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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:VAExprs.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings VAExprs_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/VAExprs.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 ‘VAExprs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VAExprs’ version ‘1.5.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘VAExprs’ 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
  ‘original_dim’
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’
Undefined global functions or variables:
  original_dim 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
fit_vae   10.513  1.584  15.851
plot_aug   7.895  0.137   8.008
gen_exprs  7.399  0.037   7.293
* 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 ...
  ‘VAExprs.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘VAExprs.Rmd’ using rmarkdown
/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}")
Train on 300 samples, validate on 300 samples
Epoch 1/100
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 18:42:24.762728: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:357] MLIR V1 optimization pass is not enabled
2023-02-07 18:42:24.820531: W tensorflow/c/c_api.cc:291] Operation '{name:'training/Adam/z_mean/bias/v/Assign' id:540 op device:{requested: '', assigned: ''} def:{{{node training/Adam/z_mean/bias/v/Assign}} = AssignVariableOp[_has_manual_control_dependencies=true, dtype=DT_FLOAT, validate_shape=false](training/Adam/z_mean/bias/v, training/Adam/z_mean/bias/v/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.
/usr/local/lib/python3.10/dist-packages/keras/engine/training_v1.py:2333: 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
2023-02-07 18:42:25.268500: W tensorflow/c/c_api.cc:291] Operation '{name:'loss/mul' id:210 op device:{requested: '', assigned: ''} def:{{{node loss/mul}} = Mul[T=DT_FLOAT, _has_manual_control_dependencies=true](loss/mul/x, loss/dense_2_loss/value)}}' 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.
Epoch 2/100
Epoch 3/100
Epoch 4/100
Epoch 5/100
Epoch 6/100
Epoch 7/100
Epoch 8/100
Epoch 9/100
Epoch 10/100
Epoch 11/100
Epoch 12/100
Epoch 13/100
Epoch 14/100
Epoch 15/100
Epoch 16/100
Epoch 17/100
Epoch 18/100
Epoch 19/100
Epoch 20/100
Epoch 21/100
Epoch 22/100
Epoch 23/100
Epoch 24/100
Epoch 25/100
Epoch 26/100
Epoch 27/100
Epoch 28/100
Epoch 29/100
Epoch 30/100
Epoch 31/100
Epoch 32/100
Epoch 33/100
Epoch 34/100
Epoch 35/100
Epoch 36/100
Epoch 37/100
Epoch 38/100
Epoch 39/100
Epoch 40/100
Epoch 41/100
Epoch 42/100
Epoch 43/100
Epoch 44/100
/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,
2023-02-07 18:42:35.841361: W tensorflow/c/c_api.cc:291] Operation '{name:'z_mean/BiasAdd' id:49 op device:{requested: '', assigned: ''} def:{{{node z_mean/BiasAdd}} = BiasAdd[T=DT_FLOAT, _has_manual_control_dependencies=true, data_format="NHWC"](z_mean/MatMul, z_mean/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.
2023-02-07 18:42:37.401250: W tensorflow/c/c_api.cc:291] Operation '{name:'dense_2_1/Sigmoid' id:147 op device:{requested: '', assigned: ''} def:{{{node dense_2_1/Sigmoid}} = Sigmoid[T=DT_FLOAT, _has_manual_control_dependencies=true](dense_2_1/BiasAdd)}}' 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.
Killed

* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL VAExprs
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘VAExprs’ ...
** using staged installation
** R
** 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 (VAExprs)

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(VAExprs)
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("VAExprs")
/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 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 21.835   1.432  24.821