Aaron Lun
| Snapshot Date: 2025-03-19 13:40 -0400 (Wed, 19 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/basilisk |
| git_branch: devel |
| git_last_commit: 33efb9e |
| git_last_commit_date: 2025-03-19 06:03:55 -0400 (Wed, 19 Mar 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-20 11:44 -0400 (Thu, 20 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4458 |
| 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 139/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| basilisk 1.19.2 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | 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: 1.19.2 |
| 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_1.19.2.tar.gz |
| StartedAt: 2025-03-19 18:19:58 -0400 (Wed, 19 Mar 2025) |
| EndedAt: 2025-03-19 18:23:12 -0400 (Wed, 19 Mar 2025) |
| EllapsedTime: 193.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: basilisk.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_1.19.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/basilisk.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.19.2’
* 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-3.21-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 14.222 3.868 25.101
createLocalBasiliskEnv 6.516 1.803 11.650
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
── Error ('test-package.R:14:5'): internal test package installs correctly ─────
Error in `checkForRemoteErrors(lapply(cl, recvResult))`: one node produced an error: ModuleNotFoundError: No module named 'test_dummy'
Run `reticulate::py_last_error()` for details.
Backtrace:
▆
1. └─son.of.basilisk::test() at test-package.R:14:5
2. └─basilisk::basiliskRun(...)
3. └─parallel::clusterCall(proc, fun = fun, ...)
4. └─parallel:::checkForRemoteErrors(lapply(cl, recvResult))
[ FAIL 5 | WARN 1 | SKIP 1 | PASS 34 ]
Error: Test failures
In addition: Warning message:
In for (call in calls) { : closing unused connection 5 (<-localhost:11506)
Execution halted
* 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: 1 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-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-arm64/Resources/library’ * installing *source* package ‘basilisk’ ... ** this is package ‘basilisk’ version ‘1.19.2’ ** 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.fail
R Under development (unstable) (2025-03-02 r87868) -- "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
> if (.Platform$OS.type != "windows") test_check("basilisk")
Using Python: /Users/biocbuild/.pyenv/versions/3.12.9/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 (24.3.1)
Collecting pip
Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-77.0.1-py3-none-any.whl.metadata (6.7 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Virtual environment 'install-test-client/my_package_A' successfully created.
Using virtual environment 'install-test-client/my_package_A' ...
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
Downloading python_dateutil-2.8.2-py2.py3-none-any.whl.metadata (8.2 kB)
Collecting pytz==2024.1
Downloading pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting numpy>=1.26.0 (from pandas==2.2.3)
Using cached numpy-2.2.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
Using cached tzdata-2025.1-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)
Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Downloading pytz-2024.1-py2.py3-none-any.whl (505 kB)
Using cached numpy-2.2.4-cp312-cp312-macosx_11_0_arm64.whl (14.1 MB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2025.1-py2.py3-none-any.whl (346 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.2.4 pandas-2.2.3 python-dateutil-2.8.2 pytz-2024.1 six-1.17.0 tzdata-2025.1
Using Python: /Users/biocbuild/.pyenv/versions/3.12.9/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 (24.3.1)
Collecting pip
Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-77.0.1-py3-none-any.whl.metadata (6.7 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Virtual environment 'install-test-client/my_package_B' successfully created.
Using virtual environment 'install-test-client/my_package_B' ...
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
Downloading pytz-2023.4-py2.py3-none-any.whl.metadata (22 kB)
Collecting numpy>=1.26.0 (from pandas==2.2.2)
Using cached numpy-2.2.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.2)
Using cached tzdata-2025.1-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)
Downloading pytz-2023.4-py2.py3-none-any.whl (506 kB)
Using cached numpy-2.2.4-cp312-cp312-macosx_11_0_arm64.whl (14.1 MB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2025.1-py2.py3-none-any.whl (346 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.2.4 pandas-2.2.2 python-dateutil-2.8.2 pytz-2023.4 six-1.17.0 tzdata-2025.1
Using Python: /Users/biocbuild/.pyenv/versions/3.12.9/bin/python3.12
Creating virtual environment '/Users/biocbuild/bbs-3.21-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.19.2' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in ./install-test-client/locality/1.19.2/lib/python3.12/site-packages (24.3.1)
Collecting pip
Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-77.0.1-py3-none-any.whl.metadata (6.7 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Virtual environment '/Users/biocbuild/bbs-3.21-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.19.2' successfully created.
