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This page was generated on 2025-10-31 09:43 -0400 (Fri, 31 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences" 917
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Package 22/230HostnameOS / ArchINSTALLBUILDCHECK
basilisk.utils 1.23.0  (landing page)
Aaron Lun
Snapshot Date: 2025-10-31 06:00 -0400 (Fri, 31 Oct 2025)
git_url: https://git.bioconductor.org/packages/basilisk.utils
git_branch: devel
git_last_commit: 2b3958b
git_last_commit_date: 2025-10-29 10:56:58 -0400 (Wed, 29 Oct 2025)
teran2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  

CHECK results for basilisk.utils on teran2

To the developers/maintainers of the basilisk.utils 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.utils
Version: 1.23.0
Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:basilisk.utils.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings basilisk.utils_1.23.0.tar.gz
StartedAt: 2025-10-31 07:39:29 -0400 (Fri, 31 Oct 2025)
EndedAt: 2025-10-31 07:40:44 -0400 (Fri, 31 Oct 2025)
EllapsedTime: 75.0 seconds
RetCode: 0
Status:   OK  
CheckDir: basilisk.utils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:basilisk.utils.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings basilisk.utils_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/basilisk.utils.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘basilisk.utils/DESCRIPTION’ ... OK
* this is package ‘basilisk.utils’ version ‘1.23.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

The Date field is over a month old.
* 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/basilisk.utils.Rcheck/00check.log’
for details.

Installation output

basilisk.utils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL basilisk.utils
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘basilisk.utils’ ...
** this is package ‘basilisk.utils’ version ‘1.23.0’
** 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) (2025-10-28 r88973) -- "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.utils)

Attaching package: 'basilisk.utils'

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

    find

> test_check("basilisk.utils")
Channels:
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /tmp/Rtmpv7qyY9/file1d34ff33a5dfe8/foo/biocconda/more-test-env

  added / updated specs:
    - pandas


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-hda65f42_8 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.44-h1aa0949_4 
  libblas            conda-forge/linux-64::libblas-3.9.0-38_h4a7cf45_openblas 
  libcblas           conda-forge/linux-64::libcblas-3.9.0-38_h0358290_openblas 
  libexpat           conda-forge/linux-64::libexpat-2.7.1-hecca717_0 
  libffi             conda-forge/linux-64::libffi-3.5.2-h9ec8514_0 
  libgcc             conda-forge/linux-64::libgcc-15.2.0-h767d61c_7 
  libgfortran        conda-forge/linux-64::libgfortran-15.2.0-h69a702a_7 
  libgfortran5       conda-forge/linux-64::libgfortran5-15.2.0-hcd61629_7 
  libgomp            conda-forge/linux-64::libgomp-15.2.0-h767d61c_7 
  liblapack          conda-forge/linux-64::liblapack-3.9.0-38_h47877c9_openblas 
  liblzma            conda-forge/linux-64::liblzma-5.8.1-hb9d3cd8_2 
  libmpdec           conda-forge/linux-64::libmpdec-4.0.0-hb9d3cd8_0 
  libopenblas        conda-forge/linux-64::libopenblas-0.3.30-pthreads_h94d23a6_3 
  libsqlite          conda-forge/linux-64::libsqlite-3.50.4-h0c1763c_0 
  libstdcxx          conda-forge/linux-64::libstdcxx-15.2.0-h8f9b012_7 
  libuuid            conda-forge/linux-64::libuuid-2.41.2-he9a06e4_0 
  libzlib            conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 
  ncurses            conda-forge/linux-64::ncurses-6.5-h2d0b736_3 
  numpy              conda-forge/linux-64::numpy-2.3.4-py314h2b28147_0 
  openssl            conda-forge/linux-64::openssl-3.5.4-h26f9b46_0 
  pandas             conda-forge/linux-64::pandas-2.3.3-py314ha0b5721_1 
  pip                conda-forge/noarch::pip-25.2-pyh145f28c_0 
  python             conda-forge/linux-64::python-3.14.0-h32b2ec7_102_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/linux-64::readline-8.2-h8c095d6_2 
  six                conda-forge/noarch::six-1.17.0-pyhe01879c_1 
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_hd72426e_102 
  tzdata             conda-forge/noarch::tzdata-2025b-h78e105d_0 
  zstd               conda-forge/linux-64::zstd-1.5.7-hb8e6e7a_2 


