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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:DeepPINCS.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DeepPINCS_1.2.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/DeepPINCS.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DeepPINCS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DeepPINCS' version '1.2.2'
* 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 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 14.92   1.28   14.99
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/DeepPINCS.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch DeepPINCS
###
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* installing to library 'C:/Users/biocbuild/bbs-3.14-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
  converting help for package 'DeepPINCS'
    finding HTML links ... done
    SARS_CoV2_3CL_Protease                  html  
    antiviral_drug                          html  
    cpi_model                               html  
    encoder_in_out                          html  
    example_bioassay                        html  
    example_cci                             html  
    example_chem                            html  
    example_cpi                             html  
    example_pd                              html  
    example_ppi                             html  
    example_prot                            html  
    get_canonical_smiles                    html  
    get_fingerprint                         html  
    get_graph_structure_node_feature        html  
    get_seq_encode_pad                      html  
    metric_concordance_index                html  
    metric_f1_score                         html  
    multiple_sampling_generator             html  
    seq_check                               html  
    seq_preprocessing                       html  
** 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)
Making 'packages.html' ... done

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
2022-04-12 18:23:25.000615: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2
Train on 100 samples, validate on 100 samples

 16/100 [===>..........................] - ETA: 6s - loss: 0.6943 - accuracy: 0.3750
100/100 [==============================] - 1s 15ms/sample - loss: 0.6923 - accuracy: 0.4900 - val_loss: 0.6921 - val_accuracy: 0.4800
Train on 100 samples, validate on 100 samples

 16/100 [===>..........................] - ETA: 5s - loss: 0.6983 - accuracy: 0.4375
100/100 [==============================] - 1s 12ms/sample - loss: 0.6946 - accuracy: 0.4600 - val_loss: 0.6918 - val_accuracy: 0.5900
Train on 100 samples, validate on 100 samples

 16/100 [===>..........................] - ETA: 5s - loss: 0.7025 - accuracy: 0.3750
100/100 [==============================] - 1s 14ms/sample - loss: 0.6904 - accuracy: 0.5400 - val_loss: 0.6895 - val_accuracy: 0.5300
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 11 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
  85.75    2.06   81.34