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How to run_app with download file

Open bitcometz opened this issue 4 months ago • 0 comments

Hello, thanks for this great tool !

After installing the tool, I run :

spatialLIBD::run_app()
/public1/home/a8s000003/.cache/R/ExperimentHub
  does not exist, create directory? (yes/no): no
using temporary cache /tmp/RtmpDnE3Wx/BiocFileCache
  |======================================================================| 100%

snapshotDate(): 2023-10-24
adding rname 'https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1'
Error in BiocFileCache::bfcrpath(bfc, url) : 
  not all 'rnames' found or unique.
In addition: Warning messages:
1: download failed
  web resource path: ‘https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1’
  local file path: ‘/tmp/RtmpDnE3Wx/BiocFileCache/2ffccf59374ec3_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1’
  reason: Timeout was reached [www.dropbox.com]:
Connection timed out after 10002 milliseconds 
2: bfcadd() failed; resource removed
  rid: BFC3
  fpath: ‘https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1’
  reason: download failed 
3: In value[[3L]](cond) : 
trying to add rname 'https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1' produced error:
  bfcadd() failed; see warnings()

The error above is likely because my computer cannot connect to the internet. Therefore, I have downloaded the relevant files, but I don't know how to use these files to start the app. I would appreciate your help. Thank you.

> load("/public1/home/a8s000003/share/analysis/zhangjinbo/notebooks/spatialLIBD/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata")
> ls()
[1] "sce"
> spatialLIBD::run_app(sce = sce)
snapshotDate(): 2023-10-24
adding rname 'https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1'
Error in BiocFileCache::bfcrpath(bfc, url) : 
  not all 'rnames' found or unique.
In addition: Warning messages:
1: download failed
  web resource path: ‘https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1’
  local file path: ‘/tmp/RtmpDnE3Wx/BiocFileCache/2ffccf528d849c_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1’
  reason: Timeout was reached [www.dropbox.com]:
Connection timed out after 10002 milliseconds 
2: bfcadd() failed; resource removed
  rid: BFC4
  fpath: ‘https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1’
  reason: download failed 
3: In value[[3L]](cond) : 
trying to add rname 'https://www.dropbox.com/s/f4wcvtdq428y73p/Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata?dl=1' produced error:
  bfcadd() failed; see warnings()

Best

bitcometz avatar Oct 14 '25 03:10 bitcometz