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

## Package Plan ##

  environment location: /tmp/Rtmpv7qyY9/file1d34ff33a5dfe8/foo/biocconda/test-env

  added / updated specs:
    - hdf5


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 
  c-ares             conda-forge/linux-64::c-ares-1.34.5-hb9d3cd8_0 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0 
  hdf5               conda-forge/linux-64::hdf5-1.14.6-nompi_h6e4c0c1_103 
  keyutils           conda-forge/linux-64::keyutils-1.6.3-hb9d3cd8_0 
  krb5               conda-forge/linux-64::krb5-1.21.3-h659f571_0 
  libaec             conda-forge/linux-64::libaec-1.1.4-h3f801dc_0 
  libcurl            conda-forge/linux-64::libcurl-8.16.0-h4e3cde8_0 
  libedit            conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0 
  libev              conda-forge/linux-64::libev-4.33-hd590300_2 
  libgcc             conda-forge/linux-64::libgcc-15.2.0-h767d61c_7 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_7 
  libgfortran        conda-forge/linux-64::libgfortran-15.2.0-h69a702a_7 
  libgfortran5       conda-forge/linux-64::libgfortran5-15.2.0-hcd61629_7 
  libgomp            conda-forge/linux-64::libgomp-15.2.0-h767d61c_7 
  libnghttp2         conda-forge/linux-64::libnghttp2-1.67.0-had1ee68_0 
  libssh2            conda-forge/linux-64::libssh2-1.11.1-hcf80075_0 
  libstdcxx          conda-forge/linux-64::libstdcxx-15.2.0-h8f9b012_7 
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-15.2.0-h4852527_7 
  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-3.5.4-h26f9b46_0 
  zstd               conda-forge/linux-64::zstd-1.5.7-hb8e6e7a_2 


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

## Package Plan ##

  environment location: /tmp/Rtmpv7qyY9/file1d34ff39ba665c/test_env/1.0.0

  added / updated specs:
    - hdf5


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 
  c-ares             conda-forge/linux-64::c-ares-1.34.5-hb9d3cd8_0 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0 
  hdf5               conda-forge/linux-64::hdf5-1.14.6-nompi_h6e4c0c1_103 
  keyutils           conda-forge/linux-64::keyutils-1.6.3-hb9d3cd8_0 
  krb5               conda-forge/linux-64::krb5-1.21.3-h659f571_0 
  libaec             conda-forge/linux-64::libaec-1.1.4-h3f801dc_0 
  libcurl            conda-forge/linux-64::libcurl-8.16.0-h4e3cde8_0 
  libedit            conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0 
  libev              conda-forge/linux-64::libev-4.33-hd590300_2 
  libgcc             conda-forge/linux-64::libgcc-15.2.0-h767d61c_7 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_7 
  libgfortran        conda-forge/linux-64::libgfortran-15.2.0-h69a702a_7 
  libgfortran5       conda-forge/linux-64::libgfortran5-15.2.0-hcd61629_7 
  libgomp            conda-forge/linux-64::libgomp-15.2.0-h767d61c_7 
  libnghttp2         conda-forge/linux-64::libnghttp2-1.67.0-had1ee68_0 
  libssh2            conda-forge/linux-64::libssh2-1.11.1-hcf80075_0 
  libstdcxx          conda-forge/linux-64::libstdcxx-15.2.0-h8f9b012_7 
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-15.2.0-h4852527_7 
  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-3.5.4-h26f9b46_0 
  zstd               conda-forge/linux-64::zstd-1.5.7-hb8e6e7a_2 


