I am running k-means clustering in R on a dataset with 636,688 rows and 7 columns using the standard stats package: kmeans(dataset, centers = 100, nstart = 25
stats
kmeans(dataset, centers = 100, nstart = 25
Had the same problem, seems to have something to do with available memory.
Running Garbage Collection before the function worked for me:
gc()
or reference:
Increasing (or decreasing) the memory available to R processes