##############################################################################
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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
###
##############################################################################
##############################################################################


* 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 19.289  1.173  23.347
* 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 ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘DeepPINCS.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}")
Epoch 1/20

1/6 [====>.........................] - ETA: 12s - loss: 0.6912 - accuracy: 0.5156
4/6 [===================>..........] - ETA: 0s - loss: 0.6930 - accuracy: 0.5039 
6/6 [==============================] - 3s 130ms/step - loss: 0.6911 - accuracy: 0.5086 - val_loss: 0.6888 - val_accuracy: 0.4867
Epoch 2/20

1/6 [====>.........................] - ETA: 0s - loss: 0.6813 - accuracy: 0.5312
4/6 [===================>..........] - ETA: 0s - loss: 0.6810 - accuracy: 0.5820
6/6 [==============================] - 0s 42ms/step - loss: 0.6832 - accuracy: 0.5657 - val_loss: 0.6846 - val_accuracy: 0.5000
Epoch 3/20

1/6 [====>.........................] - ETA: 0s - loss: 0.6925 - accuracy: 0.5156
4/6 [===================>..........] - ETA: 0s - loss: 0.6821 - accuracy: 0.5508
6/6 [==============================] - 0s 43ms/step - loss: 0.6783 - accuracy: 0.5629 - val_loss: 0.6799 - val_accuracy: 0.5333
Epoch 4/20

1/6 [====>.........................] - ETA: 0s - loss: 0.6855 - accuracy: 0.4219
3/6 [==============>...............] - ETA: 0s - loss: 0.6732 - accuracy: 0.5677
5/6 [========================>.....] - ETA: 0s - loss: 0.6744 - accuracy: 0.5625
6/6 [==============================] - 0s 47ms/step - loss: 0.6726 - accuracy: 0.5714 - val_loss: 0.6763 - val_accuracy: 0.5467
Epoch 5/20

1/6 [====>.........................] - ETA: 0s - loss: 0.6795 - accuracy: 0.5312
3/6 [==============>...............] - ETA: 0s - loss: 0.6674 - accuracy: 0.5365
5/6 [========================>.....] - ETA: 0s - loss: 0.6659 - accuracy: 0.5906
6/6 [==============================] - 0s 39ms/step - loss: 0.6672 - accuracy: 0.5800 - val_loss: 0.6716 - val_accuracy: 0.5400
Epoch 6/20

1/6 [====>.........................] - ETA: 0s - loss: 0.6597 - accuracy: 0.5938
3/6 [==============>...............] - ETA: 0s - loss: 0.6592 - accuracy: 0.5885
5/6 [========================>.....] - ETA: 0s - loss: 0.6627 - accuracy: 0.5938
6/6 [==============================] - 0s 45ms/step - loss: 0.6614 - accuracy: 0.5943 - val_loss: 0.6663 - val_accuracy: 0.5400
Epoch 7/20

1/6 [====>.........................] - ETA: 0s - loss: 0.6698 - accuracy: 0.5781
4/6 [===================>..........] - ETA: 0s - loss: 0.6527 - accuracy: 0.6406
6/6 [==============================] - 0s 42ms/step - loss: 0.6547 - accuracy: 0.6171 - val_loss: 0.6602 - val_accuracy: 0.5733
Epoch 8/20

1/6 [====>.........................] - ETA: 0s - loss: 0.6394 - accuracy: 0.6250
3/6 [==============>...............] - ETA: 0s - loss: 0.6502 - accuracy: 0.6198
6/6 [==============================] - ETA: 0s - loss: 0.6494 - accuracy: 0.6286
6/6 [==============================] - 0s 43ms/step - loss: 0.6494 - accuracy: 0.6286 - val_loss: 0.6520 - val_accuracy: 0.6800
Epoch 9/20

1/6 [====>.........................] - ETA: 0s - loss: 0.6539 - accuracy: 0.6250
3/6 [==============>...............] - ETA: 0s - loss: 0.6441 - accuracy: 0.6354
6/6 [==============================] - ETA: 0s - loss: 0.6398 - accuracy: 0.6571
6/6 [==============================] - 0s 43ms/step - loss: 0.6398 - accuracy: 0.6571 - val_loss: 0.6457 - val_accuracy: 0.6267
Epoch 10/20

