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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 velociraptor
###
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* checking for file ‘velociraptor/DESCRIPTION’ ... OK
* preparing ‘velociraptor’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘velociraptor.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 13.7.8 using python-build 2.6.12-2-g2afd173)

Inspect or clean up the working tree at /var/folders/dc/2xck8b8s0_3gymbxnrltzxhm0000gs/T/python-build.20251118021102.14391
Results logged to /var/folders/dc/2xck8b8s0_3gymbxnrltzxhm0000gs/T/python-build.20251118021102.14391.log

Last 10 log lines:
ld: warning: search path '/Users/biocbuild/.pyenv/versions/3.12.10/lib' not found
ld: Undefined symbols:
  _mkfifoat, referenced from:
      _os_mkfifo in 127.arm64.thinlto.o
  _mknodat, referenced from:
      _os_mknod in 127.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 velociraptor.Rmd:75-82 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.12.10 failed
---
Backtrace:
     ▆
  1. ├─velociraptor::scvelo(...)
  2. └─velociraptor::scvelo(...)
  3.   └─velociraptor (local) .local(x, ...)
  4.     ├─methods::callNextMethod(x, ..., sf.X = sf.X, dimred = dimred)
  5.     │ └─base::eval(call, callEnv)
  6.     │   └─base::eval(call, callEnv)
  7.     └─velociraptor (local) .nextMethod(x, ..., sf.X = sf.X, dimred = dimred)
  8.       └─velociraptor (local) .local(x, ...)
  9.         └─velociraptor:::.scvelo(...)
 10.           └─basilisk::basiliskRun(...)
 11.             └─basilisk::basiliskStart(...)
 12.               └─basilisk::obtainEnvironmentPath(env)
 13.                 └─basilisk::setupBasiliskEnv(...)
 14.                   ├─base::suppressMessages(install_python(version))
 15.                   │ └─base::withCallingHandlers(...)
 16.                   └─reticulate::install_python(version)
 17.                     └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Error: Vignette re-building failed.
Execution halted