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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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Error Message #44

Closed AmbroiseGecko closed 4 years ago

AmbroiseGecko commented 4 years ago

Hi there, I tried to run PathFindR recently and whichever dataset I use, I obtain the following error messages at the end:

Is it possible to know what is going on? Thank you!!

| | 0%Cannot download KGML file for: hsa03010 Here's the original error message: |============= | 10%Cannot download KGML file for: hsa03040 Here's the original error message: |=========================== | 20%Cannot download KGML file for: hsa04110 Here's the original error message: |======================================== | 30%Cannot download KGML file for: hsa00190 Here's the original error message: |===================================================== | 40%Cannot download KGML file for: hsa05203 Here's the original error message: |================================================================== | 50%Cannot download KGML file for: hsa05130 Here's the original error message: |================================================================================ | 60%Cannot download KGML file for: hsa04218 Here's the original error message: |============================================================================================= | 70%Cannot download KGML file for: hsa04141 Here's the original error message: |========================================================================================================== | 80%Cannot download KGML file for: hsa05169 Here's the original error message: |======================================================================================================================== | 90%Cannot download KGML file for: hsa04810 Here's the original error message: |=====================================================================================================================================| 100% Saving colored pathway diagrams of 0 KEGG pathways

Error in utils::txtProgressBar(min = 0, max = length(pw_vis_list), style = 3) : must have 'max' > 'min' In addition: Warning message: In pathfindR::input_processing(input, p_val_threshold, pin_path, : The gene column was turned into character from factor.

egeulgen commented 4 years ago

please install and try with the latest development version:

install.packages("devtools") # if you have not installed "devtools"
devtools::install_github("egeulgen/pathfindR")
egeulgen commented 4 years ago

@AmbroiseGecko has the development version resolved your issue?

AmbroiseGecko commented 4 years ago

@egeulgen . Thanks, I just tried and yes it works beautifully. Thanks a lot!