Aaron Lun
| Snapshot Date: 2025-11-12 13:40 -0500 (Wed, 12 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/basilisk |
| git_branch: devel |
| git_last_commit: b653397 |
| git_last_commit_date: 2025-10-29 10:56:48 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4013 |
| 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 143/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| basilisk 1.23.0 (landing page) Aaron Lun
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the basilisk package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/basilisk.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: basilisk |
| Version: 1.23.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basilisk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basilisk_1.23.0.tar.gz |
| StartedAt: 2025-11-12 18:01:40 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 18:07:41 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 360.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: basilisk.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basilisk.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basilisk_1.23.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/basilisk.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.23.0’
* 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 ... NOTE
Found the following hidden files and directories:
inst/example/.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 ‘basilisk’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/basilisk.Rcheck/00install.out’ for details.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
basiliskStart 14.916 4.445 46.304
createLocalBasiliskEnv 7.049 2.265 24.055
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/basilisk.Rcheck/00check.log’
for details.
basilisk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL basilisk ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘basilisk’ ... ** this is package ‘basilisk’ version ‘1.23.0’ ** using non-staged installation via StagedInstall field ** 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 * DONE (basilisk)
basilisk.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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.
> library(testthat)
> library(basilisk)
Loading required package: reticulate
> test_check("basilisk")
Using Python: /Users/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment 'install-test-client/my_package_A' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in ./install-test-client/my_package_A/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.3-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'pandas==2.2.3', 'python-dateutil==2.8.2', 'pytz==2024.1'
Collecting pandas==2.2.3
Using cached pandas-2.2.3-cp312-cp312-macosx_11_0_arm64.whl.metadata (89 kB)
Collecting python-dateutil==2.8.2
Using cached python_dateutil-2.8.2-py2.py3-none-any.whl.metadata (8.2 kB)
Collecting pytz==2024.1
Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting numpy>=1.26.0 (from pandas==2.2.3)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting six>=1.5 (from python-dateutil==2.8.2)
Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Using cached pandas-2.2.3-cp312-cp312-macosx_11_0_arm64.whl (11.4 MB)
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Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.3.4 pandas-2.2.3 python-dateutil-2.8.2 pytz-2024.1 six-1.17.0 tzdata-2025.2
Virtual environment 'install-test-client/my_package_A' successfully created.
Using Python: /Users/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment 'install-test-client/my_package_B' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in ./install-test-client/my_package_B/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.3-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'pandas==2.2.2', 'python-dateutil==2.8.2', 'pytz==2023.4'
Collecting pandas==2.2.2
Using cached pandas-2.2.2-cp312-cp312-macosx_11_0_arm64.whl.metadata (19 kB)
Collecting python-dateutil==2.8.2
Using cached python_dateutil-2.8.2-py2.py3-none-any.whl.metadata (8.2 kB)
Collecting pytz==2023.4
Using cached pytz-2023.4-py2.py3-none-any.whl.metadata (22 kB)
Collecting numpy>=1.26.0 (from pandas==2.2.2)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.2)
Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting six>=1.5 (from python-dateutil==2.8.2)
Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Using cached pandas-2.2.2-cp312-cp312-macosx_11_0_arm64.whl (11.3 MB)
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Using cached pytz-2023.4-py2.py3-none-any.whl (506 kB)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl (14.2 MB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.3.4 pandas-2.2.2 python-dateutil-2.8.2 pytz-2023.4 six-1.17.0 tzdata-2025.2
Virtual environment 'install-test-client/my_package_B' successfully created.
Using Python: /Users/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment '/Users/biocbuild/bbs-3.23-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.23.0' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in ./install-test-client/locality/1.23.0/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.3-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'pandas==2.2.3', 'python-dateutil==2.8.2', 'pytz==2024.1'
Collecting pandas==2.2.3
Using cached pandas-2.2.3-cp312-cp312-macosx_11_0_arm64.whl.metadata (89 kB)
Collecting python-dateutil==2.8.2
Using cached python_dateutil-2.8.2-py2.py3-none-any.whl.metadata (8.2 kB)
Collecting pytz==2024.1
Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting numpy>=1.26.0 (from pandas==2.2.3)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting six>=1.5 (from python-dateutil==2.8.2)
Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Using cached pandas-2.2.3-cp312-cp312-macosx_11_0_arm64.whl (11.4 MB)
Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl (14.2 MB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.3.4 pandas-2.2.3 python-dateutil-2.8.2 pytz-2024.1 six-1.17.0 tzdata-2025.2
Virtual environment '/Users/biocbuild/bbs-3.23-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.23.0' successfully created.
