Back to Long Tests report for BioC 3.21

This page was generated on 2025-04-26 23:55 -0400 (Sat, 26 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4832
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4574
merida1macOS 12.7.5 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
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 3/30HostnameOS / ArchCHECK
basilisk 1.20.0  (landing page)
Aaron Lun
Snapshot Date: 2025-04-26 09:55 -0400 (Sat, 26 Apr 2025)
git_url: https://git.bioconductor.org/packages/basilisk
git_branch: RELEASE_3_21
git_last_commit: 072c38e
git_last_commit_date: 2025-04-15 11:54:33 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  OK  

CHECK results for basilisk on merida1

To the developers/maintainers of the basilisk package:
- 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.

raw results


Summary

Package: basilisk
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no basilisk_1.20.0.tar.gz
StartedAt: 2025-04-26 16:01:22 -0400 (Sat, 26 Apr 2025)
EndedAt: 2025-04-26 16:07:30 -0400 (Sat, 26 Apr 2025)
EllapsedTime: 367.1 seconds
RetCode: 0
Status:   OK  
CheckDir: basilisk.Rcheck
Warnings: 0

Tests output

basilisk.Rcheck/tests/testthat.Rout


R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(basilisk)
Loading required package: reticulate
> test_check("basilisk")
* 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)
Retrieving notices: ...working... done
Channels:
 - conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/son.of.basilisk/0.99.0/env1

  added / updated specs:
    - python=3.12.8


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2025.4.26  |       hbd8a1cb_0         149 KB  conda-forge
    pip-25.1                   |     pyh8b19718_0         1.2 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         1.3 MB

The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-hfdf4475_7 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.4.26-hbd8a1cb_0 
  libexpat           conda-forge/osx-64::libexpat-2.7.0-h240833e_0 
  libffi             conda-forge/osx-64::libffi-3.4.6-h281671d_1 
  liblzma            conda-forge/osx-64::liblzma-5.8.1-hd471939_0 
  libsqlite          conda-forge/osx-64::libsqlite-3.49.1-hdb6dae5_2 
  libzlib            conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2 
  ncurses            conda-forge/osx-64::ncurses-6.5-h0622a9a_3 
  openssl            conda-forge/osx-64::openssl-3.5.0-hc426f3f_0 
  pip                conda-forge/noarch::pip-25.1-pyh8b19718_0 
  python             conda-forge/osx-64::python-3.12.8-h9ccd52b_1_cpython 
  readline           conda-forge/osx-64::readline-8.2-h7cca4af_2 
  setuptools         conda-forge/noarch::setuptools-79.0.1-pyhff2d567_0 
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1 
  tzdata             conda-forge/noarch::tzdata-2025b-h78e105d_0 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.11.3
    latest version: 25.3.1

Please update conda by running

    $ conda update -n base -c conda-forge conda



# All requested packages already installed.

Channels:
 - conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.11.3
    latest version: 25.3.1

Please update conda by running

    $ conda update -n base -c conda-forge conda



## Package Plan ##

  environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/son.of.basilisk/0.99.0/env1

  added / updated specs:
    - pandas=2.2.3
    - python=3.12.8


The following NEW packages will be INSTALLED:

  libblas            conda-forge/osx-64::libblas-3.9.0-31_h7f60823_openblas 
  libcblas           conda-forge/osx-64::libcblas-3.9.0-31_hff6cab4_openblas 
  libcxx             conda-forge/osx-64::libcxx-20.1.3-hf95d169_0 
  libgfortran        conda-forge/osx-64::libgfortran-14.2.0-hef36b68_105 
  libgfortran5       conda-forge/osx-64::libgfortran5-14.2.0-h58528f3_105 
  liblapack          conda-forge/osx-64::liblapack-3.9.0-31_h236ab99_openblas 
  libopenblas        conda-forge/osx-64::libopenblas-0.3.29-openmp_hbf64a52_0 
  llvm-openmp        conda-forge/osx-64::llvm-openmp-20.1.3-ha54dae1_0 
  numpy              conda-forge/osx-64::numpy-2.2.5-py312h6693b03_0 
  pandas             conda-forge/osx-64::pandas-2.2.3-py312hec45ffd_3 
  python-dateutil    conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_1 
  python-tzdata      conda-forge/noarch::python-tzdata-2025.2-pyhd8ed1ab_0 
  python_abi         conda-forge/noarch::python_abi-3.12-7_cp312 
  pytz               conda-forge/noarch::pytz-2025.2-pyhd8ed1ab_0 
  six                conda-forge/noarch::six-1.17.0-pyhd8ed1ab_0 



