Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 817/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenProSeq 1.4.2  (landing page)
Dongmin Jung
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/GenProSeq
git_branch: RELEASE_3_17
git_last_commit: 54af195
git_last_commit_date: 2023-05-24 07:38:10 -0400 (Wed, 24 May 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for GenProSeq on kjohnson2


To the developers/maintainers of the GenProSeq package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: GenProSeq
Version: 1.4.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenProSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenProSeq_1.4.2.tar.gz
StartedAt: 2023-10-17 22:00:16 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 22:03:16 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 180.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GenProSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenProSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenProSeq_1.4.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GenProSeq.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenProSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenProSeq’ version ‘1.4.2’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenProSeq’ 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 ... NOTE
fit_VAE: no visible binding for global variable ‘z_mean’
fit_VAE: no visible binding for global variable ‘z_log_stddev’
fit_VAE : vae_loss: no visible binding for global variable
  ‘z_log_stddev’
fit_VAE : vae_loss: no visible binding for global variable ‘z_mean’
layer_embedding_token_position : <anonymous>: no visible global
  function definition for ‘super’
layer_embedding_token_position : <anonymous>: no visible binding for
  global variable ‘self’
layer_transformer_encoder : <anonymous>: no visible global function
  definition for ‘super’
layer_transformer_encoder : <anonymous>: no visible binding for global
  variable ‘self’
Undefined global functions or variables:
  self super z_log_stddev z_mean
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
     user system elapsed
ART 8.106  1.648  19.922
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GenProSeq.Rcheck/00check.log’
for details.

Installation output

GenProSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenProSeq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘GenProSeq’ ...
** using staged installation
** R
** data
** 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 (GenProSeq)

