Aaron Lun
| Snapshot Date: 2026-04-19 13:40 -0400 (Sun, 19 Apr 2026) |
| 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 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-20 11:37 -0400 (Mon, 20 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4961 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4690 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 146/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| basilisk 1.23.0 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
| See other builds for basilisk in R Universe. | ||||||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: basilisk |
| Version: 1.23.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings basilisk_1.23.0.tar.gz |
| StartedAt: 2026-04-17 02:51:32 -0000 (Fri, 17 Apr 2026) |
| EndedAt: 2026-04-17 03:02:17 -0000 (Fri, 17 Apr 2026) |
| EllapsedTime: 644.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: basilisk.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings basilisk_1.23.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/basilisk.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 ‘/home/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 loading without being on the library search path ... 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 39.643 2.89 96.594
createLocalBasiliskEnv 19.933 1.30 35.999
* 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:
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-setupBasiliskEnv.R:35:5'): setupBasiliskEnv will install Python 2.7 if requested ──
Error: installation of Python 2.7.18 failed
Backtrace:
▆
1. └─basilisk::setupBasiliskEnv(target, "python=2.7.18") at test-setupBasiliskEnv.R:35:5
2. ├─base::suppressMessages(install_python(version))
3. │ └─base::withCallingHandlers(...)
4. └─reticulate::install_python(version)
5. └─reticulate:::stopf("installation of Python %s failed", version)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 60 ]
Error: Test failures
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
‘/home/biocbuild/bbs-3.23-bioc/meat/basilisk.Rcheck/00check.log’
for details.
basilisk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL basilisk ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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.fail
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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: /home/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-26.0.1-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.46.3-py3-none-any.whl.metadata (2.4 kB)
Collecting setuptools
Using cached setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
Collecting packaging>=24.0 (from wheel)
Using cached packaging-26.1-py3-none-any.whl.metadata (3.5 kB)
Using cached pip-26.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.46.3-py3-none-any.whl (30 kB)
Using cached setuptools-82.0.1-py3-none-any.whl (1.0 MB)
Using cached packaging-26.1-py3-none-any.whl (95 kB)
Installing collected packages: setuptools, pip, packaging, wheel
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed packaging-26.1 pip-26.0.1 setuptools-82.0.1 wheel-0.46.3
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-manylinux2014_aarch64.manylinux_2_17_aarch64.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-2.4.4-cp312-cp312-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl.metadata (6.6 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
Using cached tzdata-2026.1-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-manylinux2014_aarch64.manylinux_2_17_aarch64.whl (15.2 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-2.4.4-cp312-cp312-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl (15.7 MB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2026.1-py2.py3-none-any.whl (348 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.4.4 pandas-2.2.3 python-dateutil-2.8.2 pytz-2024.1 six-1.17.0 tzdata-2026.1
Virtual environment 'install-test-client/my_package_A' successfully created.
Using Python: /home/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-26.0.1-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.46.3-py3-none-any.whl.metadata (2.4 kB)
Collecting setuptools
Using cached setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
Collecting packaging>=24.0 (from wheel)
Using cached packaging-26.1-py3-none-any.whl.metadata (3.5 kB)
Using cached pip-26.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.46.3-py3-none-any.whl (30 kB)
Using cached setuptools-82.0.1-py3-none-any.whl (1.0 MB)
Using cached packaging-26.1-py3-none-any.whl (95 kB)
Installing collected packages: setuptools, pip, packaging, wheel
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed packaging-26.1 pip-26.0.1 setuptools-82.0.1 wheel-0.46.3
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-manylinux_2_17_aarch64.manylinux2014_aarch64.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-2.4.4-cp312-cp312-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl.metadata (6.6 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.2)
Using cached tzdata-2026.1-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-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (15.2 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-2.4.4-cp312-cp312-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl (15.7 MB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2026.1-py2.py3-none-any.whl (348 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.4.4 pandas-2.2.2 python-dateutil-2.8.2 pytz-2023.4 six-1.17.0 tzdata-2026.1
Virtual environment 'install-test-client/my_package_B' successfully created.
