Error Loading Experiment from SimBenchData Package
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ksankaran • 0
@e4769b8d
Last seen 44 minutes ago
United States

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
Bioconductor • 110 views
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Entering edit mode

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.

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Entering edit mode

Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.

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