hosted in TileDB Cloud, tiledb_101_singlecell_r.ipynb. For your convenience,
below is the code to create soma-exp-pbmc3k using TileDB-SOMA-R:

library(tiledb)
library(tiledbsoma)
suppressPackageStartupMessages(library(Seurat))

show_package_versions()

rds_uri <- "tiledb://TileDB-Inc/scanpy_pbmc3k_processed_rds"
rds_path <- "pbmc3k_processed.rds"

if (!file.exists(rds_path)) {
  if (!tiledb_filestore_uri_export(rds_path, rds_uri)) {
    stop("Failed to export RDS file from TileDB Cloud")
  }
}

pbmc3k <- readRDS(rds_path)
pbmc3k

Graphs(pbmc3k)

write_soma(pbmc3k, uri = "soma-exp-pbmc3k")

experiment <- SOMAExperimentOpen("soma-exp-pbmc3k")

[DarioS]

Ah, I had skipped the Python section because I thought that it is not relevant to R users.

[DarioS]

But it still fails. Has the data set in the cloud been deleted?

> rds_path
  "pbmc3k_processed.rds"
> rds_uri
  "tiledb://TileDB-Inc/scanpy_pbmc3k_processed_rds"
> tiledb_filestore_uri_export(rds_path, rds_uri)
  Error: Error exporting file from filestore

[aaronwolen]

Thanks for following up, @DarioS, and thanks to @jdblischak for jumping in to help.

The "Error exporting file from filestore" is likely an authentication issue, not a missing file. The RDS at tiledb://TileDB-Inc/scanpy_pbmc3k_processed_rds is hosted on TileDB Cloud and requires a valid account token to access it.

If you don't have an account already, sign up at https://cloud.tiledb.com. Once logged in, go to your account settings and create an API token (look for "API Tokens" under your profile menu). Use the token to define the env variable TILEDB_REST_TOKEN. The tiledb package reads this environment variable at load time to authenticate requests.

With the token in place, tiledb_filestore_uri_export should be able to download the RDS from TileDB Cloud and the rest of the tutorial should proceed normally.

Let us know if you run into any trouble after setting the token.

Also worth noting we have newer single-cell tutorials available on TileDB Academy that may be easier to follow than the Medium post.

[DarioS]

It appears that new registrations have been closed.

[aaronwolen]

Apologies for the runaround, @DarioS. You're right that signups aren't currently open, so the token approach won't work for you. We're in the middle of some platform changes on the hosting side, and a few of the older tutorial assets like this one are caught up in the transition.

To get you unblocked, I'll attach a gzipped copy of pbmc3k_processed.rds to this issue shortly. Once you have it locally, you can skip the tiledb_filestore_uri_export step entirely and pick up from readRDS.

pbmc3k_processed.rds.gz