############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data basilisk ### ############################################################################## ############################################################################## * checking for file ‘basilisk/DESCRIPTION’ ... OK * preparing ‘basilisk’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘motivation.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.20251117191608.38825 Results logged to /var/folders/dc/2xck8b8s0_3gymbxnrltzxhm0000gs/T/python-build.20251117191608.38825.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 motivation.Rmd:251-256 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! installation of Python 3.12.10 failed --- Backtrace: ▆ 1. └─basilisk::createLocalBasiliskEnv(...) 2. └─basilisk::setupBasiliskEnv(envpath, ...) 3. ├─base::suppressMessages(install_python(version)) 4. │ └─base::withCallingHandlers(...) 5. └─reticulate::install_python(version) 6. └─reticulate:::stopf("installation of Python %s failed", version) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'motivation.Rmd' failed with diagnostics: installation of Python 3.12.10 failed --- failed re-building ‘motivation.Rmd’ SUMMARY: processing the following file failed: ‘motivation.Rmd’ Error: Vignette re-building failed. Execution halted