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This page was generated on 2025-09-18 11:40 -0400 (Thu, 18 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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 1492/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoProc 2.2.4  (landing page)
Vincent Carey
Snapshot Date: 2025-09-15 13:40 -0400 (Mon, 15 Sep 2025)
git_url: https://git.bioconductor.org/packages/ontoProc
git_branch: RELEASE_3_21
git_last_commit: 67dc810
git_last_commit_date: 2025-08-10 15:18:15 -0400 (Sun, 10 Aug 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


BUILD results for ontoProc on kunpeng2

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.

raw results


Summary

Package: ontoProc
Version: 2.2.4
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data ontoProc
StartedAt: 2025-09-16 10:16:46 -0000 (Tue, 16 Sep 2025)
EndedAt: 2025-09-16 10:34:42 -0000 (Tue, 16 Sep 2025)
EllapsedTime: 1076.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/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: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.20.0/ontoProc/2.2.4/bsklenv

  added / updated specs:
    - python=3.12.8


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-aarch64::bzip2-1.0.8-h4777abc_8 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.8.3-hbd8a1cb_0 
  ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.44-h5e2c951_1 
  libexpat           conda-forge/linux-aarch64::libexpat-2.7.1-hfae3067_0 
  libffi             conda-forge/linux-aarch64::libffi-3.4.6-he21f813_1 
  libgcc             conda-forge/linux-aarch64::libgcc-15.1.0-he277a41_5 
  libgcc-ng          conda-forge/linux-aarch64::libgcc-ng-15.1.0-he9431aa_5 
  libgomp            conda-forge/linux-aarch64::libgomp-15.1.0-he277a41_5 
  liblzma            conda-forge/linux-aarch64::liblzma-5.8.1-h86ecc28_2 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.1-h86ecc28_1 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.50.4-h022381a_0 
  libuuid            conda-forge/linux-aarch64::libuuid-2.41.1-h3e4203c_0 
  libxcrypt          conda-forge/linux-aarch64::libxcrypt-4.4.36-h31becfc_1 
  libzlib            conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2 
  ncurses            conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3 
  openssl            conda-forge/linux-aarch64::openssl-3.5.2-h8e36d6e_0 
  pip                conda-forge/noarch::pip-25.2-pyh8b19718_0 
  python             conda-forge/linux-aarch64::python-3.12.8-h1683364_1_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8382b9d_2 
  setuptools         conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.13-noxft_h5688188_102 
  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: linux-aarch64
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: linux-aarch64
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: /home/biocbuild/.cache/R/basilisk/1.20.0/ontoProc/2.2.4/bsklenv

  added / updated specs:
    - h5py=3.13.0
    - python=3.12.8


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    h5py-3.13.0                |nompi_py312h4f270de_101         1.3 MB  conda-forge
    hdf5-1.14.6                |nompi_h587839b_103         3.7 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         5.0 MB

The following NEW packages will be INSTALLED:

