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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_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DeepPINCS.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.17.0’
* 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 20.612  3.485  24.006
* 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-3.22-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/4.5-x86_64/Resources/library’
* installing *source* package ‘DeepPINCS’ ...
** this is package ‘DeepPINCS’ version ‘1.17.0’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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")
2025-06-23 20:02:27.194452: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
/Library/Python/3.9/site-packages/urllib3/__init__.py:34: NotOpenSSLWarning: urllib3 v2 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with 'LibreSSL 2.8.3'. See: https://github.com/urllib3/urllib3/issues/3020
  warnings.warn(

1/7 [===>..........................] - ETA: 10s - loss: 0.7052 - accuracy: 0.5000
7/7 [==============================] - 2s 69ms/step - loss: 0.6971 - accuracy: 0.4900 - val_loss: 0.6893 - val_accuracy: 0.6400

1/7 [===>..........................] - ETA: 9s - loss: 0.6858 - accuracy: 0.5625
7/7 [==============================] - 2s 63ms/step - loss: 0.6814 - accuracy: 0.5200 - val_loss: 0.6855 - val_accuracy: 0.4500

1/7 [===>..........................] - ETA: 11s - loss: 0.6866 - accuracy: 0.5000
6/7 [========================>.....] - ETA: 0s - loss: 0.6774 - accuracy: 0.5312 
7/7 [==============================] - 2s 66ms/step - loss: 0.6796 - accuracy: 0.5200 - val_loss: 0.6929 - val_accuracy: 0.4800

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 200ms/step
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 11 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
 78.603   4.227  76.661