Tests output

GenProSeq.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(GenProSeq)
Loading required package: keras
Loading required package: mclust
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.
> 
> test_check("GenProSeq")
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 - attr(*, "class")= chr "py_config"
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 $ libpython           : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/config-3.9-"| __truncated__
 $ pythonhome          : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9:/Library/Developer/Comman"| __truncated__
 $ pythonpath          : chr "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/reticulate/config:/Library/Developer/Comma"| __truncated__
 $ prefix              : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ exec_prefix         : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ base_exec_prefix    : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.9.6 (default, Oct 18 2022, 12:41:40)  [Clang 14.0.0 (clang-1400.0.29.202)]"
 $ version             : chr "3.9"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : chr "False"
 $ numpy               :List of 2
  ..$ path   : chr "/Library/Python/3.9/site-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 3
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/Users/biocbuild/Library/Python/3.9/lib/python/site-packages/tensorflow"
 $ available           : logi TRUE
 $ python_versions     : chr "/usr/bin/python3"
 $ forced              : chr "RETICULATE_PYTHON"
 - attr(*, "class")= chr "py_config"
List of 20
 $ python              : chr "/usr/bin/python3"
 $ libpython           : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/config-3.9-"| __truncated__
 $ pythonhome          : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9:/Library/Developer/Comman"| __truncated__
 $ pythonpath          : chr "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/reticulate/config:/Library/Developer/Comma"| __truncated__
 $ prefix              : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ exec_prefix         : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ base_exec_prefix    : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.9.6 (default, Oct 18 2022, 12:41:40)  [Clang 14.0.0 (clang-1400.0.29.202)]"
 $ version             : chr "3.9"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : chr "False"
 $ numpy               :List of 2
  ..$ path   : chr "/Library/Python/3.9/site-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 3
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/Users/biocbuild/Library/Python/3.9/lib/python/site-packages/tensorflow"
 $ available           : logi TRUE
 $ python_versions     : chr "/usr/bin/python3"
 $ forced              : chr "RETICULATE_PYTHON"
 - attr(*, "class")= chr "py_config"
List of 20
 $ python              : chr "/usr/bin/python3"
 $ libpython           : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/config-3.9-"| __truncated__
 $ pythonhome          : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9:/Library/Developer/Comman"| __truncated__
 $ pythonpath          : chr "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/reticulate/config:/Library/Developer/Comma"| __truncated__
 $ prefix              : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ exec_prefix         : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ base_exec_prefix    : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.9.6 (default, Oct 18 2022, 12:41:40)  [Clang 14.0.0 (clang-1400.0.29.202)]"
 $ version             : chr "3.9"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : chr "False"
 $ numpy               :List of 2
  ..$ path   : chr "/Library/Python/3.9/site-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 3
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/Users/biocbuild/Library/Python/3.9/lib/python/site-packages/tensorflow"
 $ available           : logi TRUE
 $ python_versions     : chr "/usr/bin/python3"
 $ forced              : chr "RETICULATE_PYTHON"
 - attr(*, "class")= chr "py_config"
List of 20
 $ python              : chr "/usr/bin/python3"
 $ libpython           : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/config-3.9-"| __truncated__
 $ pythonhome          : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9:/Library/Developer/Comman"| __truncated__
 $ pythonpath          : chr "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/reticulate/config:/Library/Developer/Comma"| __truncated__
 $ prefix              : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ exec_prefix         : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ base_exec_prefix    : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.9.6 (default, Oct 18 2022, 12:41:40)  [Clang 14.0.0 (clang-1400.0.29.202)]"
 $ version             : chr "3.9"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : chr "False"
 $ numpy               :List of 2
  ..$ path   : chr "/Library/Python/3.9/site-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 3
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/Users/biocbuild/Library/Python/3.9/lib/python/site-packages/tensorflow"
 $ available           : logi TRUE
 $ python_versions     : chr "/usr/bin/python3"
 $ forced              : chr "RETICULATE_PYTHON"
 - attr(*, "class")= chr "py_config"
List of 20
 $ python              : chr "/usr/bin/python3"
 $ libpython           : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/config-3.9-"| __truncated__
 $ pythonhome          : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9:/Library/Developer/Comman"| __truncated__
 $ pythonpath          : chr "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/reticulate/config:/Library/Developer/Comma"| __truncated__
 $ prefix              : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ exec_prefix         : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ base_exec_prefix    : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.9.6 (default, Oct 18 2022, 12:41:40)  [Clang 14.0.0 (clang-1400.0.29.202)]"
 $ version             : chr "3.9"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : chr "False"
 $ numpy               :List of 2
  ..$ path   : chr "/Library/Python/3.9/site-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 3
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/Users/biocbuild/Library/Python/3.9/lib/python/site-packages/tensorflow"
 $ available           : logi TRUE
 $ python_versions     : chr "/usr/bin/python3"
 $ forced              : chr "RETICULATE_PYTHON"
 - attr(*, "class")= chr "py_config"
List of 20
 $ python              : chr "/usr/bin/python3"
 $ libpython           : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/config-3.9-"| __truncated__
 $ pythonhome          : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9:/Library/Developer/Comman"| __truncated__
 $ pythonpath          : chr "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/reticulate/config:/Library/Developer/Comma"| __truncated__
 $ prefix              : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ exec_prefix         : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ base_exec_prefix    : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.9.6 (default, Oct 18 2022, 12:41:40)  [Clang 14.0.0 (clang-1400.0.29.202)]"
