qpBayes cannot load the package adaptivetau

[DONG-Wenjie]

Hello, I encountered the following error when running qpBayes. I installed qpBrute in a virtual environment using conda, following the steps provided on this GitHub page. The software seems to indicate that the R package adaptivetau cannot be loaded, but the package is already installed in the environment. Has anyone experienced the same error? What is the problem with it and how could I fix it?

The error messages are as follows: " multiprocess.pool.RemoteTraceback: """ Traceback (most recent call last): File "/gpfs/home/dongwj/anaconda3/envs/qpbrute/lib/python3.8/site-packages/multiprocess/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/gpfs/home/dongwj/anaconda3/envs/qpbrute/lib/python3.8/site-packages/multiprocess/pool.py", line 48, in mapstar return list(map(args)) File "/gpfs/home/dongwj/anaconda3/envs/qpbrute/lib/python3.8/site-packages/pathos/helpers/mp_helper.py", line 15, in func = lambda args: f(*args) File "/gpfs/home/dongwj/anaconda3/envs/qpbrute/lib/python3.8/site-packages/qpbrute/qpbayes.py", line 212, in model_likelihood run_cmd( File "/gpfs/home/dongwj/anaconda3/envs/qpbrute/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 /gpfs/home/dongwj/anaconda3/envs/qpbrute/lib/python3.8/site-packages/qpbrute/rscript/model_likelihood.R qpbrute_sim4pop_1 5e30802d1fde qpbrute_sim4pop_1/dstats/qpbrute_sim4pop_1.csv 2 5 2000000 1100000 """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/gpfs/home/dongwj/anaconda3/envs/qpbrute/bin/qpBayes", line 8, in sys.exit(qpbayes()) File "/gpfs/home/dongwj/anaconda3/envs/qpbrute/lib/python3.8/site-packages/qpbrute/qpbayes.py", line 372, in qpbayes calculate_bayes_factors( File "/gpfs/home/dongwj/anaconda3/envs/qpbrute/lib/python3.8/site-packages/qpbrute/qpbayes.py", line 291, in calculate_bayes_factors qpb.calculate_bayes_factors() File "/gpfs/home/dongwj/anaconda3/envs/qpbrute/lib/python3.8/site-packages/qpbrute/qpbayes.py", line 196, in calculate_bayes_factors pool.map(self.model_likelihood, self.graphs) File "/gpfs/home/dongwj/anaconda3/envs/qpbrute/lib/python3.8/site-packages/pathos/multiprocessing.py", line 137, in map return _pool.map(star(f), zip(*args)) # chunksize File "/gpfs/home/dongwj/anaconda3/envs/qpbrute/lib/python3.8/site-packages/multiprocess/pool.py", line 364, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/gpfs/home/dongwj/anaconda3/envs/qpbrute/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 /gpfs/home/dongwj/anaconda3/envs/qpbrute/lib/python3.8/site-packages/qpbrute/rscript/model_likelihood.R qpbrute_sim4pop_1 5e30802d1fde qpbrute_sim4pop_1/dstats/qpbrute_sim4pop_1.csv 2 5 2000000 1100000 “

Thanks a lot!!

Dong

[ekirving]

Hi Dong,

Try activating your conda environment and manually reinstalling the adaptivetau R package.

Cheers, Evan

[DONG-Wenjie]

Hi Dong,

Try activating your conda environment and manually reinstalling the adaptivetau R package.

Cheers, Evan

Great! The program seems to work fine after I manually installed a newer version of adaptivetau package. Thank you very much!!