script.R' returned non-zero exit status 127.

[cornhundred]

Hi, I'm getting an error in the MERFISH_POA.ipynb notebook on the cell

# this requires local R installation with packages 'sctransform' and 'feather'
analysis.normalize_vectors_sctransform()

the error is below:

---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
<ipython-input-21-757813b83b14> in <module>
      1 # this requires local R installation with packages 'sctransform' and 'feather'
----> 2 analysis.normalize_vectors_sctransform()

~/anaconda3/envs/merlin_env/lib/python3.6/site-packages/ssam/__init__.py in normalize_vectors_sctransform(self, use_expanded_vectors, normalize_vf)
    717             vec = np.array(self.dataset.vf[self.dataset.local_maxs], copy=True)
    718 
--> 719         norm_vec, fit_params = run_sctransform(vec)
    720         self.dataset.normalized_vectors = np.array(norm_vec)
    721 

~/anaconda3/envs/merlin_env/lib/python3.6/site-packages/ssam/__init__.py in run_sctransform(data, **kwargs)
     96         with open(rfn, "w") as f:
     97             f.write(rcmd)
---> 98         subprocess.check_output("Rscript " + rfn, shell=True)
     99         return pd.read_feather(ofn), pd.read_feather(pfn)
    100 

~/anaconda3/envs/merlin_env/lib/python3.6/subprocess.py in check_output(timeout, *popenargs, **kwargs)
    354 
    355     return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
--> 356                **kwargs).stdout
    357 
    358 

~/anaconda3/envs/merlin_env/lib/python3.6/subprocess.py in run(input, timeout, check, *popenargs, **kwargs)
    436         if check and retcode:
    437             raise CalledProcessError(retcode, process.args,
--> 438                                      output=stdout, stderr=stderr)
    439     return CompletedProcess(process.args, retcode, stdout, stderr)
    440 

CalledProcessError: Command 'Rscript /tmp/tmpb04epu5o/script.R' returned non-zero exit status 127.

I installed the R dependencies

install.packages("feather")
install.packages("sctransform")

[pjb7687]

Hi, may I ask you try loading the libraries in R? I think one of the libraries are not properly installed.