seu <- fitGMM(seu) has an issue

[vijithaduke]

fitGMM isn't working and I'm getting this error: seu <- fitGMM(seu)

Error in getGlobalsAndPackages(expr, envir = envir, globals = globals) : The total size of the 26 globals exported for future expression (‘FUN(X = structure(c(45, 2, 7, 0, 4, 14, 4, 234, 6, 9, 15, 7,; 4, 5, 1, 22, 8, 21, 0, 0, 11, 37, 11, 29, 28, 3, 11, 0, 5, 29,; 4, 220, 12, 8, 26, 6, 5, 5, 4, 24, 8, 22, 0, 0, 10, 40, 11, 29,; 42, 3, 11, 0, 5, 29, 4, 220, 12, 8, 26, 6, 5, 5, 2, 24, 8, 22,; 0, 0, 10, 40, 11, 30, 32, 3, 11, 0, 5, 29, 4, 220, 12, 8, 26,; 6, 5, 5, 2, 24, 8, 22, 0, 0, 10, 40, 11, 30, 29, 3, 11, 0, 5,; ...; 22, 55, 3, 3, 0, 4, 11, 5, 185, 7, 7, 8, 5, 4, 4, 2, 17, 6, 16,; 0, 0, 8, 20, 11, 26, 20, 2, 8, 0, 3, 32, 4, 200, 5, 4, 14, 4,; 3, 2, 0, 7, 6, 20, 0, 0, 10, 63, 10, 24, 34, 1, 5, 0, 2, 14,’) is 1.08 GiB.. This exceeds the maximum allowed size of 500.00 MiB (option 'future.globals.maxSize'). The three largest globals are ‘FUN’ (1.08 GiB of class ‘function’), ‘fitdistr’ (66.83 KiB of class ‘function’) and ‘Mclust’ (16.33 KiB of class ‘function’)

5. | stop(msg) -- | --

Please help me to resolve this. Thank you!

[jianhong]

This is memory issue. Try to decrease the processors by

library(future.apply)
plan(multisession, workers=1)
seu <- fitMM(seu) 

If it does not work, share me the seurat object. I will try to decrease the memory cost by playing the big data.

[vijithaduke]

Got it. Thank you!