code doesn't stop running

[mvereten]

Hello!

I've tried to run the vignette from https://cran.r-project.org/web/packages/ProFAST/vignettes/CosMx.html ,
and when I run this part of the code below, with the data as in the vignette,

dat_cor <- diagnostic.cor.eigs(CosMx_subset)
q_est <- attr(dat_cor, "q_est")
cat("q_est = ", q_est, '\n')

I get a "Progress:.....100%" printed out many many times, but the printing of this seems to have no end.

Is this a bug in the code by any chance?

P.S. If I stop this code and restart, none of the "Progress..."" text appears (repeated this several times, get the same phenomenon), but not sure the code is supposed to be running for hours and hours or this is a bug indeed.

Thanks,
Maria

[feiyoung]

Hi,

I have attempted to execute the provided code and it successfully completed its execution within 20 seconds. Here is a screenshot of the results:

Could you please share your output information by performing a screenshot or a copy-paste of the relevant part?

You can also refer to the package website: https://feiyoung.github.io/ProFAST/articles/CosMx.html

Best regards,

Wei Liu

[mvereten]

Hi Wei, It looks like this the first time round:
copy1.pdf

[mvereten]

And if I stop the code execution and try to rerun the code, I get this:

and nothing happens for at least half a day

[feiyoung]

Are you executing this on a server? It's possible that the resources might be limited when running tasks in root node on a server. You could try running this on your personal computer or submitting the job for execution on a server. I can also run this code on our server that does not limit the resource usage:

[mvereten]

Dear Wei,

Thanks a lot, I tried it on my laptop instead and after a few installation updates the code runs. Thank you.