Multiple platform build/check report for BioC 3.22 - CHECK results for basilisk.utils on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4810
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"	4548
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4528
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4493
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 palomino8

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: 1.21.2

Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:basilisk.utils.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings basilisk.utils_1.21.2.tar.gz

StartedAt: 2025-06-18 23:37:14 -0400 (Wed, 18 Jun 2025)

EndedAt: 2025-06-18 23:47:21 -0400 (Wed, 18 Jun 2025)

EllapsedTime: 606.7 seconds

RetCode: 0

Status: OK

CheckDir: basilisk.utils.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:basilisk.utils.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings basilisk.utils_1.21.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/basilisk.utils.Rcheck'
* using R version 4.5.0 (2025-04-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL basilisk.utils
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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)

Tests output

basilisk.utils.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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: win-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpGapyu1\file12d3c6b1438f2\foo\biocconda\more-test-env

  added / updated specs:
    - pandas


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/win-64::bzip2-1.0.8-h2466b09_7 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.6.15-h4c7d964_0 
  intel-openmp       conda-forge/win-64::intel-openmp-2024.2.1-h57928b3_1083 
  libblas            conda-forge/win-64::libblas-3.9.0-31_h641d27c_mkl 
  libcblas           conda-forge/win-64::libcblas-3.9.0-31_h5e41251_mkl 
  libexpat           conda-forge/win-64::libexpat-2.7.0-he0c23c2_0 
  libffi             conda-forge/win-64::libffi-3.4.6-h537db12_1 
  libhwloc           conda-forge/win-64::libhwloc-2.11.2-default_ha69328c_1001 
  libiconv           conda-forge/win-64::libiconv-1.18-h135ad9c_1 
  liblapack          conda-forge/win-64::liblapack-3.9.0-31_h1aa476e_mkl 
  liblzma            conda-forge/win-64::liblzma-5.8.1-h2466b09_2 
  libmpdec           conda-forge/win-64::libmpdec-4.0.0-h2466b09_0 
  libsqlite          conda-forge/win-64::libsqlite-3.50.1-h67fdade_0 
  libwinpthread      conda-forge/win-64::libwinpthread-12.0.0.r4.gg4f2fc60ca-h57928b3_9 
  libxml2            conda-forge/win-64::libxml2-2.13.8-h442d1da_0 
  libzlib            conda-forge/win-64::libzlib-1.3.1-h2466b09_2 
  mkl                conda-forge/win-64::mkl-2024.2.2-h66d3029_15 
  numpy              conda-forge/win-64::numpy-2.3.0-py313hefb8edb_0 
  openssl            conda-forge/win-64::openssl-3.5.0-ha4e3fda_1 
  pandas             conda-forge/win-64::pandas-2.3.0-py313hf91d08e_0 
  pip                conda-forge/noarch::pip-25.1.1-pyh145f28c_0 
  python             conda-forge/win-64::python-3.13.5-h7de537c_102_cp313 
  python-dateutil    conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_1 
  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 
  six                conda-forge/noarch::six-1.17.0-pyhd8ed1ab_0 
  tbb                conda-forge/win-64::tbb-2021.13.0-h62715c5_1 
  tk                 conda-forge/win-64::tk-8.6.13-h2c6b04d_2 
  tzdata             conda-forge/noarch::tzdata-2025b-h78e105d_0 
  ucrt               conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_1 
  vc                 conda-forge/win-64::vc-14.3-h2b53caa_26 
  vc14_runtime       conda-forge/win-64::vc14_runtime-14.42.34438-hfd919c2_26 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: win-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpGapyu1\file12d3c6b1438f2\foo\biocconda\test-env

