pandoc-citeproc is not available!

[sbbmu]

When I try the example code below, I got this error "Error in .check_pandoc(ignore_pandoc) : pandoc-citeproc is not available!".

library("GeneTonic")
library("macrophage")
happy_hour(dds = dds_macrophage,
           res_de = res_de,
           res_enrich = res_enrich,
           annotation_obj = anno_df,
           project_id = "examplerun",
           mygenesets = res_enrich$gs_id[c(1:5,11,31)],
           mygenes = c("ENSG00000125347",
                       "ENSG00000172399",
                       "ENSG00000137496")
)

Error in .check_pandoc(ignore_pandoc) : pandoc-citeproc is not available!

I have installed pandoc. But pandoc-citeproc is discontinued. I am using Windows 10. Any suggestions?

> Sys.which("pandoc-citeproc")
pandoc-citeproc 
             "" 

[federicomarini]

Nice catch - I think I never had to experience that so I could not really test that out.

I hope a simple check whether pandoc is available should suffice to ensure that all works correctly. In the meantime, you can edit the source of the happy_hour function and safely ignore the lines that check for the presence of pandoc-citeproc

Federico

[federicomarini]

... or alternatively, without the need of editing source code - just call happy_hour() setting the ignore_pandoc argument to TRUE. This will likely raise a warning but at least it won't interrupt the execution of the function.

[federicomarini]

Does it work in your hands as well @sbbmu ? If so, I could close the issue!