##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DNAcycP2.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings DNAcycP2_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/DNAcycP2.Rcheck'
* using R version 4.5.0 (2025-04-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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 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 8.08   3.84   94.39
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL DNAcycP2
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

C:\Users\BIOCBU~1\BASILI~1\121~1.0\0\Lib\site-packages\conda\base\context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. 

To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:

  conda config --add channels defaults

For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html

  deprecated.topic(
C:\Users\BIOCBU~1\BASILI~1\121~1.0\0\Lib\site-packages\conda\base\context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. 

To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:

  conda config --add channels defaults

For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html

  deprecated.topic(
C:\Users\BIOCBU~1\BASILI~1\121~1.0\0\Lib\site-packages\conda\base\context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. 

To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:

  conda config --add channels defaults

For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html

  deprecated.topic(
2025-05-09 01:21:55.562134: 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: SSE SSE2 SSE3 SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 1s 891ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 31ms/step
Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 1s 719ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 31ms/step
Reading sequences...
Predicting cyclizability...

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

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 16ms/step
Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 1s 844ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 31ms/step
Reading sequences...
Predicting cyclizability...
WARNING:tensorflow:5 out of the last 9 calls to <function Model.make_predict_function.<locals>.predict_function at 0x0000018B6D249080> 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 766ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 31ms/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 0x0000018B69E9F920> 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 875ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 31ms/step
Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 1s 766ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 31ms/step


RUNIT TEST PROTOCOL -- Fri May  9 01:22:12 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 
  22.43    2.96   42.59