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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DeepPINCS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DeepPINCS_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DeepPINCS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeepPINCS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeepPINCS’ version ‘1.14.0’
* 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 code 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                40.843  6.779  94.316
metric_concordance_index  6.644  1.248  11.482
metric_f1_score           6.675  0.659   8.364
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/DeepPINCS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DeepPINCS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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")

1/7 [===>..........................] - ETA: 28s - loss: 0.7156 - accuracy: 0.4375
2/7 [=======>......................] - ETA: 1s - loss: 0.7172 - accuracy: 0.3750 
6/7 [========================>.....] - ETA: 0s - loss: 0.7005 - accuracy: 0.5417WARNING:tensorflow:Callback method `on_train_batch_end` is slow compared to the batch time (batch time: 0.0183s vs `on_train_batch_end` time: 0.0457s). Check your callbacks.

7/7 [==============================] - 6s 277ms/step - loss: 0.6996 - accuracy: 0.5500 - val_loss: 0.6883 - val_accuracy: 0.5400

1/7 [===>..........................] - ETA: 26s - loss: 0.6938 - accuracy: 0.5000
2/7 [=======>......................] - ETA: 0s - loss: 0.6918 - accuracy: 0.5312 
4/7 [================>.............] - ETA: 0s - loss: 0.6912 - accuracy: 0.5156
7/7 [==============================] - 5s 158ms/step - loss: 0.6873 - accuracy: 0.5200 - val_loss: 0.6893 - val_accuracy: 0.4800

1/7 [===>..........................] - ETA: 41s - loss: 0.6910 - accuracy: 0.5000
5/7 [====================>.........] - ETA: 0s - loss: 0.6929 - accuracy: 0.4375 
7/7 [==============================] - 8s 164ms/step - loss: 0.6902 - accuracy: 0.4600 - val_loss: 0.6902 - val_accuracy: 0.5000

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 1s 518ms/step
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 11 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
180.857  12.414 242.698