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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ttgsea_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ttgsea.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ttgsea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ttgsea’ version ‘1.2.1’
* 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 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
predict_model 22.828  3.131  12.695
fit_model     20.696  2.489  13.406
text_token    11.711  1.392   6.794
token_vector  10.353  0.480   6.473
* 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:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ttgsea
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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")
2022-04-12 09:48:35.428245: 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-3.14-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.14-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.14-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.14-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server:/home/biocbuild/bbs-3.14-bioc/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-11-openjdk-amd64/lib/server
2022-04-12 09:48:35.428295: 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.
2022-04-12 09:48:38.118020: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
2022-04-12 09:48:38.119627: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
2022-04-12 09:48:38.180830: E tensorflow/stream_executor/cuda/cuda_driver.cc:328] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected
2022-04-12 09:48:38.180885: 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
2022-04-12 09:48:38.181436: 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.
2022-04-12 09:48:38.185292: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
2022-04-12 09:48:38.523049: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2)
2022-04-12 09:48:38.523966: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 2200000000 Hz

 1/45 [..............................] - ETA: 1:57 - loss: 1.5953 - pearson_correlation: -0.0222
 3/45 [=>............................] - ETA: 1s - loss: 1.6337 - pearson_correlation: 0.0570   
 6/45 [===>..........................] - ETA: 1s - loss: 1.6141 - pearson_correlation: 0.0734
 9/45 [=====>........................] - ETA: 0s - loss: 1.6239 - pearson_correlation: 0.0890
11/45 [======>.......................] - ETA: 0s - loss: 1.6264 - pearson_correlation: 0.0953
13/45 [=======>......................] - ETA: 0s - loss: 1.6219 - pearson_correlation: 0.0998
15/45 [=========>....................] - ETA: 0s - loss: 1.6164 - pearson_correlation: 0.1026
17/45 [==========>...................] - ETA: 0s - loss: 1.6105 - pearson_correlation: 0.1050
19/45 [===========>..................] - ETA: 0s - loss: 1.6047 - pearson_correlation: 0.1065
21/45 [=============>................] - ETA: 0s - loss: 1.5998 - pearson_correlation: 0.1068
23/45 [==============>...............] - ETA: 0s - loss: 1.5953 - pearson_correlation: 0.1070
25/45 [===============>..............] - ETA: 0s - loss: 1.5904 - pearson_correlation: 0.1079
27/45 [=================>............] - ETA: 0s - loss: 1.5864 - pearson_correlation: 0.1091
30/45 [===================>..........] - ETA: 0s - loss: 1.5820 - pearson_correlation: 0.1112
32/45 [====================>.........] - ETA: 0s - loss: 1.5797 - pearson_correlation: 0.1127
34/45 [=====================>........] - ETA: 0s - loss: 1.5775 - pearson_correlation: 0.1143
36/45 [=======================>......] - ETA: 0s - loss: 1.5761 - pearson_correlation: 0.1152
39/45 [=========================>....] - ETA: 0s - loss: 1.5745 - pearson_correlation: 0.1169
41/45 [==========================>...] - ETA: 0s - loss: 1.5738 - pearson_correlation: 0.1180
44/45 [============================>.] - ETA: 0s - loss: 1.5728 - pearson_correlation: 0.1190
45/45 [==============================] - 4s 26ms/step - loss: 1.5723 - pearson_correlation: 0.1194
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 22.235   3.768  16.328