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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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

Package 322/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cfTools 1.8.0  (landing page)
Ran Hu
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/cfTools
git_branch: RELEASE_3_21
git_last_commit: c1e7735
git_last_commit_date: 2025-05-31 22:39:51 -0400 (Sat, 31 May 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for cfTools on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: cfTools
Version: 1.8.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data cfTools
StartedAt: 2025-10-13 23:31:47 -0000 (Mon, 13 Oct 2025)
EndedAt: 2025-10-13 23:34:12 -0000 (Mon, 13 Oct 2025)
EllapsedTime: 145.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R 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
Channels:
 - conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.20.0/cfTools/1.8.0/new_env

  added / updated specs:
    - python=3.8


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-aarch64::bzip2-1.0.8-h4777abc_8 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0 
  ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.44-h9df1782_2 
  libffi             conda-forge/linux-aarch64::libffi-3.5.2-hd65408f_0 
  libgcc             conda-forge/linux-aarch64::libgcc-15.2.0-he277a41_7 
  libgcc-ng          conda-forge/linux-aarch64::libgcc-ng-15.2.0-he9431aa_7 
  libgomp            conda-forge/linux-aarch64::libgomp-15.2.0-he277a41_7 
  liblzma            conda-forge/linux-aarch64::liblzma-5.8.1-h86ecc28_2 
  liblzma-devel      conda-forge/linux-aarch64::liblzma-devel-5.8.1-h86ecc28_2 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.1-h86ecc28_1 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.50.4-h022381a_0 
  libuuid            conda-forge/linux-aarch64::libuuid-2.41.2-h3e4203c_0 
  libxcrypt          conda-forge/linux-aarch64::libxcrypt-4.4.36-h31becfc_1 
  libzlib            conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2 
  ncurses            conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3 
  openssl            conda-forge/linux-aarch64::openssl-3.5.4-h8e36d6e_0 
  pip                conda-forge/noarch::pip-24.3.1-pyh8b19718_0 
  python             conda-forge/linux-aarch64::python-3.8.20-hbf90c55_2_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8382b9d_2 
  setuptools         conda-forge/noarch::setuptools-75.3.0-pyhd8ed1ab_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.13-noxft_h5688188_102 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_0 
  xz                 conda-forge/linux-aarch64::xz-5.8.1-h2dbfc1b_2 
  xz-gpl-tools       conda-forge/linux-aarch64::xz-gpl-tools-5.8.1-h2dbfc1b_2 
  xz-tools           conda-forge/linux-aarch64::xz-tools-5.8.1-h86ecc28_2 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - conda-forge
Platform: linux-aarch64
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: 25.9.1

Please update conda by running

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



# All requested packages already installed.

Channels:
 - conda-forge
Platform: linux-aarch64
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