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nolanlab / spade

SPADE: Spanning Tree Progression of Density Normalized Events
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Problem with "Example Usage" #97

Closed givison closed 9 years ago

givison commented 9 years ago

I've tried running through the "example usage" tutorial, and step 2 doesn't seem to work as written. First, I ran into an error with the use of "downsampling_samples" argument, which has been addressed in another thread (should say "downsampling_target_number" in the example if I understand correctly). It would be helpful if the documentation were updated, it still says the argument is called "downsampling_samples"

Next, I got the error "Error in loadNamespace(name) : there is no package called ‘igraph0’" Googling suggests to me that I should change the text of the SPADE.driver command to just say 'igraph' here, since igraph0 is has been removed from the CRAN repository--is this correct?

Thanks for making this great tool!

zbjornson commented 9 years ago

Sorry, another spot I forgot to update. I think it's all correct now. Please reopen if it still doesn't work for you.

givison commented 9 years ago

Running the new code in the example, I get: "Error in .Call("R_igraph_get_shortest_paths", graph, as.igraph.vs(graph, : At iterators.c:759 : Cannot create iterator, invalid vertex id, Invalid vertex id"

jpabbuehl commented 9 years ago

Hi I am also running into the same error, both with my fcs files and the example file At iterators.c:759 : Cannot create iterator, invalid vertex id, Invalid vertex id Possibly, the error might come from a function at a given vertice that is not listed in graph vertices.