I'm not understanding how to do indirect subscripting in %dopar% or in llply( .parallel = TRUE). My actual use-case is a list of formulas, then generating a list of glmer results in a first foreach %dopar%, then calling PBmodcomp on specific pairs of results in a separate foreach %dopar%. My toy example, using numeric indices rather than names of objects in the lists, works fine for %do% but not %dopar%, and fine for alply without .parallel = TRUE but not with .parallel = TRUE. [My real example with glmer and indexing lists by names rather than by integers works with %do% but not %dopar%.]
library(doParallel) library(foreach) library(plyr) cl <- makePSOCKcluster(2) # tiny for toy example registerDoParallel(cl) mB <- c(1,2,1,3,4,10) MO <- c("Full", "noYS", "noYZ", "noYSZS", "noS", "noZ", "noY", "justS", "justZ", "noSZ", "noYSZ") # Works testouts <- foreach(i = 1:length(mB)) %do% { # mB[i] MO[mB[i]] } testouts # all NA testouts2 <- foreach(i = 1:length(mB)) %dopar% { # mB[i] MO[mB[i]] } testouts2 # Works testouts3 <- alply(mB, 1, .fun = function(i) { MO[mB[i]]} ) testouts3 # fails "$ operator is invalid for atomic vectors" testouts4 <- alply(mB, 1, .fun = function(i) { MO[mB[i]]}, .parallel = TRUE, .paropts = list(.export=ls(.GlobalEnv))) testouts4 stopCluster(cl) I've tried various combinations of double brackets like MO[mB[[i]]], to no avail. mB[i] instead of MO[mB[i]] works in all 4 and returns a list of the numbers. I've tried .export(c("MO", "mB")) but just get the message that those objects are already exported.
I assume that there's something I misunderstand about evaluation of expressions like MO[mB[i]] in different environments, but there may be other things I misunderstand, too.
sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252
attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base
other attached packages: [1] plyr_1.8.4 doParallel_1.0.13 iterators_1.0.9 foreach_1.5.0
loaded via a namespace (and not attached): [1] compiler_3.5.1
tools_3.5.1 listenv_0.7.0 Rcpp_0.12.17 [5] codetools_0.2-15 digest_0.6.15 globals_0.12.1 future_1.8.1
[9] fortunes_1.5-5
