Multiple platform build/check report for BioC 3.21 - BUILD results for cfTools on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4824
palomino7	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4566
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4604
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4545
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4579
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*

BUILD results for cfTools on palomino7

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

Version: 1.8.0

Command: chmod a+r cfTools -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe --arch x64 CMD build --keep-empty-dirs --no-resave-data cfTools

StartedAt: 2025-08-14 17:58:23 -0400 (Thu, 14 Aug 2025)

EndedAt: 2025-08-14 18:06:19 -0400 (Thu, 14 Aug 2025)

EllapsedTime: 476.4 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r cfTools -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe --arch x64 CMD build --keep-empty-dirs --no-resave-data cfTools
###
##############################################################################
##############################################################################


* checking for file 'cfTools/DESCRIPTION' ... OK
* preparing 'cfTools':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'cfTools-vignette.Rmd' using rmarkdown
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: C:\Users\biocbuild\.basilisk\1.20.0\cfTools\1.8.0\new_env

  added / updated specs:
    - python=3.8


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-2025.8.3-h4c7d964_0 
  libffi             conda-forge/win-64::libffi-3.4.6-h537db12_1 
  liblzma            conda-forge/win-64::liblzma-5.8.1-h2466b09_2 
  liblzma-devel      conda-forge/win-64::liblzma-devel-5.8.1-h2466b09_2 
  libsqlite          conda-forge/win-64::libsqlite-3.50.4-hf5d6505_0 
  libzlib            conda-forge/win-64::libzlib-1.3.1-h2466b09_2 
  openssl            conda-forge/win-64::openssl-3.5.2-h725018a_0 
  pip                conda-forge/noarch::pip-24.3.1-pyh8b19718_0 
  python             conda-forge/win-64::python-3.8.20-hfaddaf0_2_cpython 
  setuptools         conda-forge/noarch::setuptools-75.3.0-pyhd8ed1ab_0 
  tk                 conda-forge/win-64::tk-8.6.13-h2c6b04d_2 
  ucrt               conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_1 
  vc                 conda-forge/win-64::vc-14.3-h41ae7f8_31 
  vc14_runtime       conda-forge/win-64::vc14_runtime-14.44.35208-h818238b_31 
  vcomp14            conda-forge/win-64::vcomp14-14.44.35208-h818238b_31 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_0 
  xz                 conda-forge/win-64::xz-5.8.1-h208afaa_2 
  xz-tools           conda-forge/win-64::xz-tools-5.8.1-h2466b09_2 


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


==> WARNING: A newer version of conda exists. <==
    current version: 24.11.3
    latest version: 25.7.0

Please update conda by running

    $ conda update -n base -c conda-forge conda



# All requested packages already installed.

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:

  - tensorflow=2.10.0*

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.



Quitting from cfTools-vignette.Rmd:164-167 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! one or more Python packages failed to install [error code 1]
---
Backtrace:
    ▆
 1. └─cfTools::MergePEReads(PEReads)
 2.   └─basilisk::basiliskStart(my_env)
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         └─reticulate::conda_install(...)
 6.           └─reticulate:::stopf(fmt, result)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'cfTools-vignette.Rmd' failed with diagnostics:
one or more Python packages failed to install [error code 1]
--- failed re-building 'cfTools-vignette.Rmd'

SUMMARY: processing the following file failed:
  'cfTools-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted