############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data DOtools ### ############################################################################## ############################################################################## * checking for file ‘DOtools/DESCRIPTION’ ... OK * preparing ‘DOtools’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘DOtools.Rmd’ using rmarkdown 2025-12-04 18:58:34.628 R[81465:87104296] XType: com.apple.fonts is not accessible. 2025-12-04 18:58:34.629 R[81465:87104296] XType: XTFontStaticRegistry is enabled. 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 2.6.15) Inspect or clean up the working tree at /tmp/python-build.20251204185932.85856 Results logged to /tmp/python-build.20251204185932.85856.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: *** [sharedinstall] Error 71 Quitting from DOtools.Rmd:279-286 [annotation] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! installation of Python 3.14.0 failed --- Backtrace: ▆ 1. └─DOtools::DO.CellTypist(...) 2. └─zellkonverter::writeH5AD(...) 3. └─basilisk::basiliskRun(...) 4. └─basilisk::basiliskStart(...) 5. └─basilisk::obtainEnvironmentPath(env) 6. └─basilisk::setupBasiliskEnv(...) 7. ├─base::suppressMessages(install_python(version)) 8. │ └─base::withCallingHandlers(...) 9. └─reticulate::install_python(version) 10. └─reticulate:::stopf("installation of Python %s failed", version) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'DOtools.Rmd' failed with diagnostics: installation of Python 3.14.0 failed --- failed re-building ‘DOtools.Rmd’ SUMMARY: processing the following file failed: ‘DOtools.Rmd’ Error: Vignette re-building failed. Execution halted