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digitalcytometry / ecotyper

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
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Error in tutorial 1 #58

Closed mao223 closed 1 year ago

mao223 commented 1 year ago

Good day, I am going through the tutorial (running on my local computer) and I am getting this error when running Rscript EcoTyper_recovery_bulk.R -d Carcinoma -m example_data/bulk_lung_data.txt -a example_data/bulk_lung_annotation.txt -c Tissue -o RecoveryOutput

Running cell state recovery on: CD8.T.cells...
Running cell state recovery on: Mast.cells...
Running cell state recovery on: NK.cells...
Running cell state recovery on: PCs...
Running cell state recovery on: CD4.T.cells...
Running cell state recovery on: PMNs...
Running cell state recovery on: Fibroblasts...
Running cell state recovery on: Dendritic.cells...
Running cell state recovery on: Monocytes.and.Macrophages...
Running cell state recovery on: B.cells...
Error in getFromNamespace(device_info[3], ns = device_info[2])(temp_image) : 
  unable to open /var/folders/37/wkndqrfs33dg5gvv556h0gcm0000gn/T//RtmpNV47Cg/.heatmap_body_8e298dcba81b6519e384a7170581a0ad_1_11b1b60531ec4.png
Execution halted
Error in getFromNamespace(device_info[3], ns = device_info[2])(temp_image) : 
  unable to open /var/folders/37/wkndqrfs33dg5gvv556h0gcm0000gn/T//Rtmpzqv484/.heatmap_body_8e298dcba81b6519e384a7170581a0ad_1_11b25214c019b.png
Execution halted
Error in getFromNamespace(device_info[3], ns = device_info[2])(temp_image) : 
  unable to open /var/folders/37/wkndqrfs33dg5gvv556h0gcm0000gn/T//Rtmp3edupD/.heatmap_body_8e298dcba81b6519e384a7170581a0ad_1_11b1e210a8a79.png
Execution halted
Error in getFromNamespace(device_info[3], ns = device_info[2])(temp_image) : 
  unable to open /var/folders/37/wkndqrfs33dg5gvv556h0gcm0000gn/T//Rtmpkt85uO/.heatmap_body_8e298dcba81b6519e384a7170581a0ad_1_11b1d2f21e2bb.png
Execution halted
Error in getFromNamespace(device_info[3], ns = device_info[2])(temp_image) : 
  unable to open /var/folders/37/wkndqrfs33dg5gvv556h0gcm0000gn/T//Rtmp5xkdBp/.heatmap_body_8e298dcba81b6519e384a7170581a0ad_1_11b191ec257ca.png
Execution halted
Error in getFromNamespace(device_info[3], ns = device_info[2])(temp_image) : 
  unable to open /var/folders/37/wkndqrfs33dg5gvv556h0gcm0000gn/T//RtmpWZu59c/.heatmap_body_8e298dcba81b6519e384a7170581a0ad_1_11b22244c36a9.png
Execution halted
Error in getFromNamespace(device_info[3], ns = device_info[2])(temp_image) : 
  unable to open /var/folders/37/wkndqrfs33dg5gvv556h0gcm0000gn/T//Rtmp4QReWK/.heatmap_body_8e298dcba81b6519e384a7170581a0ad_1_11b1756aad2f9.png
Execution halted
Error in getFromNamespace(device_info[3], ns = device_info[2])(temp_image) : 
  unable to open /var/folders/37/wkndqrfs33dg5gvv556h0gcm0000gn/T//Rtmp7XOKYS/.heatmap_body_8e298dcba81b6519e384a7170581a0ad_1_11b241c4aebce.png
Execution halted
Running cell state recovery on: Epithelial.cells...
Running cell state recovery on: Endothelial.cells...
Error in getFromNamespace(device_info[3], ns = device_info[2])(temp_image) : 
  unable to open /var/folders/37/wkndqrfs33dg5gvv556h0gcm0000gn/T//RtmpIIsIOv/.heatmap_body_8e298dcba81b6519e384a7170581a0ad_1_11b20380c2954.png
Execution halted
Error in getFromNamespace(device_info[3], ns = device_info[2])(temp_image) : 
  unable to open /var/folders/37/wkndqrfs33dg5gvv556h0gcm0000gn/T//RtmpxkUesE/.heatmap_body_8e298dcba81b6519e384a7170581a0ad_1_11b2667611af6.png
Execution halted
Error in getFromNamespace(device_info[3], ns = device_info[2])(temp_image) : 
  unable to open /var/folders/37/wkndqrfs33dg5gvv556h0gcm0000gn/T//RtmpECyGiy/.heatmap_body_8e298dcba81b6519e384a7170581a0ad_1_11bc13747b11b.png
Execution halted
Error in getFromNamespace(device_info[3], ns = device_info[2])(temp_image) : 
  unable to open /var/folders/37/wkndqrfs33dg5gvv556h0gcm0000gn/T//Rtmphm7geC/.heatmap_body_8e298dcba81b6519e384a7170581a0ad_1_11bb6640ea8d4.png
Execution halted
Error in RunJobQueue() : 
  EcoTyper failed. Please check the error message above!
Execution halted

I was wondering if I could get guidance on figuring out the source of the error and how I could get it to run. Thank you very much!

mao223 commented 1 year ago

Hi just to follow up, I got it to work after finding installing xquartz, see: https://github.com/jokergoo/EnrichedHeatmap/issues/59#issuecomment-1168156778

I also have an M1 Mac. Just mentioning in case someone else encounters this problem. Thank you for a great tool!