scRNAseq Download Errors
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Entering edit mode
Dario Strbenac ★ 1.5k
@dario-strbenac-5916
Last seen 2 hours ago
Australia

I am using a standard home Wi-Fi connection in Australia and getting errors when I download a data set from scRNAseq. From the start of execution until the error message takes 18 minutes. Average transfer speed appeared to be around 4 Mbps. Any mirrors located in Asia-Pacific I could choose somehow? Also, I wonder if such functions could allow the user to choose 100 genes and 100 cells, for instance, to download instead of the full data set.

> mouse.brain.romanov <- scRNAseq::RomanovBrainData(ensembl = TRUE)

snapshotDate(): 2023-04-13
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
downloading 1 resources
retrieving 1 resource

loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
downloading 1 resources
retrieving 1 resource

loading from cache
using temporary cache C:\Users\Dario\AppData\Local\Temp\RtmpW2ln90/BiocFileCache

87% Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) : 
  bfcadd() failed; see warnings()
In addition: Warning messages:
1: download failed
  web resource path: 'https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3'
  local file path: 'C:\Users\Dario\AppData\Local\Temp\RtmpW2ln90/BiocFileCache/1c98484752ce_annotationhub.sqlite3'
  reason: transfer closed with 15694848 bytes remaining to read 
2: bfcadd() failed; resource removed
  rid: BFC1
  fpath: 'https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3'
  reason: download failed
scRNAseq • 568 views
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Entering edit mode

BiocFileCache uses httr::GET to retrieve the files so perhaps there is a way to increase the timeout?

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