Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 551/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
densvis 1.19.0 (landing page) Alan O'Callaghan
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
To the developers/maintainers of the densvis package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/densvis.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: densvis |
Version: 1.19.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data densvis |
StartedAt: 2025-08-08 16:07:29 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 16:07:51 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 22.2 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### 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 2025-08-08 16:07:36.870 R[24539:486034593] XType: Using static font registry. Quitting from densvis.Rmd:122-130 [run-densmap] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> 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