| 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 744/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FLAMES 2.4.1 (landing page) Changqing Wang
| 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 | ERROR | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the FLAMES package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FLAMES.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: FLAMES |
| Version: 2.4.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data FLAMES |
| StartedAt: 2025-11-17 22:28:41 -0500 (Mon, 17 Nov 2025) |
| EndedAt: 2025-11-17 23:00:17 -0500 (Mon, 17 Nov 2025) |
| EllapsedTime: 1896.1 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 FLAMES
###
##############################################################################
##############################################################################
* checking for file ‘FLAMES/DESCRIPTION’ ... OK
* preparing ‘FLAMES’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘FLAMES_vignette.Rmd’ using rmarkdown
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.11.9.tar.xz...
-> https://www.python.org/ftp/python/3.11.9/Python-3.11.9.tar.xz
Installing Python-3.11.9...
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.20251117223311.71133
Results logged to /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T/python-build.20251117223311.71133.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
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.11.9.tar.xz...
-> https://www.python.org/ftp/python/3.11.9/Python-3.11.9.tar.xz
Installing Python-3.11.9...
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.20251117224001.5356
Results logged to /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T/python-build.20251117224001.5356.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
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.11.9.tar.xz...
-> https://www.python.org/ftp/python/3.11.9/Python-3.11.9.tar.xz
Installing Python-3.11.9...
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.20251117224644.51484
Results logged to /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T/python-build.20251117224644.51484.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
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.11.9.tar.xz...
-> https://www.python.org/ftp/python/3.11.9/Python-3.11.9.tar.xz
Installing Python-3.11.9...
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.20251117225336.92002
Results logged to /var/folders/v1/y6dg5h4n163dzmrfl6t_r5480000gp/T/python-build.20251117225336.92002.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 FLAMES_vignette.Rmd:168-173 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! installation of Python 3.11.9 failed
---
Backtrace:
▆
1. ├─FLAMES::run_step(mspipeline, "barcode_demultiplex")
2. └─FLAMES::run_step(mspipeline, "barcode_demultiplex")
3. ├─FLAMES:::barcode_demultiplex(pipeline)
4. └─FLAMES:::barcode_demultiplex(pipeline)
5. └─base::lapply(...)
6. └─FLAMES (local) FUN(X[[i]], ...)
7. └─FLAMES::find_barcode(...)
8. └─FLAMES::cutadapt(...)
9. └─basilisk::basiliskRun(...)
10. └─basilisk::basiliskStart(...)
11. └─basilisk::obtainEnvironmentPath(env)
12. └─basilisk::setupBasiliskEnv(...)
13. ├─base::suppressMessages(install_python(version))
14. │ └─base::withCallingHandlers(...)
15. └─reticulate::install_python(version)
16. └─reticulate:::stopf("installation of Python %s failed", version)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'FLAMES_vignette.Rmd' failed with diagnostics:
installation of Python 3.11.9 failed
--- failed re-building ‘FLAMES_vignette.Rmd’
SUMMARY: processing the following file failed:
‘FLAMES_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted