Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-09-18 11:40 -0400 (Thu, 18 Sep 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" | 4827 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R 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 1492/2341 | 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 | |||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
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 |
############################################################################## ############################################################################## ### ### 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... hdf5-1.14.6 | 3.7 MB | | 0% h5py-3.13.0 | 1.3 MB | | 0% [A hdf5-1.14.6 | 3.7 MB | ## | 21% h5py-3.13.0 | 1.3 MB | 1 | 1% [A h5py-3.13.0 | 1.3 MB | 2 | 2% [A h5py-3.13.0 | 1.3 MB | 7 | 7% [A h5py-3.13.0 | 1.3 MB | 9 | 10% [A h5py-3.13.0 | 1.3 MB | #2 | 12% [A h5py-3.13.0 | 1.3 MB | #4 | 14% [A hdf5-1.14.6 | 3.7 MB | #####1 | 51% h5py-3.13.0 | 1.3 MB | #6 | 17% [A hdf5-1.14.6 | 3.7 MB | ######7 | 68% hdf5-1.14.6 | 3.7 MB | #######8 | 79% h5py-3.13.0 | 1.3 MB | #9 | 19% [A hdf5-1.14.6 | 3.7 MB | ########9 | 90% 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h5py-3.13.0 | 1.3 MB | ########2 | 83% [A h5py-3.13.0 | 1.3 MB | #########2 | 92% [A h5py-3.13.0 | 1.3 MB | ########## | 100% [A h5py-3.13.0 | 1.3 MB | ########## | 100% [A h5py-3.13.0 | 1.3 MB | ########## | 100% [A [A done Preparing transaction: - \ done Verifying transaction: / - \ | / - \ | / - done Executing transaction: | / - \ | / - \ | / - \ | / - \ | / - \ done Collecting owlready2==0.47 Downloading owlready2-0.47.tar.gz (27.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 27.3/27.3 MB 971.2 kB/s 0:00:27 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting bioregistry==0.12.4 Downloading bioregistry-0.12.4-py3-none-any.whl.metadata (35 kB) Collecting requests (from bioregistry==0.12.4) Using cached 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sortedcontainers-2.4.0-py2.py3-none-any.whl (29 kB) Using cached tqdm-4.67.1-py3-none-any.whl (78 kB) 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