Long Tests report for BioC 3.21 - CHECK results for basilisk on nebbiolo1

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"	4547
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
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*

CHECK results for basilisk on nebbiolo1

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: 1.19.3

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no basilisk_1.19.3.tar.gz

StartedAt: 2025-03-22 16:01:08 -0400 (Sat, 22 Mar 2025)

EndedAt: 2025-03-22 16:03:15 -0400 (Sat, 22 Mar 2025)

EllapsedTime: 127.0 seconds

RetCode: 0

Status: OK

CheckDir: basilisk.Rcheck

Warnings: 0

Tests output

basilisk.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
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")
* 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)
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/son.of.basilisk/0.99.0/env1

  added / updated specs:
    - python=3.12.8


The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 
  ca-certificates    conda-forge/linux-64::ca-certificates-2025.1.31-hbcca054_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_4 
  libexpat           conda-forge/linux-64::libexpat-2.6.4-h5888daf_0 
  libffi             conda-forge/linux-64::libffi-3.4.6-h2dba641_0 
  libgcc             conda-forge/linux-64::libgcc-14.2.0-h767d61c_2 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_2 
  libgomp            conda-forge/linux-64::libgomp-14.2.0-h767d61c_2 
  liblzma            conda-forge/linux-64::liblzma-5.6.4-hb9d3cd8_0 
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hd590300_0 
  libsqlite          conda-forge/linux-64::libsqlite-3.49.1-hee588c1_2 
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  libzlib            conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 
  ncurses            conda-forge/linux-64::ncurses-6.5-h2d0b736_3 
  openssl            conda-forge/linux-64::openssl-3.4.1-h7b32b05_0 
  pip                conda-forge/noarch::pip-25.0.1-pyh8b19718_0 
  python             conda-forge/linux-64::python-3.12.8-h9e4cc4f_1_cpython 
  readline           conda-forge/linux-64::readline-8.2-h8c095d6_2 
  setuptools         conda-forge/noarch::setuptools-75.8.2-pyhff2d567_0 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 
  tzdata             conda-forge/noarch::tzdata-2025a-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: linux-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: 25.1.1

Please update conda by running

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



# All requested packages already installed.

Channels:
 - conda-forge
Platform: linux-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: 25.1.1

Please update conda by running

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



## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/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/linux-64::libblas-3.9.0-31_h59b9bed_openblas 
  libcblas           conda-forge/linux-64::libcblas-3.9.0-31_he106b2a_openblas 
  libgfortran        conda-forge/linux-64::libgfortran-14.2.0-h69a702a_2 
  libgfortran5       conda-forge/linux-64::libgfortran5-14.2.0-hf1ad2bd_2 
  liblapack          conda-forge/linux-64::liblapack-3.9.0-31_h7ac8fdf_openblas 
  libopenblas        conda-forge/linux-64::libopenblas-0.3.29-pthreads_h94d23a6_0 
  libstdcxx          conda-forge/linux-64::libstdcxx-14.2.0-h8f9b012_2 
  numpy              conda-forge/linux-64::numpy-2.2.4-py312h72c5963_0 
  pandas             conda-forge/linux-64::pandas-2.2.3-py312hf9745cd_1 
  python-dateutil    conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_1 
  python-tzdata      conda-forge/noarch::python-tzdata-2025.1-pyhd8ed1ab_0 
  python_abi         conda-forge/linux-64::python_abi-3.12-5_cp312 
  pytz               conda-forge/noarch::pytz-2024.1-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: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/son.of.basilisk/0.99.0/env2

  added / updated specs:
    - python=3.12.8


The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 
  ca-certificates    conda-forge/linux-64::ca-certificates-2025.1.31-hbcca054_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_4 
  libexpat           conda-forge/linux-64::libexpat-2.6.4-h5888daf_0 
  libffi             conda-forge/linux-64::libffi-3.4.6-h2dba641_0 
  libgcc             conda-forge/linux-64::libgcc-14.2.0-h767d61c_2 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_2 
  libgomp            conda-forge/linux-64::libgomp-14.2.0-h767d61c_2 
  liblzma            conda-forge/linux-64::liblzma-5.6.4-hb9d3cd8_0 
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hd590300_0 
  libsqlite          conda-forge/linux-64::libsqlite-3.49.1-hee588c1_2 
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  libzlib            conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 
  ncurses            conda-forge/linux-64::ncurses-6.5-h2d0b736_3 
  openssl            conda-forge/linux-64::openssl-3.4.1-h7b32b05_0 
  pip                conda-forge/noarch::pip-25.0.1-pyh8b19718_0 
  python             conda-forge/linux-64::python-3.12.8-h9e4cc4f_1_cpython 
  readline           conda-forge/linux-64::readline-8.2-h8c095d6_2 
  setuptools         conda-forge/noarch::setuptools-75.8.2-pyhff2d567_0 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 
  tzdata             conda-forge/noarch::tzdata-2025a-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: linux-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: 25.1.1

