Multiple platform build/check report for BioC 3.23 - CHECK results for basilisk.utils on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4869
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "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.utils on kjohnson3

To the developers/maintainers of the basilisk.utils package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/basilisk.utils.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.

raw results

Summary

Package: basilisk.utils

Version: 1.23.1

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basilisk.utils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basilisk.utils_1.23.1.tar.gz

StartedAt: 2025-12-03 19:02:03 -0500 (Wed, 03 Dec 2025)

EndedAt: 2025-12-03 19:06:47 -0500 (Wed, 03 Dec 2025)

EllapsedTime: 283.4 seconds

RetCode: 0

Status: OK

CheckDir: basilisk.utils.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basilisk.utils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basilisk.utils_1.23.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/basilisk.utils.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘basilisk.utils/DESCRIPTION’ ... OK
* this is package ‘basilisk.utils’ version ‘1.23.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘basilisk.utils’ can be installed ... OK
* 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 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
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

basilisk.utils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL basilisk.utils
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘basilisk.utils’ ...
** this is package ‘basilisk.utils’ version ‘1.23.1’
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (basilisk.utils)

Tests output

basilisk.utils.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.utils)

Attaching package: 'basilisk.utils'

The following object is masked from 'package:utils':

    find

> test_check("basilisk.utils")
Channels:
 - conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpRhIJpC/filea4b11826f2bb/foo/biocconda/more-test-env

  added / updated specs:
    - pandas


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libblas-3.11.0             |3_h51639a9_openblas          18 KB  conda-forge
    libcblas-3.11.0            |3_hb0561ab_openblas          18 KB  conda-forge
    liblapack-3.11.0           |3_hd9741b5_openblas          18 KB  conda-forge
    llvm-openmp-21.1.7         |       h4a912ad_0         279 KB  conda-forge
    python-3.14.1              |h40d2674_100_cp314        13.0 MB  conda-forge
    zstd-1.5.7                 |       hbf9d68e_6         423 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        13.7 MB

The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/osx-arm64::_openmp_mutex-4.5-7_kmp_llvm 
  bzip2              conda-forge/osx-arm64::bzip2-1.0.8-hd037594_8 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.11.12-hbd8a1cb_0 
  libblas            conda-forge/osx-arm64::libblas-3.11.0-3_h51639a9_openblas 
  libcblas           conda-forge/osx-arm64::libcblas-3.11.0-3_hb0561ab_openblas 
  libcxx             conda-forge/osx-arm64::libcxx-21.1.7-hf598326_0 
  libexpat           conda-forge/osx-arm64::libexpat-2.7.3-haf25636_0 
  libffi             conda-forge/osx-arm64::libffi-3.5.2-he5f378a_0 
  libgcc             conda-forge/osx-arm64::libgcc-15.2.0-hcbb3090_14 
  libgfortran        conda-forge/osx-arm64::libgfortran-15.2.0-h07b0088_14 
  libgfortran5       conda-forge/osx-arm64::libgfortran5-15.2.0-hdae7583_14 
  liblapack          conda-forge/osx-arm64::liblapack-3.11.0-3_hd9741b5_openblas 
  liblzma            conda-forge/osx-arm64::liblzma-5.8.1-h39f12f2_2 
  libmpdec           conda-forge/osx-arm64::libmpdec-4.0.0-h5505292_0 
  libopenblas        conda-forge/osx-arm64::libopenblas-0.3.30-openmp_ha158390_3 
  libsqlite          conda-forge/osx-arm64::libsqlite-3.51.1-h9a5124b_0 
  libzlib            conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2 
  llvm-openmp        conda-forge/osx-arm64::llvm-openmp-21.1.7-h4a912ad_0 
  ncurses            conda-forge/osx-arm64::ncurses-6.5-h5e97a16_3 
  numpy              conda-forge/osx-arm64::numpy-2.3.5-py314h5b5928d_0 
  openssl            conda-forge/osx-arm64::openssl-3.6.0-h5503f6c_0 
  pandas             conda-forge/osx-arm64::pandas-2.3.3-py314ha3d490a_2 
  pip                conda-forge/noarch::pip-25.3-pyh145f28c_0 
  python             conda-forge/osx-arm64::python-3.14.1-h40d2674_100_cp314 
  python-dateutil    conda-forge/noarch::python-dateutil-2.9.0.post0-pyhe01879c_2 
  python-tzdata      conda-forge/noarch::python-tzdata-2025.2-pyhd8ed1ab_0 
  python_abi         conda-forge/noarch::python_abi-3.14-8_cp314 
  pytz               conda-forge/noarch::pytz-2025.2-pyhd8ed1ab_0 
  readline           conda-forge/osx-arm64::readline-8.2-h1d1bf99_2 
  six                conda-forge/noarch::six-1.17.0-pyhe01879c_1 
  tk                 conda-forge/osx-arm64::tk-8.6.13-h892fb3f_3 
  tzdata             conda-forge/noarch::tzdata-2025b-h78e105d_0 
  zstd               conda-forge/osx-arm64::zstd-1.5.7-hbf9d68e_6 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpRhIJpC/filea4b11826f2bb/foo/biocconda/test-env

