Bioconductor Single Package Builder - Build History

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URL:  https://git.bioconductor.org/packages/BatChef
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo2 Linux (Ubuntu 24.04.3 LTS)/x86_64   ERROR     skipped     skipped     skipped  

nebbiolo2 Summary

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Package: BatChef
Version: 0.99.1
RVersion: 4.5
BiocVersion: 3.22
BuildCommand: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BatChef
BuildTime: 10 minutes 45.17 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: BatChef_20251003164006
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: BatChef. Starting Build package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 1.

nebbiolo2 BUILD SRC output

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 R CMD BUILD

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* checking for file ‘BatChef/DESCRIPTION’ ... OK
* preparing ‘BatChef’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘batch_correction.Rmd’ using rmarkdown
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Downloading Python-3.10.12.tar.xz...
-> https://www.python.org/ftp/python/3.10.12/Python-3.10.12.tar.xz
Installing Python-3.10.12...
Installed Python-3.10.12 to /home/pkgbuild/.pyenv/versions/3.10.12
Requirement already satisfied: pip in /var/cache/basilisk/1.21.5/BatChef/0.99.1/py_env/lib/python3.10/site-packages (23.0.1)
Collecting pip
  Using cached pip-25.2-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 /var/cache/basilisk/1.21.5/BatChef/0.99.1/py_env/lib/python3.10/site-packages (65.5.0)
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 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
  Attempting uninstall: pip
    Found existing installation: pip 23.0.1
    Uninstalling pip-23.0.1:
      Successfully uninstalled pip-23.0.1
Successfully installed pip-25.2 setuptools-80.9.0 wheel-0.45.1
Collecting scanorama==1.7.4
  Downloading scanorama-1.7.4-py3-none-any.whl.metadata (525 bytes)
Collecting scanpy==1.10.1
  Downloading scanpy-1.10.1-py3-none-any.whl.metadata (8.6 kB)
Collecting python-igraph==0.11.4
  Downloading python_igraph-0.11.4-py3-none-any.whl.metadata (2.8 kB)
Collecting leidenalg==0.10.2
  Using cached leidenalg-0.10.2-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (10 kB)
Collecting scikit-learn==1.4.2
  Downloading scikit_learn-1.4.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting anndata==0.10.7
  Downloading anndata-0.10.7-py3-none-any.whl.metadata (6.6 kB)
Collecting bbknn==1.6.0
  Downloading bbknn-1.6.0-py3-none-any.whl.metadata (8.2 kB)
Collecting scvi-tools==1.1.2
  Downloading scvi_tools-1.1.2-py3-none-any.whl.metadata (12 kB)
Collecting lightning==2.0.9.post0
  Downloading lightning-2.0.9.post0-py3-none-any.whl.metadata (41 kB)
ERROR: Ignored the following versions that require a different python version: 0.12.0 Requires-Python >=3.11; 0.12.0rc1 Requires-Python >=3.11; 0.12.0rc2 Requires-Python >=3.11; 0.12.0rc3 Requires-Python >=3.11; 0.12.0rc4 Requires-Python >=3.11; 0.12.1 Requires-Python >=3.11; 0.12.2 Requires-Python >=3.11; 1.4.0 Requires-Python >=3.11
ERROR: Could not find a version that satisfies the requirement openssl==3.2.0 (from versions: none)
ERROR: No matching distribution found for openssl==3.2.0

Quitting from batch_correction.Rmd:144-153 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'scanorama==1.7.4'", "'scanpy==1.10.1'", "'python-igraph==0.11.4'", "'leidenalg==0.10.2'", "'scikit-learn==1.4.2'", "'anndata==0.10.7'", "'bbknn==1.6.0'", "'scvi-tools==1.1.2'", "'lightning==2.0.9.post0'", "'openssl==3.2.0'"
---
Backtrace:
    ▆
 1. ├─BatChef::batchCorrect(...)
 2. └─BatChef::batchCorrect(...)
 3.   ├─base::do.call(scanoramaRun, args)
 4.   └─BatChef (local) `<fn>`(input = `<list>`, return_dimred = TRUE)
 5.     └─basilisk::basiliskStart(py_env)
 6.       └─basilisk::obtainEnvironmentPath(env)
 7.         └─basilisk::setupBasiliskEnv(...)
 8.           └─reticulate::virtualenv_create(...)
 9.             └─reticulate:::pip_install(python, packages)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'batch_correction.Rmd' failed with diagnostics:
Error installing package(s): "'scanorama==1.7.4'", "'scanpy==1.10.1'", "'python-igraph==0.11.4'", "'leidenalg==0.10.2'", "'scikit-learn==1.4.2'", "'anndata==0.10.7'", "'bbknn==1.6.0'", "'scvi-tools==1.1.2'", "'lightning==2.0.9.post0'", "'openssl==3.2.0'"
--- failed re-building ‘batch_correction.Rmd’

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

Error: Vignette re-building failed.
Execution halted

nebbiolo2 CHECK output

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nebbiolo2 BUILD BIN output
 
                    			
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