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This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4013
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Package 1493/2325HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 2.5.0  (landing page)
Vincent Carey
Snapshot Date: 2025-11-12 13:40 -0500 (Wed, 12 Nov 2025)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: devel
git_last_commit: a09f239
git_last_commit_date: 2025-10-29 19:20:08 -0500 (Wed, 29 Oct 2025)
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for ontoProc on kjohnson3

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.

raw results


Summary

Package: ontoProc
Version: 2.5.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ontoProc
StartedAt: 2025-11-12 16:51:58 -0500 (Wed, 12 Nov 2025)
EndedAt: 2025-11-12 16:54:18 -0500 (Wed, 12 Nov 2025)
EllapsedTime: 139.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ontoProc
###
##############################################################################
##############################################################################


* checking for file ‘ontoProc/DESCRIPTION’ ... OK
* preparing ‘ontoProc’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘ontoProc.Rmd’ using rmarkdown
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.23.0/ontoProc/2.5.0/bsklenv/lib/python3.12/site-packages (25.0.1)
Collecting pip
  Using cached pip-25.3-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
  Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
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-25.3 setuptools-80.9.0 wheel-0.45.1
Collecting h5py==3.13.0
  Using cached h5py-3.13.0-cp312-cp312-macosx_11_0_arm64.whl.metadata (2.5 kB)
Collecting owlready2==0.47
  Using cached owlready2-0.47-cp312-cp312-macosx_11_0_arm64.whl
Collecting bioregistry==0.12.4
  Using cached bioregistry-0.12.4-py3-none-any.whl.metadata (35 kB)
Collecting numpy>=1.19.3 (from h5py==3.13.0)
  Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting requests (from bioregistry==0.12.4)
  Using cached requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)
Collecting tqdm (from bioregistry==0.12.4)
  Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)
Collecting pystow>=0.1.13 (from bioregistry==0.12.4)
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Collecting click (from bioregistry==0.12.4)
  Using cached click-8.3.0-py3-none-any.whl.metadata (2.6 kB)
Collecting more_click>=0.1.2 (from bioregistry==0.12.4)
  Using cached more_click-0.1.3-py3-none-any.whl.metadata (14 kB)
Collecting pydantic>=2.0 (from pydantic[email]>=2.0->bioregistry==0.12.4)
  Downloading pydantic-2.12.4-py3-none-any.whl.metadata (89 kB)
Collecting curies>=0.7.0 (from bioregistry==0.12.4)
  Downloading curies-0.12.4-py3-none-any.whl.metadata (14 kB)
Collecting typing-extensions (from curies>=0.7.0->bioregistry==0.12.4)
  Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
Collecting annotated-types>=0.6.0 (from pydantic>=2.0->pydantic[email]>=2.0->bioregistry==0.12.4)
  Using cached annotated_types-0.7.0-py3-none-any.whl.metadata (15 kB)
Collecting pydantic-core==2.41.5 (from pydantic>=2.0->pydantic[email]>=2.0->bioregistry==0.12.4)
  Downloading pydantic_core-2.41.5-cp312-cp312-macosx_11_0_arm64.whl.metadata (7.3 kB)
Collecting typing-inspection>=0.4.2 (from pydantic>=2.0->pydantic[email]>=2.0->bioregistry==0.12.4)
  Using cached typing_inspection-0.4.2-py3-none-any.whl.metadata (2.6 kB)
Collecting email-validator>=2.0.0 (from pydantic[email]>=2.0->bioregistry==0.12.4)
  Using cached email_validator-2.3.0-py3-none-any.whl.metadata (26 kB)
Collecting dnspython>=2.0.0 (from email-validator>=2.0.0->pydantic[email]>=2.0->bioregistry==0.12.4)
  Using cached dnspython-2.8.0-py3-none-any.whl.metadata (5.7 kB)
Collecting idna>=2.0.0 (from email-validator>=2.0.0->pydantic[email]>=2.0->bioregistry==0.12.4)
  Using cached idna-3.11-py3-none-any.whl.metadata (8.4 kB)
Collecting charset_normalizer<4,>=2 (from requests->bioregistry==0.12.4)
  Using cached charset_normalizer-3.4.4-cp312-cp312-macosx_10_13_universal2.whl.metadata (37 kB)
Collecting urllib3<3,>=1.21.1 (from requests->bioregistry==0.12.4)
  Using cached urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)
Collecting certifi>=2017.4.17 (from requests->bioregistry==0.12.4)
  Downloading certifi-2025.11.12-py3-none-any.whl.metadata (2.5 kB)
Using cached h5py-3.13.0-cp312-cp312-macosx_11_0_arm64.whl (2.9 MB)
Using cached bioregistry-0.12.4-py3-none-any.whl (5.4 MB)
Downloading curies-0.12.4-py3-none-any.whl (68 kB)
Using cached more_click-0.1.3-py3-none-any.whl (12 kB)
Using cached numpy-2.3.4-cp312-cp312-macosx_11_0_arm64.whl (14.2 MB)
Downloading pydantic-2.12.4-py3-none-any.whl (463 kB)
Downloading pydantic_core-2.41.5-cp312-cp312-macosx_11_0_arm64.whl (1.9 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.9/1.9 MB 9.9 MB/s  0:00:00
Using cached annotated_types-0.7.0-py3-none-any.whl (13 kB)
Using cached email_validator-2.3.0-py3-none-any.whl (35 kB)
Using cached dnspython-2.8.0-py3-none-any.whl (331 kB)
Using cached idna-3.11-py3-none-any.whl (71 kB)
Using cached pystow-0.7.11-py3-none-any.whl (43 kB)
Using cached typing_extensions-4.15.0-py3-none-any.whl (44 kB)
Using cached typing_inspection-0.4.2-py3-none-any.whl (14 kB)
Using cached click-8.3.0-py3-none-any.whl (107 kB)
Using cached requests-2.32.5-py3-none-any.whl (64 kB)
Using cached charset_normalizer-3.4.4-cp312-cp312-macosx_10_13_universal2.whl (208 kB)
Using cached urllib3-2.5.0-py3-none-any.whl (129 kB)
Downloading certifi-2025.11.12-py3-none-any.whl (159 kB)
Using cached tqdm-4.67.1-py3-none-any.whl (78 kB)
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-2025.11.12 charset_normalizer-3.4.4 click-8.3.0 curies-0.12.4 dnspython-2.8.0 email-validator-2.3.0 h5py-3.13.0 idna-3.11 more_click-0.1.3 numpy-2.3.4 owlready2-0.47 pydantic-2.12.4 pydantic-core-2.41.5 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
2025-11-12 16:52:29.275 R[93240:2820087] XType: Using static font registry.
Warning in doTryCatch(return(expr), name, parentenv, handler) :
  zero-length arrow is of indeterminate angle and so skipped

Quitting from ontoProc.Rmd:167-172 [gethpca]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'celldex'
---
Backtrace:
    ▆
 1. └─base::library(celldex)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ontoProc.Rmd' failed with diagnostics:
there is no package called 'celldex'
--- failed re-building ‘ontoProc.Rmd’

--- re-building ‘owlents.Rmd’ using rmarkdown
--- finished re-building ‘owlents.Rmd’

SUMMARY: processing the following file failed:
  ‘ontoProc.Rmd’

Error: Vignette re-building failed.
Execution halted