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I'm trying to load the ExperimentHub experiments shared in the SimBenchData package. I tried loading the data from the first experiment:
library(ExperimentHub)
library(SimBenchData)
eh <- ExperimentHub()
alldata <- query(eh, "SimBenchData")
alldata[["EH5384"]]
But I see the following error:
library(ExperimentHub)
#> Loading required package: BiocGenerics
#> Loading required package: generics
#>
#> Attaching package: 'generics'
#> The following objects are masked from 'package:base':
#>
#> as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#> setequal, union
#>
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#>
#> IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#>
#> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
#> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
#> get, grep, grepl, is.unsorted, lapply, Map, mapply, match, mget,
#> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
#> rbind, Reduce, rownames, sapply, saveRDS, table, tapply, unique,
#> unsplit, which.max, which.min
#> Loading required package: AnnotationHub
#> Loading required package: BiocFileCache
#> Loading required package: dbplyr
library(SimBenchData)
eh <- ExperimentHub()
alldata <- query(eh, "SimBenchData")
alldata[["EH5384"]]
#> see ?SimBenchData and browseVignettes('SimBenchData') for documentation
#> loading from cache
#> require("Seurat")
#> Error loading resource.
#> attempting to re-download
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
#> Error: failed to load resource
#> name: EH5384
#> title: 293T cell line
#> reason: C stack usage 7954960 is too close to the limit
My first attempt to solve this was to raise my system's ulimit. I checked ulimit -H -s
in my terminal, and set it to my maximum allowed using ulimit -s 65520
. The same code above now yields a different error message, which seems to suggest an unaccounted for recursion. Could anyone point me in the right direction? I'm really looking forward to using these datasets. Thank you!!
> eh <- ExperimentHub()
alldata <- query(eh, "SimBenchData")
alldata[["EH5384"]]
snapshotDate(): 2025-09-22
> alldata <- query(eh, "SimBenchData")
> alldata[["EH5384"]]
see ?SimBenchData and browseVignettes('SimBenchData') for documentation
loading from cache
Error loading resource.
attempting to re-download
downloading 1 resources
retrieving 1 resource
loading from cache
Error: failed to load resource
name: EH5384
title: 293T cell line
reason: node stack overflow
I'm using Bioconductor 3.22:
r$> packageVersion("BiocVersion")
[1] '3.22.0'
Here is my session information.
r$> sessionInfo()
R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices
[4] utils datasets methods
[7] base
loaded via a namespace (and not attached):
[1] digest_0.6.37
[2] R6_2.6.1
[3] fastmap_1.2.0
[4] xfun_0.53
[5] magrittr_2.0.4
[6] glue_1.8.0
[7] tibble_3.3.0
[8] knitr_1.50
[9] pkgconfig_2.0.3
[10] htmltools_0.5.8.1
[11] rmarkdown_2.29
[12] lifecycle_1.0.4
[13] ps_1.9.1
[14] cli_3.6.5
[15] processx_3.8.6
[16] callr_3.7.6
[17] vctrs_0.6.5
[18] reprex_2.1.1
[19] withr_3.0.2
[20] compiler_4.5.1
[21] rstudioapi_0.17.1
[22] tools_4.5.1
[23] clipr_0.8.0
[24] pillar_1.11.1
[25] evaluate_1.0.5
[26] yaml_2.3.10
[27] rlang_1.1.6
[28] jsonlite_2.0.0
[29] fs_1.6.6
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release/data/experiment/manuals/SimBenchData/man/SimBenchData.pdf I see that Seurat is only suggested, so not installed by default upon installation.
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.