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R CMD BUILD
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* checking for file ‘OAtools/DESCRIPTION’ ... OK
* preparing ‘OAtools’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘OAtools.Rmd’ using rmarkdown
Downloading Python-3.13.5.tar.xz...
-> https://www.python.org/ftp/python/3.13.5/Python-3.13.5.tar.xz
Installing Python-3.13.5...
BUILD FAILED (Ubuntu 24.04 using python-build 2.6.20-3-g82f4de5)
Inspect or clean up the working tree at /tmp/python-build.20260121113400.3007867
Results logged to /tmp/python-build.20260121113400.3007867.log
Last 10 log lines:
0:01:33 load avg: 3.22 [42/43] test_xml_etree
0:01:34 load avg: 3.22 [42/43] test_xml_etree passed
0:01:34 load avg: 3.22 [43/43] test_xml_etree_c
0:01:35 load avg: 3.22 [43/43] test_xml_etree_c passed
Total duration: 1 min 35 sec
Total tests: run=9,367 failures=1 skipped=211
Total test files: run=43/43 failed=1
Result: FAILURE
make: *** [Makefile:902: profile-run-stamp] Error 2
Quitting from OAtools.Rmd:283-290 [regression-fit_curve]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `purrr::map()`:
i In index: 1.
i With name: well_2321.
Caused by error:
! installation of Python 3.13.5 failed
---
Backtrace:
▆
1. └─OAtools::computeModels(se = se, assay_name = "fluo_reporter")
2. └─purrr::map(...)
3. └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
4. ├─purrr:::with_indexed_errors(...)
5. │ └─base::withCallingHandlers(...)
6. ├─purrr:::call_with_cleanup(...)
7. └─OAtools (local) .f(.x[[i]], ...)
8. └─OAtools:::.runFitCurve(...)
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)
17. └─base::stop(sprintf(fmt, ...), call. = call.)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'OAtools.Rmd' failed with diagnostics:
i In index: 1.
i With name: well_2321.
Caused by error:
! installation of Python 3.13.5 failed
--- failed re-building ‘OAtools.Rmd’
SUMMARY: processing the following file failed:
‘OAtools.Rmd’
Error: Vignette re-building failed.
Execution halted