Fastcluster

Significant faster clustering algorithm for R and python.
http://math.stanford.edu/~muellner/fastcluster.html#2

Quick test on RStudio.swmed.edu:

system.time(pheatmap(test,color=hmcols,cluster_rows=TRUE,cluster_cols=FALSE,legend=FALSE,show_rownames=FALSE,show_colnames=FALSE,clustering_method="complete",clustering_distance_rows="correlation"))

238.219 seconds

library("fastcluster")

system.time(pheatmap(test,color=hmcols,cluster_rows=TRUE,cluster_cols=FALSE,legend=FALSE,show_rownames=FALSE,show_colnames=FALSE,clustering_method="complete",clustering_distance_rows="correlation"))

28.176 seconds