Multiple platform build/check report for BioC 3.22 - BUILD results for densvis on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4615
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"	4610
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4598
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4668
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 merida1

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: 1.20.1

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

StartedAt: 2025-11-17 21:51:51 -0500 (Mon, 17 Nov 2025)

EndedAt: 2025-11-17 21:58:14 -0500 (Mon, 17 Nov 2025)

EllapsedTime: 382.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### 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
2025-11-17 21:52:53.666 R[46456:22278280] XType: com.apple.fonts is not accessible.
2025-11-17 21:52:53.667 R[46456:22278280] XType: XTFontStaticRegistry is enabled.
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.12.10.tar.xz...
-> https://www.python.org/ftp/python/3.12.10/Python-3.12.10.tar.xz
Installing Python-3.12.10...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.12-2-g2afd173)

Inspect or clean up the working tree at /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T/python-build.20251117215405.49106
Results logged to /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T/python-build.20251117215405.49106.log

Last 10 log lines:
Undefined symbols for architecture x86_64:
  "_mkfifoat", referenced from:
      _os_mkfifo in 127.x86_64.thinlto.o
  "_mknodat", referenced from:
      _os_mknod in 127.x86_64.thinlto.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [Programs/_freeze_module] Error 1
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2

Quitting from densvis.Rmd:122-130 [run-densmap]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.12.10 failed
---
Backtrace:
    ▆
 1. └─densvis::densmap(data[, 1:2], dens_frac = 0.5, dens_lambda = 0.5)
 2.   └─densvis::umap(..., densmap = TRUE)
 3.     └─basilisk::basiliskStart(python_env)
 4.       └─basilisk::obtainEnvironmentPath(env)
 5.         └─basilisk::setupBasiliskEnv(...)
 6.           ├─base::suppressMessages(install_python(version))
 7.           │ └─base::withCallingHandlers(...)
 8.           └─reticulate::install_python(version)
 9.             └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'densvis.Rmd' failed with diagnostics:
installation of Python 3.12.10 failed
--- failed re-building ‘densvis.Rmd’

SUMMARY: processing the following file failed:
  ‘densvis.Rmd’

Error: Vignette re-building failed.
Execution halted