ModuleNotFoundError: No module named 'tables' on 1.3.1
f6v opened this issue · comments
I'm running R
code to calculate the gene scores from ATAC data and running into the issue which already has been described: #61
Here's my code:
atac_counts = # A data frame with loci in rows and cells in columns
gene_scores <- ATACCalculateGenescore(atac_counts, organism = "GRCh38")
I get the following error:
Error in py_run_file_impl(file, local, convert) :
ModuleNotFoundError: No module named 'tables'
Detailed traceback:
File "<string>", line 10, in <module>
File "/kyukon/data/gent/vo/000/gvo00027/multimodal_omics_GRN/maestro_env/lib/R/library/reticulate/python/rpytools/loader.py", line 19, in _import_hook
module = _import(
Calls: ATACCalculateGenescore -> source_python -> py_run_file -> py_run_file_impl
I installed MAESTRO
through conda
. pytables 3.6.1
seems to be installed in the environment(if that's the package in question). Am I missing something?
Thanks!
Hi!
If you run
library(reticulate)
use_python("~/miniconda2/envs/MAESTRO_1.3.2/bin/python3.8",required = TRUE)
and try:
import("tables")
If the module loaded successfully, it should be fixed.
@baigal628 thanks! That works.
Hi Gali,
I tried reticulate to install miniconda in R, and run ATACCalculateGenescore function. However, error shows below:
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'tables'
I tried "import('tables') above, but error persists: ModuleNotFoundError: No module named 'tables'.
On Ubuntu, I solved this problem using this command:
sudo apt-get install python3-tables