| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-11-20 12:07 -0500 (Thu, 20 Nov 2025).
| 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 | ||||
| Package 2313/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| velociraptor 1.20.0 (landing page) Kevin Rue-Albrecht
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the velociraptor package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/velociraptor.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: velociraptor |
| Version: 1.20.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data velociraptor |
| StartedAt: 2025-11-18 02:10:31 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 02:12:42 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 131.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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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 velociraptor
###
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* checking for file ‘velociraptor/DESCRIPTION’ ... OK
* preparing ‘velociraptor’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘velociraptor.Rmd’ using rmarkdown
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 13.7.8 using python-build 2.6.12-2-g2afd173)
Inspect or clean up the working tree at /var/folders/dc/2xck8b8s0_3gymbxnrltzxhm0000gs/T/python-build.20251118021102.14391
Results logged to /var/folders/dc/2xck8b8s0_3gymbxnrltzxhm0000gs/T/python-build.20251118021102.14391.log
Last 10 log lines:
ld: warning: search path '/Users/biocbuild/.pyenv/versions/3.12.10/lib' not found
ld: Undefined symbols:
_mkfifoat, referenced from:
_os_mkfifo in 127.arm64.thinlto.o
_mknodat, referenced from:
_os_mknod in 127.arm64.thinlto.o
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 velociraptor.Rmd:75-82 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.12.10 failed
---
Backtrace:
▆
1. ├─velociraptor::scvelo(...)
2. └─velociraptor::scvelo(...)
3. └─velociraptor (local) .local(x, ...)
4. ├─methods::callNextMethod(x, ..., sf.X = sf.X, dimred = dimred)
5. │ └─base::eval(call, callEnv)
6. │ └─base::eval(call, callEnv)
7. └─velociraptor (local) .nextMethod(x, ..., sf.X = sf.X, dimred = dimred)
8. └─velociraptor (local) .local(x, ...)
9. └─velociraptor:::.scvelo(...)
10. └─basilisk::basiliskRun(...)
11. └─basilisk::basiliskStart(...)
12. └─basilisk::obtainEnvironmentPath(env)
13. └─basilisk::setupBasiliskEnv(...)
14. ├─base::suppressMessages(install_python(version))
15. │ └─base::withCallingHandlers(...)
16. └─reticulate::install_python(version)
17. └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'velociraptor.Rmd' failed with diagnostics:
installation of Python 3.12.10 failed
--- failed re-building ‘velociraptor.Rmd’
SUMMARY: processing the following file failed:
‘velociraptor.Rmd’
Error: Vignette re-building failed.
Execution halted