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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DNAcycP2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DNAcycP2_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DNAcycP2.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* 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 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 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 4.503  0.937  15.466
* 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

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DNAcycP2
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 248ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 11ms/step
Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 267ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 14ms/step
Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 208ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 8ms/step
Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 248ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 11ms/step
Reading sequences...
Predicting cyclizability...
WARNING:tensorflow:5 out of the last 9 calls to <function Model.make_predict_function.<locals>.predict_function at 0x2c6cbe520> 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 247ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 10ms/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
WARNING:tensorflow:6 out of the last 11 calls to <function Model.make_predict_function.<locals>.predict_function at 0x2c8d76840> 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.
Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 394ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 11ms/step
Reading sequences...
Predicting cyclizability...

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 195ms/step

1/1 [==============================] - ETA: 0s
1/1 [==============================] - 0s 9ms/step


RUNIT TEST PROTOCOL -- Fri Aug  8 19:11:00 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 
  7.549   0.765   8.644