| 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 |
BUILD results for ontoProc on palomino7
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
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### chmod a+r ontoProc -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe 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: win-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: C:\Users\biocbuild\.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/win-64::bzip2-1.0.8-h2466b09_7
ca-certificates conda-forge/noarch::ca-certificates-2025.8.3-h4c7d964_0
libexpat conda-forge/win-64::libexpat-2.7.1-hac47afa_0
libffi conda-forge/win-64::libffi-3.4.6-h537db12_1
liblzma conda-forge/win-64::liblzma-5.8.1-h2466b09_2
libsqlite conda-forge/win-64::libsqlite-3.50.4-hf5d6505_0
libzlib conda-forge/win-64::libzlib-1.3.1-h2466b09_2
openssl conda-forge/win-64::openssl-3.5.2-h725018a_0
pip conda-forge/noarch::pip-25.2-pyh8b19718_0
python conda-forge/win-64::python-3.12.8-h3f84c4b_1_cpython
setuptools conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0
tk conda-forge/win-64::tk-8.6.13-h2c6b04d_2
tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0
ucrt conda-forge/win-64::ucrt-10.0.22621.0-h57928b3_1
vc conda-forge/win-64::vc-14.3-h41ae7f8_31
vc14_runtime conda-forge/win-64::vc14_runtime-14.44.35208-h818238b_31
vcomp14 conda-forge/win-64::vcomp14-14.44.35208-h818238b_31
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: win-64
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: win-64
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: C:\Users\biocbuild\.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
---------------------------|-----------------
libblas-3.9.0 | 34_h5709861_mkl 69 KB conda-forge
libcblas-3.9.0 | 34_h2a3cdd5_mkl 69 KB conda-forge
libiconv-1.18 | hc1393d2_2 681 KB conda-forge
liblapack-3.9.0 | 34_hf9ab0e9_mkl 80 KB conda-forge
llvm-openmp-20.1.8 | hfa2b4ca_1 287 KB conda-forge
mkl-2024.2.2 | h57928b3_16 98.3 MB conda-forge
------------------------------------------------------------
Total: 99.5 MB
The following NEW packages will be INSTALLED:
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/win-64::h5py-3.13.0-nompi_py312h4e244af_101
hdf5 conda-forge/win-64::hdf5-1.14.6-nompi_he30205f_103
krb5 conda-forge/win-64::krb5-1.21.3-hdf4eb48_0
libaec conda-forge/win-64::libaec-1.1.4-h20038f6_0
libblas conda-forge/win-64::libblas-3.9.0-34_h5709861_mkl
libcblas conda-forge/win-64::libcblas-3.9.0-34_h2a3cdd5_mkl
libcurl conda-forge/win-64::libcurl-8.14.1-h88aaa65_0
libhwloc conda-forge/win-64::libhwloc-2.12.1-default_h88281d1_1000
libiconv conda-forge/win-64::libiconv-1.18-hc1393d2_2
liblapack conda-forge/win-64::liblapack-3.9.0-34_hf9ab0e9_mkl
libssh2 conda-forge/win-64::libssh2-1.11.1-h9aa295b_0
libwinpthread conda-forge/win-64::libwinpthread-12.0.0.r4.gg4f2fc60ca-h57928b3_9
libxml2 conda-forge/win-64::libxml2-2.13.8-h741aa76_1
llvm-openmp conda-forge/win-64::llvm-openmp-20.1.8-hfa2b4ca_1
mkl conda-forge/win-64::mkl-2024.2.2-h57928b3_16
numpy conda-forge/win-64::numpy-2.3.2-py312ha72d056_0
python_abi conda-forge/noarch::python_abi-3.12-8_cp312
tbb conda-forge/win-64::tbb-2021.13.0-h18a62a1_2
Downloading and Extracting Packages: ...working...
