##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DeProViR
###
##############################################################################
##############################################################################


* checking for file ‘DeProViR/DESCRIPTION’ ... OK
* preparing ‘DeProViR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DeProViR_tutorial.Rmd’ using rmarkdown
/Users/biocbuild/Library/Python/3.9/lib/python/site-packages/urllib3/__init__.py:35: NotOpenSSLWarning: urllib3 v2 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with 'LibreSSL 2.8.3'. See: https://github.com/urllib3/urllib3/issues/3020
  warnings.warn(

Quitting from DeProViR_tutorial.Rmd:217-246 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_call_impl()`:
! ValueError: Unrecognized keyword arguments passed to Embedding: {'input_length': 1000, 'weights': [array([[ 0.      ,  0.      ,  0.      , ...,  0.      ,  0.      ,
         0.      ],
       [-0.45433 ,  1.0234  ,  0.024278, ..., -0.43769 ,  1.0169  ,
        -0.26706 ],
       [-0.27086 ,  0.044006, -0.02026 , ..., -0.4923  ,  0.63687 ,
         0.23642 ],
       ...,
       [-0.20314 ,  0.50467 , -0.25223 , ..., -0.34618 , -0.18627 ,
        -0.31606 ],
       [ 0.29492 ,  0.56874 , -0.20245 , ..., -0.16875 ,  0.51895 ,
        -0.50086 ],
       [-0.11752 ,  0.97272 , -0.29021 , ..., -0.50598 , -0.28476 ,
        -0.70045 ]])]}
Run `reticulate::py_last_error()` for details.
---
Backtrace:
     ▆
  1. ├─DeProViR::modelTraining(...)
  2. │ └─... %>% layer_dropout(rate = 0.3)
  3. ├─keras::layer_dropout(., rate = 0.3)
  4. │ └─keras::create_layer(...)
  5. ├─keras::bidirectional(., layer_lstm(units = layer_lstm))
  6. │ └─keras::create_layer(keras$layers$Bidirectional, object, args)
  7. ├─keras::layer_max_pooling_1d(., pool_size = pool_size)
  8. │ └─keras::create_layer(...)
  9. ├─keras::layer_conv_1d(...)
 10. │ └─keras::create_layer(keras$layers$Conv1D, object, args)
 11. ├─keras::layer_conv_1d(...)
 12. │ └─keras::create_layer(keras$layers$Conv1D, object, args)
 13. └─keras::layer_embedding(...)
 14.   └─keras::create_layer(keras$layers$Embedding, object, args)
 15.     ├─base::do.call(layer_class, args)
 16.     └─reticulate (local) `<python.builtin.type>`(...)
 17.       └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'DeProViR_tutorial.Rmd' failed with diagnostics:
ValueError: Unrecognized keyword arguments passed to Embedding: {'input_length': 1000, 'weights': [array([[ 0.      ,  0.      ,  0.      , ...,  0.      ,  0.      ,
         0.      ],
       [-0.45433 ,  1.0234  ,  0.024278, ..., -0.43769 ,  1.0169  ,
        -0.26706 ],
       [-0.27086 ,  0.044006, -0.02026 , ..., -0.4923  ,  0.63687 ,
         0.23642 ],
       ...,
       [-0.20314 ,  0.50467 , -0.25223 , ..., -0.34618 , -0.18627 ,
        -0.31606 ],
       [ 0.29492 ,  0.56874 , -0.20245 , ..., -0.16875 ,  0.51895 ,
        -0.50086 ],
       [-0.11752 ,  0.97272 , -0.29021 , ..., -0.50598 , -0.28476 ,
        -0.70045 ]])]}
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘DeProViR_tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘DeProViR_tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted