optim.pml not stopping iterating

[nemartins]

After updating to phangorn 2.5.3, a codon tree with ~30 nodes that previously converged quickly with optim.pml(model="codon1",optBf=T,optNni=T) now iterates forever, without any (visible) changes in the likelihood. I've tried to reduce the number of nodes, but the problem persists, and if I remove the topology optimization it converges quickly.

3 
optimize base frequencies:  -4171.912 --> -4171.912 
optimize rate matrix:  -4171.912 --> -4171.912 
optimize edge weights:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 
3 
optimize base frequencies:  -4171.912 --> -4171.912 
optimize rate matrix:  -4171.912 --> -4171.912 
optimize edge weights:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 
3 
optimize base frequencies:  -4171.912 --> -4171.912 
optimize rate matrix:  -4171.912 --> -4171.912 
optimize edge weights:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 
3 
optimize base frequencies:  -4171.912 --> -4171.912 
optimize rate matrix:  -4171.912 --> -4171.912 
optimize edge weights:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 
3 
optimize base frequencies:  -4171.912 --> -4171.912 
optimize rate matrix:  -4171.912 --> -4171.912 
optimize edge weights:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 
optimize topology:  -4171.912 --> -4171.912 

[KlausVigo]

Hi @nemartins,
can you send me your data set [email protected] ? Regards, Klaus