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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MOFA2
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* checking for file ‘MOFA2/DESCRIPTION’ ... OK
* preparing ‘MOFA2’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MEFISTO_temporal.Rmd’ using rmarkdown
2025-03-19 17:46:43.454 R[75994:446143670] XType: com.apple.fonts is not accessible.
2025-03-19 17:46:43.454 R[75994:446143670] XType: XTFontStaticRegistry is enabled.
python-build: use openssl from homebrew
python-build: use readline from homebrew
Downloading Python-3.10.5.tar.xz...
-> https://www.python.org/ftp/python/3.10.5/Python-3.10.5.tar.xz
Installing Python-3.10.5...
python-build: use readline from homebrew
python-build: use ncurses from homebrew
python-build: use zlib from xcode sdk
Installed Python-3.10.5 to /Users/biocbuild/.pyenv/versions/3.10.5
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/MOFA2/1.17.0/mofa_env/lib/python3.10/site-packages (22.0.4)
Collecting pip
  Using cached pip-25.0.1-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 /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/MOFA2/1.17.0/mofa_env/lib/python3.10/site-packages (58.1.0)
Collecting setuptools
  Using cached setuptools-77.0.1-py3-none-any.whl (1.3 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 22.0.4
    Uninstalling pip-22.0.4:
      Successfully uninstalled pip-22.0.4
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
ERROR: Could not find a version that satisfies the requirement python==3.10.5 (from versions: none)
ERROR: No matching distribution found for python==3.10.5

Quitting from MEFISTO_temporal.Rmd:95-98 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'python==3.10.5'", "'numpy==1.23.1'", "'scipy==1.8.1'", "'pandas==1.4.3'", "'h5py==3.6.0'", "'scikit-learn==1.1.1'", "'dtw-python==1.2.2'", "'mofapy2==0.7.0'"
---
Backtrace:
    ▆
 1. └─MOFA2::run_mofa(sm, outfile, use_basilisk = TRUE)
 2.   └─basilisk::basiliskStart(mofa_env)
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         └─reticulate::virtualenv_install(...)
 6.           └─reticulate:::pip_install(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MEFISTO_temporal.Rmd' failed with diagnostics:
Error installing package(s): "'python==3.10.5'", "'numpy==1.23.1'", "'scipy==1.8.1'", "'pandas==1.4.3'", "'h5py==3.6.0'", "'scikit-learn==1.1.1'", "'dtw-python==1.2.2'", "'mofapy2==0.7.0'"
--- failed re-building ‘MEFISTO_temporal.Rmd’

--- re-building ‘downstream_analysis.Rmd’ using rmarkdown
--- finished re-building ‘downstream_analysis.Rmd’

--- re-building ‘getting_started_R.Rmd’ using rmarkdown
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/MOFA2/1.17.0/mofa_env/lib/python3.10/site-packages (22.0.4)
Collecting pip
  Using cached pip-25.0.1-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 /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/MOFA2/1.17.0/mofa_env/lib/python3.10/site-packages (58.1.0)
Collecting setuptools
  Using cached setuptools-77.0.1-py3-none-any.whl (1.3 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 22.0.4
    Uninstalling pip-22.0.4:
      Successfully uninstalled pip-22.0.4
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
ERROR: Could not find a version that satisfies the requirement python==3.10.5 (from versions: none)
ERROR: No matching distribution found for python==3.10.5

Quitting from getting_started_R.Rmd:212-215 [unnamed-chunk-14]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'python==3.10.5'", "'numpy==1.23.1'", "'scipy==1.8.1'", "'pandas==1.4.3'", "'h5py==3.6.0'", "'scikit-learn==1.1.1'", "'dtw-python==1.2.2'", "'mofapy2==0.7.0'"
---
Backtrace:
    ▆
 1. └─MOFA2::run_mofa(MOFAobject, outfile, use_basilisk = TRUE)
 2.   └─basilisk::basiliskStart(mofa_env)
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         └─reticulate::virtualenv_install(...)
 6.           └─reticulate:::pip_install(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'getting_started_R.Rmd' failed with diagnostics:
Error installing package(s): "'python==3.10.5'", "'numpy==1.23.1'", "'scipy==1.8.1'", "'pandas==1.4.3'", "'h5py==3.6.0'", "'scikit-learn==1.1.1'", "'dtw-python==1.2.2'", "'mofapy2==0.7.0'"
--- failed re-building ‘getting_started_R.Rmd’

SUMMARY: processing the following files failed:
  ‘MEFISTO_temporal.Rmd’ ‘getting_started_R.Rmd’

Error: Vignette re-building failed.
Execution halted