Using virtual environment '/Users/biocbuild/bbs-3.21-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.19.2' ...
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-2.2.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
Using cached tzdata-2025.1-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-2.2.4-cp312-cp312-macosx_11_0_arm64.whl (14.1 MB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2025.1-py2.py3-none-any.whl (346 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.2.4 pandas-2.2.3 python-dateutil-2.8.2 pytz-2024.1 six-1.17.0 tzdata-2025.1
Using Python: /Users/biocbuild/.pyenv/versions/3.12.9/bin/python3.12
Creating virtual environment '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp60HaiV/file121e37bcbcf8f/1.19.2/basilisk/1.19.2/test' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp60HaiV/file121e37bcbcf8f/1.19.2/basilisk/1.19.2/test/lib/python3.12/site-packages (24.3.1)
Collecting pip
Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-77.0.1-py3-none-any.whl.metadata (6.7 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Virtual environment '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp60HaiV/file121e37bcbcf8f/1.19.2/basilisk/1.19.2/test' successfully created.
Using virtual environment '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//Rtmp60HaiV/file121e37bcbcf8f/1.19.2/basilisk/1.19.2/test' ...
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-2.2.4-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-2025.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
Using cached tzdata-2025.1-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-2.2.4-cp312-cp312-macosx_11_0_arm64.whl (14.1 MB)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Using cached pytz-2025.1-py2.py3-none-any.whl (507 kB)
Using cached tzdata-2025.1-py2.py3-none-any.whl (346 kB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.2.4 pandas-2.2.3 python-dateutil-2.9.0.post0 pytz-2025.1 six-1.17.0 tzdata-2025.1
* 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/3.12.9/bin/python3.12
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/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/1.19.2/son.of.basilisk/0.99.0/env1/lib/python3.12/site-packages (24.3.1)
Collecting pip
Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 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-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/son.of.basilisk/0.99.0/env1' successfully created.
Using virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/son.of.basilisk/0.99.0/env1' ...
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-2.2.4-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-2025.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
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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)
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Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
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Using cached tzdata-2025.1-py2.py3-none-any.whl (346 kB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.2.4 pandas-2.2.3 python-dateutil-2.9.0.post0 pytz-2025.1 six-1.17.0 tzdata-2025.1
sys:1: FutureWarning: pandas.Float64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead.
sys:1: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead.
sys:1: FutureWarning: pandas.UInt64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead.
Using Python: /Users/biocbuild/.pyenv/versions/3.12.9/bin/python3.12
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/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/1.19.2/son.of.basilisk/0.99.0/env2/lib/python3.12/site-packages (24.3.1)
Collecting pip
Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-77.0.1-py3-none-any.whl.metadata (6.7 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/son.of.basilisk/0.99.0/env2' successfully created.
Using virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/son.of.basilisk/0.99.0/env2' ...
