Vincent Carey
| Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/ontoProc |
| git_branch: devel |
| git_last_commit: 8aa7338 |
| git_last_commit_date: 2025-10-08 11:44:19 -0400 (Wed, 08 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-11 12:07 -0400 (Sat, 11 Oct 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" | 4864 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
| 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 1502/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ontoProc 2.3.11 (landing page) Vincent Carey
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the ontoProc package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ontoProc.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: ontoProc |
| Version: 2.3.11 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data ontoProc |
| StartedAt: 2025-10-10 02:44:27 -0000 (Fri, 10 Oct 2025) |
| EndedAt: 2025-10-10 02:47:13 -0000 (Fri, 10 Oct 2025) |
| EllapsedTime: 166.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data ontoProc
###
##############################################################################
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* checking for file ‘ontoProc/DESCRIPTION’ ... OK
* preparing ‘ontoProc’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ontoProc.Rmd’ using rmarkdown
Requirement already satisfied: pip in /home/biocbuild/.cache/R/basilisk/1.21.5/ontoProc/2.3.11/bsklenv/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-25.2-py3-none-any.whl.metadata (4.7 kB)
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Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed pip-25.2 setuptools-80.9.0 wheel-0.45.1
Collecting h5py==3.13.0
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Installing collected packages: urllib3, typing-extensions, tqdm, owlready2, numpy, idna, dnspython, click, charset_normalizer, certifi, annotated-types, typing-inspection, requests, pydantic-core, more_click, h5py, email-validator, pystow, pydantic, curies, bioregistry
Successfully installed annotated-types-0.7.0 bioregistry-0.12.4 certifi-2025.10.5 charset_normalizer-3.4.3 click-8.3.0 curies-0.12.1 dnspython-2.8.0 email-validator-2.3.0 h5py-3.13.0 idna-3.10 more_click-0.1.2 numpy-2.3.3 owlready2-0.47 pydantic-2.12.0 pydantic-core-2.41.1 pystow-0.7.11 requests-2.32.5 tqdm-4.67.1 typing-extensions-4.15.0 typing-inspection-0.4.2 urllib3-2.5.0
Warning in doTryCatch(return(expr), name, parentenv, handler) :
zero-length arrow is of indeterminate angle and so skipped
Quitting from ontoProc.Rmd:125-141 [donew]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_call_impl()`:
! owlready2.base.OwlReadyOntologyParsingError: NTriples parsing error (or unrecognized file format) in /home/biocbuild/tmp/RtmpCO3xum/file362a524bd63c64.
Run `reticulate::py_last_error()` for details.
---
Backtrace:
▆
1. └─ontoProc::setup_entities2(tf)
2. └─basilisk::basiliskRun(...)
3. └─ontoProc (local) fun(...)
4. └─o2$get_ontology(owlfn)$load()
5. └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ontoProc.Rmd' failed with diagnostics:
owlready2.base.OwlReadyOntologyParsingError: NTriples parsing error (or unrecognized file format) in /home/biocbuild/tmp/RtmpCO3xum/file362a524bd63c64.
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘ontoProc.Rmd’
--- re-building ‘owlents.Rmd’ using rmarkdown
Quitting from owlents.Rmd:33-45 [getcl]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_call_impl()`:
! owlready2.base.OwlReadyOntologyParsingError: NTriples parsing error (or unrecognized file format) in /home/biocbuild/tmp/RtmpCO3xum/file362a52446a00b3.
Run `reticulate::py_last_error()` for details.
---
Backtrace:
▆
1. └─ontoProc::setup_entities2(tf)
2. └─basilisk::basiliskRun(...)
3. └─ontoProc (local) fun(...)
4. └─o2$get_ontology(owlfn)$load()
5. └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'owlents.Rmd' failed with diagnostics:
owlready2.base.OwlReadyOntologyParsingError: NTriples parsing error (or unrecognized file format) in /home/biocbuild/tmp/RtmpCO3xum/file362a52446a00b3.
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘owlents.Rmd’
SUMMARY: processing the following files failed:
‘ontoProc.Rmd’ ‘owlents.Rmd’
Error: Vignette re-building failed.
Execution halted