##############################################################################
##############################################################################
###
### 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_1.21.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/basilisk.utils.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 option ‘--no-vignettes’
* checking for file ‘basilisk.utils/DESCRIPTION’ ... OK
* this is package ‘basilisk.utils’ version ‘1.21.2’
* 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘basilisk.utils’ ...
** this is package ‘basilisk.utils’ version ‘1.21.2’
** 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)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
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.utils)

Attaching package: 'basilisk.utils'

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

    find

> test_check("basilisk.utils")
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: /tmp/RtmpUC75JU/file15462519586b1/foo/biocconda/more-test-env

  added / updated specs:
    - pandas


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-2025.7.9-hbd8a1cb_0 
  libblas            conda-forge/osx-64::libblas-3.9.0-32_h7f60823_openblas 
  libcblas           conda-forge/osx-64::libcblas-3.9.0-32_hff6cab4_openblas 
  libcxx             conda-forge/osx-64::libcxx-20.1.8-hf95d169_0 
  libexpat           conda-forge/osx-64::libexpat-2.7.0-h240833e_0 
  libffi             conda-forge/osx-64::libffi-3.4.6-h281671d_1 
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-14_2_0_h51e75f0_103 
  libgfortran5       conda-forge/osx-64::libgfortran5-14.2.0-h51e75f0_103 
  liblapack          conda-forge/osx-64::liblapack-3.9.0-32_h236ab99_openblas 
  liblzma            conda-forge/osx-64::liblzma-5.8.1-hd471939_2 
  libmpdec           conda-forge/osx-64::libmpdec-4.0.0-h6e16a3a_0 
  libopenblas        conda-forge/osx-64::libopenblas-0.3.30-openmp_hbf64a52_0 
  libsqlite          conda-forge/osx-64::libsqlite-3.50.2-h39a8b3b_2 
  libzlib            conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2 
  llvm-openmp        conda-forge/osx-64::llvm-openmp-20.1.7-ha54dae1_0 
  ncurses            conda-forge/osx-64::ncurses-6.5-h0622a9a_3 
  numpy              conda-forge/osx-64::numpy-2.3.1-py313hc518a0f_0 
  openssl            conda-forge/osx-64::openssl-3.5.1-hc426f3f_0 
  pandas             conda-forge/osx-64::pandas-2.3.1-py313h366a99e_0 
  pip                conda-forge/noarch::pip-25.1.1-pyh145f28c_0 
  python             conda-forge/osx-64::python-3.13.5-hc3a4c56_102_cp313 
  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-3.13-7_cp313 
  pytz               conda-forge/noarch::pytz-2025.2-pyhd8ed1ab_0 
  readline           conda-forge/osx-64::readline-8.2-h7cca4af_2 
  six                conda-forge/noarch::six-1.17.0-pyhd8ed1ab_0 
  tk                 conda-forge/osx-64::tk-8.6.13-hf689a15_2 
  tzdata             conda-forge/noarch::tzdata-2025b-h78e105d_0 


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

## Package Plan ##

  environment location: /tmp/RtmpUC75JU/file15462519586b1/foo/biocconda/test-env

  added / updated specs:
    - hdf5


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    hdf5-1.14.6                |nompi_hc8237f9_102         3.4 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         3.4 MB

The following NEW packages will be INSTALLED:

  c-ares             conda-forge/osx-64::c-ares-1.34.5-hf13058a_0 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.7.9-hbd8a1cb_0 
  hdf5               conda-forge/osx-64::hdf5-1.14.6-nompi_hc8237f9_102 
  krb5               conda-forge/osx-64::krb5-1.21.3-h37d8d59_0 
  libaec             conda-forge/osx-64::libaec-1.1.4-ha6bc127_0 
  libcurl            conda-forge/osx-64::libcurl-8.14.1-h5dec5d8_0 
  libcxx             conda-forge/osx-64::libcxx-20.1.8-hf95d169_0 
  libedit            conda-forge/osx-64::libedit-3.1.20250104-pl5321ha958ccf_0 
  libev              conda-forge/osx-64::libev-4.33-h10d778d_2 
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-14_2_0_h51e75f0_103 
  libgfortran5       conda-forge/osx-64::libgfortran5-14.2.0-h51e75f0_103 
  libnghttp2         conda-forge/osx-64::libnghttp2-1.64.0-hc7306c3_0 
  libssh2            conda-forge/osx-64::libssh2-1.11.1-hed3591d_0 
  libzlib            conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2 
  llvm-openmp        conda-forge/osx-64::llvm-openmp-20.1.7-ha54dae1_0 
  ncurses            conda-forge/osx-64::ncurses-6.5-h0622a9a_3 
  openssl            conda-forge/osx-64::openssl-3.5.1-hc426f3f_0 
  zstd               conda-forge/osx-64::zstd-1.5.7-h8210216_2 