Using Python: /Users/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpRPXrRD/file150104fbbeeff/1.23.0/basilisk/1.23.0/test' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpRPXrRD/file150104fbbeeff/1.23.0/basilisk/1.23.0/test/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.3-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'pandas==2.2.3'
Collecting pandas==2.2.3
Using cached pandas-2.2.3-cp312-cp312-macosx_11_0_arm64.whl.metadata (89 kB)
Collecting numpy>=1.26.0 (from pandas==2.2.3)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting python-dateutil>=2.8.2 (from pandas==2.2.3)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas==2.2.3)
Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas==2.2.3)
Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Using cached pandas-2.2.3-cp312-cp312-macosx_11_0_arm64.whl (11.4 MB)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl (14.2 MB)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.3.4 pandas-2.2.3 python-dateutil-2.9.0.post0 pytz-2025.2 six-1.17.0 tzdata-2025.2
Virtual environment '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpRPXrRD/file150104fbbeeff/1.23.0/basilisk/1.23.0/test' successfully created.
* installing *source* package ‘son.of.basilisk’ ...
** this is package ‘son.of.basilisk’ version ‘0.99.0’
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (son.of.basilisk)
Using Python: /Users/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.23.0/son.of.basilisk/0.99.0/env1' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.23.0/son.of.basilisk/0.99.0/env1/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.3-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'pandas==2.2.3'
Collecting pandas==2.2.3
Using cached pandas-2.2.3-cp312-cp312-macosx_11_0_arm64.whl.metadata (89 kB)
Collecting numpy>=1.26.0 (from pandas==2.2.3)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting python-dateutil>=2.8.2 (from pandas==2.2.3)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas==2.2.3)
Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas==2.2.3)
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Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.3.4 pandas-2.2.3 python-dateutil-2.9.0.post0 pytz-2025.2 six-1.17.0 tzdata-2025.2
Virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.23.0/son.of.basilisk/0.99.0/env1' successfully created.
Using Python: /Users/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.23.0/son.of.basilisk/0.99.0/env2' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.23.0/son.of.basilisk/0.99.0/env2/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.3-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'scikit-learn==1.6.1'
Collecting scikit-learn==1.6.1
Using cached scikit_learn-1.6.1-cp312-cp312-macosx_12_0_arm64.whl.metadata (31 kB)
Collecting numpy>=1.19.5 (from scikit-learn==1.6.1)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting scipy>=1.6.0 (from scikit-learn==1.6.1)
Using cached scipy-1.16.3-cp312-cp312-macosx_12_0_arm64.whl.metadata (62 kB)
Collecting joblib>=1.2.0 (from scikit-learn==1.6.1)
Using cached joblib-1.5.2-py3-none-any.whl.metadata (5.6 kB)
Collecting threadpoolctl>=3.1.0 (from scikit-learn==1.6.1)
Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
Using cached scikit_learn-1.6.1-cp312-cp312-macosx_12_0_arm64.whl (11.2 MB)
Using cached joblib-1.5.2-py3-none-any.whl (308 kB)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl (14.2 MB)
Using cached scipy-1.16.3-cp312-cp312-macosx_12_0_arm64.whl (28.9 MB)
Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
Installing collected packages: threadpoolctl, numpy, joblib, scipy, scikit-learn
Successfully installed joblib-1.5.2 numpy-2.3.4 scikit-learn-1.6.1 scipy-1.16.3 threadpoolctl-3.6.0
Virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.23.0/son.of.basilisk/0.99.0/env2' successfully created.
Using Python: /Users/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.23.0/son.of.basilisk/0.99.0/env3' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.23.0/son.of.basilisk/0.99.0/env3/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.3-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
Virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.23.0/son.of.basilisk/0.99.0/env3' successfully created.
Processing /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpRPXrRD/Rlib.15010220bffec/son.of.basilisk/test_dummy
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: test_dummy
Building wheel for test_dummy (pyproject.toml): started
Building wheel for test_dummy (pyproject.toml): finished with status 'done'
Created wheel for test_dummy: filename=test_dummy-0.1-py3-none-any.whl size=1312 sha256=4f2985d3a81d958402afb7c6a56fdd29c05ab6879f6c8d5a8157dd0dce8398b2
Stored in directory: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/pip-ephem-wheel-cache-v8cn2rk0/wheels/8f/f1/07/03a5f9f151288536dcffb59f10c5d16535aa21f4239020a10c
Successfully built test_dummy
Installing collected packages: test_dummy
Successfully installed test_dummy-0.1
Using Python: /Users/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment 'install-test-client/thingo' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in ./install-test-client/thingo/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.3-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'pandas==2.2.3', 'python-dateutil==2.8.2', 'pytz==2024.1'
Collecting pandas==2.2.3
Using cached pandas-2.2.3-cp312-cp312-macosx_11_0_arm64.whl.metadata (89 kB)
Collecting python-dateutil==2.8.2
Using cached python_dateutil-2.8.2-py2.py3-none-any.whl.metadata (8.2 kB)
Collecting pytz==2024.1
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Collecting numpy>=1.26.0 (from pandas==2.2.3)
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Collecting tzdata>=2022.7 (from pandas==2.2.3)
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Collecting six>=1.5 (from python-dateutil==2.8.2)
Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Using cached pandas-2.2.3-cp312-cp312-macosx_11_0_arm64.whl (11.4 MB)
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Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.3.4 pandas-2.2.3 python-dateutil-2.8.2 pytz-2024.1 six-1.17.0 tzdata-2025.2
Virtual environment 'install-test-client/thingo' successfully created.
