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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:DeepPINCS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings DeepPINCS_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DeepPINCS.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 ‘DeepPINCS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeepPINCS’ version ‘1.7.0’
* 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 ‘DeepPINCS’ 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_cpi: no visible binding for global variable ‘compound’
fit_cpi: no visible binding for global variable ‘compound_args’
fit_cpi: no visible binding for global variable ‘protein’
fit_cpi: no visible binding for global variable ‘protein_args’
fit_cpi: no visible binding for global variable ‘max_atoms’
gcn_in_out : initialize: no visible global function definition for
  ‘super’
gcn_in_out : call: no visible binding for global variable ‘self’
gcn_in_out : <anonymous>: no visible binding for global variable ‘self’
gcn_in_out: no visible binding for global variable ‘temp_units’
multiple_sampling_generator : <anonymous>: no visible binding for
  global variable ‘batch_start’
Undefined global functions or variables:
  batch_start compound compound_args max_atoms protein protein_args
  self super temp_units
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
cpi_model 19.144  1.144  23.599
* 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 ...
  ‘DeepPINCS.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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

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(DeepPINCS)
Loading required package: keras
> 
> test_check("DeepPINCS")
/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}")

1/7 [===>..........................] - ETA: 13s - loss: 0.6893 - accuracy: 0.5625
7/7 [==============================] - ETA: 0s - loss: 0.6896 - accuracy: 0.5100 
7/7 [==============================] - 3s 80ms/step - loss: 0.6896 - accuracy: 0.5100 - val_loss: 0.6907 - val_accuracy: 0.4800

1/7 [===>..........................] - ETA: 13s - loss: 0.7125 - accuracy: 0.3750
6/7 [========================>.....] - ETA: 0s - loss: 0.6958 - accuracy: 0.5312 
7/7 [==============================] - 3s 81ms/step - loss: 0.6943 - accuracy: 0.5500 - val_loss: 0.6872 - val_accuracy: 0.5400

1/7 [===>..........................] - ETA: 15s - loss: 0.7016 - accuracy: 0.5000
5/7 [====================>.........] - ETA: 0s - loss: 0.6930 - accuracy: 0.5375 
7/7 [==============================] - 3s 81ms/step - loss: 0.6926 - accuracy: 0.5100 - val_loss: 0.6928 - val_accuracy: 0.4900

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 256ms/step
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 11 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
 99.786   1.444  94.729