##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ttgsea.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ttgsea_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ttgsea.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.0.0’
* 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 ‘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     28.223  3.328  21.593
predict_model 27.538  3.561  19.172
text_token    12.506  0.634   7.145
token_vector   9.921  0.829   5.476
bi_gru         3.966  0.627   6.293
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ttgsea
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
2021-10-14 11:59:39.738748: I tensorflow/stream_executor/platform/default/dso_loader.cc:48] Successfully opened dynamic library libcudart.so.10.1
2021-10-14 11:59:41.898100: I tensorflow/stream_executor/platform/default/dso_loader.cc:48] Successfully opened dynamic library libcuda.so.1
2021-10-14 11:59:41.925571: E tensorflow/stream_executor/cuda/cuda_driver.cc:314] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected
2021-10-14 11:59:41.925694: 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
2021-10-14 11:59:41.926116: 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.
2021-10-14 11:59:41.940693: I tensorflow/core/platform/profile_utils/cpu_utils.cc:104] CPU Frequency: 2200000000 Hz
2021-10-14 11:59:41.945096: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x564ab5bcf910 initialized for platform Host (this does not guarantee that XLA will be used). Devices:
2021-10-14 11:59:41.945180: I tensorflow/compiler/xla/service/service.cc:176]   StreamExecutor device (0): Host, Default Version

 1/45 [..............................] - ETA: 0s - loss: 1.7519 - pearson_correlation: -0.1605
 3/45 [=>............................] - ETA: 1s - loss: 1.6498 - pearson_correlation: 0.0405 
 4/45 [=>............................] - ETA: 1s - loss: 1.7379 - pearson_correlation: 0.0693
 6/45 [===>..........................] - ETA: 1s - loss: 1.6818 - pearson_correlation: 0.1519
 7/45 [===>..........................] - ETA: 1s - loss: 1.6584 - pearson_correlation: 0.1273
 9/45 [=====>........................] - ETA: 1s - loss: 1.6377 - pearson_correlation: 0.1450
11/45 [======>.......................] - ETA: 1s - loss: 1.5811 - pearson_correlation: 0.1242
13/45 [=======>......................] - ETA: 1s - loss: 1.5551 - pearson_correlation: 0.1529
15/45 [=========>....................] - ETA: 1s - loss: 1.5425 - pearson_correlation: 0.1493
16/45 [=========>....................] - ETA: 1s - loss: 1.5518 - pearson_correlation: 0.1548
18/45 [===========>..................] - ETA: 1s - loss: 1.5481 - pearson_correlation: 0.1257
20/45 [============>.................] - ETA: 1s - loss: 1.5476 - pearson_correlation: 0.1179
21/45 [=============>................] - ETA: 1s - loss: 1.5379 - pearson_correlation: 0.1262
23/45 [==============>...............] - ETA: 1s - loss: 1.5295 - pearson_correlation: 0.1206
25/45 [===============>..............] - ETA: 0s - loss: 1.5256 - pearson_correlation: 0.1325
27/45 [=================>............] - ETA: 0s - loss: 1.5310 - pearson_correlation: 0.1440
28/45 [=================>............] - ETA: 0s - loss: 1.5175 - pearson_correlation: 0.1350
30/45 [===================>..........] - ETA: 0s - loss: 1.5131 - pearson_correlation: 0.1395
32/45 [====================>.........] - ETA: 0s - loss: 1.5227 - pearson_correlation: 0.1466
33/45 [=====================>........] - ETA: 0s - loss: 1.5254 - pearson_correlation: 0.1448
35/45 [======================>.......] - ETA: 0s - loss: 1.5539 - pearson_correlation: 0.1322
36/45 [=======================>......] - ETA: 0s - loss: 1.5579 - pearson_correlation: 0.1311
38/45 [========================>.....] - ETA: 0s - loss: 1.5746 - pearson_correlation: 0.1429
39/45 [=========================>....] - ETA: 0s - loss: 1.5830 - pearson_correlation: 0.1448
40/45 [=========================>....] - ETA: 0s - loss: 1.5733 - pearson_correlation: 0.1411
41/45 [==========================>...] - ETA: 0s - loss: 1.5754 - pearson_correlation: 0.1459
42/45 [===========================>..] - ETA: 0s - loss: 1.5698 - pearson_correlation: 0.1480
43/45 [===========================>..] - ETA: 0s - loss: 1.5664 - pearson_correlation: 0.1470
44/45 [============================>.] - ETA: 0s - loss: 1.5678 - pearson_correlation: 0.1490
45/45 [==============================] - ETA: 0s - loss: 1.5706 - pearson_correlation: 0.1387
45/45 [==============================] - 2s 49ms/step - loss: 1.5706 - pearson_correlation: 0.1387
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 29.847   5.020  19.476