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Error: could not find function "graph.adjacency"
Execution halted

> source('~/Dropbox/Study/Spring17/RA/bmd/sims_run_methods.R', echo=TRUE)

> library(MASS)

> library(Matrix)

> library(lpbrim)

> source("bmd.R")

> source("formatBRIM.R")

> # Set desired list of sample sizes to try
> ns <- c(100, 500)

> saveDir <- "sims"

> # Set rho_knobs
> rho_knobs <- c(0, 1)

> # Do we do BRIM?
> doBRIM <- FALSE

> for (rcount in 1:length(rho_knobs)) {
+   
+   for (ncount in 1:length(ns)) {
+     
+     # make filename
+     fn <- paste0("rcount=", rcount, "_" .... [TRUNCATED] 
Beginning method.

doing test save
fn is sims/BMD_saves/1.RData 

#-----------------------------------------

loopCount 1 

length remainingX =  500 
length remainingY =  250 
OL_count =  0 
Dud_count =  0 
comm_starter =  653 (Y = 153) 
getting, checking initial sets
........chunk 1 
Initial set is size 12 (12, 0)

Error: object 'B_newy' not found