Multiple platform build/check report for BioC 3.20 - BUILD results for cfTools on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4426
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 palomino8

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: 1.6.0

Command: chmod a+r cfTools -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe --arch x64 CMD build --keep-empty-dirs --no-resave-data cfTools

StartedAt: 2025-03-31 17:54:49 -0400 (Mon, 31 Mar 2025)

EndedAt: 2025-03-31 18:00:11 -0400 (Mon, 31 Mar 2025)

EllapsedTime: 321.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r cfTools -R && F:\biocbuild\bbs-3.20-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\1.18.0\cfTools\1.6.0\new_env

  added / updated specs:
    - python=3.8


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libffi-3.4.6               |       h537db12_1          44 KB  conda-forge
    vc-14.3                    |      h2b53caa_26          17 KB  conda-forge
    vc14_runtime-14.42.34438   |      hfd919c2_26         733 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         795 KB

The following NEW packages will be INSTALLED:

  bzip2              conda-forge/win-64::bzip2-1.0.8-h2466b09_7 
  ca-certificates    conda-forge/win-64::ca-certificates-2025.1.31-h56e8100_0 
  libffi             conda-forge/win-64::libffi-3.4.6-h537db12_1 
  liblzma            conda-forge/win-64::liblzma-5.6.4-h2466b09_0 
  liblzma-devel      conda-forge/win-64::liblzma-devel-5.6.4-h2466b09_0 
  libsqlite          conda-forge/win-64::libsqlite-3.49.1-h67fdade_2 
  libzlib            conda-forge/win-64::libzlib-1.3.1-h2466b09_2 
  openssl            conda-forge/win-64::openssl-3.4.1-ha4e3fda_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-h5226925_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 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_0 
  xz                 conda-forge/win-64::xz-5.6.4-h208afaa_0 
  xz-tools           conda-forge/win-64::xz-tools-5.6.4-h2466b09_0 


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: 24.3.0
    latest version: 25.3.0

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... 
Quitting from cfTools-vignette.Rmd:164-167 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! one or more Python packages failed to install [error code 5]
---
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 5]
--- failed re-building 'cfTools-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted