Multiple platform build/check report for BioC 3.22 - BUILD results for densvis on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4810
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"	4548
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4528
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4493
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*

BUILD results for densvis on kjohnson3

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.

raw results

Summary

Package: densvis

Version: 1.19.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data densvis

StartedAt: 2025-06-18 16:06:24 -0400 (Wed, 18 Jun 2025)

EndedAt: 2025-06-18 16:06:46 -0400 (Wed, 18 Jun 2025)

EllapsedTime: 22.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data densvis
###
##############################################################################
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* 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
2025-06-18 16:06:32.226 R[901:122292069] 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