Same error message, suggested fix did not work

[alymatz]

Hi! I am having the same error as discussed previously on Jan 28: "Error in utils::txtProgressBar(min = 0, max = length(pw_vis_list), style = 3) : must have 'max' > 'min'" In response to the previous poster, you suggested downloading a new update. I did so and restarted my computer but there was no change. I am connected to the internet and my connection is strong. I would like to visualize my results if possible. Thank you for your consideration! Sincerely, Alyssa

[egeulgen]

Hey @alymatz, Have you tried to download the latest development version? This can be achieved via pak:

install.packages("pak") # if you have not installed "pak"
pak::pkg_install("egeulgen/pathfindR")

This issue was fixed. If installing the latest development version does not work, please provide the script you run and the exact error you get. Best, -E

[alymatz]

Hi E, I installed the latest version and still got the same error. Here is more of the script, if more is needed please let me know! I am very new to R.

output<-run_pathfindR(m) There is already a directory named "pathfindR_Results". Writing the result to "pathfindR_Results(8)" not to overwrite any previous results.

Testing input

The input looks OK

Processing input. Converting gene symbols,

if necessary (and if human gene symbols provided) Number of genes provided in input: 119 Number of genes in input after p-value filtering: 79 pathfindR cannot handle p values < 1e-13. These were changed to 1e-13

Could not find any interactions for 23 (29.11%) genes in the PIN Final number of genes in input: 56

Performing Active Subnetwork Search and Enrichment

Processing the enrichment results over all iterations

Annotating involved genes and visualizing enriched terms

Downloading pathway diagrams of 10 KEGG pathways

| | 0%Cannot download KGML file for: hsa04062 Here's the original error message: |=========== | 10%Cannot download KGML file for: hsa04630 Here's the original error message: |===================== | 20%Cannot download KGML file for: hsa04061 Here's the original error message: |================================ | 30%Cannot download KGML file for: hsa04620 Here's the original error message: |========================================== | 40%Cannot download KGML file for: hsa05145 Here's the original error message: |===================================================== | 50%Cannot download KGML file for: hsa05235 Here's the original error message: |================================================================ | 60%Cannot download KGML file for: hsa04668 Here's the original error message: |========================================================================== | 70%Cannot download KGML file for: hsa04657 Here's the original error message: |===================================================================================== | 80%Cannot download KGML file for: hsa05164 Here's the original error message: |=============================================================================================== | 90%Cannot download KGML file for: hsa04621 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]

ok I think pak is installing the latest release on github. Do you mind installing the development via devtools:

devtools::install_github("egeulgen/pathfindR")

[alymatz]

Yes! Thank you!! -Alyssa