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ChiLiubio / microeco

An R package for data analysis in microbial community ecology
GNU General Public License v3.0
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R Session Aborted R encountered a fatal error The session was terminated #345

Open makerer5 opened 2 months ago

makerer5 commented 2 months ago

Hi Chi When I updated 'microeco' to V 1.6.0, I used the following code to plot the microbial network: t1 <- trans_network$new(dataset = group_PR, cor_method = NULL, taxa_level = "OTU", filter_thres = 0.001); t1$ cal_network(network_method = "SpiecEasi", SpiecEasi_method = "mb"). I encountered Rstudio crashing situation when I ran other code without any problem. Does this code conflict with R? Maker image 2024-04-05 233726

ChiLiubio commented 2 months ago

Hi Maker. Could you please attach your data group_PR so that I can use my PC to reproduce it? To save the data, please follow the steps in the tutorial (https://chiliubio.github.io/microeco_tutorial/notes.html#save-function) and attach the compressed object.Message ID: @.***>

makerer5 commented 2 months ago

dataset.zip Thanks, this is my data. I also ran into the following problem: t1$get_node_table(node_roles = TRUE) The nodes (364) with NaN in z will be filtered ... Error in private$assign_module_roles(zp) : No valid result obtained for this network!

ChiLiubio commented 2 months ago

Hi. Yes. I tested the steps using both windows and linux server and different microeco versions. All the sessions crashed. I am still not sure why it happened. If no available z value is found, please use node_roles = FALSE in get_node_table function.

makerer5 commented 2 months ago

This is the case, but the good news is: I used "SpiecEasi" to build the co-occurrence network for other data without any errors. It seems that this data has a special structure. Maybe I should check the amplicon process. Anyway, thank you for your help!