| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
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%
h5py-3.13.0 | 1.3 MB | ## | 20% [A
hdf5-1.14.6 | 3.7 MB | #########6 | 97%
h5py-3.13.0 | 1.3 MB | ##2 | 23% [A
hdf5-1.14.6 | 3.7 MB | ########## | 100%
h5py-3.13.0 | 1.3 MB | ##4 | 24% [A
hdf5-1.14.6 | 3.7 MB | ########## | 100%
h5py-3.13.0 | 1.3 MB | ##5 | 25% [A
h5py-3.13.0 | 1.3 MB | ##6 | 26% [A
h5py-3.13.0 | 1.3 MB | ###3 | 34% [A
h5py-3.13.0 | 1.3 MB | ###7 | 37% [A
h5py-3.13.0 | 1.3 MB | ###9 | 40% [A
h5py-3.13.0 | 1.3 MB | ####2 | 42% [A
h5py-3.13.0 | 1.3 MB | ####4 | 44% [A
h5py-3.13.0 | 1.3 MB | ####6 | 47% [A
h5py-3.13.0 | 1.3 MB | ####9 | 49% [A
h5py-3.13.0 | 1.3 MB | #####1 | 52% [A
h5py-3.13.0 | 1.3 MB | #####4 | 54% [A
h5py-3.13.0 | 1.3 MB | #####6 | 56% [A
h5py-3.13.0 | 1.3 MB | #####8 | 59% [A
h5py-3.13.0 | 1.3 MB | ###### | 60% [A
h5py-3.13.0 | 1.3 MB | ######2 | 62% [A
h5py-3.13.0 | 1.3 MB | ######3 | 64% [A
h5py-3.13.0 | 1.3 MB | ######6 | 66% [A
h5py-3.13.0 | 1.3 MB | ######8 | 68% [A
h5py-3.13.0 | 1.3 MB | #######2 | 72% [A
h5py-3.13.0 | 1.3 MB | #######6 | 77% [A
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)
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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)
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Using cached requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)
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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-0.7.8-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)
Downloading 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)
Downloading pydantic-2.11.9-py3-none-any.whl.metadata (68 kB)
Collecting curies>=0.7.0 (from bioregistry==0.12.4)
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Collecting pytrie (from curies>=0.7.0->bioregistry==0.12.4)
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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)
Downloading 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)
Downloading pydantic_core-2.33.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (6.8 kB)
Collecting typing-inspection>=0.4.0 (from pydantic>=2.0->pydantic[email]>=2.0->bioregistry==0.12.4)
Downloading 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)
Downloading 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)
Downloading 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-3.10-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)
Using cached charset_normalizer-3.4.3-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.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)
Downloading bioregistry-0.12.4-py3-none-any.whl (5.4 MB)
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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