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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ttgsea.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ttgsea_1.3.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ttgsea.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ttgsea/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ttgsea' version '1.3.1'
* 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 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 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     16.50   0.59   21.32
predict_model 13.09   0.37   26.28
bi_gru         3.65   1.09    6.94
text_token     1.73   0.05   14.25
token_vector   1.58   0.13   13.77
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ttgsea
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ttgsea' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ttgsea'
    finding HTML links ... done
    bi_gru                                  html  
    bi_lstm                                 html  
    fit_model                               html  
    metric_pearson_correlation              html  
    plot_model                              html  
    predict_model                           html  
    sampling_generator                      html  
    text_token                              html  
    token_vector                            html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'ggmsa' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'midasHLA' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
2022-03-17 20:35:39.747673: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'cudart64_101.dll'; dlerror: cudart64_101.dll not found
2022-03-17 20:35:39.748090: 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.
2022-03-17 20:35:42.420238: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'nvcuda.dll'; dlerror: nvcuda.dll not found
2022-03-17 20:35:42.420556: W tensorflow/stream_executor/cuda/cuda_driver.cc:312] failed call to cuInit: UNKNOWN ERROR (303)
2022-03-17 20:35:42.420903: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:169] retrieving CUDA diagnostic information for host: riesling1
2022-03-17 20:35:42.421201: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:176] hostname: riesling1
2022-03-17 20:35:42.421932: 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
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2022-03-17 20:35:42.442271: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x5eae1eb0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2022-03-17 20:35:42.442703: I tensorflow/compiler/xla/service/service.cc:176]   StreamExecutor device (0): Host, Default Version

 1/45 [..............................] - ETA: 0s - loss: 1.4274 - pearson_correlation: 0.0527
 4/45 [=>............................] - ETA: 0s - loss: 1.5843 - pearson_correlation: 0.0133
 8/45 [====>.........................] - ETA: 0s - loss: 1.5621 - pearson_correlation: -0.0053
12/45 [=======>......................] - ETA: 0s - loss: 1.5854 - pearson_correlation: 0.0448 
16/45 [=========>....................] - ETA: 0s - loss: 1.5853 - pearson_correlation: 0.0370
20/45 [============>.................] - ETA: 0s - loss: 1.6135 - pearson_correlation: 0.0589
24/45 [===============>..............] - ETA: 0s - loss: 1.6210 - pearson_correlation: 0.0705
28/45 [=================>............] - ETA: 0s - loss: 1.5810 - pearson_correlation: 0.0876
33/45 [=====================>........] - ETA: 0s - loss: 1.5754 - pearson_correlation: 0.1034
36/45 [=======================>......] - ETA: 0s - loss: 1.5812 - pearson_correlation: 0.1035
39/45 [=========================>....] - ETA: 0s - loss: 1.5672 - pearson_correlation: 0.1119
42/45 [===========================>..] - ETA: 0s - loss: 1.5521 - pearson_correlation: 0.1181
45/45 [==============================] - 1s 17ms/step - loss: 1.5555 - pearson_correlation: 0.1149
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
  23.46    1.73   20.28