Downloading and Extracting Packages: ...working... done
Preparing transaction: - \ done
Verifying transaction: / - \ | / - \ | / done
Executing transaction: \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
Channels:
 - conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/son.of.basilisk/0.99.0/env2

  added / updated specs:
    - python=3.12.8


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-hfdf4475_7 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.4.26-hbd8a1cb_0 
  libexpat           conda-forge/osx-64::libexpat-2.7.0-h240833e_0 
  libffi             conda-forge/osx-64::libffi-3.4.6-h281671d_1 
  liblzma            conda-forge/osx-64::liblzma-5.8.1-hd471939_0 
  libsqlite          conda-forge/osx-64::libsqlite-3.49.1-hdb6dae5_2 
  libzlib            conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2 
  ncurses            conda-forge/osx-64::ncurses-6.5-h0622a9a_3 
  openssl            conda-forge/osx-64::openssl-3.5.0-hc426f3f_0 
  pip                conda-forge/noarch::pip-25.1-pyh8b19718_0 
  python             conda-forge/osx-64::python-3.12.8-h9ccd52b_1_cpython 
  readline           conda-forge/osx-64::readline-8.2-h7cca4af_2 
  setuptools         conda-forge/noarch::setuptools-79.0.1-pyhff2d567_0 
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1 
  tzdata             conda-forge/noarch::tzdata-2025b-h78e105d_0 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.11.3
    latest version: 25.3.1

Please update conda by running

    $ conda update -n base -c conda-forge conda



# All requested packages already installed.

Channels:
 - conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.11.3
    latest version: 25.3.1

Please update conda by running

    $ conda update -n base -c conda-forge conda



## Package Plan ##

  environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/son.of.basilisk/0.99.0/env2

  added / updated specs:
    - python=3.12.8
    - scikit-learn=1.6.1


The following NEW packages will be INSTALLED:

  joblib             conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_1 
  libblas            conda-forge/osx-64::libblas-3.9.0-31_h7f60823_openblas 
  libcblas           conda-forge/osx-64::libcblas-3.9.0-31_hff6cab4_openblas 
  libcxx             conda-forge/osx-64::libcxx-20.1.3-hf95d169_0 
  libgfortran        conda-forge/osx-64::libgfortran-14.2.0-hef36b68_105 
  libgfortran5       conda-forge/osx-64::libgfortran5-14.2.0-h58528f3_105 
  liblapack          conda-forge/osx-64::liblapack-3.9.0-31_h236ab99_openblas 
  libopenblas        conda-forge/osx-64::libopenblas-0.3.29-openmp_hbf64a52_0 
  llvm-openmp        conda-forge/osx-64::llvm-openmp-20.1.3-ha54dae1_0 
  numpy              conda-forge/osx-64::numpy-2.2.5-py312h6693b03_0 
  python_abi         conda-forge/noarch::python_abi-3.12-7_cp312 
  scikit-learn       conda-forge/osx-64::scikit-learn-1.6.1-py312he1a5313_0 
  scipy              conda-forge/osx-64::scipy-1.15.2-py312hd04560d_0 
  threadpoolctl      conda-forge/noarch::threadpoolctl-3.6.0-pyhecae5ae_0 



Downloading and Extracting Packages: ...working... done
Preparing transaction: - done
Verifying transaction: | / - \ | / - \ | / done
Executing transaction: \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
Channels:
 - conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/son.of.basilisk/0.99.0/env3

  added / updated specs:
    - python=3.12.8


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-hfdf4475_7 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.4.26-hbd8a1cb_0 
  libexpat           conda-forge/osx-64::libexpat-2.7.0-h240833e_0 
  libffi             conda-forge/osx-64::libffi-3.4.6-h281671d_1 
  liblzma            conda-forge/osx-64::liblzma-5.8.1-hd471939_0 
  libsqlite          conda-forge/osx-64::libsqlite-3.49.1-hdb6dae5_2 
  libzlib            conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2 
  ncurses            conda-forge/osx-64::ncurses-6.5-h0622a9a_3 
  openssl            conda-forge/osx-64::openssl-3.5.0-hc426f3f_0 
  pip                conda-forge/noarch::pip-25.1-pyh8b19718_0 
  python             conda-forge/osx-64::python-3.12.8-h9ccd52b_1_cpython 
  readline           conda-forge/osx-64::readline-8.2-h7cca4af_2 
  setuptools         conda-forge/noarch::setuptools-79.0.1-pyhff2d567_0 
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1 
  tzdata             conda-forge/noarch::tzdata-2025b-h78e105d_0 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.11.3
    latest version: 25.3.1

Please update conda by running

    $ conda update -n base -c conda-forge conda



# All requested packages already installed.

Channels:
 - conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.11.3
    latest version: 25.3.1

Please update conda by running

    $ conda update -n base -c conda-forge conda



# All requested packages already installed.

Processing /private/tmp/RtmpoTxPel/Rlib.c5df7285ba3c/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
  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=9ec6e54ebb111ddc0ad8583c6a2a08addf3b5f9e0529484e77e61c2ab3bbf68d
  Stored in directory: /private/tmp/pip-ephem-wheel-cache-vcvozyzk/wheels/fa/bb/f4/98373edc182035d9223b858405eb7145da143747a98a662536
Successfully built test_dummy
Installing collected packages: test_dummy
Successfully installed test_dummy-0.1
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
110.533  43.901 320.366

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no basilisk_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/basilisk.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘basilisk/DESCRIPTION’ ... OK
* this is package ‘basilisk’ version ‘1.20.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  inst/example/.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘basilisk’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/basilisk.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  basiliskStart.Rd: activateEnvironment, getExternalDir
  listPackages.Rd: installConda
  useBasiliskEnv.Rd: activateEnvironment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/basilisk.Rcheck/00check.log’
for details.

Installation output

basilisk.Rcheck/00install.out

* installing *source* package ‘basilisk’ ...
** this is package ‘basilisk’ version ‘1.20.0’
** 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)