Gabriele Sales
| Snapshot Date: 2025-10-31 13:45 -0400 (Fri, 31 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/spatialDE |
| git_branch: RELEASE_3_22 |
| git_last_commit: dfd143b |
| git_last_commit_date: 2025-10-29 11:11:31 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-01 12:04 -0400 (Sat, 01 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 | ||||
| Package 2078/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| spatialDE 1.16.0 (landing page) Gabriele Sales
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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. |
| Package: spatialDE |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data spatialDE |
| StartedAt: 2025-10-31 18:55:53 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 19:01:09 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 316.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
###
### /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 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 readline from homebrew
python-build: use ncurses from homebrew
python-build: use zlib from xcode sdk
BUILD FAILED (OS X 12.7.6 using python-build 2.6.12)
Inspect or clean up the working tree at /tmp/python-build.20251031185640.66327
Results logged to /tmp/python-build.20251031185640.66327.log
Last 10 log lines:
"_mkfifoat", referenced from:
_os_mkfifo in lto.o
"_mknodat", referenced from:
_os_mknod in lto.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[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