Cannot run example dataset

[nbruse]

Hey,

It is probably an issue with the installation, but I cannot even execute the run_pathfindr function on the example dataset without getting this error. The progress bar also only shows up after the whole process is done.

> library(pathfindR)
> head(RA_input)
  Gene.symbol      logFC    adj.P.Val
1     FAM110A -0.6939359 3.408699e-06
2      RNASE2  1.3535040 1.008499e-05
3      S100A8  1.5448338 3.466386e-05
4      S100A9  1.0280904 2.262617e-04
5      TEX261 -0.3235994 2.262617e-04
6    ARHGAP17 -0.6919330 2.708081e-04
> RA_output <- run_pathfindR(RA_input)
`n_processes` is set to `iterations` because `iterations` < `n_processes`
There is already a directory named "pathfindR_Results".
Writing the result to "pathfindR_Results(3)" 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: 572
Number of genes in input after p-value filtering: 572

Could not find any interactions for 11 (1.92%) genes in the PIN
Final number of genes in input: 561
## 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: hsa03040
Here's the original error message:
  |================                                                                                                                                                |  10%Cannot download KGML file for: hsa00190
Here's the original error message:
  |================================                                                                                                                                |  20%Cannot download KGML file for: hsa05012
Here's the original error message:
  |================================================                                                                                                                |  30%Cannot download KGML file for: hsa04932
Here's the original error message:
  |================================================================                                                                                                |  40%Cannot download KGML file for: hsa03410
Here's the original error message:
  |================================================================================                                                                                |  50%Cannot download KGML file for: hsa05010
Here's the original error message:
  |================================================================================================                                                                |  60%Cannot download KGML file for: hsa04064
Here's the original error message:
  |================================================================================================================                                                |  70%Cannot download KGML file for: hsa05016
Here's the original error message:
  |================================================================================================================================                                |  80%Cannot download KGML file for: hsa04714
Here's the original error message:
  |================================================================================================================================================                |  90%Cannot download KGML file for: hsa03013
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'

Is this a known error?

Thank you for your time.

[egeulgen]

None of the KEGG pathways could be downloaded, please check your internet connection. If visualization is not necessary, set visualize_enriched_terms=FALSE in run_pathfindR().

The error was: because no pathway diagrams could be downloaded, there were 0 diagrams to color. Because the progress bar for coloring requires the minimum and maximum (both 0 in this case), it failed.

The latest commit fixes this issue. If you'd like, please download the latest development version via:

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

[alymatz]

Hi! I am having the same issue as discussed above, I installed the latest development version as suggested and there has been no change. My internet is connected and strong and I restarted my computer as well. I am using my own data for this analysis. I did wish to visualize the results. Thank you for your consideration! Sincerely, Alyssa

[kratzera]

Hej, I try to visualise KEGG pathways of my data, but it gives me the following error: Here's the original error message: 'color.pathway.by.objects()' failed to extract KEGG image path from response. Cannot download PNG file: NA Here's the original error message: invalid 'url' argument I get that for all pathways.

Here is my data I try to run: GenesUpDownP1_KEGG_processed <- input_processing(GenesUpDownP1.df, pin_name_path="KEGG",convert2alias = TRUE) visualize_terms( result_df = GenesUpDownP1_GO_KEGG, input_processed = GenesUpDownP1_KEGG_processed, hsa_KEGG = TRUE, pin_name_path = "KEGG" )

Thank you for your help! H

[egeulgen]

Can you share the data you use for this (GenesUpDownP1_KEGG_processed and GenesUpDownP1_GO_KEGG) as RDS files?Best,-EOn 5 Jun 2023, at 22:41, kratzera @.***> wrote: Hej, I try to visualise KEGG pathways of my data, but it gives me the following error: Here's the original error message: 'color.pathway.by.objects()' failed to extract KEGG image path from response. Cannot download PNG file: NA Here's the original error message: invalid 'url' argument I get that for all pathways. Here is my data I try to run: GenesUpDownP1_KEGG_processed <- input_processing(GenesUpDownP1.df, pin_name_path="KEGG",convert2alias = TRUE) visualize_terms( result_df = GenesUpDownP1_GO_KEGG, input_processed = GenesUpDownP1_KEGG_processed, hsa_KEGG = TRUE, pin_name_path = "KEGG" ) Thank you for your help! H

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[kratzera]

Hej there, Thank you for your reply. I am still very new to this, but I manage bit by bit to work with it and I think your script is great. It’s probably sthg small that I cannot see that is wrong. Please find attached the files you asked for:

Best and thanks, Heidi

On 13. Jun 2023, at 21:19, Ege Ulgen @.***> wrote:

Can you share the data you use for this (GenesUpDownP1_KEGG_processed and GenesUpDownP1_GO_KEGG) as RDS files?Best,-EOn 5 Jun 2023, at 22:41, kratzera @.***> wrote: Hej, I try to visualise KEGG pathways of my data, but it gives me the following error: Here's the original error message: 'color.pathway.by.objects()' failed to extract KEGG image path from response. Cannot download PNG file: NA Here's the original error message: invalid 'url' argument I get that for all pathways. Here is my data I try to run: GenesUpDownP1_KEGG_processed <- input_processing(GenesUpDownP1.df, pin_name_path="KEGG",convert2alias = TRUE) visualize_terms( result_df = GenesUpDownP1_GO_KEGG, input_processed = GenesUpDownP1_KEGG_processed, hsa_KEGG = TRUE, pin_name_path = "KEGG" ) Thank you for your help! H

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you modified the open/close state.Message ID: @.***> — Reply to this email directly, view it on GitHub https://github.com/egeulgen/pathfindR/issues/28#issuecomment-1589888649, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADU6KHLEI5VXUH2Q7WBUQZTXLC4MXANCNFSM4KMTM7LQ. You are receiving this because you commented.

[egeulgen]

hello again, I think attachments via mail don't work, can you try sending from github web?

[kratzera]

hello again, sorry for the late reply. My colleague managed to make it work on his PC (not Mac), but I ran actually into more problems in the last weeks. I updated my Rstudio to Version 2023.06.0+421 and R to 4.3.1 and now I get a fatal error when I try to run pathfindR (see image). Any recommendations/suggestions? Thanks again for your help!