  added / updated specs:
    - hdf5


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/noarch::ca-certificates-2025.6.15-h4c7d964_0 
  hdf5               conda-forge/win-64::hdf5-1.14.6-nompi_hd5d9e70_101 
  krb5               conda-forge/win-64::krb5-1.21.3-hdf4eb48_0 
  libaec             conda-forge/win-64::libaec-1.1.4-h20038f6_0 
  libcurl            conda-forge/win-64::libcurl-8.14.1-h88aaa65_0 
  libssh2            conda-forge/win-64::libssh2-1.11.1-h9aa295b_0 
  libzlib            conda-forge/win-64::libzlib-1.3.1-h2466b09_2 
  openssl            conda-forge/win-64::openssl-3.5.0-ha4e3fda_1 
  ucrt               conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_1 
  vc                 conda-forge/win-64::vc-14.3-h2b53caa_26 
  vc14_runtime       conda-forge/win-64::vc14_runtime-14.42.34438-hfd919c2_26 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Retrieving notices: ...working... done
Channels:
 - conda-forge
Platform: win-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpGapyu1\file12d3c7fe8cfd\test_env\1.0.0

  added / updated specs:
    - hdf5


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/noarch::ca-certificates-2025.6.15-h4c7d964_0 
  hdf5               conda-forge/win-64::hdf5-1.14.6-nompi_hd5d9e70_101 
  krb5               conda-forge/win-64::krb5-1.21.3-hdf4eb48_0 
  libaec             conda-forge/win-64::libaec-1.1.4-h20038f6_0 
  libcurl            conda-forge/win-64::libcurl-8.14.1-h88aaa65_0 
  libssh2            conda-forge/win-64::libssh2-1.11.1-h9aa295b_0 
  libzlib            conda-forge/win-64::libzlib-1.3.1-h2466b09_2 
  openssl            conda-forge/win-64::openssl-3.5.0-ha4e3fda_1 
  ucrt               conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_1 
  vc                 conda-forge/win-64::vc-14.3-h2b53caa_26 
  vc14_runtime       conda-forge/win-64::vc14_runtime-14.42.34438-hfd919c2_26 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: win-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpGapyu1\file12d3c7fe8cfd\test_env\1.0.1

  added / updated specs:
    - hdf5


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/noarch::ca-certificates-2025.6.15-h4c7d964_0 
  hdf5               conda-forge/win-64::hdf5-1.14.6-nompi_hd5d9e70_101 
  krb5               conda-forge/win-64::krb5-1.21.3-hdf4eb48_0 
  libaec             conda-forge/win-64::libaec-1.1.4-h20038f6_0 
  libcurl            conda-forge/win-64::libcurl-8.14.1-h88aaa65_0 
  libssh2            conda-forge/win-64::libssh2-1.11.1-h9aa295b_0 
  libzlib            conda-forge/win-64::libzlib-1.3.1-h2466b09_2 
  openssl            conda-forge/win-64::openssl-3.5.0-ha4e3fda_1 
  ucrt               conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_1 
  vc                 conda-forge/win-64::vc-14.3-h2b53caa_26 
  vc14_runtime       conda-forge/win-64::vc14_runtime-14.42.34438-hfd919c2_26 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: win-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpGapyu1\file12d3c7fe8cfd\test_env\1.0.0

  added / updated specs:
    - hdf5


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/noarch::ca-certificates-2025.6.15-h4c7d964_0 
  hdf5               conda-forge/win-64::hdf5-1.14.6-nompi_hd5d9e70_101 
  krb5               conda-forge/win-64::krb5-1.21.3-hdf4eb48_0 
  libaec             conda-forge/win-64::libaec-1.1.4-h20038f6_0 
  libcurl            conda-forge/win-64::libcurl-8.14.1-h88aaa65_0 
  libssh2            conda-forge/win-64::libssh2-1.11.1-h9aa295b_0 
  libzlib            conda-forge/win-64::libzlib-1.3.1-h2466b09_2 
  openssl            conda-forge/win-64::openssl-3.5.0-ha4e3fda_1 
  ucrt               conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_1 
  vc                 conda-forge/win-64::vc-14.3-h2b53caa_26 
  vc14_runtime       conda-forge/win-64::vc14_runtime-14.42.34438-hfd919c2_26 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: win-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 
   0.93    0.43  566.46

Example timings

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

name	user	system	elapsed
binaryPath	0	0	0
configureEnvironments	0	0	0
createEnvironment	0	0	0
defaults	0.00	0.01	0.02
download	0	0	0
find	0.00	0.00	4.37