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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 OSCA.intro
###
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* checking for file ‘OSCA.intro/DESCRIPTION’ ... OK
* preparing ‘OSCA.intro’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'stub.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
--- finished re-building ‘stub.Rmd’

"/Library/Frameworks/R.framework/Resources/bin/R" -e "work.dir <- rebook::bookCache('OSCA.intro'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)"

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> work.dir <- rebook::bookCache('OSCA.intro'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)
# 
# 
# processing file: getting-datasets.Rmd
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# 38/42 [unnamed-chunk-18]
# 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.20251024064713.70636
# Results logged to /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/python-build.20251024064713.70636.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[3]: *** [Programs/_freeze_module] Error 1
# make[2]: *** [profile-gen-stamp] Error 2
# make[1]: *** [profile-run-stamp] Error 2
# Error: installation of Python 3.14.0 failed
# 
# Quitting from getting-datasets.Rmd:231-236 [unnamed-chunk-18]
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# <error/rlang_error>
# Error:
# ! installation of Python 3.14.0 failed
# ---
# Backtrace:
#     ▆
#  1. └─zellkonverter::readH5AD(demo)
#  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)
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# 
# Execution halted

Error in compileChapter(path) : 
  failed to compile '~/Library/Caches/rebook/OSCA.intro/1.17.1/getting-datasets.Rmd'
Calls: <Anonymous> ... .precompile_book -> .locked_compile_chapter -> compileChapter
Execution halted
make: *** [compiled] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted