Error: Will not launch future due to the size of the globals 4.98 GiB exceeds 2.93 GiB

[danli349]

Hello,

Thanks a lot for this great tool! How can I resolve the error when I run the following code?

cellchat <- subsetData(cellchat) # This step is necessary even if using the whole database
future::plan("multisession", workers = 12) # do parallel
cellchat <- identifyOverExpressedGenes(cellchat)
cellchat <- identifyOverExpressedInteractions(cellchat)

execution.time = Sys.time() - ptm
print(as.numeric(execution.time, units = "secs"))

Error: Will not launch future due to the size of the globals 4.98 GiB exceeds 2.93 GiB. The total size of the 9 globals exported for future expression ('{; "# future::getGlobalsAndPackages(): wrapping the original future"; "# expression in do.call(), because function called uses '...'  "; "# as a global variable                                         "; do.call(function(...) {; "# future::getGlobalsAndPackages(): FUN() uses '...' internally "; ...; }; }, args = future.call.arguments); }') is 2.49 GiB The three largest globals are '...future.FUN' (2.49 GiB of class 'function'), 'complexSubunits' (23.57 KiB of class 'list') and 'features.sig' (12.55 KiB of class 'character')
Traceback:

1. unlist(x = my.sapply(X = 1:nrow(complexSubunits), FUN = function(x) {
 .     complexsubunitsV <- unlist(complexSubunits[x, ], use.names = F)
 .     complexsubunitsV <- complexsubunitsV[complexsubunitsV != 
 .         ""]
 .     if (length(intersect(complexsubunitsV, features.sig)) > 0 & 
 .         all(complexsubunitsV %in% gene.use)) {
 .         return(x)
 .     }
 . }))
2. my.sapply(X = 1:nrow(complexSubunits), FUN = function(x) {
 .     complexsubunitsV <- unlist(complexSubunits[x, ], use.names = F)
 .     complexsubunitsV <- complexsubunitsV[complexsubunitsV != 
 .         ""]
 .     if (length(intersect(complexsubunitsV, features.sig)) > 0 & 
 .         all(complexsubunitsV %in% gene.use)) {
 .         return(x)
 .     }
 . })
3. future_lapply(X = X, FUN = FUN, ..., future.envir = future.envir, 
 .     future.label = future.label)
4. future_xapply(FUN = FUN, nX = nX, chunk_args = X, args = list(...), 
 .     get_chunk = `chunkWith[[`, expr = expr, envir = envir, future.envir = future.envir, 
 .     future.globals = future.globals, future.packages = future.packages, 
 .     future.scheduling = future.scheduling, future.chunk.size = future.chunk.size, 
 .     future.stdout = future.stdout, future.conditions = future.conditions, 
 .     future.seed = future.seed, future.label = future.label, fcn_name = fcn_name, 
 .     args_name = args_name, debug = debug)
5. future(expr, substitute = FALSE, envir = future.envir, stdout = future.stdout, 
 .     conditions = future.conditions, globals = globals_ii, packages = packages_ii, 
 .     seed = future.seed, label = labels[ii])
6. run(future)
7. run.Future(future)
8. validateFutureGlobals(backend, future)
9. validateFutureGlobals.FutureBackend(backend, future)
10. stop(FutureError(msg, future = future))

[Bejsernia]

options(future.globals.maxSize = 50 * 1024 * 1024 * 1024)

@danli349 run this command may help