Please update conda by running

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



# All requested packages already installed.

Channels:
 - conda-forge
Platform: linux-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: 25.1.1

Please update conda by running

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



## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/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/linux-64::libblas-3.9.0-31_h59b9bed_openblas 
  libcblas           conda-forge/linux-64::libcblas-3.9.0-31_he106b2a_openblas 
  libgfortran        conda-forge/linux-64::libgfortran-14.2.0-h69a702a_2 
  libgfortran5       conda-forge/linux-64::libgfortran5-14.2.0-hf1ad2bd_2 
  liblapack          conda-forge/linux-64::liblapack-3.9.0-31_h7ac8fdf_openblas 
  libopenblas        conda-forge/linux-64::libopenblas-0.3.29-pthreads_h94d23a6_0 
  libstdcxx          conda-forge/linux-64::libstdcxx-14.2.0-h8f9b012_2 
  numpy              conda-forge/linux-64::numpy-2.2.4-py312h72c5963_0 
  python_abi         conda-forge/linux-64::python_abi-3.12-5_cp312 
  scikit-learn       conda-forge/linux-64::scikit-learn-1.6.1-py312h7a48858_0 
  scipy              conda-forge/linux-64::scipy-1.15.2-py312ha707e6e_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: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.19.3/son.of.basilisk/0.99.0/env3

  added / updated specs:
    - python=3.12.8


The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 
  ca-certificates    conda-forge/linux-64::ca-certificates-2025.1.31-hbcca054_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_4 
  libexpat           conda-forge/linux-64::libexpat-2.6.4-h5888daf_0 
  libffi             conda-forge/linux-64::libffi-3.4.6-h2dba641_0 
  libgcc             conda-forge/linux-64::libgcc-14.2.0-h767d61c_2 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_2 
  libgomp            conda-forge/linux-64::libgomp-14.2.0-h767d61c_2 
  liblzma            conda-forge/linux-64::liblzma-5.6.4-hb9d3cd8_0 
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hd590300_0 
  libsqlite          conda-forge/linux-64::libsqlite-3.49.1-hee588c1_2 
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 
  libzlib            conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 
  ncurses            conda-forge/linux-64::ncurses-6.5-h2d0b736_3 
  openssl            conda-forge/linux-64::openssl-3.4.1-h7b32b05_0 
  pip                conda-forge/noarch::pip-25.0.1-pyh8b19718_0 
  python             conda-forge/linux-64::python-3.12.8-h9e4cc4f_1_cpython 
  readline           conda-forge/linux-64::readline-8.2-h8c095d6_2 
  setuptools         conda-forge/noarch::setuptools-75.8.2-pyhff2d567_0 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 
  tzdata             conda-forge/noarch::tzdata-2025a-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: linux-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: 25.1.1

Please update conda by running

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



# All requested packages already installed.

Channels:
 - conda-forge
Platform: linux-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: 25.1.1

Please update conda by running

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



# All requested packages already installed.

Processing /tmp/Rtmp8xYZUH/Rlib.e323e2a1937f9/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=1310 sha256=bcb776c0bab0bde001a49c8c2ae86e53a08e88c67888b370b83cbe7e6b2f567d
  Stored in directory: /tmp/pip-ephem-wheel-cache-59ql7r0d/wheels/eb/b0/a2/8c922298fcb281b88446629ec7a5d7cbe0d2d8b7386c8eaf45
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 
 74.059  14.676  95.915

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no basilisk_1.19.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/basilisk.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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
* 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 ‘1.19.3’
* 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-3.21-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 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 ... 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
  ‘/home/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 ‘1.19.3’
** 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)