Ran Hu
| Snapshot Date: 2025-08-05 13:25 -0400 (Tue, 05 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/cfTools |
| git_branch: devel |
| git_last_commit: 970eb2d |
| git_last_commit_date: 2025-07-15 15:25:12 -0400 (Tue, 15 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-06 13:56 -0400 (Wed, 06 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4813 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
| 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 320/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cfTools 1.9.0 (landing page) Ran Hu
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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: 1.9.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cfTools |
| StartedAt: 2025-08-05 15:50:24 -0400 (Tue, 05 Aug 2025) |
| EndedAt: 2025-08-05 15:50:50 -0400 (Tue, 05 Aug 2025) |
| EllapsedTime: 26.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cfTools
###
##############################################################################
##############################################################################
* 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 13.7.1 using python-build 2.6.5-2-gbd9d13b)
Inspect or clean up the working tree at /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/python-build.20250805155043.96268
Results logged to /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/python-build.20250805155043.96268.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