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-2.2.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting scipy>=1.6.0 (from scikit-learn==1.6.1)
Using cached scipy-1.15.2-cp312-cp312-macosx_12_0_arm64.whl.metadata (61 kB)
Collecting joblib>=1.2.0 (from scikit-learn==1.6.1)
Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 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-1.4.2-py3-none-any.whl (301 kB)
Using cached numpy-2.2.4-cp312-cp312-macosx_11_0_arm64.whl (14.1 MB)
Using cached scipy-1.15.2-cp312-cp312-macosx_12_0_arm64.whl (30.2 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-1.4.2 numpy-2.2.4 scikit-learn-1.6.1 scipy-1.15.2 threadpoolctl-3.6.0
Using Python: /Users/biocbuild/.pyenv/versions/3.12.9/bin/python3.12
Creating virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/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/1.19.2/son.of.basilisk/0.99.0/env3/lib/python3.12/site-packages (24.3.1)
Collecting pip
Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-77.0.1-py3-none-any.whl.metadata (6.7 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Installing packages: numpy
Collecting numpy
Using cached numpy-2.2.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Using cached numpy-2.2.4-cp312-cp312-macosx_11_0_arm64.whl (14.1 MB)
Installing collected packages: numpy
Successfully installed numpy-2.2.4
Virtual environment '/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/son.of.basilisk/0.99.0/env3' successfully created.
Processing /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp60HaiV/Rlib.121e3500db593/son.of.basilisk/test_dummy
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: test_dummy
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=4a33f6cea695c070cfe8e158a0423b7c7e0f0fd0e5406310371e2b91ebc70501
Stored in directory: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/pip-ephem-wheel-cache-b1069qqq/wheels/ff/9b/d0/ad205a3401e385da01a93bc242b81f2b5bffa9d3eab4bf0ad0
Successfully built test_dummy
Installing collected packages: test_dummy
Successfully installed test_dummy-0.1
Using Python: /Users/biocbuild/.pyenv/versions/3.12.9/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 (24.3.1)
Collecting pip
Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
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Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Virtual environment 'install-test-client/thingo' successfully created.
Using virtual environment 'install-test-client/thingo' ...
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-2.2.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
Using cached tzdata-2025.1-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-2025.1-py2.py3-none-any.whl (346 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.2.4 pandas-2.2.3 python-dateutil-2.8.2 pytz-2024.1 six-1.17.0 tzdata-2025.1
Using Python: /Users/biocbuild/.pyenv/versions/3.12.9/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 (24.3.1)
Collecting pip
Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 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-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Virtual environment 'install-test-client/thingo' successfully created.
Using virtual environment 'install-test-client/thingo' ...
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-2.2.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.2)
Using cached tzdata-2025.1-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 six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2025.1-py2.py3-none-any.whl (346 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.2.4 pandas-2.2.2 python-dateutil-2.8.2 pytz-2023.4 six-1.17.0 tzdata-2025.1
Using Python: /Users/biocbuild/.pyenv/versions/3.12.9/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 (24.3.1)
Collecting pip
Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
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Collecting setuptools
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Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Installing packages: numpy
Collecting numpy
Using cached numpy-2.2.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Using cached numpy-2.2.4-cp312-cp312-macosx_11_0_arm64.whl (14.1 MB)
Installing collected packages: numpy
Successfully installed numpy-2.2.4
Virtual environment 'install-test-client/thingo' successfully created.
Processing /Library/Frameworks/R.framework/Versions/4.5-arm64/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
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=dd51512df34d190086c8e9621001c72a821c10c866add6dd3d9b23436c3e593c
Stored in directory: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/pip-ephem-wheel-cache-1aqxqbvt/wheels/63/4f/f8/61e0e800854b1157bfbb32ed373d1be82ac2739e2387c298aa
Successfully built test_dummy
Installing collected packages: test_dummy
Successfully installed test_dummy-0.1
Using Python: /Users/biocbuild/.pyenv/versions/3.12.9/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 (24.3.1)
Collecting pip
Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-77.0.1-py3-none-any.whl.metadata (6.7 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Virtual environment 'install-test-client/thingo' successfully created.
Using virtual environment 'install-test-client/thingo' ...
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/3.12.9/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 (24.3.1)
Collecting pip
Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-77.0.1-py3-none-any.whl.metadata (6.7 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Virtual environment 'install-test-client/thingo' successfully created.
