Long Tests report for BioC 3.19 - CHECK results for basilisk on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4758
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4492
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4506
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 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: 1.16.0

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_1.16.0.tar.gz

StartedAt: 2024-06-22 16:01:19 -0400 (Sat, 22 Jun 2024)

EndedAt: 2024-06-22 16:12:04 -0400 (Sat, 22 Jun 2024)

EllapsedTime: 644.1 seconds

RetCode: 0

Status: OK

CheckDir: basilisk.Rcheck

Warnings: 0

Tests output

basilisk.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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’ ...
** 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)
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /private/var/cache/basilisk/1.16.0/son.of.basilisk/0.99.0/env1

  added / updated specs:
    - python=3.9.12


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    setuptools-70.1.0          |     pyhd8ed1ab_0         484 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         484 KB

The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
  ca-certificates    conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
  libffi             conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
  libsqlite          conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0
  libzlib            conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
  ncurses            conda-forge/osx-64::ncurses-6.5-h5846eda_0
  openssl            conda-forge/osx-64::openssl-3.3.1-h87427d6_0
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
  readline           conda-forge/osx-64::readline-8.2-h9e318b2_1
  setuptools         conda-forge/noarch::setuptools-70.1.0-pyhd8ed1ab_0
  sqlite             conda-forge/osx-64::sqlite-3.46.0-h28673e1_0
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/osx-64::xz-5.2.6-h775f41a_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /private/var/cache/basilisk/1.16.0/son.of.basilisk/0.99.0/env1

  added / updated specs:
    - pandas=1.4.3
    - python-dateutil=2.8.2
    - python=3.9.12
    - pytz=2022.2.1


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    llvm-openmp-18.1.8         |       h15ab845_0         294 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         294 KB

The following NEW packages will be INSTALLED:

  libblas            conda-forge/osx-64::libblas-3.9.0-22_osx64_openblas
  libcblas           conda-forge/osx-64::libcblas-3.9.0-22_osx64_openblas
  libcxx             conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
  libgfortran5       conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
  liblapack          conda-forge/osx-64::liblapack-3.9.0-22_osx64_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.27-openmp_hfef2a42_0
  llvm-openmp        conda-forge/osx-64::llvm-openmp-18.1.8-h15ab845_0
  numpy              conda-forge/osx-64::numpy-1.26.4-py39h28c39a1_0
  pandas             conda-forge/osx-64::pandas-1.4.3-py39hf72b562_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
  python_abi         conda-forge/osx-64::python_abi-3.9-4_cp39
  pytz               conda-forge/noarch::pytz-2022.2.1-pyhd8ed1ab_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0



Downloading and Extracting Packages

llvm-openmp-18.1.8   | 294 KB    |            |   0% 
llvm-openmp-18.1.8   | 294 KB    | 5          |   5% 
llvm-openmp-18.1.8   | 294 KB    | ########## | 100% 
llvm-openmp-18.1.8   | 294 KB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
sys:1: FutureWarning: pandas.Float64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead.
sys:1: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead.
sys:1: FutureWarning: pandas.UInt64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /private/var/cache/basilisk/1.16.0/son.of.basilisk/0.99.0/env2

  added / updated specs:
    - python=3.9.12


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
  ca-certificates    conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
  libffi             conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
  libsqlite          conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0
  libzlib            conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
  ncurses            conda-forge/osx-64::ncurses-6.5-h5846eda_0
  openssl            conda-forge/osx-64::openssl-3.3.1-h87427d6_0
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
  readline           conda-forge/osx-64::readline-8.2-h9e318b2_1
  setuptools         conda-forge/noarch::setuptools-70.1.0-pyhd8ed1ab_0
  sqlite             conda-forge/osx-64::sqlite-3.46.0-h28673e1_0
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/osx-64::xz-5.2.6-h775f41a_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /private/var/cache/basilisk/1.16.0/son.of.basilisk/0.99.0/env2

  added / updated specs:
    - python-dateutil=2.8.1
    - python=3.9.12
    - pytz=2022.1
    - scikit-learn=1.1.1


The following NEW packages will be INSTALLED:

  joblib             conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_0
  libblas            conda-forge/osx-64::libblas-3.9.0-22_osx64_openblas
  libcblas           conda-forge/osx-64::libcblas-3.9.0-22_osx64_openblas
  libcxx             conda-forge/osx-64::libcxx-17.0.6-h88467a6_0
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
  libgfortran5       conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
  liblapack          conda-forge/osx-64::liblapack-3.9.0-22_osx64_openblas
  libopenblas        conda-forge/osx-64::libopenblas-0.3.27-openmp_hfef2a42_0
  llvm-openmp        conda-forge/osx-64::llvm-openmp-18.1.8-h15ab845_0
  numpy              conda-forge/osx-64::numpy-1.26.4-py39h28c39a1_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  python_abi         conda-forge/osx-64::python_abi-3.9-4_cp39
  pytz               conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
  scikit-learn       conda-forge/osx-64::scikit-learn-1.1.1-py39hafe9688_0
  scipy              conda-forge/osx-64::scipy-1.13.1-py39h038d4f4_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  threadpoolctl      conda-forge/noarch::threadpoolctl-3.5.0-pyhc1e730c_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /private/var/cache/basilisk/1.16.0/son.of.basilisk/0.99.0/env3

  added / updated specs:
    - python=3.9.12


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
  ca-certificates    conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
  libffi             conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
  libsqlite          conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0
  libzlib            conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
  ncurses            conda-forge/osx-64::ncurses-6.5-h5846eda_0
  openssl            conda-forge/osx-64::openssl-3.3.1-h87427d6_0
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/osx-64::python-3.9.12-h1cc4136_1_cpython
  readline           conda-forge/osx-64::readline-8.2-h9e318b2_1
  setuptools         conda-forge/noarch::setuptools-70.1.0-pyhd8ed1ab_0
  sqlite             conda-forge/osx-64::sqlite-3.46.0-h28673e1_0
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/osx-64::xz-5.2.6-h775f41a_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

Processing /private/tmp/Rtmp11LEqE/Rlib.efd354ea085d/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=1281 sha256=8088fee94815ac683e5505aa8827bfbbe95bdc15f7a4b12771edfb24517b6827
  Stored in directory: /private/tmp/pip-ephem-wheel-cache-3xyl2hgy/wheels/c3/d5/61/c215ae0db937281feaba6f9eb4f3dfbc99e9d75df6f4833de4
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 
448.721  60.894 594.246

'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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/basilisk.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* 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 ‘1.16.0’
* 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-3.19-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 ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/basilisk.Rcheck/00check.log’
for details.

Installation output

basilisk.Rcheck/00install.out

* installing *source* package ‘basilisk’ ...
** 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)