| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-20 12:04 -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 329/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cfTools 1.10.0 (landing page) Ran Hu
| 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 | OK | OK | ||||||||||
|
To the developers/maintainers of the cfTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cfTools.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: cfTools |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cfTools |
| StartedAt: 2025-11-17 21:04:43 -0500 (Mon, 17 Nov 2025) |
| EndedAt: 2025-11-17 21:07:15 -0500 (Mon, 17 Nov 2025) |
| EllapsedTime: 151.6 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 cfTools
###
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* checking for file ‘cfTools/DESCRIPTION’ ... OK
* preparing ‘cfTools’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘cfTools-vignette.Rmd’ using rmarkdown
python-build: use openssl from homebrew
python-build: use readline from homebrew
Downloading Python-3.8.20.tar.xz...
-> https://www.python.org/ftp/python/3.8.20/Python-3.8.20.tar.xz
Installing Python-3.8.20...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk
BUILD FAILED (OS X 12.7.6 using python-build 2.6.12-2-g2afd173)
Inspect or clean up the working tree at /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T/python-build.20251117210655.54017
Results logged to /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T/python-build.20251117210655.54017.log
Last 10 log lines:
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for --with-pydebug... no
checking for --with-trace-refs... no
checking for --with-assertions... no
checking for --enable-optimizations... yes
checking PROFILE_TASK... -m test --pgo
checking for --with-lto... yes
checking for llvm-ar... no
configure: error: llvm-ar is required for a --with-lto build with clang but could not be found.
make: *** No targets specified and no makefile found. Stop.
Quitting from cfTools-vignette.Rmd:172-175 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.8 failed
---
Backtrace:
▆
1. └─cfTools::MergePEReads(PEReads)
2. └─basilisk::basiliskStart(my_env)
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 'cfTools-vignette.Rmd' failed with diagnostics:
installation of Python 3.8 failed
--- failed re-building ‘cfTools-vignette.Rmd’
SUMMARY: processing the following file failed:
‘cfTools-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted