Dongmin Jung
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/GenProSeq |
| git_branch: RELEASE_3_18 |
| git_last_commit: b262d91 |
| git_last_commit_date: 2023-10-24 11:40:41 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:11 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 833/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenProSeq 1.6.0 (landing page) Dongmin Jung
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
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. |
| Package: GenProSeq |
| Version: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2024-04-17 14:59:33 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 15:01:25 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 112.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenProSeq.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/GenProSeq.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenProSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenProSeq’ version ‘1.6.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ART 5.692 0.968 6.888
* 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-3.18-bioc-mac-arm64/meat/GenProSeq.Rcheck/00check.log’
for details.
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)
GenProSeq.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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 6.1
Type 'citation("mclust")' for citing this R package in publications.
>
> test_check("GenProSeq")
List of 22
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List of 22
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List of 22
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List of 22
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List of 22
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List of 22
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List of 22
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List of 22
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$ 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"
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$ virtualenv : chr ""
$ virtualenv_activate : chr ""
$ executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ base_executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
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$ 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 "/Library/Python/3.9/site-packages/tensorflow"
$ available : logi TRUE
$ python_versions : chr "/usr/bin/python3"
$ forced : chr "RETICULATE_PYTHON"
- attr(*, "class")= chr "py_config"
List of 22
$ 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 ""
$ executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ base_executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ version_string : chr "3.9.6 (default, Aug 11 2023, 19:44:49) [Clang 15.0.0 (clang-1500.0.40.1)]"
$ 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 "/Library/Python/3.9/site-packages/tensorflow"
$ available : logi TRUE
$ python_versions : chr "/usr/bin/python3"
$ forced : chr "RETICULATE_PYTHON"
- attr(*, "class")= chr "py_config"
List of 22
$ 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"
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$ virtualenv : chr ""
$ virtualenv_activate : chr ""
$ executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ base_executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
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$ conda : chr "False"
$ numpy :List of 2
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..$ version:Class 'numeric_version' hidden list of 1
.. ..$ : int [1:3] 1 24 3
$ required_module : chr "tensorflow"
$ required_module_path: chr "/Library/Python/3.9/site-packages/tensorflow"
$ available : logi TRUE
$ python_versions : chr "/usr/bin/python3"
$ forced : chr "RETICULATE_PYTHON"
- attr(*, "class")= chr "py_config"
List of 22
$ 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 ""
$ executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ base_executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ version_string : chr "3.9.6 (default, Aug 11 2023, 19:44:49) [Clang 15.0.0 (clang-1500.0.40.1)]"
$ 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 "/Library/Python/3.9/site-packages/tensorflow"
$ available : logi TRUE
$ python_versions : chr "/usr/bin/python3"
$ forced : chr "RETICULATE_PYTHON"
- attr(*, "class")= chr "py_config"
List of 22
$ 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 ""
$ executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ base_executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ version_string : chr "3.9.6 (default, Aug 11 2023, 19:44:49) [Clang 15.0.0 (clang-1500.0.40.1)]"
$ 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 "/Library/Python/3.9/site-packages/tensorflow"
$ available : logi TRUE
$ python_versions : chr "/usr/bin/python3"
$ forced : chr "RETICULATE_PYTHON"
- attr(*, "class")= chr "py_config"
List of 22
$ 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 ""
$ executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ base_executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ version_string : chr "3.9.6 (default, Aug 11 2023, 19:44:49) [Clang 15.0.0 (clang-1500.0.40.1)]"
$ 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 "/Library/Python/3.9/site-packages/tensorflow"
$ available : logi TRUE
$ python_versions : chr "/usr/bin/python3"
$ forced : chr "RETICULATE_PYTHON"
- attr(*, "class")= chr "py_config"
List of 22
$ 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 ""
$ executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ base_executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ version_string : chr "3.9.6 (default, Aug 11 2023, 19:44:49) [Clang 15.0.0 (clang-1500.0.40.1)]"
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$ anaconda : logi FALSE
$ conda : chr "False"
$ numpy :List of 2
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..$ version:Class 'numeric_version' hidden list of 1
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$ required_module : chr "tensorflow"
$ required_module_path: chr "/Library/Python/3.9/site-packages/tensorflow"
$ available : logi TRUE
$ python_versions : chr "/usr/bin/python3"
$ forced : chr "RETICULATE_PYTHON"
- attr(*, "class")= chr "py_config"
List of 22
$ 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 ""
$ executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ base_executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ version_string : chr "3.9.6 (default, Aug 11 2023, 19:44:49) [Clang 15.0.0 (clang-1500.0.40.1)]"
$ version : chr "3.9"
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$ 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 "/Library/Python/3.9/site-packages/tensorflow"
$ available : logi TRUE
$ python_versions : chr "/usr/bin/python3"
$ forced : chr "RETICULATE_PYTHON"
- attr(*, "class")= chr "py_config"
List of 22
$ 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 ""
$ executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ base_executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ version_string : chr "3.9.6 (default, Aug 11 2023, 19:44:49) [Clang 15.0.0 (clang-1500.0.40.1)]"
$ 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 "/Library/Python/3.9/site-packages/tensorflow"
$ available : logi TRUE
$ python_versions : chr "/usr/bin/python3"
$ forced : chr "RETICULATE_PYTHON"
- attr(*, "class")= chr "py_config"
List of 22
$ 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 ""
$ executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ base_executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ version_string : chr "3.9.6 (default, Aug 11 2023, 19:44:49) [Clang 15.0.0 (clang-1500.0.40.1)]"
$ 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 "/Library/Python/3.9/site-packages/tensorflow"
$ available : logi TRUE
$ python_versions : chr "/usr/bin/python3"
$ forced : chr "RETICULATE_PYTHON"
- attr(*, "class")= chr "py_config"
List of 22
$ 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 ""
$ executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ base_executable : chr "/Library/Developer/CommandLineTools/usr/bin/python3"
$ version_string : chr "3.9.6 (default, Aug 11 2023, 19:44:49) [Clang 15.0.0 (clang-1500.0.40.1)]"
$ 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 "/Library/Python/3.9/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
13.535 1.044 13.751
GenProSeq.Rcheck/GenProSeq-Ex.timings
| name | user | system | elapsed | |
| ART | 5.692 | 0.968 | 6.888 | |
| GAN | 0.014 | 0.003 | 0.017 | |
| VAE | 0.017 | 0.004 | 0.020 | |
| prot_seq_check | 0.009 | 0.002 | 0.012 | |
| prot_vec | 0.754 | 0.026 | 0.784 | |
| transformer | 0.011 | 0.002 | 0.013 | |