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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DeProViR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DeProViR_1.1.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DeProViR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘DeProViR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeProViR’ version ‘1.1.0’
* package encoding: UTF-8
* 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 ‘DeProViR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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
encodeHostSeq    74.042  2.768  78.986
encodeViralSeq   58.801  2.655  61.456
predInteractions 59.157  0.811  59.329
gloveImport      57.552  1.156  58.706
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/DeProViR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL DeProViR
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘DeProViR’ ...
** using staged installation
** R
** inst
** 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 (DeProViR)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> BiocGenerics:::testPackage('DeProViR')
2024-07-05 22:20:53.243132: I tensorflow/core/util/port.cc:110] 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`.
2024-07-05 22:20:53.246943: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2024-07-05 22:20:53.334003: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2024-07-05 22:20:53.334556: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-07-05 22:20:54.393530: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-07-05 22:20:56.900057: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_2_grad/concat/split_2/split_dim' with dtype int32
	 [[{{node gradients/split_2_grad/concat/split_2/split_dim}}]]
2024-07-05 22:20:56.901435: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_grad/concat/split/split_dim' with dtype int32
	 [[{{node gradients/split_grad/concat/split/split_dim}}]]
2024-07-05 22:20:56.902632: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_1_grad/concat/split_1/split_dim' with dtype int32
	 [[{{node gradients/split_1_grad/concat/split_1/split_dim}}]]
2024-07-05 22:20:57.061049: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/ReverseV2_grad/ReverseV2/ReverseV2/axis' with dtype int32 and shape [1]
	 [[{{node gradients/ReverseV2_grad/ReverseV2/ReverseV2/axis}}]]
2024-07-05 22:20:57.112609: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_2_grad/concat/split_2/split_dim' with dtype int32
	 [[{{node gradients/split_2_grad/concat/split_2/split_dim}}]]
2024-07-05 22:20:57.113892: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_grad/concat/split/split_dim' with dtype int32
	 [[{{node gradients/split_grad/concat/split/split_dim}}]]
2024-07-05 22:20:57.115063: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_1_grad/concat/split_1/split_dim' with dtype int32
	 [[{{node gradients/split_1_grad/concat/split_1/split_dim}}]]
2024-07-05 22:20:57.398358: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_2_grad/concat/split_2/split_dim' with dtype int32
	 [[{{node gradients/split_2_grad/concat/split_2/split_dim}}]]
2024-07-05 22:20:57.399630: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_grad/concat/split/split_dim' with dtype int32
	 [[{{node gradients/split_grad/concat/split/split_dim}}]]
2024-07-05 22:20:57.400821: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_1_grad/concat/split_1/split_dim' with dtype int32
	 [[{{node gradients/split_1_grad/concat/split_1/split_dim}}]]
2024-07-05 22:20:57.556426: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/ReverseV2_grad/ReverseV2/ReverseV2/axis' with dtype int32 and shape [1]
	 [[{{node gradients/ReverseV2_grad/ReverseV2/ReverseV2/axis}}]]
2024-07-05 22:20:57.606344: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_2_grad/concat/split_2/split_dim' with dtype int32
	 [[{{node gradients/split_2_grad/concat/split_2/split_dim}}]]
2024-07-05 22:20:57.607614: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_grad/concat/split/split_dim' with dtype int32
	 [[{{node gradients/split_grad/concat/split/split_dim}}]]
2024-07-05 22:20:57.608784: I tensorflow/core/common_runtime/executor.cc:1197] [/device:CPU:0] (DEBUG INFO) Executor start aborting (this does not indicate an error and you can ignore this message): INVALID_ARGUMENT: You must feed a value for placeholder tensor 'gradients/split_1_grad/concat/split_1/split_dim' with dtype int32
	 [[{{node gradients/split_1_grad/concat/split_1/split_dim}}]]
Setting levels: control = 0, case = 1
Setting direction: controls < cases


RUNIT TEST PROTOCOL -- Fri Jul  5 22:20:58 2024 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
DeProViR RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 71.959   2.723  74.341