Qiang Hu
| Snapshot Date: 2025-11-03 13:45 -0500 (Mon, 03 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/Rcwl |
| git_branch: RELEASE_3_22 |
| git_last_commit: 0b6281a |
| git_last_commit_date: 2025-10-29 10:50:00 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-04 12:04 -0500 (Tue, 04 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" | 4902 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4692 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 1735/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rcwl 1.26.0 (landing page) Qiang Hu
| 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 Rcwl package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rcwl.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: Rcwl |
| Version: 1.26.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Rcwl |
| StartedAt: 2025-11-03 18:24:06 -0500 (Mon, 03 Nov 2025) |
| EndedAt: 2025-11-03 18:34:08 -0500 (Mon, 03 Nov 2025) |
| EllapsedTime: 602.2 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 Rcwl
###
##############################################################################
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* checking for file ‘Rcwl/DESCRIPTION’ ... OK
* preparing ‘Rcwl’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Rcwl.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.20251103182435.98168
Results logged to /tmp/python-build.20251103182435.98168.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 Rcwl.Rmd:118-120 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.11 failed
---
Backtrace:
▆
1. └─Rcwl::install_cwltool()
2. └─basilisk::basiliskStart(env_Rcwl)
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 'Rcwl.Rmd' failed with diagnostics:
installation of Python 3.11 failed
--- failed re-building ‘Rcwl.Rmd’
SUMMARY: processing the following file failed:
‘Rcwl.Rmd’
Error: Vignette re-building failed.
Execution halted