############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data StatescopeR ### ############################################################################## ############################################################################## * checking for file ‘StatescopeR/DESCRIPTION’ ... OK * preparing ‘StatescopeR’: * checking DESCRIPTION meta-information ... OK * installing the package (it is needed to build vignettes) * creating vignettes ... ERROR --- re-building ‘StatescopeR.Rmd’ using rmarkdown python-build: use openssl from homebrew python-build: use readline from homebrew Downloading Python-3.7.17.tar.xz... -> https://www.python.org/ftp/python/3.7.17/Python-3.7.17.tar.xz Installing Python-3.7.17... patching file 'Doc/library/ctypes.rst' patching file 'Lib/test/test_unicode.py' patching file 'Modules/_ctypes/_ctypes.c' patching file 'Modules/_ctypes/callproc.c' patching file 'Modules/_ctypes/ctypes.h' patching file setup.py patching file 'Misc/NEWS.d/next/Core and Builtins/2020-06-30-04-44-29.bpo-41100.PJwA6F.rst' patching file 'Modules/_decimal/libmpdec/mpdecimal.h' patching file setup.py patching file setup.py 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 2.6.20-3-g82f4de5) Inspect or clean up the working tree at /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/python-build.20260123175706.3533 Results logged to /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/python-build.20260123175706.3533.log Last 10 log lines: incomplete block on file /usr/bin/install -c checking for a thread-safe mkdir -p... ./install-sh -c -d checking for --with-pydebug... no checking for --with-assertions... no checking for --enable-optimizations... yes checking for --with-lto... yes checking for llvm-ar... no configure: error: llvm-ar is required for a --with-lto build with clang but could not be found. make: *** No targets specified and no makefile found. Stop. Quitting from StatescopeR.Rmd:124-153 [Prepare StatescopeR input] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! installation of Python 3.7 failed --- Backtrace: ▆ 1. └─StatescopeR::select_genes(scRNAseq, 30L, 50L, labels = scRNAseq$`cell type`) 2. └─basilisk::basiliskStart(autogenes, testload = c("autogenes")) 3. └─basilisk::obtainEnvironmentPath(env) 4. └─basilisk::setupBasiliskEnv(...) 5. ├─base::suppressMessages(install_python(version)) 6. │ └─base::withCallingHandlers(...) 7. └─reticulate::install_python(version) 8. └─reticulate:::stopf("installation of Python %s failed", version) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'StatescopeR.Rmd' failed with diagnostics: installation of Python 3.7 failed --- failed re-building ‘StatescopeR.Rmd’ SUMMARY: processing the following file failed: ‘StatescopeR.Rmd’ Error: Vignette re-building failed. Execution halted