Multiple platform build/check report for BioC 3.23 - BUILD results for DOtools on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4826
lconway	macOS 12.7.6 Monterey	x86_64	R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"	4561
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4562
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 DOtools on lconway

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

Version: 1.1.0

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

StartedAt: 2025-11-17 17:01:40 -0500 (Mon, 17 Nov 2025)

EndedAt: 2025-11-17 17:08:19 -0500 (Mon, 17 Nov 2025)

EllapsedTime: 399.5 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 DOtools
###
##############################################################################
##############################################################################


* checking for file ‘DOtools/DESCRIPTION’ ... OK
* preparing ‘DOtools’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘DOtools.Rmd’ using rmarkdown
2025-11-17 17:02:54.749 R[10749:15737965] XType: Using static font registry.
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.14.0.tar.xz...
-> https://www.python.org/ftp/python/3.14.0/Python-3.14.0.tar.xz
Installing Python-3.14.0...
python-build: use readline from homebrew
python-build: use ncurses 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 /tmp/python-build.20251117170334.20298
Results logged to /tmp/python-build.20251117170334.20298.log

Last 10 log lines:
Undefined symbols for architecture x86_64:
  "_mkfifoat", referenced from:
      _os_mkfifo in 158.x86_64.thinlto.o
  "_mknodat", referenced from:
      _os_mknod in 158.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 DOtools.Rmd:279-286 [annotation]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.14.0 failed
---
Backtrace:
     ▆
  1. └─DOtools::DO.CellTypist(...)
  2.   └─zellkonverter::writeH5AD(...)
  3.     └─basilisk::basiliskRun(...)
  4.       └─basilisk::basiliskStart(...)
  5.         └─basilisk::obtainEnvironmentPath(env)
  6.           └─basilisk::setupBasiliskEnv(...)
  7.             ├─base::suppressMessages(install_python(version))
  8.             │ └─base::withCallingHandlers(...)
  9.             └─reticulate::install_python(version)
 10.               └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'DOtools.Rmd' failed with diagnostics:
installation of Python 3.14.0 failed
--- failed re-building ‘DOtools.Rmd’

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

Error: Vignette re-building failed.
Execution halted