  added / updated specs:
    - hdf5


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    hdf5-1.14.6                |nompi_hd3baa01_104         3.1 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         3.1 MB

The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/osx-arm64::_openmp_mutex-4.5-7_kmp_llvm 
  c-ares             conda-forge/osx-arm64::c-ares-1.34.5-h5505292_0 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.11.12-hbd8a1cb_0 
  hdf5               conda-forge/osx-arm64::hdf5-1.14.6-nompi_hd3baa01_104 
  krb5               conda-forge/osx-arm64::krb5-1.21.3-h237132a_0 
  libaec             conda-forge/osx-arm64::libaec-1.1.4-h51d1e36_0 
  libcurl            conda-forge/osx-arm64::libcurl-8.17.0-hdece5d2_0 
  libcxx             conda-forge/osx-arm64::libcxx-21.1.7-hf598326_0 
  libedit            conda-forge/osx-arm64::libedit-3.1.20250104-pl5321hafb1f1b_0 
  libev              conda-forge/osx-arm64::libev-4.33-h93a5062_2 
  libgcc             conda-forge/osx-arm64::libgcc-15.2.0-hcbb3090_14 
  libgfortran        conda-forge/osx-arm64::libgfortran-15.2.0-h07b0088_14 
  libgfortran5       conda-forge/osx-arm64::libgfortran5-15.2.0-hdae7583_14 
  libnghttp2         conda-forge/osx-arm64::libnghttp2-1.67.0-hc438710_0 
  libssh2            conda-forge/osx-arm64::libssh2-1.11.1-h1590b86_0 
  libzlib            conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2 
  llvm-openmp        conda-forge/osx-arm64::llvm-openmp-21.1.7-h4a912ad_0 
  ncurses            conda-forge/osx-arm64::ncurses-6.5-h5e97a16_3 
  openssl            conda-forge/osx-arm64::openssl-3.6.0-h5503f6c_0 
  zstd               conda-forge/osx-arm64::zstd-1.5.7-hbf9d68e_6 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpRhIJpC/filea4b162e1169f/test_env/1.0.0

  added / updated specs:
    - hdf5


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/osx-arm64::_openmp_mutex-4.5-7_kmp_llvm 
  c-ares             conda-forge/osx-arm64::c-ares-1.34.5-h5505292_0 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.11.12-hbd8a1cb_0 
  hdf5               conda-forge/osx-arm64::hdf5-1.14.6-nompi_hd3baa01_104 
  krb5               conda-forge/osx-arm64::krb5-1.21.3-h237132a_0 
  libaec             conda-forge/osx-arm64::libaec-1.1.4-h51d1e36_0 
  libcurl            conda-forge/osx-arm64::libcurl-8.17.0-hdece5d2_0 
  libcxx             conda-forge/osx-arm64::libcxx-21.1.7-hf598326_0 
  libedit            conda-forge/osx-arm64::libedit-3.1.20250104-pl5321hafb1f1b_0 
  libev              conda-forge/osx-arm64::libev-4.33-h93a5062_2 
  libgcc             conda-forge/osx-arm64::libgcc-15.2.0-hcbb3090_14 
  libgfortran        conda-forge/osx-arm64::libgfortran-15.2.0-h07b0088_14 
  libgfortran5       conda-forge/osx-arm64::libgfortran5-15.2.0-hdae7583_14 
  libnghttp2         conda-forge/osx-arm64::libnghttp2-1.67.0-hc438710_0 
  libssh2            conda-forge/osx-arm64::libssh2-1.11.1-h1590b86_0 
  libzlib            conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2 
  llvm-openmp        conda-forge/osx-arm64::llvm-openmp-21.1.7-h4a912ad_0 
  ncurses            conda-forge/osx-arm64::ncurses-6.5-h5e97a16_3 
  openssl            conda-forge/osx-arm64::openssl-3.6.0-h5503f6c_0 
  zstd               conda-forge/osx-arm64::zstd-1.5.7-hbf9d68e_6 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpRhIJpC/filea4b162e1169f/test_env/1.0.1

