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JMP and R connection issue

abmayfield

I just saw a cool webinar today on using some features in R that are not available in JMP via JSL. I am specifically talking about t-SNE: Data visualization with t-SNE and UMAP .

I am running JMP 14 on Mac OS 10.13 (High Sierra) and, according to the add-in link above, the R version to get is 3.3.3, so I downloaded that, restarted, and followed this: https://www.jmp.com/support/help/en/15.1/index.shtml#page/jmp/installing-r.shtml#. I cannot get even the very simple script in this trouble-shooting guide to work, not an error, just nothing. The JMP scripting guide is written for Windows, but I tried manually setting the "set environmental variable" to the applications folder, but that did not work either. R works and is stored in my Applications folder. I had older versions of R on my computer, but I deleted them (and restarted afterwards). I made it to where I can read and write files (it is my personal computer, and I am the administrator), yet even "R Init ();" does nothing.

As of a few months ago, JMP14, R ver. 3.3.3., and MAC OS10.13 were all theoretically compatible. Did anything happen in the meantime that would have made it to where I can no longer use R via the script window?

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cwillden

I think JMP Tech Support may be the fastest solution path for you. It might take some time for another Mac user connecting JMP to R to see this.

abmayfield

Nay you worry, they are on the case (though thus far stumped). My goal is to, once we figure out the issue, post the solution here so that other Mac users looking to run R via JSL don't run into the same issue.

@abmayfield Yeah, Mac had some versioning issues previously. One of the Mac users was able to connect to R and managed to run this Embedding add-in but it was a while ago and many factors have changed. I hope the tech support will figure it out for you.

abmayfield

I figured it out! It is actually an R vs. Mac issue.

https://community.rstudio.com/t/i-can-t-install-packages-on-r-studio-non-zero-exit-status/52135

If you try to install the Rtsne package on a Mac, R will install it, then immediately delete it and give you all kinds of weird error messages UNLESS you install it via the Mac-specific registry mentioned in this link (https://mac.R-project.org). This is the kind of thing that makes me prefer JMP over R. Even installing a simple data package with R took me 36 hours to trouble-shoot and figure out. Could t-SNE be integrated into the next version of JMP Genomics maybe?

There is a weird, but minor, JMP issue, though. "R Init" does not work at all on my Mac. Only "R is connected" will cause JMP and R to sync. From reading various posts, it seems like BOTH should be able to connect to R, so it's strange that "R Init" fails to do so. In other words, Mac users on 10.13 with R 3.3.3 will need to use "R is connected" not "R Init" to use R via JSL.