Unable to Read Font "helvetica"

evofish commented 3 years ago

Hello all this is my first time using pathfindR and I am having an issue running the example dataset "RA_input" as test.

When I just run the command:

run_pathfindR(RA_input)

I get the following

_n_processes is set to iterations because iterations < n_processes There is already a directory named "pathfindR_Results". Writing the result to "pathfindR_Results(5)" 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 5 (0.87%) genes in the PIN Final number of genes in input: 567

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

|===========================================================================================| 100% Saving colored pathway diagrams of 10 KEGG pathways

| | 0%

Error in grid.Call(CstringMetric, as.graphicsAnnot(x$label)) : rsession: UnableToReadFont `helvetica' @ error/annotate.c/RenderFreetype/1396

It seems like the error is the lack of helvetica con my computer, which I have no idea how to solve. This is the first time I see this type of error for any sort of graph or analysis I have run with R.

This is with R 4.1.1 and I had to "force" install some of the BioConductor dependencies to make it run. I also had a to install the latest version of Java available for mac (14) to make the pipeline work.

Any suggestions would be greatly appreciated.

evofish commented 3 years ago

egeulgen commented 3 years ago

hey @evofish,

You can find Helvetica here. While the font installation depends on your operating system, it's usually fairly easy (googling for it should help).

Hope this helps, Best, -E

evofish commented 3 years ago

Unfortunately it is much more complex than that. I have helvetica installed on my Mac by default, and it is on every user's library. When I run ggplot2 on itself I have no issue.

The issue only comes up when I run pathfindr, giving me the error message: "Error in grid.Call(CstringMetric, as.graphicsAnnot(x$label)) : rsession: UnableToReadFont `helvetica' @ error/annotate.c/RenderFreetype/1396"

If I try to run ggplot2 after running pathfindr I get the same error message from above.

Is it possible that pathfindr is looking for fonts on a different folder? could this be triggered by one of the multiple dependencies? Any suggestion helps. Thanks again

egeulgen commented 3 years ago

hello again, Some search revealed that this is an issue with magick (one of the dependencies). The solution provided here suggests installing GhostScript via homebrew should resolve the issue:

brew install gs

Hope this resolves the issue, Best, -E

evofish commented 3 years ago

Thanks it is working properly now. I appreciate your support !

egeulgen / pathfindR