Aaron Lun
| Snapshot Date: 2025-07-23 13:25 -0400 (Wed, 23 Jul 2025) |
| git_url: https://git.bioconductor.org/packages/basilisk |
| git_branch: devel |
| git_last_commit: e93af07 |
| git_last_commit_date: 2025-05-19 16:40:18 -0400 (Mon, 19 May 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-07-24 12:10 -0400 (Thu, 24 Jul 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4792 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4530 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4573 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4514 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4510 |
| 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 139/2311 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| basilisk 1.21.5 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.21.5 |
| 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_1.21.5.tar.gz |
| StartedAt: 2025-07-23 19:12:51 -0400 (Wed, 23 Jul 2025) |
| EndedAt: 2025-07-23 19:23:15 -0400 (Wed, 23 Jul 2025) |
| EllapsedTime: 623.8 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_1.21.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/basilisk.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.21.5’
* 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-3.22-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 42.230 11.171 86.315
createLocalBasiliskEnv 20.339 5.457 44.496
* 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-3.22-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/4.5-x86_64/Resources/library’ * installing *source* package ‘basilisk’ ... ** this is package ‘basilisk’ version ‘1.21.5’ ** 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 version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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-25.1.1-py3-none-any.whl.metadata (3.6 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-25.1.1-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-25.1.1 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_10_9_x86_64.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-2.3.1-cp312-cp312-macosx_10_13_x86_64.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_10_9_x86_64.whl (12.5 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-2.3.1 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-25.1.1-py3-none-any.whl.metadata (3.6 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-25.1.1-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-25.1.1 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_10_9_x86_64.whl.metadata (19 kB)
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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-2.3.1-cp312-cp312-macosx_10_13_x86_64.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_10_9_x86_64.whl (12.5 MB)
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Using cached pytz-2023.4-py2.py3-none-any.whl (506 kB)
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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-2.3.1 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-3.22-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.21.5' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in ./install-test-client/locality/1.21.5/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 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-25.1.1-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-25.1.1 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_10_9_x86_64.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-2.3.1-cp312-cp312-macosx_10_13_x86_64.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_10_9_x86_64.whl (12.5 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-2.3.1-cp312-cp312-macosx_10_13_x86_64.whl (20.9 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-2.3.1 pandas-2.2.3 python-dateutil-2.8.2 pytz-2024.1 six-1.17.0 tzdata-2025.2
Virtual environment '/Users/biocbuild/bbs-3.22-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.21.5' successfully created.
Using Python: /Users/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment '/tmp/RtmpHMUO8o/file1347113eed076/1.21.5/basilisk/1.21.5/test' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /private/tmp/RtmpHMUO8o/file1347113eed076/1.21.5/basilisk/1.21.5/test/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 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-25.1.1-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-25.1.1 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_10_9_x86_64.whl.metadata (89 kB)
Collecting numpy>=1.26.0 (from pandas==2.2.3)
Using cached numpy-2.3.1-cp312-cp312-macosx_10_13_x86_64.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_10_9_x86_64.whl (12.5 MB)
Using cached numpy-2.3.1-cp312-cp312-macosx_10_13_x86_64.whl (20.9 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-2.3.1 pandas-2.2.3 python-dateutil-2.9.0.post0 pytz-2025.2 six-1.17.0 tzdata-2025.2
Virtual environment '/tmp/RtmpHMUO8o/file1347113eed076/1.21.5/basilisk/1.21.5/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 '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-25.1.1-py3-none-any.whl.metadata (3.6 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-25.1.1-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-25.1.1 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_10_9_x86_64.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-2.3.1-cp312-cp312-macosx_10_13_x86_64.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)
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Using cached pandas-2.2.3-cp312-cp312-macosx_10_9_x86_64.whl (12.5 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-2.3.1 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-25.1.1-py3-none-any.whl.metadata (3.6 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-25.1.1-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-25.1.1 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_10_9_x86_64.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-2.3.1-cp312-cp312-macosx_10_13_x86_64.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_10_9_x86_64.whl (12.5 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-2.3.1-cp312-cp312-macosx_10_13_x86_64.whl (20.9 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-2.3.1 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-25.1.1-py3-none-any.whl.metadata (3.6 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-25.1.1-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-25.1.1 setuptools-80.9.0 wheel-0.45.1
Virtual environment 'install-test-client/thingo' successfully created.
Processing /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/basilisk/example/inst/test_dummy
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: test_dummy
DEPRECATION: Building 'test_dummy' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'test_dummy'. Discussion can be found at https://github.com/pypa/pip/issues/6334
Building wheel for test_dummy (setup.py): started
Building wheel for test_dummy (setup.py): finished with status 'done'
Created wheel for test_dummy: filename=test_dummy-0.1-py3-none-any.whl size=1312 sha256=f4435f55c64f9d12979a2f57daeb64d44e78ffd9c04d5ff43085f665830ca7ae
Stored in directory: /private/tmp/pip-ephem-wheel-cache-jtiv86sv/wheels/86/b2/c4/5767c45b04c9771c703581b7e406e45815abc591f667de76a3
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-25.1.1-py3-none-any.whl.metadata (3.6 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-25.1.1-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-25.1.1 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-25.1.1-py3-none-any.whl.metadata (3.6 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-25.1.1-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-25.1.1 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_10_9_x86_64.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-2.3.1-cp312-cp312-macosx_10_13_x86_64.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_10_9_x86_64.whl (12.5 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-2.3.1-cp312-cp312-macosx_10_13_x86_64.whl (20.9 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-2.3.1 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
245.373 66.175 420.521
basilisk.Rcheck/basilisk-Ex.timings
| name | user | system | elapsed | |
| BasiliskEnvironment-class | 0.002 | 0.000 | 0.002 | |
| PyPiLink | 0 | 0 | 0 | |
| basiliskOptions | 0.000 | 0.000 | 0.001 | |
| basiliskStart | 42.230 | 11.171 | 86.315 | |
| clearExternalDir | 0.000 | 0.000 | 0.001 | |
| configureBasiliskEnv | 0 | 0 | 0 | |
| createLocalBasiliskEnv | 20.339 | 5.457 | 44.496 | |
| getBinaries | 0 | 0 | 0 | |
| getExternalDir | 0 | 0 | 0 | |
| getSystemDir | 0.000 | 0.001 | 0.000 | |
| listPackages | 0.399 | 0.100 | 0.532 | |
| lockExternalDir | 0.003 | 0.001 | 0.005 | |
| obtainEnvironmentPath | 0.000 | 0.001 | 0.001 | |
| platform | 0.000 | 0.001 | 0.001 | |
| setupBasiliskEnv | 0 | 0 | 0 | |
| useBasiliskEnv | 0.260 | 0.056 | 0.238 | |