Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-06-19 12:02 -0400 (Thu, 19 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4810
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4548
kjohnson3macOS 13.7.1 Venturaarm644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4528
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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

Package 1890/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scifer 1.11.3  (landing page)
Rodrigo Arcoverde Cerveira
Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025)
git_url: https://git.bioconductor.org/packages/scifer
git_branch: devel
git_last_commit: b4b323c
git_last_commit_date: 2025-06-11 05:53:55 -0400 (Wed, 11 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'flowCore' which is only available as a source package that needs compilation
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

BUILD results for scifer on nebbiolo2

To the developers/maintainers of the scifer package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scifer.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: scifer
Version: 1.11.3
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 scifer
StartedAt: 2025-06-18 19:20:54 -0400 (Wed, 18 Jun 2025)
EndedAt: 2025-06-18 19:22:49 -0400 (Wed, 18 Jun 2025)
EllapsedTime: 115.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 scifer
###
##############################################################################
##############################################################################


* checking for file ‘scifer/DESCRIPTION’ ... OK
* preparing ‘scifer’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘scifer_walkthrough.Rmd’ using rmarkdown
Requirement already satisfied: pip in /home/biocbuild/.cache/R/basilisk/1.21.5/scifer/1.11.3/igblast_wrap_basilisk/lib/python3.9/site-packages (23.0.1)
Collecting pip
  Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Requirement already satisfied: setuptools in /home/biocbuild/.cache/R/basilisk/1.21.5/scifer/1.11.3/igblast_wrap_basilisk/lib/python3.9/site-packages (58.1.0)
Collecting setuptools
  Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 58.1.0
    Uninstalling setuptools-58.1.0:
      Successfully uninstalled setuptools-58.1.0
  Attempting uninstall: pip
    Found existing installation: pip 23.0.1
    Uninstalling pip-23.0.1:
      Successfully uninstalled pip-23.0.1
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
ERROR: Could not find a version that satisfies the requirement igblast==1.22.0 (from versions: none)
ERROR: No matching distribution found for igblast==1.22.0

Quitting from scifer_walkthrough.Rmd:246-254 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'igblast==1.22.0'", "'cffi==1.16.0'", "'python-isal==1.6.1'", "'pip==24.0'", "'pycparser==2.22'", "'setuptools==70.1.1'", "'wheel==0.43.0'", "'xopen==2.0.1'", "'python-zlib-ng==0.4.3'", "'zstandard==0.22.0'", "'dnaio==1.2.1'"
---
Backtrace:
    ▆
 1. └─scifer::igblast(...)
 2.   └─basilisk::basiliskStart(env)
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         └─reticulate::virtualenv_create(...)
 6.           └─reticulate:::pip_install(python, packages)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'scifer_walkthrough.Rmd' failed with diagnostics:
Error installing package(s): "'igblast==1.22.0'", "'cffi==1.16.0'", "'python-isal==1.6.1'", "'pip==24.0'", "'pycparser==2.22'", "'setuptools==70.1.1'", "'wheel==0.43.0'", "'xopen==2.0.1'", "'python-zlib-ng==0.4.3'", "'zstandard==0.22.0'", "'dnaio==1.2.1'"
--- failed re-building ‘scifer_walkthrough.Rmd’

SUMMARY: processing the following file failed:
  ‘scifer_walkthrough.Rmd’

Error: Vignette re-building failed.
Execution halted