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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:GenProSeq.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings GenProSeq_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GenProSeq.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenProSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenProSeq’ version ‘1.6.0’
* 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 loading without being on the library search path ... 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...
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GenProSeq.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL GenProSeq
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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")
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 26 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
 11.203   1.071  15.938