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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ttgsea_1.7.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ttgsea.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘ttgsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ttgsea’ version ‘1.7.1’
* 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 ‘ttgsea’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
fit_model     22.797  2.766  14.048
predict_model 21.970  3.003  12.883
text_token    10.262  0.452   6.808
token_vector  10.088  0.548   6.413
bi_gru         3.063  0.992   5.641
* 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 ...
  ‘ttgsea.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ttgsea
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘ttgsea’ ...
** using staged installation
** R
** 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 (ttgsea)

R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
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(ttgsea)
Loading required package: keras
> 
> test_check("ttgsea")
2023-04-12 10:05:31.496938: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] 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
2023-04-12 10:05:31.496990: 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.
2023-04-12 10:05:34.243011: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
2023-04-12 10:05:34.244124: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
2023-04-12 10:05:34.281866: E tensorflow/stream_executor/cuda/cuda_driver.cc:328] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected
2023-04-12 10:05:34.281914: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (nebbiolo2): /proc/driver/nvidia/version does not exist
2023-04-12 10:05:34.282296: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-04-12 10:05:34.285212: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
2023-04-12 10:05:34.601945: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2)
2023-04-12 10:05:34.602817: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 2200000000 Hz

 1/45 [..............................] - ETA: 2:03 - loss: 1.6149 - pearson_correlation: 0.1648
 3/45 [=>............................] - ETA: 1s - loss: 1.5483 - pearson_correlation: 0.0698  
 5/45 [==>...........................] - ETA: 1s - loss: 1.5292 - pearson_correlation: 0.0435
 7/45 [===>..........................] - ETA: 1s - loss: 1.5088 - pearson_correlation: 0.0365
10/45 [=====>........................] - ETA: 1s - loss: 1.4898 - pearson_correlation: 0.0351
13/45 [=======>......................] - ETA: 0s - loss: 1.4875 - pearson_correlation: 0.0388
16/45 [=========>....................] - ETA: 0s - loss: 1.4893 - pearson_correlation: 0.0406
19/45 [===========>..................] - ETA: 0s - loss: 1.4954 - pearson_correlation: 0.0434
22/45 [=============>................] - ETA: 0s - loss: 1.5027 - pearson_correlation: 0.0455
24/45 [===============>..............] - ETA: 0s - loss: 1.5079 - pearson_correlation: 0.0467
27/45 [=================>............] - ETA: 0s - loss: 1.5135 - pearson_correlation: 0.0487
30/45 [===================>..........] - ETA: 0s - loss: 1.5189 - pearson_correlation: 0.0518
33/45 [=====================>........] - ETA: 0s - loss: 1.5230 - pearson_correlation: 0.0550
36/45 [=======================>......] - ETA: 0s - loss: 1.5269 - pearson_correlation: 0.0596
39/45 [=========================>....] - ETA: 0s - loss: 1.5304 - pearson_correlation: 0.0647
42/45 [===========================>..] - ETA: 0s - loss: 1.5331 - pearson_correlation: 0.0693
45/45 [==============================] - ETA: 0s - loss: 1.5351 - pearson_correlation: 0.0735
45/45 [==============================] - 4s 24ms/step - loss: 1.5357 - pearson_correlation: 0.0748
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 24.982   4.771  17.373