MOFA2
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20 hours ago •
bioFAM
bioFAM
Error in py_call_impl(callable, dots$args, dots$keywords): AttributeError: Module 'scipy' has no attribute 'random'
I have installed a conda env with mofapy.
> reticulate::py_config()
python: /home/roy/miniconda3/envs/mofa/bin/python
libpython: /home/roy/miniconda3/envs/mofa/lib/libpython3.10.so
pythonhome: /home/roy/miniconda3/envs/mofa:/home/roy/miniconda3/envs/mofa
version: 3.10.6 (main, Oct 24 2022, 16:07:47) [GCC 11.2.0]
numpy: /home/roy/miniconda3/envs/mofa/lib/python3.10/site-packages/numpy
numpy_version: 1.23.4
mofapy2: /home/roy/miniconda3/envs/mofa/lib/python3.10/site-packages/mofapy2
But, I can't get run_mofa to work.
run_mofa(mo,outfile,use_basilisk=FALSE)
Connecting to the mofapy2 python package using reticulate (use_basilisk = FALSE)...
Please make sure to manually specify the right python binary when loading R with reticulate::use_python(..., force=TRUE) or the right conda environment with reticulate::use_condaenv(..., force=TRUE)
If you prefer to let us automatically install a conda environment with 'mofapy2' installed using the 'basilisk' package, please use the argument 'use_basilisk = TRUE'
Warning: The latest mofapy2 version is 0.6.4, you are using 0.6.7. Please upgrade with 'pip install mofapy2'Warning: mofapy2_0.6.4 is not detected in the specified python binary, see reticulate::py_config(). Setting use_basilisk = TRUE...Connecting to the mofapy2 package using basilisk.
Then , I reinstalled mofapy to an older version: 0.6.4. This worked a little bit more and crashed at this error:
Connecting to the mofapy2 python package using reticulate (use_basilisk = FALSE)...
Please make sure to manually specify the right python binary when loading R with reticulate::use_python(..., force=TRUE) or the right conda environment with reticulate::use_condaenv(..., force=TRUE)
If you prefer to let us automatically install a conda environment with 'mofapy2' installed using the 'basilisk' package, please use the argument 'use_basilisk = TRUE'
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#########################################################
Successfully loaded view='view_1' group='group1' with N=200 samples and D=1000 features...
Successfully loaded view='view_2' group='group1' with N=200 samples and D=1000 features...
Model options:
- Automatic Relevance Determination prior on the factors: False
- Automatic Relevance Determination prior on the weights: True
- Spike-and-slab prior on the factors: False
- Spike-and-slab prior on the weights: True
Likelihoods:
- View 0 (view_1): gaussian
- View 1 (view_2): gaussian
Error in py_call_impl(callable, dots$args, dots$keywords) :
AttributeError: Module 'scipy' has no attribute 'random'
Here is a complete reprex:
library(MOFA2)
#>
#> Attaching package: 'MOFA2'
#> The following object is masked from 'package:stats':
#>
#> predict
reticulate::use_condaenv("mofa")
data <- make_example_data(
n_views = 2,
n_samples = 200,
n_features = 1000,
n_factors = 10
)[[1]]
m <- create_mofa(data)
#> Creating MOFA object from a list of matrices (features as rows, sample as columns)...
data_opts <- get_default_data_options(m)
model_opts <- get_default_model_options(m)
train_opts <- get_default_training_options(m)
mo <- prepare_mofa(
object = m,
data_options = data_opts,
model_options = model_opts,
training_options = train_opts
)
#> Checking data options...
#> Checking training options...
#> Checking model options...
outfile <- file.path(getwd(),"mofa.hdf5")
mot <- run_mofa(mo,outfile,use_basilisk=FALSE)
#> Connecting to the mofapy2 python package using reticulate (use_basilisk = FALSE)...
#> Please make sure to manually specify the right python binary when loading R with reticulate::use_python(..., force=TRUE) or the right conda environment with reticulate::use_condaenv(..., force=TRUE)
#> If you prefer to let us automatically install a conda environment with 'mofapy2' installed using the 'basilisk' package, please use the argument 'use_basilisk = TRUE'
#> Error in py_call_impl(callable, dots$args, dots$keywords): AttributeError: Module 'scipy' has no attribute 'random'
Created on 2022-10-26 with reprex v2.0.2
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
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#> collate en_GB.UTF-8
#> ctype en_GB.UTF-8
#> date 2022-10-26
#> pandoc 2.18 @ /usr/lib/rstudio/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
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#>
#> [1] /home/roy/miniconda3/envs/r-4.1/lib/R/library
#>
#> ─ Python configuration ───────────────────────────────────────────────────────
#> python: /home/roy/miniconda3/envs/mofa/bin/python
#> libpython: /home/roy/miniconda3/envs/mofa/lib/libpython3.10.so
#> pythonhome: /home/roy/miniconda3/envs/mofa:/home/roy/miniconda3/envs/mofa
#> version: 3.10.6 (main, Oct 24 2022, 16:07:47) [GCC 11.2.0]
#> numpy: /home/roy/miniconda3/envs/mofa/lib/python3.10/site-packages/numpy
#> numpy_version: 1.23.4
#> mofapy2: /home/roy/miniconda3/envs/mofa/lib/python3.10/site-packages/mofapy2
#>
#> NOTE: Python version was forced by use_python function
#>
#> ──────────────────────────────────────────────────────────────────────────────