Using Python: /Users/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment 'install-test-client/thingo' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in ./install-test-client/thingo/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.3-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'pandas==2.2.2', 'python-dateutil==2.8.2', 'pytz==2023.4'
Collecting pandas==2.2.2
Using cached pandas-2.2.2-cp312-cp312-macosx_11_0_arm64.whl.metadata (19 kB)
Collecting python-dateutil==2.8.2
Using cached python_dateutil-2.8.2-py2.py3-none-any.whl.metadata (8.2 kB)
Collecting pytz==2023.4
Using cached pytz-2023.4-py2.py3-none-any.whl.metadata (22 kB)
Collecting numpy>=1.26.0 (from pandas==2.2.2)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.2)
Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting six>=1.5 (from python-dateutil==2.8.2)
Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Using cached pandas-2.2.2-cp312-cp312-macosx_11_0_arm64.whl (11.3 MB)
Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Using cached pytz-2023.4-py2.py3-none-any.whl (506 kB)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl (14.2 MB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.3.4 pandas-2.2.2 python-dateutil-2.8.2 pytz-2023.4 six-1.17.0 tzdata-2025.2
Virtual environment 'install-test-client/thingo' successfully created.
Using Python: /Users/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment 'install-test-client/thingo' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in ./install-test-client/thingo/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.3-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
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Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
Virtual environment 'install-test-client/thingo' successfully created.
Processing /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/basilisk/example/inst/test_dummy
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: test_dummy
Building wheel for test_dummy (pyproject.toml): started
Building wheel for test_dummy (pyproject.toml): finished with status 'done'
Created wheel for test_dummy: filename=test_dummy-0.1-py3-none-any.whl size=1312 sha256=c091aa72befaa7e84ab8cf339794a55afb0b8cb2dfe334bb1d369c9d154560e7
Stored in directory: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/pip-ephem-wheel-cache-cw8l_1t4/wheels/40/22/43/026d83aa8a75b3f56036c298a1bdc99052ce736ed5088638cc
Successfully built test_dummy
Installing collected packages: test_dummy
Successfully installed test_dummy-0.1
Using Python: /Users/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment 'install-test-client/thingo' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in ./install-test-client/thingo/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.3-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'WHHEEEEEEEEEEEEEEEEEE==0.0.1'
ERROR: Could not find a version that satisfies the requirement WHHEEEEEEEEEEEEEEEEEE==0.0.1 (from versions: none)
ERROR: No matching distribution found for WHHEEEEEEEEEEEEEEEEEE==0.0.1
Using Python: /Users/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment 'install-test-client/thingo' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in ./install-test-client/thingo/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.3-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
Installing packages: 'pandas==2.2.3', 'python-dateutil==2.8.2', 'pytz==2024.1'
Collecting pandas==2.2.3
Using cached pandas-2.2.3-cp312-cp312-macosx_11_0_arm64.whl.metadata (89 kB)
Collecting python-dateutil==2.8.2
Using cached python_dateutil-2.8.2-py2.py3-none-any.whl.metadata (8.2 kB)
Collecting pytz==2024.1
Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting numpy>=1.26.0 (from pandas==2.2.3)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting six>=1.5 (from python-dateutil==2.8.2)
Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Using cached pandas-2.2.3-cp312-cp312-macosx_11_0_arm64.whl (11.4 MB)
Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl (14.2 MB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.3.4 pandas-2.2.3 python-dateutil-2.8.2 pytz-2024.1 six-1.17.0 tzdata-2025.2
Virtual environment 'install-test-client/thingo' successfully created.
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 60 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Mac (1): 'test-setupBasiliskEnv.R:32:5'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 60 ]
>
> proc.time()
user system elapsed
115.374 33.914 262.135
basilisk.Rcheck/basilisk-Ex.timings
| name | user | system | elapsed | |
| BasiliskEnvironment-class | 0.001 | 0.000 | 0.002 | |
| PyPiLink | 0 | 0 | 0 | |
| basiliskOptions | 0.000 | 0.000 | 0.001 | |
| basiliskStart | 14.916 | 4.445 | 46.304 | |
| clearExternalDir | 0 | 0 | 0 | |
| configureBasiliskEnv | 0 | 0 | 0 | |
| createLocalBasiliskEnv | 7.049 | 2.265 | 24.055 | |
| getBinaries | 0 | 0 | 0 | |
| getExternalDir | 0 | 0 | 0 | |
| getSystemDir | 0 | 0 | 0 | |
| listPackages | 0.148 | 0.046 | 0.221 | |
| lockExternalDir | 0.001 | 0.001 | 0.002 | |
| obtainEnvironmentPath | 0.000 | 0.000 | 0.001 | |
| platform | 0 | 0 | 0 | |
| setupBasiliskEnv | 0 | 0 | 0 | |
| useBasiliskEnv | 0.108 | 0.026 | 0.100 | |