element. Please specify either 'title' or 'pagetitle' in the metadata, e.g. by using --metadata pagetitle="..." on the command line. Falling back to 'stub.knit' --- 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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 # 1/42 # 2/42 [setup] # 3/42 # 4/42 [unnamed-chunk-1] # 5/42 # 6/42 [unnamed-chunk-2] # 7/42 # 8/42 [unnamed-chunk-3] # 9/42 # 10/42 [unnamed-chunk-4] # 11/42 # 12/42 [unnamed-chunk-5] # 13/42 # 14/42 [unnamed-chunk-6] # 15/42 # 16/42 [unnamed-chunk-7] # 17/42 # 18/42 [unnamed-chunk-8] # 19/42 # 20/42 [unnamed-chunk-9] # 21/42 # 22/42 [unnamed-chunk-10] # 23/42 # 24/42 [unnamed-chunk-11] # 25/42 # 26/42 [unnamed-chunk-12] # 27/42 # 28/42 [unnamed-chunk-13] # 29/42 # 30/42 [unnamed-chunk-14] # 31/42 # 32/42 [unnamed-chunk-15] # 33/42 # 34/42 [unnamed-chunk-16] # 35/42 # 36/42 [unnamed-chunk-17] # 37/42 # 38/42 [unnamed-chunk-18] # Downloading openssl-3.6.0.tar.gz... # -> https://github.com/openssl/openssl/releases/download/openssl-3.6.0/openssl-3.6.0.tar.gz # Installing openssl-3.6.0... # Installed openssl-3.6.0 to /Users/biocbuild/.pyenv/versions/3.14.0 # Downloading readline-8.3.tar.gz... # -> https://pyenv.github.io/pythons/fe5383204467828cd495ee8d1d3c037a7eba1389c22bc6a041f627976f9061cc # Installing readline-8.3... # Installed readline-8.3 to /Users/biocbuild/.pyenv/versions/3.14.0 # 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 zlib from xcode sdk # # BUILD FAILED (OS X 12.7.6 using python-build 2.6.22-2-gb2a43bb) # # Inspect or clean up the working tree at /tmp/python-build.20260206074434.87737 # Results logged to /tmp/python-build.20260206074434.87737.log # # Last 10 log lines: # /usr/bin/install -c -m 755 Modules/_posixshmem.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_posixshmem.cpython-314-darwin.so # /usr/bin/install -c -m 755 Modules/_multiprocessing.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_multiprocessing.cpython-314-darwin.so # /usr/bin/install -c -m 755 Modules/_ctypes.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_ctypes.cpython-314-darwin.so # /usr/bin/install -c -m 755 Modules/_curses.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_curses.cpython-314-darwin.so # /usr/bin/install -c -m 755 Modules/_curses_panel.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_curses_panel.cpython-314-darwin.so # /usr/bin/install -c -m 755 Modules/_sqlite3.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_sqlite3.cpython-314-darwin.so # /usr/bin/install -c -m 755 Modules/_ssl.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_ssl.cpython-314-darwin.so # /usr/bin/install -c -m 755 Modules/_hashlib.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_hashlib.cpython-314-darwin.so # install: Modules/_hashlib.cpython-314-darwin.so: No such file or directory # make[1]: *** [sharedinstall] Error 71 # 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) # # 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/1.18.0/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

############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.intro ### ############################################################################## ############################################################################## * 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 element. Please specify either 'title' or 'pagetitle' in the metadata, e.g. by using --metadata pagetitle="..." on the command line. Falling back to 'stub.knit' --- 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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 # 1/42 # 2/42 [setup] # 3/42 # 4/42 [unnamed-chunk-1] # 5/42 # 6/42 [unnamed-chunk-2] # 7/42 # 8/42 [unnamed-chunk-3] # 9/42 # 10/42 [unnamed-chunk-4] # 11/42 # 12/42 [unnamed-chunk-5] # 13/42 # 14/42 [unnamed-chunk-6] # 15/42 # 16/42 [unnamed-chunk-7] # 17/42 # 18/42 [unnamed-chunk-8] # 19/42 # 20/42 [unnamed-chunk-9] # 21/42 # 22/42 [unnamed-chunk-10] # 23/42 # 24/42 [unnamed-chunk-11] # 25/42 # 26/42 [unnamed-chunk-12] # 27/42 # 28/42 [unnamed-chunk-13] # 29/42 # 30/42 [unnamed-chunk-14] # 31/42 # 32/42 [unnamed-chunk-15] # 33/42 # 34/42 [unnamed-chunk-16] # 35/42 # 36/42 [unnamed-chunk-17] # 37/42 # 38/42 [unnamed-chunk-18] # Downloading openssl-3.6.0.tar.gz... # -> https://github.com/openssl/openssl/releases/download/openssl-3.6.0/openssl-3.6.0.tar.gz # Installing openssl-3.6.0... # Installed openssl-3.6.0 to /Users/biocbuild/.pyenv/versions/3.14.0 # Downloading readline-8.3.tar.gz... # -> https://pyenv.github.io/pythons/fe5383204467828cd495ee8d1d3c037a7eba1389c22bc6a041f627976f9061cc # Installing readline-8.3... # Installed readline-8.3 to /Users/biocbuild/.pyenv/versions/3.14.0 # 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 zlib from xcode sdk # # BUILD FAILED (OS X 12.7.6 using python-build 2.6.22-2-gb2a43bb) # # Inspect or clean up the working tree at /tmp/python-build.20260206074434.87737 # Results logged to /tmp/python-build.20260206074434.87737.log # # Last 10 log lines: # /usr/bin/install -c -m 755 Modules/_posixshmem.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_posixshmem.cpython-314-darwin.so # /usr/bin/install -c -m 755 Modules/_multiprocessing.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_multiprocessing.cpython-314-darwin.so # /usr/bin/install -c -m 755 Modules/_ctypes.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_ctypes.cpython-314-darwin.so # /usr/bin/install -c -m 755 Modules/_curses.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_curses.cpython-314-darwin.so # /usr/bin/install -c -m 755 Modules/_curses_panel.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_curses_panel.cpython-314-darwin.so # /usr/bin/install -c -m 755 Modules/_sqlite3.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_sqlite3.cpython-314-darwin.so # /usr/bin/install -c -m 755 Modules/_ssl.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_ssl.cpython-314-darwin.so # /usr/bin/install -c -m 755 Modules/_hashlib.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_hashlib.cpython-314-darwin.so # install: Modules/_hashlib.cpython-314-darwin.so: No such file or directory # make[1]: *** [sharedinstall] Error 71 # 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) # # 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/1.18.0/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