Using Python: /home/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment '/home/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-26.0.1-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.46.3-py3-none-any.whl.metadata (2.4 kB)
Collecting setuptools
Using cached setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
Collecting packaging>=24.0 (from wheel)
Using cached packaging-26.1-py3-none-any.whl.metadata (3.5 kB)
Using cached pip-26.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.46.3-py3-none-any.whl (30 kB)
Using cached setuptools-82.0.1-py3-none-any.whl (1.0 MB)
Using cached packaging-26.1-py3-none-any.whl (95 kB)
Installing collected packages: setuptools, pip, packaging, wheel
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed packaging-26.1 pip-26.0.1 setuptools-82.0.1 wheel-0.46.3
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-manylinux2014_aarch64.manylinux_2_17_aarch64.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-2.4.4-cp312-cp312-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl.metadata (6.6 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
Using cached tzdata-2026.1-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-manylinux2014_aarch64.manylinux_2_17_aarch64.whl (15.2 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-2.4.4-cp312-cp312-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl (15.7 MB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2026.1-py2.py3-none-any.whl (348 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.4.4 pandas-2.2.3 python-dateutil-2.8.2 pytz-2024.1 six-1.17.0 tzdata-2026.1
Virtual environment '/home/biocbuild/bbs-3.23-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.23.0' successfully created.
Using Python: /home/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment '/home/biocbuild/tmp/RtmpE5trCD/file1557e9387af50b/1.23.0/basilisk/1.23.0/test' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /home/biocbuild/tmp/RtmpE5trCD/file1557e9387af50b/1.23.0/basilisk/1.23.0/test/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-26.0.1-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.46.3-py3-none-any.whl.metadata (2.4 kB)
Collecting setuptools
Using cached setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
Collecting packaging>=24.0 (from wheel)
Using cached packaging-26.1-py3-none-any.whl.metadata (3.5 kB)
Using cached pip-26.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.46.3-py3-none-any.whl (30 kB)
Using cached setuptools-82.0.1-py3-none-any.whl (1.0 MB)
Using cached packaging-26.1-py3-none-any.whl (95 kB)
Installing collected packages: setuptools, pip, packaging, wheel
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed packaging-26.1 pip-26.0.1 setuptools-82.0.1 wheel-0.46.3
Installing packages: 'pandas==2.2.3'
Collecting pandas==2.2.3
Using cached pandas-2.2.3-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.whl.metadata (89 kB)
Collecting numpy>=1.26.0 (from pandas==2.2.3)
Using cached numpy-2.4.4-cp312-cp312-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl.metadata (6.6 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-2026.1.post1-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
Using cached tzdata-2026.1-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-manylinux2014_aarch64.manylinux_2_17_aarch64.whl (15.2 MB)
Using cached numpy-2.4.4-cp312-cp312-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl (15.7 MB)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
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Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2026.1-py2.py3-none-any.whl (348 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.4.4 pandas-2.2.3 python-dateutil-2.9.0.post0 pytz-2026.1.post1 six-1.17.0 tzdata-2026.1
Virtual environment '/home/biocbuild/tmp/RtmpE5trCD/file1557e9387af50b/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: /home/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-26.0.1-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.46.3-py3-none-any.whl.metadata (2.4 kB)
Collecting setuptools
Using cached setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
Collecting packaging>=24.0 (from wheel)
Using cached packaging-26.1-py3-none-any.whl.metadata (3.5 kB)
Using cached pip-26.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.46.3-py3-none-any.whl (30 kB)
Using cached setuptools-82.0.1-py3-none-any.whl (1.0 MB)
Using cached packaging-26.1-py3-none-any.whl (95 kB)
Installing collected packages: setuptools, pip, packaging, wheel
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed packaging-26.1 pip-26.0.1 setuptools-82.0.1 wheel-0.46.3
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-manylinux2014_aarch64.manylinux_2_17_aarch64.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-2.4.4-cp312-cp312-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl.metadata (6.6 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.3)
Using cached tzdata-2026.1-py2.py3-none-any.whl.metadata (1.4 kB)
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Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Using cached pandas-2.2.3-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.whl (15.2 MB)
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Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Using cached tzdata-2026.1-py2.py3-none-any.whl (348 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.4.4 pandas-2.2.3 python-dateutil-2.8.2 pytz-2024.1 six-1.17.0 tzdata-2026.1
Virtual environment 'install-test-client/thingo' successfully created.
Using Python: /home/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-26.0.1-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.46.3-py3-none-any.whl.metadata (2.4 kB)
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Using cached setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
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Installing collected packages: setuptools, pip, packaging, wheel
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed packaging-26.1 pip-26.0.1 setuptools-82.0.1 wheel-0.46.3
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-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (19 kB)
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Collecting numpy>=1.26.0 (from pandas==2.2.2)
Using cached numpy-2.4.4-cp312-cp312-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl.metadata (6.6 kB)
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Using cached pandas-2.2.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (15.2 MB)
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Using cached tzdata-2026.1-py2.py3-none-any.whl (348 kB)
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.4.4 pandas-2.2.2 python-dateutil-2.8.2 pytz-2023.4 six-1.17.0 tzdata-2026.1
Virtual environment 'install-test-client/thingo' successfully created.
