Multiple platform build/check report for BioC 3.22 - BUILD results for DOtools 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"	4879
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4670
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4604
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4669
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 merida1

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: 1.0.0

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

StartedAt: 2025-12-08 19:17:01 -0500 (Mon, 08 Dec 2025)

EndedAt: 2025-12-08 19:38:29 -0500 (Mon, 08 Dec 2025)

EllapsedTime: 1288.1 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 to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DOtools.Rmd’ using rmarkdown
2025-12-08 19:19:33.000 R[21348:100855583] XType: com.apple.fonts is not accessible.
2025-12-08 19:19:33.000 R[21348:100855583] XType: XTFontStaticRegistry is enabled.
Downloading openssl-3.6.0.tar.gz...
-> https://github.com/openssl/openssl/releases/download/openssl-3.6.0/openssl-3.6.0.tar.gz
Installing openssl-3.6.0...
Installed openssl-3.6.0 to /Users/biocbuild/.pyenv/versions/3.14.0
Downloading readline-8.3.tar.gz...
-> https://pyenv.github.io/pythons/fe5383204467828cd495ee8d1d3c037a7eba1389c22bc6a041f627976f9061cc
Installing readline-8.3...
Installed readline-8.3 to /Users/biocbuild/.pyenv/versions/3.14.0
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 zlib from xcode sdk

BUILD FAILED (OS X 12.7.6 using python-build 2.6.16)

Inspect or clean up the working tree at /tmp/python-build.20251208192024.24877
Results logged to /tmp/python-build.20251208192024.24877.log

Last 10 log lines:
/usr/bin/install -c -m 755 Modules/_posixshmem.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_posixshmem.cpython-314-darwin.so
/usr/bin/install -c -m 755 Modules/_multiprocessing.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_multiprocessing.cpython-314-darwin.so
/usr/bin/install -c -m 755 Modules/_ctypes.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_ctypes.cpython-314-darwin.so
/usr/bin/install -c -m 755 Modules/_curses.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_curses.cpython-314-darwin.so
/usr/bin/install -c -m 755 Modules/_curses_panel.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_curses_panel.cpython-314-darwin.so
/usr/bin/install -c -m 755 Modules/_sqlite3.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_sqlite3.cpython-314-darwin.so
/usr/bin/install -c -m 755 Modules/_ssl.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_ssl.cpython-314-darwin.so
/usr/bin/install -c -m 755 Modules/_hashlib.cpython-314-darwin.so /Users/biocbuild/.pyenv/versions/3.14.0/lib/python3.14/lib-dynload/_hashlib.cpython-314-darwin.so
install: Modules/_hashlib.cpython-314-darwin.so: No such file or directory
make: *** [sharedinstall] Error 71

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