1/6 [====>.........................] - ETA: 0s - loss: 0.6575 - accuracy: 0.6094
4/6 [===================>..........] - ETA: 0s - loss: 0.6386 - accuracy: 0.6602
6/6 [==============================] - 0s 35ms/step - loss: 0.6312 - accuracy: 0.6914 - val_loss: 0.6361 - val_accuracy: 0.6867
Epoch 11/20

1/6 [====>.........................] - ETA: 0s - loss: 0.6364 - accuracy: 0.6719
4/6 [===================>..........] - ETA: 0s - loss: 0.6191 - accuracy: 0.6953
6/6 [==============================] - 0s 41ms/step - loss: 0.6224 - accuracy: 0.7029 - val_loss: 0.6280 - val_accuracy: 0.6867
Epoch 12/20

1/6 [====>.........................] - ETA: 0s - loss: 0.6026 - accuracy: 0.7812
3/6 [==============>...............] - ETA: 0s - loss: 0.6216 - accuracy: 0.7031
5/6 [========================>.....] - ETA: 0s - loss: 0.6131 - accuracy: 0.7156
6/6 [==============================] - 0s 46ms/step - loss: 0.6116 - accuracy: 0.7143 - val_loss: 0.6170 - val_accuracy: 0.7067
Epoch 13/20

1/6 [====>.........................] - ETA: 0s - loss: 0.5951 - accuracy: 0.7344
4/6 [===================>..........] - ETA: 0s - loss: 0.6049 - accuracy: 0.6992
6/6 [==============================] - 0s 40ms/step - loss: 0.5993 - accuracy: 0.7229 - val_loss: 0.6074 - val_accuracy: 0.7200
Epoch 14/20

1/6 [====>.........................] - ETA: 0s - loss: 0.5932 - accuracy: 0.7812
3/6 [==============>...............] - ETA: 0s - loss: 0.5930 - accuracy: 0.7500
5/6 [========================>.....] - ETA: 0s - loss: 0.5872 - accuracy: 0.7469
6/6 [==============================] - 0s 44ms/step - loss: 0.5869 - accuracy: 0.7400 - val_loss: 0.5945 - val_accuracy: 0.7200
Epoch 15/20

1/6 [====>.........................] - ETA: 0s - loss: 0.5622 - accuracy: 0.7500
3/6 [==============>...............] - ETA: 0s - loss: 0.5791 - accuracy: 0.7552
5/6 [========================>.....] - ETA: 0s - loss: 0.5707 - accuracy: 0.7750
6/6 [==============================] - 0s 46ms/step - loss: 0.5710 - accuracy: 0.7657 - val_loss: 0.5824 - val_accuracy: 0.7533
Epoch 16/20

1/6 [====>.........................] - ETA: 0s - loss: 0.5771 - accuracy: 0.6875
3/6 [==============>...............] - ETA: 0s - loss: 0.5729 - accuracy: 0.7500
6/6 [==============================] - ETA: 0s - loss: 0.5551 - accuracy: 0.7857
6/6 [==============================] - 0s 44ms/step - loss: 0.5551 - accuracy: 0.7857 - val_loss: 0.5676 - val_accuracy: 0.7467
Epoch 17/20

1/6 [====>.........................] - ETA: 0s - loss: 0.5369 - accuracy: 0.8125
3/6 [==============>...............] - ETA: 0s - loss: 0.5380 - accuracy: 0.7917
5/6 [========================>.....] - ETA: 0s - loss: 0.5365 - accuracy: 0.8031
6/6 [==============================] - 0s 37ms/step - loss: 0.5378 - accuracy: 0.8000 - val_loss: 0.5533 - val_accuracy: 0.7467
Epoch 18/20

1/6 [====>.........................] - ETA: 0s - loss: 0.5664 - accuracy: 0.7812
3/6 [==============>...............] - ETA: 0s - loss: 0.5257 - accuracy: 0.8073
5/6 [========================>.....] - ETA: 0s - loss: 0.5207 - accuracy: 0.8156
6/6 [==============================] - 0s 38ms/step - loss: 0.5187 - accuracy: 0.8143 - val_loss: 0.5389 - val_accuracy: 0.7733
Epoch 19/20

