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This page was generated on 2025-03-20 11:45 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4777
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4458
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 1477/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 2.1.7  (landing page)
Vincent Carey
Snapshot Date: 2025-03-19 13:40 -0400 (Wed, 19 Mar 2025)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: devel
git_last_commit: 091f8da
git_last_commit_date: 2025-03-13 13:01:15 -0400 (Thu, 13 Mar 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

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: 2.1.7
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ontoProc
StartedAt: 2025-03-19 17:15:32 -0400 (Wed, 19 Mar 2025)
EndedAt: 2025-03-19 17:17:44 -0400 (Wed, 19 Mar 2025)
EllapsedTime: 132.4 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 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/1.19.2/ontoProc/2.1.7/bsklenv/lib/python3.12/site-packages (24.3.1)
Collecting pip
  Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
  Using cached setuptools-77.0.1-py3-none-any.whl.metadata (6.7 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: pip
    Found existing installation: pip 24.3.1
    Uninstalling pip-24.3.1:
      Successfully uninstalled pip-24.3.1
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Collecting h5py==3.13.0
  Downloading 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-2.2.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (62 kB)
Collecting requests (from bioregistry==0.12.4)
  Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 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)
  Using cached pystow-0.7.0-py3-none-any.whl.metadata (17 kB)
Collecting click (from bioregistry==0.12.4)
  Using cached click-8.1.8-py3-none-any.whl.metadata (2.3 kB)
Collecting more_click>=0.1.2 (from bioregistry==0.12.4)
  Using cached more_click-0.1.2-py3-none-any.whl.metadata (4.3 kB)
Collecting pydantic>=2.0 (from pydantic[email]>=2.0->bioregistry==0.12.4)
  Using cached pydantic-2.10.6-py3-none-any.whl.metadata (30 kB)
Collecting curies>=0.7.0 (from bioregistry==0.12.4)
  Downloading curies-0.10.8-py3-none-any.whl.metadata (14 kB)
Collecting pytrie (from curies>=0.7.0->bioregistry==0.12.4)
  Using cached PyTrie-0.4.0-py3-none-any.whl.metadata (1.6 kB)
Collecting typing-extensions (from curies>=0.7.0->bioregistry==0.12.4)
  Using cached typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 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==2.27.2 (from pydantic>=2.0->pydantic[email]>=2.0->bioregistry==0.12.4)
  Using cached pydantic_core-2.27.2-cp312-cp312-macosx_11_0_arm64.whl.metadata (6.6 kB)
Collecting email-validator>=2.0.0 (from pydantic[email]>=2.0->bioregistry==0.12.4)
  Using cached email_validator-2.2.0-py3-none-any.whl.metadata (25 kB)
Collecting charset-normalizer<4,>=2 (from requests->bioregistry==0.12.4)
  Using cached charset_normalizer-3.4.1-cp312-cp312-macosx_10_13_universal2.whl.metadata (35 kB)
Collecting idna<4,>=2.5 (from requests->bioregistry==0.12.4)
  Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
Collecting urllib3<3,>=1.21.1 (from requests->bioregistry==0.12.4)
  Using cached urllib3-2.3.0-py3-none-any.whl.metadata (6.5 kB)
Collecting certifi>=2017.4.17 (from requests->bioregistry==0.12.4)
  Using cached certifi-2025.1.31-py3-none-any.whl.metadata (2.5 kB)
Collecting dnspython>=2.0.0 (from email-validator>=2.0.0->pydantic[email]>=2.0->bioregistry==0.12.4)
  Using cached dnspython-2.7.0-py3-none-any.whl.metadata (5.8 kB)
Collecting sortedcontainers (from pytrie->curies>=0.7.0->bioregistry==0.12.4)
  Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl.metadata (10 kB)
Downloading h5py-3.13.0-cp312-cp312-macosx_11_0_arm64.whl (2.9 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.9/2.9 MB 15.8 MB/s eta 0:00:00
Using cached bioregistry-0.12.4-py3-none-any.whl (5.4 MB)
Downloading curies-0.10.8-py3-none-any.whl (56 kB)
Using cached more_click-0.1.2-py3-none-any.whl (6.7 kB)
Using cached numpy-2.2.4-cp312-cp312-macosx_11_0_arm64.whl (14.1 MB)
Using cached pydantic-2.10.6-py3-none-any.whl (431 kB)
Using cached pydantic_core-2.27.2-cp312-cp312-macosx_11_0_arm64.whl (1.8 MB)
Using cached pystow-0.7.0-py3-none-any.whl (38 kB)
Using cached click-8.1.8-py3-none-any.whl (98 kB)
Using cached requests-2.32.3-py3-none-any.whl (64 kB)
Using cached tqdm-4.67.1-py3-none-any.whl (78 kB)
Using cached annotated_types-0.7.0-py3-none-any.whl (13 kB)
Using cached certifi-2025.1.31-py3-none-any.whl (166 kB)
Using cached charset_normalizer-3.4.1-cp312-cp312-macosx_10_13_universal2.whl (196 kB)
Using cached email_validator-2.2.0-py3-none-any.whl (33 kB)
Using cached idna-3.10-py3-none-any.whl (70 kB)
Using cached typing_extensions-4.12.2-py3-none-any.whl (37 kB)
Using cached urllib3-2.3.0-py3-none-any.whl (128 kB)
Using cached PyTrie-0.4.0-py3-none-any.whl (6.1 kB)
Using cached dnspython-2.7.0-py3-none-any.whl (313 kB)
Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB)
Installing collected packages: sortedcontainers, urllib3, typing-extensions, tqdm, pytrie, owlready2, numpy, idna, dnspython, click, charset-normalizer, certifi, annotated-types, requests, pydantic-core, more_click, h5py, email-validator, pystow, pydantic, curies, bioregistry
Successfully installed annotated-types-0.7.0 bioregistry-0.12.4 certifi-2025.1.31 charset-normalizer-3.4.1 click-8.1.8 curies-0.10.8 dnspython-2.7.0 email-validator-2.2.0 h5py-3.13.0 idna-3.10 more_click-0.1.2 numpy-2.2.4 owlready2-0.47 pydantic-2.10.6 pydantic-core-2.27.2 pystow-0.7.0 pytrie-0.4.0 requests-2.32.3 sortedcontainers-2.4.0 tqdm-4.67.1 typing-extensions-4.12.2 urllib3-2.3.0

Quitting from ontoProc.Rmd:40-44 [lkbr]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_module_import()`:
! ModuleNotFoundError: No module named 'bioregistry'
Run `reticulate::py_last_error()` for details.
---
Backtrace:
    ▆
 1. └─ontoProc::bioregistry_ols_resources()
 2.   └─basilisk::basiliskRun(...)
 3.     └─ontoProc (local) fun(...)
 4.       └─reticulate::import("bioregistry")
 5.         └─reticulate:::py_module_import(module, convert = convert)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ontoProc.Rmd' failed with diagnostics:
ModuleNotFoundError: No module named 'bioregistry'
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘ontoProc.Rmd’

--- re-building ‘owlents.Rmd’ using rmarkdown
2025-03-19 17:16:33.338 R[99165:759124946] XType: Using static font registry.
--- finished re-building ‘owlents.Rmd’

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

Error: Vignette re-building failed.
Execution halted