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

## Package Plan ##

  environment location: /tmp/Rtmpv7qyY9/file1d34ff39ba665c/test_env/1.0.1

  added / updated specs:
    - hdf5


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 
  c-ares             conda-forge/linux-64::c-ares-1.34.5-hb9d3cd8_0 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0 
  hdf5               conda-forge/linux-64::hdf5-1.14.6-nompi_h6e4c0c1_103 
  keyutils           conda-forge/linux-64::keyutils-1.6.3-hb9d3cd8_0 
  krb5               conda-forge/linux-64::krb5-1.21.3-h659f571_0 
  libaec             conda-forge/linux-64::libaec-1.1.4-h3f801dc_0 
  libcurl            conda-forge/linux-64::libcurl-8.16.0-h4e3cde8_0 
  libedit            conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0 
  libev              conda-forge/linux-64::libev-4.33-hd590300_2 
  libgcc             conda-forge/linux-64::libgcc-15.2.0-h767d61c_7 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_7 
  libgfortran        conda-forge/linux-64::libgfortran-15.2.0-h69a702a_7 
  libgfortran5       conda-forge/linux-64::libgfortran5-15.2.0-hcd61629_7 
  libgomp            conda-forge/linux-64::libgomp-15.2.0-h767d61c_7 
  libnghttp2         conda-forge/linux-64::libnghttp2-1.67.0-had1ee68_0 
  libssh2            conda-forge/linux-64::libssh2-1.11.1-hcf80075_0 
  libstdcxx          conda-forge/linux-64::libstdcxx-15.2.0-h8f9b012_7 
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-15.2.0-h4852527_7 
  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-3.5.4-h26f9b46_0 
  zstd               conda-forge/linux-64::zstd-1.5.7-hb8e6e7a_2 


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

## Package Plan ##

  environment location: /tmp/Rtmpv7qyY9/file1d34ff39ba665c/test_env/1.0.0

  added / updated specs:
    - hdf5


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 
  c-ares             conda-forge/linux-64::c-ares-1.34.5-hb9d3cd8_0 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0 
  hdf5               conda-forge/linux-64::hdf5-1.14.6-nompi_h6e4c0c1_103 
  keyutils           conda-forge/linux-64::keyutils-1.6.3-hb9d3cd8_0 
  krb5               conda-forge/linux-64::krb5-1.21.3-h659f571_0 
  libaec             conda-forge/linux-64::libaec-1.1.4-h3f801dc_0 
  libcurl            conda-forge/linux-64::libcurl-8.16.0-h4e3cde8_0 
  libedit            conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0 
  libev              conda-forge/linux-64::libev-4.33-hd590300_2 
  libgcc             conda-forge/linux-64::libgcc-15.2.0-h767d61c_7 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_7 
  libgfortran        conda-forge/linux-64::libgfortran-15.2.0-h69a702a_7 
  libgfortran5       conda-forge/linux-64::libgfortran5-15.2.0-hcd61629_7 
  libgomp            conda-forge/linux-64::libgomp-15.2.0-h767d61c_7 
  libnghttp2         conda-forge/linux-64::libnghttp2-1.67.0-had1ee68_0 
  libssh2            conda-forge/linux-64::libssh2-1.11.1-hcf80075_0 
  libstdcxx          conda-forge/linux-64::libstdcxx-15.2.0-h8f9b012_7 
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-15.2.0-h4852527_7 
  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-3.5.4-h26f9b46_0 
  zstd               conda-forge/linux-64::zstd-1.5.7-hb8e6e7a_2 


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... 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 
 34.333  14.396  57.881

Example timings

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

nameusersystemelapsed
binaryPath000
configureEnvironments0.0040.0010.005
createEnvironment0.0020.0000.004
defaults000
download0.0020.0010.003
find0.2590.0901.115