| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-14 11:46 -0400 (Thu, 14 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 1492/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ontoProc 2.2.4 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | 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. |
| Package: ontoProc |
| Version: 2.2.4 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ontoProc |
| StartedAt: 2025-08-12 05:29:57 -0400 (Tue, 12 Aug 2025) |
| EndedAt: 2025-08-12 05:33:55 -0400 (Tue, 12 Aug 2025) |
| EllapsedTime: 237.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### 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
Channels:
- conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/ontoProc/2.2.4/bsklenv
added / updated specs:
- python=3.12.8
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-arm64::bzip2-1.0.8-h99b78c6_7
ca-certificates conda-forge/noarch::ca-certificates-2025.8.3-hbd8a1cb_0
icu conda-forge/osx-arm64::icu-75.1-hfee45f7_0
libexpat conda-forge/osx-arm64::libexpat-2.7.1-hec049ff_0
libffi conda-forge/osx-arm64::libffi-3.4.6-h1da3d7d_1
liblzma conda-forge/osx-arm64::liblzma-5.8.1-h39f12f2_2
libsqlite conda-forge/osx-arm64::libsqlite-3.50.4-h4237e3c_0
libzlib conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2
ncurses conda-forge/osx-arm64::ncurses-6.5-h5e97a16_3
openssl conda-forge/osx-arm64::openssl-3.5.2-he92f556_0
pip conda-forge/noarch::pip-25.2-pyh8b19718_0
python conda-forge/osx-arm64::python-3.12.8-hc22306f_1_cpython
readline conda-forge/osx-arm64::readline-8.2-h1d1bf99_2
setuptools conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0
tk conda-forge/osx-arm64::tk-8.6.13-h892fb3f_2
tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0
wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.7.0
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.7.0
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.20.0/ontoProc/2.2.4/bsklenv
added / updated specs:
- h5py=3.13.0
- python=3.12.8
The following NEW packages will be INSTALLED:
c-ares conda-forge/osx-arm64::c-ares-1.34.5-h5505292_0
cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1
cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1
h5py conda-forge/osx-arm64::h5py-3.13.0-nompi_py312h18d8c5e_101
hdf5 conda-forge/osx-arm64::hdf5-1.14.6-nompi_he65715a_103
krb5 conda-forge/osx-arm64::krb5-1.21.3-h237132a_0
libaec conda-forge/osx-arm64::libaec-1.1.4-h51d1e36_0
libblas conda-forge/osx-arm64::libblas-3.9.0-34_h10e41b3_openblas
libcblas conda-forge/osx-arm64::libcblas-3.9.0-34_hb3479ef_openblas
libcurl conda-forge/osx-arm64::libcurl-8.14.1-h73640d1_0
libcxx conda-forge/osx-arm64::libcxx-20.1.8-hf598326_1
libedit conda-forge/osx-arm64::libedit-3.1.20250104-pl5321hafb1f1b_0
libev conda-forge/osx-arm64::libev-4.33-h93a5062_2
libgfortran conda-forge/osx-arm64::libgfortran-15.1.0-hfdf1602_0
libgfortran5 conda-forge/osx-arm64::libgfortran5-15.1.0-hb74de2c_0
liblapack conda-forge/osx-arm64::liblapack-3.9.0-34_hc9a63f6_openblas
libnghttp2 conda-forge/osx-arm64::libnghttp2-1.64.0-h6d7220d_0
libopenblas conda-forge/osx-arm64::libopenblas-0.3.30-openmp_h60d53f8_1
libssh2 conda-forge/osx-arm64::libssh2-1.11.1-h1590b86_0
llvm-openmp conda-forge/osx-arm64::llvm-openmp-20.1.8-hbb9b287_1
numpy conda-forge/osx-arm64::numpy-2.3.2-py312h2f38b44_0
python_abi conda-forge/noarch::python_abi-3.12-8_cp312
zstd conda-forge/osx-arm64::zstd-1.5.7-h6491c7d_2
Downloading and Extracting Packages: ...working... done
Preparing transaction: - done
Verifying transaction: | / - \ | / - \ | / - \ done
Executing transaction: / - \ | / - \ | / - \ | / - \ | / - \ | done
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 requests (from bioregistry==0.12.4)
Using cached requests-2.32.4-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)
Downloading pystow-0.7.5-py3-none-any.whl.metadata (17 kB)
Collecting click (from bioregistry==0.12.4)