 $ version             : chr "3.9"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : chr "False"
 $ numpy               :List of 2
  ..$ path   : chr "/Library/Python/3.9/site-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 3
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/Users/biocbuild/Library/Python/3.9/lib/python/site-packages/tensorflow"
 $ available           : logi TRUE
 $ python_versions     : chr "/usr/bin/python3"
 $ forced              : chr "RETICULATE_PYTHON"
 - attr(*, "class")= chr "py_config"
List of 20
 $ python              : chr "/usr/bin/python3"
 $ libpython           : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/config-3.9-"| __truncated__
 $ pythonhome          : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9:/Library/Developer/Comman"| __truncated__
 $ pythonpath          : chr "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/reticulate/config:/Library/Developer/Comma"| __truncated__
 $ prefix              : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ exec_prefix         : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ base_exec_prefix    : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.9.6 (default, Oct 18 2022, 12:41:40)  [Clang 14.0.0 (clang-1400.0.29.202)]"
 $ version             : chr "3.9"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : chr "False"
 $ numpy               :List of 2
  ..$ path   : chr "/Library/Python/3.9/site-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 3
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/Users/biocbuild/Library/Python/3.9/lib/python/site-packages/tensorflow"
 $ available           : logi TRUE
 $ python_versions     : chr "/usr/bin/python3"
 $ forced              : chr "RETICULATE_PYTHON"
 - attr(*, "class")= chr "py_config"
List of 20
 $ python              : chr "/usr/bin/python3"
 $ libpython           : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/config-3.9-"| __truncated__
 $ pythonhome          : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9:/Library/Developer/Comman"| __truncated__
 $ pythonpath          : chr "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/reticulate/config:/Library/Developer/Comma"| __truncated__
 $ prefix              : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ exec_prefix         : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ base_exec_prefix    : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.9.6 (default, Oct 18 2022, 12:41:40)  [Clang 14.0.0 (clang-1400.0.29.202)]"
 $ version             : chr "3.9"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : chr "False"
 $ numpy               :List of 2
  ..$ path   : chr "/Library/Python/3.9/site-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 3
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/Users/biocbuild/Library/Python/3.9/lib/python/site-packages/tensorflow"
 $ available           : logi TRUE
 $ python_versions     : chr "/usr/bin/python3"
 $ forced              : chr "RETICULATE_PYTHON"
 - attr(*, "class")= chr "py_config"
List of 20
 $ python              : chr "/usr/bin/python3"
 $ libpython           : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/config-3.9-"| __truncated__
 $ pythonhome          : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9:/Library/Developer/Comman"| __truncated__
 $ pythonpath          : chr "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/reticulate/config:/Library/Developer/Comma"| __truncated__
 $ prefix              : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ exec_prefix         : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ base_exec_prefix    : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.9.6 (default, Oct 18 2022, 12:41:40)  [Clang 14.0.0 (clang-1400.0.29.202)]"
 $ version             : chr "3.9"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : chr "False"
 $ numpy               :List of 2
  ..$ path   : chr "/Library/Python/3.9/site-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 3
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/Users/biocbuild/Library/Python/3.9/lib/python/site-packages/tensorflow"
 $ available           : logi TRUE
 $ python_versions     : chr "/usr/bin/python3"
 $ forced              : chr "RETICULATE_PYTHON"
 - attr(*, "class")= chr "py_config"
List of 20
 $ python              : chr "/usr/bin/python3"
 $ libpython           : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/config-3.9-"| __truncated__
 $ pythonhome          : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9:/Library/Developer/Comman"| __truncated__
 $ pythonpath          : chr "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/reticulate/config:/Library/Developer/Comma"| __truncated__
 $ prefix              : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ exec_prefix         : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ base_exec_prefix    : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.9.6 (default, Oct 18 2022, 12:41:40)  [Clang 14.0.0 (clang-1400.0.29.202)]"
 $ version             : chr "3.9"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : chr "False"
 $ numpy               :List of 2
  ..$ path   : chr "/Library/Python/3.9/site-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 3
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/Users/biocbuild/Library/Python/3.9/lib/python/site-packages/tensorflow"
 $ available           : logi TRUE
 $ python_versions     : chr "/usr/bin/python3"
 $ forced              : chr "RETICULATE_PYTHON"
 - attr(*, "class")= chr "py_config"
List of 20
 $ python              : chr "/usr/bin/python3"
 $ libpython           : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/config-3.9-"| __truncated__
 $ pythonhome          : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9:/Library/Developer/Comman"| __truncated__
 $ pythonpath          : chr "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/reticulate/config:/Library/Developer/Comma"| __truncated__
 $ prefix              : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ exec_prefix         : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ base_exec_prefix    : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.9.6 (default, Oct 18 2022, 12:41:40)  [Clang 14.0.0 (clang-1400.0.29.202)]"
 $ version             : chr "3.9"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : chr "False"
 $ numpy               :List of 2
  ..$ path   : chr "/Library/Python/3.9/site-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 3
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/Users/biocbuild/Library/Python/3.9/lib/python/site-packages/tensorflow"
 $ available           : logi TRUE
 $ python_versions     : chr "/usr/bin/python3"
 $ forced              : chr "RETICULATE_PYTHON"
 - attr(*, "class")= chr "py_config"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
 13.048   1.093  20.235

Example timings

GenProSeq.Rcheck/GenProSeq-Ex.timings

nameusersystemelapsed
ART 8.106 1.64819.922
GAN0.0260.0040.040
VAE0.0310.0040.053
prot_seq_check0.2320.0050.368
prot_vec0.4270.0410.724
transformer0.0230.0040.036