Back to Build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-05-10 10:04:32 -0000 (Wed, 10 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6211
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CHECK results for GenProSeq on kunpeng1


To the developers/maintainers of the GenProSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenProSeq.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 802/2194HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenProSeq 1.5.0  (landing page)
Dongmin Jung
Snapshot Date: 2023-05-08 19:11:19 -0000 (Mon, 08 May 2023)
git_url: https://git.bioconductor.org/packages/GenProSeq
git_branch: devel
git_last_commit: 71654d7
git_last_commit_date: 2023-04-25 15:36:58 -0000 (Tue, 25 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: GenProSeq
Version: 1.5.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenProSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GenProSeq_1.5.0.tar.gz
StartedAt: 2023-05-09 17:02:52 -0000 (Tue, 09 May 2023)
EndedAt: 2023-05-09 17:04:39 -0000 (Tue, 09 May 2023)
EllapsedTime: 107.1 seconds
RetCode: 0
Status:   OK  
CheckDir: GenProSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenProSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GenProSeq_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenProSeq.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘GenProSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenProSeq’ version ‘1.5.0’
* 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
* 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 ...
  ‘GenProSeq.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/GenProSeq.Rcheck/00check.log’
for details.

Installation output

GenProSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenProSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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 Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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")
List of 20
 $ python              : chr "/usr/bin/python3"
 $ libpython           : chr "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
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 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 "/usr/lib/python3.10/config-3.10-aarch64-linux-gnu/libpython3.10.so"
 $ pythonhome          : chr "//usr://usr"
 $ pythonpath          : chr "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/reticulate/config:/usr/lib/python310."| __truncated__
 $ prefix              : chr "/usr"
 $ exec_prefix         : chr "/usr"
 $ base_exec_prefix    : chr "/usr"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.10.6 (main, Mar 10 2023, 10:55:28) [GCC 11.3.0]"
 $ version             : chr "3.10"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : logi FALSE
 $ numpy               :List of 2
  ..$ path   : chr "/usr/local/lib/python3.10/dist-packages/numpy"
  ..$ version:Class 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 1 24 1
 $ required_module     : chr "tensorflow"
 $ required_module_path: chr "/usr/local/lib/python3.10/dist-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 
  7.538   0.722   8.084

Example timings

GenProSeq.Rcheck/GenProSeq-Ex.timings

nameusersystemelapsed
ART2.5180.2822.852
GAN0.2760.0040.280
VAE0.0200.0000.021
prot_seq_check0.0190.0000.020
prot_vec0.4400.0560.496
transformer0.0120.0080.019