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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
2025-12-19 04:39:18.657 R[65590:324662083] XType: Using static font registry.
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.12.12.tar.xz...
-> https://www.python.org/ftp/python/3.12.12/Python-3.12.12.tar.xz
Installing Python-3.12.12...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 13.7.8 using python-build 2.6.17)

Inspect or clean up the working tree at /tmp/python-build.20251219043925.66418
Results logged to /tmp/python-build.20251219043925.66418.log

Last 10 log lines:
/usr/bin/install -c -m 755 Modules/select.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/select.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_socket.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_socket.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/syslog.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/syslog.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/termios.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/termios.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_posixshmem.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_posixshmem.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_multiprocessing.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_multiprocessing.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_ctypes.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_ctypes.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_curses.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_curses.cpython-312-darwin.so
install: Modules/_curses.cpython-312-darwin.so: No such file or directory
make: *** [sharedinstall] Error 71

Quitting from MEFISTO_temporal.Rmd:95-98 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.12.12 failed
---
Backtrace:
    ▆
 1. └─MOFA2::run_mofa(sm, outfile, use_basilisk = TRUE)
 2.   └─basilisk::basiliskStart(mofa_env)
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         ├─base::suppressMessages(install_python(version))
 6.         │ └─base::withCallingHandlers(...)
 7.         └─reticulate::install_python(version)
 8.           └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MEFISTO_temporal.Rmd' failed with diagnostics:
installation of Python 3.12.12 failed
--- 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
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.12.12.tar.xz...
-> https://www.python.org/ftp/python/3.12.12/Python-3.12.12.tar.xz
Installing Python-3.12.12...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 13.7.8 using python-build 2.6.17)

Inspect or clean up the working tree at /tmp/python-build.20251219045000.87357
Results logged to /tmp/python-build.20251219045000.87357.log

Last 10 log lines:
/usr/bin/install -c -m 755 Modules/select.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/select.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_socket.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_socket.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/syslog.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/syslog.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/termios.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/termios.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_posixshmem.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_posixshmem.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_multiprocessing.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_multiprocessing.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_ctypes.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_ctypes.cpython-312-darwin.so
/usr/bin/install -c -m 755 Modules/_curses.cpython-312-darwin.so /Users/biocbuild/.pyenv/versions/3.12.12/lib/python3.12/lib-dynload/_curses.cpython-312-darwin.so
install: Modules/_curses.cpython-312-darwin.so: No such file or directory
make: *** [sharedinstall] Error 71

Quitting from getting_started_R.Rmd:212-215 [unnamed-chunk-14]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.12.12 failed
---
Backtrace:
    ▆
 1. └─MOFA2::run_mofa(MOFAobject, outfile, use_basilisk = TRUE)
 2.   └─basilisk::basiliskStart(mofa_env)
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         ├─base::suppressMessages(install_python(version))
 6.         │ └─base::withCallingHandlers(...)
 7.         └─reticulate::install_python(version)
 8.           └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'getting_started_R.Rmd' failed with diagnostics:
installation of Python 3.12.12 failed
--- 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