  c-ares             conda-forge/linux-aarch64::c-ares-1.34.5-h86ecc28_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/linux-aarch64::h5py-3.13.0-nompi_py312h4f270de_101 
  hdf5               conda-forge/linux-aarch64::hdf5-1.14.6-nompi_h587839b_103 
  keyutils           conda-forge/linux-aarch64::keyutils-1.6.3-h86ecc28_0 
  krb5               conda-forge/linux-aarch64::krb5-1.21.3-h50a48e9_0 
  libaec             conda-forge/linux-aarch64::libaec-1.1.4-h1e66f74_0 
  libblas            conda-forge/linux-aarch64::libblas-3.9.0-35_haddc8a3_openblas 
  libcblas           conda-forge/linux-aarch64::libcblas-3.9.0-35_hd72aa62_openblas 
  libcurl            conda-forge/linux-aarch64::libcurl-8.14.1-h6702fde_0 
  libedit            conda-forge/linux-aarch64::libedit-3.1.20250104-pl5321h976ea20_0 
  libev              conda-forge/linux-aarch64::libev-4.33-h31becfc_2 
  libgfortran        conda-forge/linux-aarch64::libgfortran-15.1.0-he9431aa_5 
  libgfortran5       conda-forge/linux-aarch64::libgfortran5-15.1.0-hbc25352_5 
  liblapack          conda-forge/linux-aarch64::liblapack-3.9.0-35_h88aeb00_openblas 
  libnghttp2         conda-forge/linux-aarch64::libnghttp2-1.67.0-ha888d0e_0 
  libopenblas        conda-forge/linux-aarch64::libopenblas-0.3.30-pthreads_h9d3fd7e_2 
  libssh2            conda-forge/linux-aarch64::libssh2-1.11.1-h18c354c_0 
  libstdcxx          conda-forge/linux-aarch64::libstdcxx-15.1.0-h3f4de04_5 
  libstdcxx-ng       conda-forge/linux-aarch64::libstdcxx-ng-15.1.0-hf1166c9_5 
  numpy              conda-forge/linux-aarch64::numpy-2.3.3-py312h6615c27_0 
  python_abi         conda-forge/noarch::python_abi-3.12-8_cp312 
  zstd               conda-forge/linux-aarch64::zstd-1.5.7-hbcf94c1_2 



Downloading and Extracting Packages: ...working...
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h5py-3.13.0          | 1.3 MB    | ######     |  60% 

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                                                      done
Preparing transaction: - \ done
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Collecting owlready2==0.47
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Building wheels for collected packages: owlready2
  Building wheel for owlready2 (pyproject.toml): started
  Building wheel for owlready2 (pyproject.toml): finished with status 'done'
  Created wheel for owlready2: filename=owlready2-0.47-cp312-cp312-linux_aarch64.whl size=23849771 sha256=d91d33b57635e0a741ace3714e63edb5ccc10bf5692089b391106bd78d6fe316
  Stored in directory: /home/biocbuild/.cache/pip/wheels/a8/81/8a/f76909ab0a8a17ce3735a6b9501344c545be5098d54b66adfc
Successfully built owlready2
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-0.10.23 dnspython-2.8.0 email-validator-2.3.0 idna-3.10 more_click-0.1.2 owlready2-0.47 pydantic-2.11.9 pydantic-core-2.33.2 pystow-0.7.8 pytrie-0.4.0 requests-2.32.5 sortedcontainers-2.4.0 tqdm-4.67.1 typing-extensions-4.15.0 typing-inspection-0.4.1 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:121-124 [donew]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `mat[, term_index]`:
! subscript out of bounds
---
Backtrace:
     ▆
  1. └─ontoProc::onto_plot2(cl, gsub(":", "_", stab$tag))
  2.   └─ontologyPlot::onto_plot(ont, terms2use, ...)
  3.     ├─base::lapply(...)
  4.     │ └─ontologyPlot (local) FUN(X[[i]], ...)
  5.     │   └─(function() {...
  6.     └─ontologyPlot::remove_uninformative_terms(ontology, term_sets)
  7.       └─ontologyPlot:::remove_uninformative_once(...)
  8.         └─base::sapply(...)
  9.           └─base::lapply(X = X, FUN = FUN, ...)
 10.             └─ontologyPlot (local) FUN(X[[i]], ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ontoProc.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘ontoProc.Rmd’

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

Quitting from owlents.Rmd:33-47 [getcl]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.util_download()`:
! bfcadd() failed; see warnings()
---
Backtrace:
    ▆
 1. └─ontoProc::owl2cache(url = "http://purl.obolibrary.org/obo/cl.owl")
 2.   ├─BiocFileCache::bfcadd(...)
 3.   └─BiocFileCache::bfcadd(...)
 4.     └─BiocFileCache:::.util_download(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'owlents.Rmd' failed with diagnostics:
bfcadd() failed; see warnings()
--- failed re-building ‘owlents.Rmd’

SUMMARY: processing the following files failed:
  ‘ontoProc.Rmd’ ‘owlents.Rmd’

Error: Vignette re-building failed.
Execution halted