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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenProSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings GenProSeq_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenProSeq.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GenProSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenProSeq’ version ‘1.3.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenProSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fit_VAE: no visible binding for global variable ‘z_mean’
fit_VAE: no visible binding for global variable ‘z_log_stddev’
fit_VAE : vae_loss: no visible binding for global variable
  ‘z_log_stddev’
fit_VAE : vae_loss: no visible binding for global variable ‘z_mean’
layer_embedding_token_position : <anonymous>: no visible global
  function definition for ‘super’
layer_embedding_token_position : <anonymous>: no visible binding for
  global variable ‘self’
layer_transformer_encoder : <anonymous>: no visible global function
  definition for ‘super’
layer_transformer_encoder : <anonymous>: no visible binding for global
  variable ‘self’
Undefined global functions or variables:
  self super z_log_stddev z_mean
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GenProSeq-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VAE
> ### Title: Variational autoencoder for generating protein sequences
> ### Aliases: fit_VAE gen_VAE
> 
> ### ** Examples
> 
> if (keras::is_keras_available() & reticulate::py_available()) {
+     data("example_luxA")
+     label <- substr(example_luxA, 3, 3)
+     
+     # model parameters
+     length_seq <- 360
+     embedding_dim <- 8
+     batch_size <- 128
+     epochs <- 2
+     
+     # CVAE
+     VAE_result <- fit_VAE(prot_seq = example_luxA,
+                         label = label,
+                         length_seq = length_seq,
+                         embedding_dim = embedding_dim,
+                         embedding_args = list(iter = 20),
+                         intermediate_encoder_layers = list(layer_dense(units = 128),
+                                                             layer_dense(units = 16)),
+                         intermediate_decoder_layers = list(layer_dense(units = 16),
+                                                             layer_dense(units = 128)),
+                         prot_seq_val = example_luxA,
+                         label_val = label,
+                         epochs = epochs,
+                         batch_size = batch_size,
+                         use_generator = FALSE,
+                         optimizer = keras::optimizer_adam(clipnorm = 0.1),
+                         callbacks = keras::callback_early_stopping(
+                             monitor = "val_loss",
+                             patience = 10,
+                             restore_best_weights = TRUE))
+     gen_prot_VAE_I <- gen_VAE(VAE_result, label = rep("I", 100), num_seq = 100)
+     gen_prot_VAE_L <- gen_VAE(VAE_result, label = rep("L", 100), num_seq = 100)
+     
+     
+     ### from preprocessing
+     VAE_result2 <- fit_VAE(intermediate_encoder_layers = list(layer_dense(units = 128),
+                                                             layer_dense(units = 16)),
+                             intermediate_decoder_layers = list(layer_dense(units = 16),
+                                                             layer_dense(units = 128)),
+                             epochs = epochs, batch_size = batch_size,
+                             preprocessing = VAE_result$preprocessing,
+                             use_generator = FALSE,
+                             optimizer = keras::optimizer_adam(clipnorm = 0.1),
+                             callbacks = keras::callback_early_stopping(
+                                 monitor = "val_loss",
+                                 patience = 10,
+                                 restore_best_weights = TRUE))
+     gen_prot_VAE2_I <- gen_VAE(VAE_result2, label = rep("I", 100), num_seq = 100)
+     gen_prot_VAE2_L <- gen_VAE(VAE_result2, label = rep("L", 100), num_seq = 100)
+ }
pre-processing...
training...
In training : Error: AttributeError: 'Adam' object has no attribute 'get_updates'


/usr/local/lib/python3.10/dist-packages/keras/engine/training_v1.py:2357: UserWarning: `Model.state_updates` will be removed in a future version. This property should not be used in TensorFlow 2.0, as `updates` are applied automatically.
  updates=self.state_updates,
WARNING:tensorflow:OMP_NUM_THREADS is no longer used by the default Keras config. To configure the number of threads, use tf.config.threading APIs.