Downloading Python-2.7.18.tar.xz...
-> https://www.python.org/ftp/python/2.7.18/Python-2.7.18.tar.xz
Installing Python-2.7.18...
/home/biocbuild/.local/share/r-reticulate/pyenv/plugins/python-build/bin/python-build: line 2048: patch: command not found
BUILD FAILED (openEuler 24.03 using python-build 2.6.27-1-g46e4e6a)
Inspect or clean up the working tree at /home/biocbuild/tmp/python-build.20260417030101.1422370
Results logged to /home/biocbuild/tmp/python-build.20260417030101.1422370.log
Last 10 log lines:
~/tmp/python-build.20260417030101.1422370 ~/bbs-3.23-bioc/meat/basilisk.Rcheck/tests/testthat
~/tmp/python-build.20260417030101.1422370/Python-2.7.18 ~/tmp/python-build.20260417030101.1422370 ~/bbs-3.23-bioc/meat/basilisk.Rcheck/tests/testthat
Using Python: /home/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
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Using cached packaging-26.1-py3-none-any.whl (95 kB)
Installing collected packages: setuptools, pip, packaging, wheel
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed packaging-26.1 pip-26.0.1 setuptools-82.0.1 wheel-0.46.3
Virtual environment 'install-test-client/thingo' successfully created.
Processing /home/biocbuild/R/R-devel_2025-02-19/site-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=83d71d57ac234d29efc7a479fca4dc527d8a3e4dc256c4cbbb7a4b84efb07503
Stored in directory: /home/biocbuild/tmp/pip-ephem-wheel-cache-6rz0flae/wheels/26/cd/d9/536b7fac5ac9387e87d9966c9135cff83dc81cb9d4aa102865
Successfully built test_dummy
Installing collected packages: test_dummy
Successfully installed test_dummy-0.1
Using Python: /home/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
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Using cached packaging-26.1-py3-none-any.whl (95 kB)
Installing collected packages: setuptools, pip, packaging, wheel
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed packaging-26.1 pip-26.0.1 setuptools-82.0.1 wheel-0.46.3
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: /home/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
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Installing collected packages: setuptools, pip, packaging, wheel
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed packaging-26.1 pip-26.0.1 setuptools-82.0.1 wheel-0.46.3
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-manylinux2014_aarch64.manylinux_2_17_aarch64.whl.metadata (89 kB)
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Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, pandas
Successfully installed numpy-2.4.4 pandas-2.2.3 python-dateutil-2.8.2 pytz-2024.1 six-1.17.0 tzdata-2026.1
Virtual environment 'install-test-client/thingo' successfully created.
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 60 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-setupBasiliskEnv.R:35:5'): setupBasiliskEnv will install Python 2.7 if requested ──
Error: installation of Python 2.7.18 failed
Backtrace:
▆
1. └─basilisk::setupBasiliskEnv(target, "python=2.7.18") at test-setupBasiliskEnv.R:35:5
2. ├─base::suppressMessages(install_python(version))
3. │ └─base::withCallingHandlers(...)
4. └─reticulate::install_python(version)
5. └─reticulate:::stopf("installation of Python %s failed", version)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 60 ]
Error: Test failures
Execution halted
basilisk.Rcheck/basilisk-Ex.timings
| name | user | system | elapsed | |
| BasiliskEnvironment-class | 0.003 | 0.000 | 0.004 | |
| PyPiLink | 0 | 0 | 0 | |
| basiliskOptions | 0.000 | 0.000 | 0.001 | |
| basiliskStart | 39.643 | 2.890 | 96.594 | |
| clearExternalDir | 0 | 0 | 0 | |
| configureBasiliskEnv | 0 | 0 | 0 | |
| createLocalBasiliskEnv | 19.933 | 1.300 | 35.999 | |
| getBinaries | 0 | 0 | 0 | |
| getExternalDir | 0 | 0 | 0 | |
| getSystemDir | 0.000 | 0.000 | 0.001 | |
| listPackages | 0.317 | 0.054 | 0.440 | |
| lockExternalDir | 0.002 | 0.000 | 0.003 | |
| obtainEnvironmentPath | 0.001 | 0.000 | 0.001 | |
| platform | 0.001 | 0.000 | 0.000 | |
| setupBasiliskEnv | 0.001 | 0.000 | 0.000 | |
| useBasiliskEnv | 0.227 | 0.019 | 0.365 | |