wget command not found

[aj12aj]

Hi,

I've been getting this issue of the wget command not found. Is there a way to fix this? tried installing the latest version too using this line: pak::pkg_install("egeulgen/pathfindR") but it gave me the same error.

output_df <- run_pathfindR(input_df)

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: 603 Number of genes in input after p-value filtering: 603 Could not find any interactions for 45 (7.59%) genes in the PIN Final number of genes in input: 548

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%sh: wget: command not found Cannot download KGML file for: hsa03050 Here's the original error message: |======= | 10%sh: wget: command not found Cannot download KGML file for: hsa00030 Here's the original error message: |============== | 20%sh: wget: command not found Cannot download KGML file for: hsa04012 Here's the original error message: |====================== | 30%sh: wget: command not found Cannot download KGML file for: hsa05161 Here's the original error message: |============================= | 40%sh: wget: command not found Cannot download KGML file for: hsa05100 Here's the original error message: |==================================== | 50%sh: wget: command not found Cannot download KGML file for: hsa05169 Here's the original error message: |=========================================== | 60%sh: wget: command not found Cannot download KGML file for: hsa04960 Here's the original error message: |================================================== | 70%sh: wget: command not found Cannot download KGML file for: hsa04714 Here's the original error message: |========================================================== | 80%sh: wget: command not found Cannot download KGML file for: hsa00190 Here's the original error message: |================================================================= | 90%sh: wget: command not found Cannot download KGML file for: hsa05205 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: There were 13 warnings (use warnings() to see them)

Thanks for the help!

[egeulgen]

You need to have wget installed on your system. Alternatively, you may use visualize_enriched_terms = TRUE for not visualizing the enriched terms.

[aj12aj]

It worked now! Thank you!

[harish0201]

I'm using the docker image as I'm encountering dependency hell while installing this on centos, but doesn't the docker image have wget installed in it?

Alternatively, is there a way to run this directly through the shell?

Currently, I'm using it like this: docker run -v $PWD:$PWD -it egeulgen/pathfindr

[egeulgen]

@harish0201 Sorry, I updated the docker images so that they have wget installed.

I'm doing the same to use it, couldn't find another way yet but I'll let you know if I can find anything more practical

[harish0201]

Thanks, should I just pull the image again?

[egeulgen]

Yes. I would suggest the dev image

-E

On 6 May 2020, at 14:12, Harish notifications@github.com wrote:

 Thanks, should I just pull the image again?

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[harish0201]

Thanks, it worked!

On Wed, May 6, 2020, 17:29 Ege Ulgen notifications@github.com wrote:

Yes. I would suggest the dev image

-E

On 6 May 2020, at 14:12, Harish notifications@github.com wrote:

 Thanks, should I just pull the image again?

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub, or unsubscribe.

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