Using cached click-8.2.1-py3-none-any.whl.metadata (2.5 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-2.11.7-py3-none-any.whl.metadata (67 kB)
Collecting curies>=0.7.0 (from bioregistry==0.12.4)
Using cached curies-0.10.19-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-4.14.1-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==2.33.2 (from pydantic>=2.0->pydantic[email]>=2.0->bioregistry==0.12.4)
Using cached pydantic_core-2.33.2-cp312-cp312-macosx_11_0_arm64.whl.metadata (6.8 kB)
Collecting typing-inspection>=0.4.0 (from pydantic>=2.0->pydantic[email]>=2.0->bioregistry==0.12.4)
Using cached typing_inspection-0.4.1-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-2.2.0-py3-none-any.whl.metadata (25 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 idna>=2.0.0 (from email-validator>=2.0.0->pydantic[email]>=2.0->bioregistry==0.12.4)
Using cached idna-3.10-py3-none-any.whl.metadata (10 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)
Collecting charset_normalizer<4,>=2 (from requests->bioregistry==0.12.4)
Downloading charset_normalizer-3.4.3-cp312-cp312-macosx_10_13_universal2.whl.metadata (36 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)
Using cached certifi-2025.8.3-py3-none-any.whl.metadata (2.4 kB)
Using cached bioregistry-0.12.4-py3-none-any.whl (5.4 MB)
Using cached curies-0.10.19-py3-none-any.whl (60 kB)
Using cached more_click-0.1.2-py3-none-any.whl (6.7 kB)
Using cached pydantic-2.11.7-py3-none-any.whl (444 kB)
Using cached pydantic_core-2.33.2-cp312-cp312-macosx_11_0_arm64.whl (1.8 MB)
Using cached annotated_types-0.7.0-py3-none-any.whl (13 kB)
Using cached email_validator-2.2.0-py3-none-any.whl (33 kB)
Using cached dnspython-2.7.0-py3-none-any.whl (313 kB)
Using cached idna-3.10-py3-none-any.whl (70 kB)
Downloading pystow-0.7.5-py3-none-any.whl (41 kB)
Using cached typing_extensions-4.14.1-py3-none-any.whl (43 kB)
Using cached typing_inspection-0.4.1-py3-none-any.whl (14 kB)
Using cached click-8.2.1-py3-none-any.whl (102 kB)
Using cached PyTrie-0.4.0-py3-none-any.whl (6.1 kB)
Using cached requests-2.32.4-py3-none-any.whl (64 kB)
Downloading charset_normalizer-3.4.3-cp312-cp312-macosx_10_13_universal2.whl (205 kB)
Using cached urllib3-2.5.0-py3-none-any.whl (129 kB)
Using cached certifi-2025.8.3-py3-none-any.whl (161 kB)
Using cached sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB)
Using cached tqdm-4.67.1-py3-none-any.whl (78 kB)
Installing collected packages: sortedcontainers, urllib3, typing-extensions, tqdm, pytrie, owlready2, idna, dnspython, click, charset_normalizer, certifi, annotated-types, typing-inspection, requests, pydantic-core, more_click, email-validator, pystow, pydantic, curies, bioregistry
Successfully installed annotated-types-0.7.0 bioregistry-0.12.4 certifi-2025.8.3 charset_normalizer-3.4.3 click-8.2.1 curies-0.10.19 dnspython-2.7.0 email-validator-2.2.0 idna-3.10 more_click-0.1.2 owlready2-0.47 pydantic-2.11.7 pydantic-core-2.33.2 pystow-0.7.5 pytrie-0.4.0 requests-2.32.4 sortedcontainers-2.4.0 tqdm-4.67.1 typing-extensions-4.14.1 typing-inspection-0.4.1 urllib3-2.5.0
2025-08-12 05:32:20.137 R[24086:290536832] XType: Using static font registry.
Warning in doTryCatch(return(expr), name, parentenv, handler) :
zero-length arrow is of indeterminate angle and so skipped
--- finished re-building ‘ontoProc.Rmd’
--- re-building ‘owlents.Rmd’ using rmarkdown
Quitting from owlents.Rmd:33-47 [getcl]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_call_impl()`:
! owlready2.base.OwlReadyOntologyParsingError: NTriples parsing error (or unrecognized file format) in /tmp/Rtmp4ZY816/file5e164abfa5f2.
Run `reticulate::py_last_error()` for details.
---
Backtrace:
▆
1. └─ontoProc::setup_entities(tf)
2. └─o2$get_ontology(owlfn)$load()
3. └─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 /tmp/Rtmp4ZY816/file5e164abfa5f2.
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘owlents.Rmd’
SUMMARY: processing the following file failed:
‘owlents.Rmd’
Error: Vignette re-building failed.
Execution halted