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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 sketchR
###
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* checking for file ‘sketchR/DESCRIPTION’ ... OK
* preparing ‘sketchR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘sketchR.Rmd’ using rmarkdown
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.12.10.tar.xz...
-> https://www.python.org/ftp/python/3.12.10/Python-3.12.10.tar.xz
Installing Python-3.12.10...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.13)

Inspect or clean up the working tree at /tmp/python-build.20251124231737.37174
Results logged to /tmp/python-build.20251124231737.37174.log

Last 10 log lines:
Undefined symbols for architecture x86_64:
  "_mkfifoat", referenced from:
      _os_mkfifo in 127.x86_64.thinlto.o
  "_mknodat", referenced from:
      _os_mknod in 127.x86_64.thinlto.o
ld: symbol(s) not found for architecture x86_64
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 sketchR.Rmd:133-138 [geosketch]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.12.10 failed
---
Backtrace:
    ▆
 1. └─sketchR::geosketch(reducedDim(pbmc3k, "PCA"), N = 800, seed = 123)
 2.   └─basilisk::basiliskRun(...)
 3.     └─basilisk::basiliskStart(...)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'sketchR.Rmd' failed with diagnostics:
installation of Python 3.12.10 failed
--- failed re-building ‘sketchR.Rmd’

--- re-building ‘sketching_workflows.Rmd’ using rmarkdown
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.12.10.tar.xz...
-> https://www.python.org/ftp/python/3.12.10/Python-3.12.10.tar.xz
Installing Python-3.12.10...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.13)

Inspect or clean up the working tree at /tmp/python-build.20251124232232.63207
Results logged to /tmp/python-build.20251124232232.63207.log

Last 10 log lines:
Undefined symbols for architecture x86_64:
  "_mkfifoat", referenced from:
      _os_mkfifo in 127.x86_64.thinlto.o
  "_mknodat", referenced from:
      _os_mknod in 127.x86_64.thinlto.o
ld: symbol(s) not found for architecture x86_64
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 sketching_workflows.Rmd:60-97 [process-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.12.10 failed
---
Backtrace:
    ▆
 1. └─snifter::fitsne(...)
 2.   └─snifter:::.create_tsne(...)
 3.     └─basilisk::basiliskStart(python_env)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'sketching_workflows.Rmd' failed with diagnostics:
installation of Python 3.12.10 failed
--- failed re-building ‘sketching_workflows.Rmd’

SUMMARY: processing the following files failed:
  ‘sketchR.Rmd’ ‘sketching_workflows.Rmd’

Error: Vignette re-building failed.
Execution halted