ekirving
commented
3 years ago Hi Kritika,
Sorry to hear that you've had some installation troubles with qpBrute
I've seen this error before, and it indicates that the R package dependencies were not properly installed (this happens sometimes with conda installations and I have yet to discover the cause).
The solution is to manually re-install the problematic package:
# activate your conda environment
conda activate qpbrute
# open an R session
R
# reinstall the package that will not load
install.packages("adaptivetau")Then try running qpBayes again.
Cheers, Evan
Hi Ervin
I have installed qpbrute using conda. I am able to run the first step, however, I get the following error when I run the qpBayes script. I am not sure which R package maybe an issue here.
Thank you very much.
Best regards Kritika
INFO: There are 98 graphs to compute Bayes factors for. multiprocess.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/balaji/anaconda3/envs/qpbrute_new/lib/python3.8/site-packages/multiprocess/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/home/balaji/anaconda3/envs/qpbrute_new/lib/python3.8/site-packages/multiprocess/pool.py", line 48, in mapstar return list(map(args)) File "/home/balaji/anaconda3/envs/qpbrute_new/lib/python3.8/site-packages/pathos/helpers/mp_helper.py", line 15, in
func = lambda args: f(*args)
File "/home/balaji/anaconda3/envs/qpbrute_new/lib/python3.8/site-packages/qpbrute/qpbayes.py", line 212, in model_likelihood
run_cmd(
File "/home/balaji/anaconda3/envs/qpbrute_new/lib/python3.8/site-packages/qpbrute/utils.py", line 67, in run_cmd
raise RuntimeError(f"ERROR: '{err}'; RETCODE:{proc.returncode}\n" + " ".join(cmd))
RuntimeError: ERROR: 'b'Error: package \xe2\x80\x98adaptivetau\xe2\x80\x99 could not be loaded\nExecution halted\n''; RETCODE:1
Rscript /home/balaji/anaconda3/envs/qpbrute_new/lib/python3.8/site-packages/qpbrute/rscript/model_likelihood.R internal_subset_3 fb088b7e76d6 internal_subset_3/dstats/internal_subset_3.csv 2 5 2000000 1100000
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/balaji/anaconda3/envs/qpbrute_new/bin/qpBayes", line 8, in
sys.exit(qpbayes())
File "/home/balaji/anaconda3/envs/qpbrute_new/lib/python3.8/site-packages/qpbrute/qpbayes.py", line 372, in qpbayes
calculate_bayes_factors(
File "/home/balaji/anaconda3/envs/qpbrute_new/lib/python3.8/site-packages/qpbrute/qpbayes.py", line 291, in calculate_bayes_factors
qpb.calculate_bayes_factors()
File "/home/balaji/anaconda3/envs/qpbrute_new/lib/python3.8/site-packages/qpbrute/qpbayes.py", line 196, in calculate_bayes_factors
pool.map(self.model_likelihood, self.graphs)
File "/home/balaji/anaconda3/envs/qpbrute_new/lib/python3.8/site-packages/pathos/multiprocessing.py", line 137, in map
return _pool.map(star(f), zip(*args)) # chunksize
File "/home/balaji/anaconda3/envs/qpbrute_new/lib/python3.8/site-packages/multiprocess/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/balaji/anaconda3/envs/qpbrute_new/lib/python3.8/site-packages/multiprocess/pool.py", line 771, in get
raise self._value
RuntimeError: ERROR: 'b'Error: package \xe2\x80\x98adaptivetau\xe2\x80\x99 could not be loaded\nExecution halted\n''; RETCODE:1
Rscript /home/balaji/anaconda3/envs/qpbrute_new/lib/python3.8/site-packages/qpbrute/rscript/model_likelihood.R internal_subset_3 fb088b7e76d6 internal_subset_3/dstats/internal_subset_3.csv 2 5 2000000 1100000