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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data NeuCA
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* checking for file ‘NeuCA/DESCRIPTION’ ... OK
* preparing ‘NeuCA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘NeuCA.Rmd’ using rmarkdown
2025-04-21 17:45:21.276961: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
/Users/biocbuild/.virtualenvs/r-keras/lib/python3.9/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(
/Users/biocbuild/.virtualenvs/r-keras/lib/python3.9/site-packages/keras/src/layers/core/dense.py:87: UserWarning: Do not pass an `input_shape`/`input_dim` argument to a layer. When using Sequential models, prefer using an `Input(shape)` object as the first layer in the model instead.
  super().__init__(activity_regularizer=activity_regularizer, **kwargs)

Quitting from NeuCA.Rmd:75-80 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_call_impl()`:
! ValueError: Only input tensors may be passed as positional arguments. The following argument value should be passed as a keyword argument: <Sequential name=sequential, built=False> (of type <class 'keras.src.models.sequential.Sequential'>)
Run `reticulate::py_last_error()` for details.
---
Backtrace:
     ▆
  1. ├─NeuCA::NeuCA(...)
  2. │ └─NeuCA:::BigNN(...)
  3. │   └─... %>% ...
  4. ├─generics::compile(...)
  5. ├─keras::layer_dense(., units = nClass, activation = last_act)
  6. │ └─keras::create_layer(...)
  7. ├─keras::layer_dense(., units = 64, activation = "relu")
  8. │ └─keras::create_layer(...)
  9. ├─keras::layer_dense(., units = 128, activation = "relu")
 10. │ └─keras::create_layer(...)
 11. └─keras::layer_dense(., units = 256, activation = "relu", input_shape = ncol(train_count))
 12.   └─keras::create_layer(...)
 13.     ├─keras:::compose_layer(object, layer)
 14.     └─keras:::compose_layer.default(object, layer)
 15.       └─reticulate (local) layer(object, ...)
 16.         └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'NeuCA.Rmd' failed with diagnostics:
ValueError: Only input tensors may be passed as positional arguments. The following argument value should be passed as a keyword argument: <Sequential name=sequential, built=False> (of type <class 'keras.src.models.sequential.Sequential'>)
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘NeuCA.Rmd’

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

Error: Vignette re-building failed.
Execution halted