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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 DOtools
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* checking for file ‘DOtools/DESCRIPTION’ ... OK
* preparing ‘DOtools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DOtools.Rmd’ using rmarkdown
2025-10-24 16:18:47.971 R[45228:540706333] XType: Using static font registry.
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.14.0.tar.xz...
-> https://www.python.org/ftp/python/3.14.0/Python-3.14.0.tar.xz
Installing Python-3.14.0...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 13.7.7 using python-build 2.6.11-2-g1b7d2f0)

Inspect or clean up the working tree at /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/python-build.20251024161904.48628
Results logged to /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/python-build.20251024161904.48628.log

Last 10 log lines:
ld: warning: search path '/Users/biocbuild/.pyenv/versions/3.14.0/lib' not found
ld: Undefined symbols:
  _mkfifoat, referenced from:
      _os_mkfifo in 158.arm64.thinlto.o
  _mknodat, referenced from:
      _os_mknod in 158.arm64.thinlto.o
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [Programs/_freeze_module] Error 1
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2

Quitting from DOtools.Rmd:279-286 [annotation]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.14.0 failed
---
Backtrace:
     ▆
  1. └─DOtools::DO.CellTypist(...)
  2.   └─zellkonverter::writeH5AD(...)
  3.     └─basilisk::basiliskRun(...)
  4.       └─basilisk::basiliskStart(...)
  5.         └─basilisk::obtainEnvironmentPath(env)
  6.           └─basilisk::setupBasiliskEnv(...)
  7.             ├─base::suppressMessages(install_python(version))
  8.             │ └─base::withCallingHandlers(...)
  9.             └─reticulate::install_python(version)
 10.               └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'DOtools.Rmd' failed with diagnostics:
installation of Python 3.14.0 failed
--- failed re-building ‘DOtools.Rmd’

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

Error: Vignette re-building failed.
Execution halted