1/6 [====>.........................] - ETA: 0s - loss: 0.5485 - accuracy: 0.7500
3/6 [==============>...............] - ETA: 0s - loss: 0.5121 - accuracy: 0.8177
5/6 [========================>.....] - ETA: 0s - loss: 0.5044 - accuracy: 0.8313
6/6 [==============================] - 0s 38ms/step - loss: 0.5002 - accuracy: 0.8400 - val_loss: 0.5246 - val_accuracy: 0.7733
Epoch 20/20

1/6 [====>.........................] - ETA: 0s - loss: 0.5107 - accuracy: 0.8281
4/6 [===================>..........] - ETA: 0s - loss: 0.4844 - accuracy: 0.8320
6/6 [==============================] - 0s 37ms/step - loss: 0.4804 - accuracy: 0.8429 - val_loss: 0.5126 - val_accuracy: 0.7800

1/5 [=====>........................] - ETA: 1s
5/5 [==============================] - 0s 7ms/step
Epoch 1/20

 1/11 [=>............................] - ETA: 16s - loss: 0.7081 - accuracy: 0.5312
11/11 [==============================] - 2s 35ms/step - loss: 0.6809 - accuracy: 0.5600 - val_loss: 0.6352 - val_accuracy: 0.6533
Epoch 2/20

 1/11 [=>............................] - ETA: 0s - loss: 0.6408 - accuracy: 0.7031
11/11 [==============================] - 0s 9ms/step - loss: 0.5953 - accuracy: 0.7371 - val_loss: 0.5950 - val_accuracy: 0.6833
Epoch 3/20

 1/11 [=>............................] - ETA: 0s - loss: 0.5139 - accuracy: 0.8281
11/11 [==============================] - 0s 9ms/step - loss: 0.5250 - accuracy: 0.7871 - val_loss: 0.5789 - val_accuracy: 0.6933
Epoch 4/20

 1/11 [=>............................] - ETA: 0s - loss: 0.4839 - accuracy: 0.7656
11/11 [==============================] - 0s 8ms/step - loss: 0.4616 - accuracy: 0.8243 - val_loss: 0.5629 - val_accuracy: 0.7067
Epoch 5/20

 1/11 [=>............................] - ETA: 0s - loss: 0.5126 - accuracy: 0.7500
11/11 [==============================] - 0s 9ms/step - loss: 0.4007 - accuracy: 0.8600 - val_loss: 0.5533 - val_accuracy: 0.7267
Epoch 6/20

 1/11 [=>............................] - ETA: 0s - loss: 0.3586 - accuracy: 0.8750
11/11 [==============================] - 0s 9ms/step - loss: 0.3514 - accuracy: 0.8829 - val_loss: 0.5455 - val_accuracy: 0.7200
Epoch 7/20

 1/11 [=>............................] - ETA: 0s - loss: 0.3416 - accuracy: 0.8906
11/11 [==============================] - 0s 9ms/step - loss: 0.3063 - accuracy: 0.9086 - val_loss: 0.5345 - val_accuracy: 0.7367
Epoch 8/20

 1/11 [=>............................] - ETA: 0s - loss: 0.2492 - accuracy: 0.9531
11/11 [==============================] - 0s 8ms/step - loss: 0.2663 - accuracy: 0.9171 - val_loss: 0.5454 - val_accuracy: 0.7367
Epoch 9/20

 1/11 [=>............................] - ETA: 0s - loss: 0.2201 - accuracy: 0.9375
11/11 [==============================] - 0s 8ms/step - loss: 0.2316 - accuracy: 0.9414 - val_loss: 0.5387 - val_accuracy: 0.7400
Epoch 10/20

 1/11 [=>............................] - ETA: 0s - loss: 0.2225 - accuracy: 0.9688
11/11 [==============================] - 0s 10ms/step - loss: 0.2022 - accuracy: 0.9471 - val_loss: 0.5452 - val_accuracy: 0.7467
Epoch 11/20

