Timeout on download

[apal6]

Hi,

Thank you for the wonderful package. I get this error when I try to load the ref data,

ref <- load.reference.map() [1] "Loading Default Reference Atlas..." [1] "/ref_TILAtlas_mouse_v1.rds not found; downloading reference TIL map from the server..." trying URL 'https://ndownloader.figshare.com/files/41398167' Content type 'application/octet-stream' length 495696162 bytes (472.7 MB) downloaded 159.4 MB Error in value[[3L]](cond) : Sorry, download failed. In addition: Warning messages: 1: In download.file(refUrl, refFileName) : downloaded length 0 != reported length 0 2: In download.file(refUrl, refFileName) : URL 'https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/41398167/ref_TILAtlas_mouse_v1.rds?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIYCQYOYV5JSSROOA/20240503/eu-west-1/s3/aws4_request&X-Amz-Date=20240503T200342Z&X-Amz-Expires=10&X-Amz-SignedHeaders=host&X-Amz-Signature=76d64b8d0649de6156c0fc8afc028427cdbc80934a7d3ba0350e5bee47ba6343': Timeout of 60 seconds was reached

How can I solve this issue?

Thank you.

[mass-a]

Hello, your log suggests that download of the reference object failed because of a download timeout (60 seconds). You can increase the timeout by setting the following option in your R session:

options(timeout = 3000)

Best -m

[apal6]

@mass-a, Thank you. That worked.

When I tried to run the classifier function, i get the following error :

`merged_obj_TIL <- ProjecTILs.classifier(merged_obj_TIL, ref, ncores = 32, split.by = "Treatment") | | 0%[1] "Using assay RNA for query" Pre-filtering cells with scGate... |==================================================================================================================================================| 100%

| | 0%[1] "Using assay RNA for query" Pre-filtering cells with scGate... |==================================================================================================================================================| 100%

failed to open the port 11106, trying a new port... | | 0%[1] "Using assay RNA for query" Pre-filtering cells with scGate... |==================================================================================================================================================| 100%

Stop worker failed with the error: wrong args for environment subassignment Error: BiocParallel errors 0 remote errors, element index: 5 unevaluated and other errors first remote error:`

> merged_obj_TIL An object of class Seurat 20138 features across 31797 samples within 1 assay Active assay: RNA (20138 features, 2000 variable features) 3 layers present: data, counts, scale.data 2 dimensional reductions calculated: pca, umap.unintegrated

I did not change anything in the environment. What do you think could be an issue?

Thank you!

[apal6]

Following up- Error: BiocParallel errors 1 remote errors, element index: 1 0 unevaluated and other errors first remote error: Error in as.vector(x): no slot of name "var.features" for this object of class "Assay5"

I am not sure why it is not recognizing the slot variables. Could you help?

Thank you