Using job::job() within RMarkdown file

[meghanmshea]

I am working on compiling one large RMarkdown file that reproduces all of the analyses for a scientific manuscript. A few of the analyses take a long time, so I've used job::job() to run them as jobs, which has worked great when I'm working through the RMarkdown file in RStudio.

But, I'd like to be able to knit the RMarkdown file to html/pdf to share with the manuscript too. But I get an error in the first chunk that includes a job::job() call when trying to render: Error in check_available(): ! You must run this from the RStudio main session. Backtrace:

1. job::job(...)
2. job:::check_available() Execution halted

Is there something I'm missing that would make it possible to render the RMarkdown even with the job sections? Or is this just fundamentally incompatible?

[psychelzh]

I think you cannot do this based on these lines:

https://github.com/lindeloev/job/blob/452600154add99982b01bd029e39e3d6f8580d44/R/misc.R#L3-L4

This function only works in an RStudio main session.

[lindeloev]

Hi @meghanmshea Sorry for the late reply, but @psychelzh is right. For your use case, you may want to look at the IDE-agnostic solutions mentioned under "See also" on https://lindeloev.github.io/job/. Namely {callr}.