mkl-2024.2.2 | 98.3 MB | | 0%
libiconv-1.18 | 681 KB | | 0% [A
llvm-openmp-20.1.8 | 287 KB | | 0% [A[A
liblapack-3.9.0 | 80 KB | | 0% [A[A[A
libcblas-3.9.0 | 69 KB | | 0% [A[A[A[A
libblas-3.9.0 | 69 KB | | 0% [A[A[A[A[A
libiconv-1.18 | 681 KB | 2 | 2% [A
libiconv-1.18 | 681 KB | ########## | 100% [A
libcblas-3.9.0 | 69 KB | ##3 | 23% [A[A[A[A
llvm-openmp-20.1.8 | 287 KB | 5 | 6% [A[A
libcblas-3.9.0 | 69 KB | ########## | 100% [A[A[A[A
liblapack-3.9.0 | 80 KB | #9 | 20% [A[A[A
llvm-openmp-20.1.8 | 287 KB | ########## | 100% [A[A
liblapack-3.9.0 | 80 KB | ########## | 100% [A[A[A
libblas-3.9.0 | 69 KB | ##3 | 23% [A[A[A[A[A
libblas-3.9.0 | 69 KB | ########## | 100% [A[A[A[A[A
mkl-2024.2.2 | 98.3 MB | | 0%
mkl-2024.2.2 | 98.3 MB | 3 | 4%
libcblas-3.9.0 | 69 KB | ########## | 100% [A[A[A[A
libcblas-3.9.0 | 69 KB | ########## | 100% [A[A[A[A
libiconv-1.18 | 681 KB | ########## | 100% [A
libiconv-1.18 | 681 KB | ########## | 100% [A
llvm-openmp-20.1.8 | 287 KB | ########## | 100% [A[A
llvm-openmp-20.1.8 | 287 KB | ########## | 100% [A[A
mkl-2024.2.2 | 98.3 MB | # | 10%
liblapack-3.9.0 | 80 KB | ########## | 100% [A[A[A
liblapack-3.9.0 | 80 KB | ########## | 100% [A[A[A
libblas-3.9.0 | 69 KB | ########## | 100% [A[A[A[A[A
libblas-3.9.0 | 69 KB | ########## | 100% [A[A[A[A[A
mkl-2024.2.2 | 98.3 MB | #8 | 18%
mkl-2024.2.2 | 98.3 MB | ##6 | 27%
mkl-2024.2.2 | 98.3 MB | ####2 | 42%
mkl-2024.2.2 | 98.3 MB | #####1 | 51%
mkl-2024.2.2 | 98.3 MB | #####9 | 59%
mkl-2024.2.2 | 98.3 MB | ######9 | 69%
mkl-2024.2.2 | 98.3 MB | #######6 | 77%
mkl-2024.2.2 | 98.3 MB | ########2 | 83%
mkl-2024.2.2 | 98.3 MB | ########8 | 88%
mkl-2024.2.2 | 98.3 MB | #########6 | 96%
mkl-2024.2.2 | 98.3 MB | ########## | 100%
mkl-2024.2.2 | 98.3 MB | ########## | 100%
[A
[A[A
[A[A[A
[A[A[A[A
[A[A[A[A[A done
Preparing transaction: - \ | / - \ done
Verifying transaction: / - \ | / - \ | / - \ | / - \ | / - \ | / - done
Executing transaction: | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
Collecting owlready2==0.47
Using cached owlready2-0.47-py3-none-any.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-0.7.6-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-win_amd64.whl.metadata (6.9 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 colorama (from click->bioregistry==0.12.4)
Using cached colorama-0.4.6-py2.py3-none-any.whl.metadata (17 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-win_amd64.whl.metadata (37 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-win_amd64.whl (2.0 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-0.7.6-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 colorama-0.4.6-py2.py3-none-any.whl (25 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-win_amd64.whl (107 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, pytrie, owlready2, idna, dnspython, colorama, charset_normalizer, certifi, annotated-types, typing-inspection, tqdm, requests, pydantic-core, email-validator, click, pystow, pydantic, more_click, curies, bioregistry
WARNING: The script normalizer.exe is installed in 'C:\Users\BIOCBU~1\BASILI~1\120~1.0\ontoProc\22D83D~1.4\bsklenv\Scripts' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
WARNING: The script tqdm.exe is installed in 'C:\Users\BIOCBU~1\BASILI~1\120~1.0\ontoProc\22D83D~1.4\bsklenv\Scripts' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
WARNING: The script email_validator.exe is installed in 'C:\Users\BIOCBU~1\BASILI~1\120~1.0\ontoProc\22D83D~1.4\bsklenv\Scripts' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
WARNING: The script pystow.exe is installed in 'C:\Users\BIOCBU~1\BASILI~1\120~1.0\ontoProc\22D83D~1.4\bsklenv\Scripts' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
WARNING: The script curies.exe is installed in 'C:\Users\BIOCBU~1\BASILI~1\120~1.0\ontoProc\22D83D~1.4\bsklenv\Scripts' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
WARNING: The script bioregistry.exe is installed in 'C:\Users\BIOCBU~1\BASILI~1\120~1.0\ontoProc\22D83D~1.4\bsklenv\Scripts' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed annotated-types-0.7.0 bioregistry-0.12.4 certifi-2025.8.3 charset_normalizer-3.4.3 click-8.2.1 colorama-0.4.6 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-0.7.6 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
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 E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpiWsc9C\file1ecb056ca2b38, line 1.
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 E:\biocbuild\bbs-3.21-bioc\tmpdir\RtmpiWsc9C\file1ecb056ca2b38, line 1.
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