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

## Package Plan ##

  environment location: /tmp/RtmpUC75JU/file154623cb9d4c8/test_env/1.0.0

  added / updated specs:
    - hdf5


The following NEW packages will be INSTALLED:

  c-ares             conda-forge/osx-64::c-ares-1.34.5-hf13058a_0 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.7.9-hbd8a1cb_0 
  hdf5               conda-forge/osx-64::hdf5-1.14.6-nompi_hc8237f9_102 
  krb5               conda-forge/osx-64::krb5-1.21.3-h37d8d59_0 
  libaec             conda-forge/osx-64::libaec-1.1.4-ha6bc127_0 
  libcurl            conda-forge/osx-64::libcurl-8.14.1-h5dec5d8_0 
  libcxx             conda-forge/osx-64::libcxx-20.1.8-hf95d169_0 
  libedit            conda-forge/osx-64::libedit-3.1.20250104-pl5321ha958ccf_0 
  libev              conda-forge/osx-64::libev-4.33-h10d778d_2 
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-14_2_0_h51e75f0_103 
  libgfortran5       conda-forge/osx-64::libgfortran5-14.2.0-h51e75f0_103 
  libnghttp2         conda-forge/osx-64::libnghttp2-1.64.0-hc7306c3_0 
  libssh2            conda-forge/osx-64::libssh2-1.11.1-hed3591d_0 
  libzlib            conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2 
  llvm-openmp        conda-forge/osx-64::llvm-openmp-20.1.7-ha54dae1_0 
  ncurses            conda-forge/osx-64::ncurses-6.5-h0622a9a_3 
  openssl            conda-forge/osx-64::openssl-3.5.1-hc426f3f_0 
  zstd               conda-forge/osx-64::zstd-1.5.7-h8210216_2 


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

## Package Plan ##

  environment location: /tmp/RtmpUC75JU/file154623cb9d4c8/test_env/1.0.1

  added / updated specs:
    - hdf5


The following NEW packages will be INSTALLED:

  c-ares             conda-forge/osx-64::c-ares-1.34.5-hf13058a_0 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.7.9-hbd8a1cb_0 
  hdf5               conda-forge/osx-64::hdf5-1.14.6-nompi_hc8237f9_102 
  krb5               conda-forge/osx-64::krb5-1.21.3-h37d8d59_0 
  libaec             conda-forge/osx-64::libaec-1.1.4-ha6bc127_0 
  libcurl            conda-forge/osx-64::libcurl-8.14.1-h5dec5d8_0 
  libcxx             conda-forge/osx-64::libcxx-20.1.8-hf95d169_0 
  libedit            conda-forge/osx-64::libedit-3.1.20250104-pl5321ha958ccf_0 
  libev              conda-forge/osx-64::libev-4.33-h10d778d_2 
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-14_2_0_h51e75f0_103 
  libgfortran5       conda-forge/osx-64::libgfortran5-14.2.0-h51e75f0_103 
  libnghttp2         conda-forge/osx-64::libnghttp2-1.64.0-hc7306c3_0 
  libssh2            conda-forge/osx-64::libssh2-1.11.1-hed3591d_0 
  libzlib            conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2 
  llvm-openmp        conda-forge/osx-64::llvm-openmp-20.1.7-ha54dae1_0 
  ncurses            conda-forge/osx-64::ncurses-6.5-h0622a9a_3 
  openssl            conda-forge/osx-64::openssl-3.5.1-hc426f3f_0 
  zstd               conda-forge/osx-64::zstd-1.5.7-h8210216_2 


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

## Package Plan ##

  environment location: /tmp/RtmpUC75JU/file154623cb9d4c8/test_env/1.0.0

  added / updated specs:
    - hdf5


The following NEW packages will be INSTALLED:

  c-ares             conda-forge/osx-64::c-ares-1.34.5-hf13058a_0 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.7.9-hbd8a1cb_0 
  hdf5               conda-forge/osx-64::hdf5-1.14.6-nompi_hc8237f9_102 
  krb5               conda-forge/osx-64::krb5-1.21.3-h37d8d59_0 
  libaec             conda-forge/osx-64::libaec-1.1.4-ha6bc127_0 
  libcurl            conda-forge/osx-64::libcurl-8.14.1-h5dec5d8_0 
  libcxx             conda-forge/osx-64::libcxx-20.1.8-hf95d169_0 
  libedit            conda-forge/osx-64::libedit-3.1.20250104-pl5321ha958ccf_0 
  libev              conda-forge/osx-64::libev-4.33-h10d778d_2 
  libgfortran        conda-forge/osx-64::libgfortran-5.0.0-14_2_0_h51e75f0_103 
  libgfortran5       conda-forge/osx-64::libgfortran5-14.2.0-h51e75f0_103 
  libnghttp2         conda-forge/osx-64::libnghttp2-1.64.0-hc7306c3_0 
  libssh2            conda-forge/osx-64::libssh2-1.11.1-hed3591d_0 
  libzlib            conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2 
  llvm-openmp        conda-forge/osx-64::llvm-openmp-20.1.7-ha54dae1_0 
  ncurses            conda-forge/osx-64::ncurses-6.5-h0622a9a_3 
  openssl            conda-forge/osx-64::openssl-3.5.1-hc426f3f_0 
  zstd               conda-forge/osx-64::zstd-1.5.7-h8210216_2 


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... failed

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

  - aaronrandompackageshouldntexist

Current channels:

  - https://conda.anaconda.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 
 72.788  35.006 113.405