Aaron Lun
| Snapshot Date: 2025-06-27 13:25 -0400 (Fri, 27 Jun 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 2025-06-28 12:05 -0400 (Sat, 28 Jun 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" | 4775 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4517 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4559 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4500 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4499 |
| 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 139/2310 | 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings basilisk_1.21.5.tar.gz |
| StartedAt: 2025-06-27 20:08:23 -0400 (Fri, 27 Jun 2025) |
| EndedAt: 2025-06-27 20:14:40 -0400 (Fri, 27 Jun 2025) |
| EllapsedTime: 376.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: basilisk.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:basilisk.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings basilisk_1.21.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/basilisk.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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 ‘/home/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 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 31.292 2.886 37.383
createLocalBasiliskEnv 15.214 1.360 19.437
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/basilisk.Rcheck/00check.log’
for details.
basilisk.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL basilisk ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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-pc-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-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-manylinux_2_17_x86_64.manylinux2014_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-manylinux_2_28_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-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.7 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-manylinux_2_28_x86_64.whl (16.6 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/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-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-manylinux_2_17_x86_64.manylinux2014_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-manylinux_2_28_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-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.7 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-manylinux_2_28_x86_64.whl (16.6 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/my_package_B' successfully created.
Using Python: /home/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment '/home/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-manylinux_2_17_x86_64.manylinux2014_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-manylinux_2_28_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-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.7 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-manylinux_2_28_x86_64.whl (16.6 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 '/home/biocbuild/bbs-3.22-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/locality/1.21.5' successfully created.
Using Python: /home/biocbuild/.pyenv/versions/3.12.10/bin/python3.12
Creating virtual environment '/tmp/RtmpxXmhxA/file36c8e34fa58cb3/1.21.5/basilisk/1.21.5/test' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /tmp/RtmpxXmhxA/file36c8e34fa58cb3/1.21.5/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-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (89 kB)
Collecting numpy>=1.26.0 (from pandas==2.2.3)
Using cached numpy-2.3.1-cp312-cp312-manylinux_2_28_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-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.7 MB)
Using cached numpy-2.3.1-cp312-cp312-manylinux_2_28_x86_64.whl (16.6 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/RtmpxXmhxA/file36c8e34fa58cb3/1.21.5/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: /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-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-manylinux_2_17_x86_64.manylinux2014_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-manylinux_2_28_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-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.7 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-manylinux_2_28_x86_64.whl (16.6 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.
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-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-manylinux_2_17_x86_64.manylinux2014_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-manylinux_2_28_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-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.7 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-manylinux_2_28_x86_64.whl (16.6 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: /home/biocbuild/.pyenv/versions/2.7.18/bin/python2.7
Creating virtual environment 'install-test-client/thingo' ...
created virtual environment CPython2.7.18.final.0-64 in 237ms
creator CPython2Posix(dest=/home/biocbuild/bbs-3.22-bioc/meat/basilisk.Rcheck/tests/testthat/install-test-client/thingo, clear=False, no_vcs_ignore=False, global=False)
seeder FromAppData(download=False, pip=bundle, wheel=bundle, setuptools=bundle, via=copy, app_data_dir=/home/biocbuild/.local/share/virtualenv)
added seed packages: pip==20.3.4, setuptools==44.1.1, wheel==0.37.1
activators NushellActivator,PythonActivator,FishActivator,CShellActivator,PowerShellActivator,BashActivator
Done!
Installing packages: pip, wheel, setuptools
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
Requirement already up-to-date: pip in ./install-test-client/thingo/lib/python2.7/site-packages (20.3.4)
Requirement already up-to-date: wheel in ./install-test-client/thingo/lib/python2.7/site-packages (0.37.1)
Requirement already up-to-date: setuptools in ./install-test-client/thingo/lib/python2.7/site-packages (44.1.1)
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-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 /home/biocbuild/bbs-3.22-bioc/R/site-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=789f999b5b3fe3c8de614fd86fa98f0deefd4cf811b2df805f25784faa39afb5
Stored in directory: /tmp/pip-ephem-wheel-cache-l3hdz1fy/wheels/1c/3f/3e/54b4df0568e1009234a2e33813d9125a0e2df35f9793be7f96
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
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: /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-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-manylinux_2_17_x86_64.manylinux2014_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-manylinux_2_28_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-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.7 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-manylinux_2_28_x86_64.whl (16.6 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 0 | PASS 62 ]
>
> proc.time()
user system elapsed
187.450 20.225 231.062
basilisk.Rcheck/basilisk-Ex.timings
| name | user | system | elapsed | |
| BasiliskEnvironment-class | 0.002 | 0.000 | 0.002 | |
| PyPiLink | 0.000 | 0.000 | 0.001 | |
| basiliskOptions | 0.000 | 0.000 | 0.001 | |
| basiliskStart | 31.292 | 2.886 | 37.383 | |
| clearExternalDir | 0 | 0 | 0 | |
| configureBasiliskEnv | 0 | 0 | 0 | |
| createLocalBasiliskEnv | 15.214 | 1.360 | 19.437 | |
| getBinaries | 0 | 0 | 0 | |
| getExternalDir | 0 | 0 | 0 | |
| getSystemDir | 0.000 | 0.000 | 0.001 | |
| listPackages | 0.251 | 0.043 | 0.294 | |
| lockExternalDir | 0.004 | 0.000 | 0.004 | |
| obtainEnvironmentPath | 0.000 | 0.002 | 0.001 | |
| platform | 0.001 | 0.000 | 0.001 | |
| setupBasiliskEnv | 0.000 | 0.000 | 0.001 | |
| useBasiliskEnv | 0.192 | 0.022 | 0.136 | |