2023-02-07 02:42:05.840527: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:357] MLIR V1 optimization pass is not enabled
2023-02-07 02:42:05.864829: W tensorflow/c/c_api.cc:291] Operation '{name:'dense_50/bias/Assign' id:179 op device:{requested: '', assigned: ''} def:{{{node dense_50/bias/Assign}} = AssignVariableOp[_has_manual_control_dependencies=true, dtype=DT_FLOAT, validate_shape=false](dense_50/bias, dense_50/bias/Initializer/zeros)}}' was changed by setting attribute after it was run by a session. This mutation will have no effect, and will trigger an error in the future. Either don't modify nodes after running them or create a new session.
generating...
2023-02-07 02:42:15.219506: W tensorflow/c/c_api.cc:291] Operation '{name:'dense_50_1/BiasAdd' id:197 op device:{requested: '', assigned: ''} def:{{{node dense_50_1/BiasAdd}} = BiasAdd[T=DT_FLOAT, _has_manual_control_dependencies=true, data_format="NHWC"](dense_50_1/MatMul, dense_50_1/BiasAdd/ReadVariableOp)}}' was changed by setting attribute after it was run by a session. This mutation will have no effect, and will trigger an error in the future. Either don't modify nodes after running them or create a new session.
post-processing...
generating...
post-processing...
training...
In training : Error: AttributeError: 'Adam' object has no attribute 'get_updates'


2023-02-07 02:42:36.556905: W tensorflow/c/c_api.cc:291] Operation '{name:'dense_54/bias/Assign' id:432 op device:{requested: '', assigned: ''} def:{{{node dense_54/bias/Assign}} = AssignVariableOp[_has_manual_control_dependencies=true, dtype=DT_FLOAT, validate_shape=false](dense_54/bias, dense_54/bias/Initializer/zeros)}}' was changed by setting attribute after it was run by a session. This mutation will have no effect, and will trigger an error in the future. Either don't modify nodes after running them or create a new session.
generating...
2023-02-07 02:42:45.916929: W tensorflow/c/c_api.cc:291] Operation '{name:'dense_55_1/BiasAdd' id:475 op device:{requested: '', assigned: ''} def:{{{node dense_55_1/BiasAdd}} = BiasAdd[T=DT_FLOAT, _has_manual_control_dependencies=true, data_format="NHWC"](dense_55_1/MatMul, dense_55_1/BiasAdd/ReadVariableOp)}}' was changed by setting attribute after it was run by a session. This mutation will have no effect, and will trigger an error in the future. Either don't modify nodes after running them or create a new session.
post-processing...
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GenProSeq.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/GenProSeq.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenProSeq
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘GenProSeq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenProSeq)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(GenProSeq)
Loading required package: keras
Loading required package: mclust
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.
> 
> test_check("GenProSeq")
/usr/local/lib/python3.10/dist-packages/tensorflow_io/python/ops/__init__.py:98: UserWarning: unable to load libtensorflow_io_plugins.so: unable to open file: libtensorflow_io_plugins.so, from paths: ['/usr/local/lib/python3.10/dist-packages/tensorflow_io/python/ops/libtensorflow_io_plugins.so']
caused by: ["[Errno 2] The file to load file system plugin from does not exist.: '/usr/local/lib/python3.10/dist-packages/tensorflow_io/python/ops/libtensorflow_io_plugins.so'"]
  warnings.warn(f"unable to load libtensorflow_io_plugins.so: {e}")
/usr/local/lib/python3.10/dist-packages/tensorflow_io/python/ops/__init__.py:104: UserWarning: file system plugins are not loaded: unable to open file: libtensorflow_io.so, from paths: ['/usr/local/lib/python3.10/dist-packages/tensorflow_io/python/ops/libtensorflow_io.so']
caused by: ['/usr/local/lib/python3.10/dist-packages/tensorflow_io/python/ops/libtensorflow_io.so: cannot open shared object file: No such file or directory']
  warnings.warn(f"file system plugins are not loaded: {e}")
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 26 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
  9.922   1.150  15.078