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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DNAcycP2.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DNAcycP2_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DNAcycP2.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘DNAcycP2/DESCRIPTION’ ... OK
* this is package ‘DNAcycP2’ 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 ‘DNAcycP2’ 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 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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
cycle 4.321  1.168   6.999
* 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: OK

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL DNAcycP2
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘DNAcycP2’ ...
** this is package ‘DNAcycP2’ version ‘1.1.0’
** 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 (DNAcycP2)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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("DNAcycP2")

Attaching package: 'DNAcycP2'

The following object is masked from 'package:stats':

    cycle

2025-06-18 22:43:54.639448: I tensorflow/core/util/port.cc:111] 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`.
2025-06-18 22:43:54.642455: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2025-06-18 22:43:54.691674: E tensorflow/compiler/xla/stream_executor/cuda/cuda_dnn.cc:9342] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
2025-06-18 22:43:54.691733: E tensorflow/compiler/xla/stream_executor/cuda/cuda_fft.cc:609] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
2025-06-18 22:43:54.691778: E tensorflow/compiler/xla/stream_executor/cuda/cuda_blas.cc:1518] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2025-06-18 22:43:54.701459: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2025-06-18 22:43:54.701734: 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.
2025-06-18 22:43:55.676643: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 1s 617ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 24ms/step
Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 499ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 32ms/step
Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 1s 512ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 23ms/step
Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 497ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 25ms/step
Reading sequences...
Predicting cyclizability...
WARNING:tensorflow:5 out of the last 9 calls to <function Model.make_predict_function.<locals>.predict_function at 0x719554157380> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for  more details.

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 493ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 24ms/step
Sequence length for ID 1: 50
Predicting cyclizability...
Chunk size: 100000, num threads: 1
Sequence length for ID 1: 50
Predicting cyclizability...
Chunk size: 100000, num threads: 1
Reading sequences...
Predicting cyclizability...
WARNING:tensorflow:6 out of the last 11 calls to <function Model.make_predict_function.<locals>.predict_function at 0x719530648860> triggered tf.function retracing. Tracing is expensive and the excessive number of tracings could be due to (1) creating @tf.function repeatedly in a loop, (2) passing tensors with different shapes, (3) passing Python objects instead of tensors. For (1), please define your @tf.function outside of the loop. For (2), @tf.function has reduce_retracing=True option that can avoid unnecessary retracing. For (3), please refer to https://www.tensorflow.org/guide/function#controlling_retracing and https://www.tensorflow.org/api_docs/python/tf/function for  more details.

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 1s 786ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 26ms/step
Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 1s 511ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 26ms/step


RUNIT TEST PROTOCOL -- Wed Jun 18 22:44:08 2025 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
DNAcycP2 RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 15.819   1.975  16.246