Bioconductor Single Package Builder - Build History

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URL: https://git.bioconductor.org/packages/OAtools

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)/x86_64	ERROR	skipped	skipped	skipped

nebbiolo1 Summary

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Package: OAtools

Version: 0.99.1

RVersion: 4.6

BiocVersion: 3.23

BuildCommand: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OAtools

BuildTime: 11 minutes 16.18 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: OAtools_20260121163237

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: OAtools. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1.

nebbiolo1 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* 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

nebbiolo1 CHECK output

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nebbiolo1 BUILD BIN output

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