 1/11 [=>............................] - ETA: 0s - loss: 0.1459 - accuracy: 1.0000
11/11 [==============================] - 0s 9ms/step - loss: 0.1765 - accuracy: 0.9600 - val_loss: 0.5429 - val_accuracy: 0.7433
Epoch 12/20

 1/11 [=>............................] - ETA: 0s - loss: 0.1910 - accuracy: 0.9688
11/11 [==============================] - 0s 8ms/step - loss: 0.1554 - accuracy: 0.9700 - val_loss: 0.5483 - val_accuracy: 0.7533
Epoch 13/20

 1/11 [=>............................] - ETA: 0s - loss: 0.1433 - accuracy: 0.9531
11/11 [==============================] - 0s 9ms/step - loss: 0.1366 - accuracy: 0.9729 - val_loss: 0.5587 - val_accuracy: 0.7567
Epoch 14/20

 1/11 [=>............................] - ETA: 0s - loss: 0.1096 - accuracy: 1.0000
11/11 [==============================] - 0s 8ms/step - loss: 0.1198 - accuracy: 0.9786 - val_loss: 0.5648 - val_accuracy: 0.7667
Epoch 15/20

 1/11 [=>............................] - ETA: 0s - loss: 0.0971 - accuracy: 0.9844
11/11 [==============================] - 0s 8ms/step - loss: 0.1056 - accuracy: 0.9800 - val_loss: 0.5671 - val_accuracy: 0.7700
Epoch 16/20

 1/11 [=>............................] - ETA: 0s - loss: 0.1195 - accuracy: 0.9844
11/11 [==============================] - 0s 10ms/step - loss: 0.0938 - accuracy: 0.9871 - val_loss: 0.5904 - val_accuracy: 0.7700
Epoch 17/20

 1/11 [=>............................] - ETA: 0s - loss: 0.0837 - accuracy: 1.0000
11/11 [==============================] - 0s 9ms/step - loss: 0.0841 - accuracy: 0.9914 - val_loss: 0.5866 - val_accuracy: 0.7600
Epoch 18/20

 1/11 [=>............................] - ETA: 0s - loss: 0.0602 - accuracy: 1.0000
11/11 [==============================] - 0s 9ms/step - loss: 0.0753 - accuracy: 0.9929 - val_loss: 0.5918 - val_accuracy: 0.7633
Epoch 19/20

 1/11 [=>............................] - ETA: 0s - loss: 0.0906 - accuracy: 1.0000
11/11 [==============================] - 0s 9ms/step - loss: 0.0668 - accuracy: 0.9929 - val_loss: 0.6118 - val_accuracy: 0.7667
Epoch 20/20

 1/11 [=>............................] - ETA: 0s - loss: 0.0602 - accuracy: 0.9844
11/11 [==============================] - 0s 9ms/step - loss: 0.0595 - accuracy: 0.9929 - val_loss: 0.6219 - val_accuracy: 0.7667

 1/10 [==>...........................] - ETA: 1s
10/10 [==============================] - 0s 2ms/step
Killed

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

Status: 1 ERROR, 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
###
##############################################################################
##############################################################################


* 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: 15s - loss: 0.7006 - accuracy: 0.5000
7/7 [==============================] - 3s 87ms/step - loss: 0.6942 - accuracy: 0.5200 - val_loss: 0.6945 - val_accuracy: 0.4800

1/7 [===>..........................] - ETA: 14s - loss: 0.6739 - accuracy: 0.5625
7/7 [==============================] - ETA: 0s - loss: 0.6782 - accuracy: 0.5400 
7/7 [==============================] - 3s 80ms/step - loss: 0.6782 - accuracy: 0.5400 - val_loss: 0.6875 - val_accuracy: 0.5500

1/7 [===>..........................] - ETA: 14s - loss: 0.7021 - accuracy: 0.2500
6/7 [========================>.....] - ETA: 0s - loss: 0.6965 - accuracy: 0.4167 
7/7 [==============================] - 3s 73ms/step - loss: 0.6961 - accuracy: 0.4300 - val_loss: 0.6893 - val_accuracy: 0.5700

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 243ms/step
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 11 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
 99.906   1.737  94.039