Closed Tommy0398 closed 3 years ago
It seems like it was related to https://github.com/egeulgen/pathfindR/issues/58 , the directory I was using was within a lot of subdirectories which I guess causes problems somehow. Performing the analysis in a folder closer to the root fixed this for some reason.
Hey @BiostormSilver, sorry I couldn’t reply earlier. Glad you resolved the issue. best, -E
Describe the bug Hi, I am having an issue running the run_pathfindR command in your package where everytime I run the command on my data it has an error involving the term_visulisations not being connected to which results in the command stopping and no output being produced.
To Reproduce My input data is DE summary data from Seurat converted into the correct format and the gene sets and PIN files im using are the ones given in the vignette: https://cran.r-project.org/web/packages/pathfindR/vignettes/non_hs_analysis.html.
This is the run_pathfindR command I'm using
And this is the error it gives
Desktop (please complete the following information):
R Session Information:
Additional context I have also tried using different databases but they also give a similar error and occasionally I get this error:
Error in { : task 1 failed - "cannot open the connection"
That occurs when using the exact same code as before just with R restarted or the objects cleared, I'm not sure what decides when that error occurs.