Using virtual environment 'install-test-client/thingo' ...
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-2.2.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
Using cached tzdata-2025.1-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-2.2.4-cp312-cp312-macosx_11_0_arm64.whl (14.1 MB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2025.1-py2.py3-none-any.whl (346 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.2.4 pandas-2.2.3 python-dateutil-2.8.2 pytz-2024.1 six-1.17.0 tzdata-2025.1
[ FAIL 5 | WARN 1 | SKIP 1 | PASS 34 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Mac aarch64 (1): 'test-setupBasiliskEnv.R:33:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-basiliskStart.R:152:5'): basilisk directly loads Python when possible ──
<callr_status_error/callr_error/rlib_error_3_0/rlib_error/error/condition>
Error: ! in callr subprocess.
Caused by error:
! `version` not identical to `test.version`.
1/1 mismatches
x[1]: "2.2.3"
y[1]: "1.5.3"
── Error ('test-basiliskStart.R:163:5'): basilisk forks when possible ──────────
<callr_status_error/callr_error/rlib_error_3_0/rlib_error/error/condition>
Error: ! in callr subprocess.
Caused by error:
! `version` not identical to `test.version`.
1/1 mismatches
x[1]: "2.2.3"
y[1]: "1.5.3"
── Error ('test-basiliskStart.R:181:5'): basilisk uses sockets correctly ───────
<callr_status_error/callr_error/rlib_error_3_0/rlib_error/error/condition>
Error: ! in callr subprocess.
Caused by error:
! `version` not identical to `test.version`.
1/1 mismatches
x[1]: "2.2.3"
y[1]: "1.5.3"
── Failure ('test-createLocalBasiliskEnv.R:21:5'): createLocalBasiliskEnv obtains the correct version of the packages ──
`pandas.ver` not identical to sub("pandas=*", "", test.pandas).
1/1 mismatches
x[1]: "1.5.3"
y[1]: "2.2.3"
── Error ('test-package.R:14:5'): internal test package installs correctly ─────
Error in `checkForRemoteErrors(lapply(cl, recvResult))`: one node produced an error: ModuleNotFoundError: No module named 'test_dummy'
Run `reticulate::py_last_error()` for details.
Backtrace:
▆
1. └─son.of.basilisk::test() at test-package.R:14:5
2. └─basilisk::basiliskRun(...)
3. └─parallel::clusterCall(proc, fun = fun, ...)
4. └─parallel:::checkForRemoteErrors(lapply(cl, recvResult))
[ FAIL 5 | WARN 1 | SKIP 1 | PASS 34 ]
Error: Test failures
In addition: Warning message:
In for (call in calls) { : closing unused connection 5 (<-localhost:11506)
Execution halted
basilisk.Rcheck/basilisk-Ex.timings
| name | user | system | elapsed | |
| BasiliskEnvironment-class | 0.001 | 0.000 | 0.001 | |
| PyPiLink | 0.001 | 0.000 | 0.000 | |
| basiliskOptions | 0.001 | 0.000 | 0.000 | |
| basiliskStart | 14.222 | 3.868 | 25.101 | |
| clearExternalDir | 0.000 | 0.000 | 0.001 | |
| configureBasiliskEnv | 0 | 0 | 0 | |
| createLocalBasiliskEnv | 6.516 | 1.803 | 11.650 | |
| getBinaries | 0 | 0 | 0 | |
| getExternalDir | 0.000 | 0.000 | 0.001 | |
| getSystemDir | 0 | 0 | 0 | |
| listPackages | 0.114 | 0.036 | 0.155 | |
| lockExternalDir | 0.001 | 0.001 | 0.002 | |
| obtainEnvironmentPath | 0 | 0 | 0 | |
| platform | 0 | 0 | 0 | |
| setupBasiliskEnv | 0 | 0 | 0 | |
| useBasiliskEnv | 0.000 | 0.000 | 0.001 | |