Error in py_module_import (sctansfer)

[Dhonveli]

Hello, I am running SAVERX with R 3.6.2. and python 3.6.10 in a conda environment. I got this error even if sctransfer (0.0.9) is present in the environment:

[1] "Input file is: ~/concatSingleCell_doubleQC.csv"
[1] "Use a pretrained model: Yes"
[1] "Data species is: Human"
[1] "Pretrained weights file is: ~/Downloads/human_Devbrain_nomanno.hdf5"
[1] "Model species is: Human"
[1] "53043 genes mapped out of 63677"
[1] "Gene names mapped, resulting file saved as: 1586351812.23148/tmpdata.rds"
[1] "Reshaped file saved as: 1586351812.23148/tmpdata.mtx"
[1] "Nonmissing indicator saved as: 1586351812.23148/tmpdata_nonmissing.txt"
[1] "Data preprocessed ..."
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'sctransfer'

The list of packages in the environment is this one:
packages in environment at /Users/chaaya/miniconda/envs/saverx:

Name Version Build Channel
absl-py 0.9.0 pypi_0 pypi
anndata 0.7.1 pypi_0 pypi
astor 0.8.1 pypi_0 pypi
ca-certificates 2020.1.1 0 anaconda
cachetools 4.1.0 pypi_0 pypi
certifi 2020.4.5.1 py36_0 anaconda
chardet 3.0.4 pypi_0 pypi
cycler 0.10.0 pypi_0 pypi
decorator 4.4.2 pypi_0 pypi
gast 0.2.2 pypi_0 pypi
get-version 2.1 pypi_0 pypi
google-auth 1.13.1 pypi_0 pypi
google-auth-oauthlib 0.4.1 pypi_0 pypi
google-pasta 0.2.0 pypi_0 pypi
grpcio 1.28.1 pypi_0 pypi
h5py 2.10.0 pypi_0 pypi
idna 2.9 pypi_0 pypi
importlib-metadata 1.6.0 pypi_0 pypi
joblib 0.14.1 pypi_0 pypi
keras 2.3.1 pypi_0 pypi
keras-applications 1.0.8 pypi_0 pypi
keras-preprocessing 1.1.0 pypi_0 pypi
kiwisolver 1.2.0 pypi_0 pypi
legacy-api-wrap 1.2 pypi_0 pypi
libcxx 4.0.1 hcfea43d_1
libcxxabi 4.0.1 hcfea43d_1
libedit 3.1.20181209 hb402a30_0
libffi 3.2.1 h475c297_4
llvmlite 0.31.0 pypi_0 pypi
markdown 3.2.1 pypi_0 pypi
matplotlib 3.2.1 pypi_0 pypi
natsort 7.0.1 pypi_0 pypi
ncurses 6.2 h0a44026_0
networkx 2.4 pypi_0 pypi
numba 0.48.0 pypi_0 pypi
numexpr 2.7.1 pypi_0 pypi
numpy 1.18.2 pypi_0 pypi
oauthlib 3.1.0 pypi_0 pypi
openssl 1.1.1 h1de35cc_0 anaconda
opt-einsum 3.2.0 pypi_0 pypi
packaging 20.3 pypi_0 pypi
pandas 1.0.3 pypi_0 pypi
patsy 0.5.1 pypi_0 pypi
pip 20.0.2 py36_1 anaconda
protobuf 3.11.3 pypi_0 pypi
pyasn1 0.4.8 pypi_0 pypi
pyasn1-modules 0.2.8 pypi_0 pypi
pyparsing 2.4.7 pypi_0 pypi
python 3.6.10 hc70fcce_1
python-dateutil 2.8.1 pypi_0 pypi
pytz 2019.3 pypi_0 pypi
pyyaml 5.3.1 pypi_0 pypi
readline 8.0 h1de35cc_0
requests 2.23.0 pypi_0 pypi
requests-oauthlib 1.3.0 pypi_0 pypi
rsa 4.0 pypi_0 pypi
scanpy 1.4.6 pypi_0 pypi
scikit-learn 0.22.2.post1 pypi_0 pypi
scipy 1.4.1 pypi_0 pypi
sctransfer 0.0.9 pypi_0 pypi
seaborn 0.10.0 pypi_0 pypi
setuptools 46.1.3 py36_0
setuptools-scm 3.5.0 pypi_0 pypi
six 1.14.0 pypi_0 pypi
sqlite 3.31.1 ha441bb4_0
statsmodels 0.11.1 pypi_0 pypi
tables 3.6.1 pypi_0 pypi
tbb 2019.0 pypi_0 pypi
tensorboard 2.1.1 pypi_0 pypi
tensorflow 2.1.0 pypi_0 pypi
tensorflow-estimator 2.1.0 pypi_0 pypi
termcolor 1.1.0 pypi_0 pypi
tk 8.6.8 ha441bb4_0
tqdm 4.45.0 pypi_0 pypi
umap-learn 0.4.0 pypi_0 pypi
urllib3 1.25.8 pypi_0 pypi
werkzeug 1.0.1 pypi_0 pypi
wheel 0.34.2 py36_0
wrapt 1.12.1 pypi_0 pypi
xz 5.2.4 h1de35cc_4
zipp 3.1.0 pypi_0 pypi
zlib 1.2.11 h1de35cc_3

Am I doing something not correct and is it fixable? Thank you in advance!

Giordano

[ayoublasri]

Hi, I had similar issue, solved running

library(reticulate)
path_to_python <- "/anaconda/bin/python"
use_python(path_to_python)