############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data densvis ### ############################################################################## ############################################################################## * checking for file ‘densvis/DESCRIPTION’ ... OK * preparing ‘densvis’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘densvis.Rmd’ using rmarkdown 2025-06-19 16:18:50.528 R[40930:131026164] XType: Using static font registry. Quitting from densvis.Rmd:122-130 [run-densmap] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `py_module_import()`: ! OSError: Could not find/load shared object file: libllvmlite.dylib Error was: dlopen(/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/densvis/1.19.0/densvis/lib/python3.11/site-packages/llvmlite/binding/libllvmlite.dylib, 0x0006): Library not loaded: @rpath/libz.1.dylib <...truncated...>/Library/Caches/org.R-project.R/R/basilisk/1.21.5/densvis/1.19.0/densvis/lib/python3.11/site-packages/llvmlite/binding/libllvmlite.dylib Reason: tried: '/Users/biocbuild/.pyenv/versions/3.11.4/lib/libz.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/biocbuild/.pyenv/versions/3.11.4/lib/libz.1.dylib' (no such file), '/opt/homebrew/lib/libz.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/libz.1.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libz.1.dylib' (no such file), '/usr/local/jdk-21.jdk/Contents/Home/lib/server/libz.1.dylib' (no such file) Run `reticulate::py_last_error()` for details. --- Backtrace: ▆ 1. └─densvis::densmap(data[, 1:2], dens_frac = 0.5, dens_lambda = 0.5) 2. └─densvis::umap(..., densmap = TRUE) 3. └─basilisk::basiliskRun(...) 4. └─densvis (local) fun(...) 5. └─reticulate::import("umap") 6. └─reticulate:::py_module_import(module, convert = convert) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'densvis.Rmd' failed with diagnostics: OSError: Could not find/load shared object file: libllvmlite.dylib Error was: dlopen(/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/densvis/1.19.0/densvis/lib/python3.11/site-packages/llvmlite/binding/libllvmlite.dylib, 0x0006): Library not loaded: @rpath/libz.1.dylib <...truncated...>/Library/Caches/org.R-project.R/R/basilisk/1.21.5/densvis/1.19.0/densvis/lib/python3.11/site-packages/llvmlite/binding/libllvmlite.dylib Reason: tried: '/Users/biocbuild/.pyenv/versions/3.11.4/lib/libz.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/biocbuild/.pyenv/versions/3.11.4/lib/libz.1.dylib' (no such file), '/opt/homebrew/lib/libz.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/libz.1.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libz.1.dylib' (no such file), '/usr/local/jdk-21.jdk/Contents/Home/lib/server/libz.1.dylib' (no such file) Run `reticulate::py_last_error()` for details. --- failed re-building ‘densvis.Rmd’ SUMMARY: processing the following file failed: ‘densvis.Rmd’ Error: Vignette re-building failed. Execution halted