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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/site-library --timings DeepPINCS_1.8.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/DeepPINCS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘DeepPINCS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeepPINCS’ version ‘1.8.3’
* 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 loading without being on the library search path ... 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 12.712  1.113  13.652
* 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/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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")
2023-10-15 20:41:26.364898: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-10-15 20:41:26.588555: I tensorflow/core/util/util.cc:169] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2023-10-15 20:41:26.594817: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
2023-10-15 20:41:26.594879: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
2023-10-15 20:41:26.625686: E tensorflow/stream_executor/cuda/cuda_blas.cc:2981] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2023-10-15 20:41:27.490677: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
2023-10-15 20:41:27.490818: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.17-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
2023-10-15 20:41:27.490840: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
2023-10-15 20:41:37.013647: E tensorflow/stream_executor/cuda/cuda_driver.cc:265] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected
2023-10-15 20:41:37.013724: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (nebbiolo1): /proc/driver/nvidia/version does not exist
2023-10-15 20:41:37.014141: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.

1/7 [===>..........................] - ETA: 7s - loss: 0.6835 - accuracy: 0.6250
7/7 [==============================] - ETA: 0s - loss: 0.6938 - accuracy: 0.5000
7/7 [==============================] - 2s 65ms/step - loss: 0.6938 - accuracy: 0.5000 - val_loss: 0.6885 - val_accuracy: 0.5900

1/7 [===>..........................] - ETA: 5s - loss: 0.6925 - accuracy: 0.6250
7/7 [==============================] - 1s 52ms/step - loss: 0.7036 - accuracy: 0.4800 - val_loss: 0.6931 - val_accuracy: 0.5200

1/7 [===>..........................] - ETA: 5s - loss: 0.7067 - accuracy: 0.4375
7/7 [==============================] - 1s 53ms/step - loss: 0.6963 - accuracy: 0.4400 - val_loss: 0.6939 - val_accuracy: 0.4800

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 183ms/step
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 11 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
 68.329   2.117  60.887