  added / updated specs:
    - hdf5


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/osx-arm64::_openmp_mutex-4.5-7_kmp_llvm 
  c-ares             conda-forge/osx-arm64::c-ares-1.34.5-h5505292_0 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.11.12-hbd8a1cb_0 
  hdf5               conda-forge/osx-arm64::hdf5-1.14.6-nompi_hd3baa01_104 
  krb5               conda-forge/osx-arm64::krb5-1.21.3-h237132a_0 
  libaec             conda-forge/osx-arm64::libaec-1.1.4-h51d1e36_0 
  libcurl            conda-forge/osx-arm64::libcurl-8.17.0-hdece5d2_0 
  libcxx             conda-forge/osx-arm64::libcxx-21.1.7-hf598326_0 
  libedit            conda-forge/osx-arm64::libedit-3.1.20250104-pl5321hafb1f1b_0 
  libev              conda-forge/osx-arm64::libev-4.33-h93a5062_2 
  libgcc             conda-forge/osx-arm64::libgcc-15.2.0-hcbb3090_14 
  libgfortran        conda-forge/osx-arm64::libgfortran-15.2.0-h07b0088_14 
  libgfortran5       conda-forge/osx-arm64::libgfortran5-15.2.0-hdae7583_14 
  libnghttp2         conda-forge/osx-arm64::libnghttp2-1.67.0-hc438710_0 
  libssh2            conda-forge/osx-arm64::libssh2-1.11.1-h1590b86_0 
  libzlib            conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2 
  llvm-openmp        conda-forge/osx-arm64::llvm-openmp-21.1.7-h4a912ad_0 
  ncurses            conda-forge/osx-arm64::ncurses-6.5-h5e97a16_3 
  openssl            conda-forge/osx-arm64::openssl-3.6.0-h5503f6c_0 
  zstd               conda-forge/osx-arm64::zstd-1.5.7-hbf9d68e_6 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpRhIJpC/filea4b162e1169f/test_env/1.0.0

  added / updated specs:
    - hdf5


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/osx-arm64::_openmp_mutex-4.5-7_kmp_llvm 
  c-ares             conda-forge/osx-arm64::c-ares-1.34.5-h5505292_0 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.11.12-hbd8a1cb_0 
  hdf5               conda-forge/osx-arm64::hdf5-1.14.6-nompi_hd3baa01_104 
  krb5               conda-forge/osx-arm64::krb5-1.21.3-h237132a_0 
  libaec             conda-forge/osx-arm64::libaec-1.1.4-h51d1e36_0 
  libcurl            conda-forge/osx-arm64::libcurl-8.17.0-hdece5d2_0 
  libcxx             conda-forge/osx-arm64::libcxx-21.1.7-hf598326_0 
  libedit            conda-forge/osx-arm64::libedit-3.1.20250104-pl5321hafb1f1b_0 
  libev              conda-forge/osx-arm64::libev-4.33-h93a5062_2 
  libgcc             conda-forge/osx-arm64::libgcc-15.2.0-hcbb3090_14 
  libgfortran        conda-forge/osx-arm64::libgfortran-15.2.0-h07b0088_14 
  libgfortran5       conda-forge/osx-arm64::libgfortran5-15.2.0-hdae7583_14 
  libnghttp2         conda-forge/osx-arm64::libnghttp2-1.67.0-hc438710_0 
  libssh2            conda-forge/osx-arm64::libssh2-1.11.1-h1590b86_0 
  libzlib            conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2 
  llvm-openmp        conda-forge/osx-arm64::llvm-openmp-21.1.7-h4a912ad_0 
  ncurses            conda-forge/osx-arm64::ncurses-6.5-h5e97a16_3 
  openssl            conda-forge/osx-arm64::openssl-3.6.0-h5503f6c_0 
  zstd               conda-forge/osx-arm64::zstd-1.5.7-hbf9d68e_6 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

PackagesNotFoundError: The following packages are not available from current channels:

  - aaronrandompackageshouldntexist

Current channels:

  - https://anaconda.mgb.org/conda-forge

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.


[ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
 23.436  24.561  55.435

Example timings

basilisk.utils.Rcheck/basilisk.utils-Ex.timings

name	user	system	elapsed
binaryPath	0.000	0.001	0.000
configureEnvironments	0	0	0
createEnvironment	0.002	0.001	0.003
defaults	0	0	0
download	0.002	0.001	0.004
find	0.221	0.149	1.229