Build/check report for BioC 3.23 - BUILD results for spatialDE on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4013
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 spatialDE on kjohnson3

To the developers/maintainers of the spatialDE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/spatialDE.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: spatialDE

Version: 1.17.0

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

StartedAt: 2025-11-12 17:16:12 -0500 (Wed, 12 Nov 2025)

EndedAt: 2025-11-12 17:18:22 -0500 (Wed, 12 Nov 2025)

EllapsedTime: 130.6 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 spatialDE
###
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* checking for file ‘spatialDE/DESCRIPTION’ ... OK
* preparing ‘spatialDE’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘spatialDE.Rmd’ using rmarkdown
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.11.14.tar.xz...
-> https://www.python.org/ftp/python/3.11.14/Python-3.11.14.tar.xz
Installing Python-3.11.14...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk

BUILD FAILED (OS X 13.7.8 using python-build 2.6.12-2-g2afd173)

Inspect or clean up the working tree at /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/python-build.20251112171631.87222
Results logged to /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/python-build.20251112171631.87222.log

Last 10 log lines:
ld: Undefined symbols:
  _mkfifoat, referenced from:
      _os_mkfifo in lto.o
  _mknodat, referenced from:
      _os_mknod in lto.o
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[3]: *** [Programs/_freeze_module] Error 1
make[2]: *** [build_all_generate_profile] Error 2
make[1]: *** [profile-gen-stamp] Error 2
make: *** [profile-run-stamp] Error 2

Quitting from spatialDE.Rmd:122-125 [stabilize]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.11 failed
---
Backtrace:
    ▆
 1. └─spatialDE::stabilize(Rep11_MOB_0)
 2.   └─basilisk::basiliskStart(spatialDE_env, testload = "scipy.optimize")
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         ├─base::suppressMessages(install_python(version))
 6.         │ └─base::withCallingHandlers(...)
 7.         └─reticulate::install_python(version)
 8.           └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'spatialDE.Rmd' failed with diagnostics:
installation of Python 3.11 failed
--- failed re-building ‘spatialDE.Rmd’

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

Error: Vignette re-building failed.
Execution halted