| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:03 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 622/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DOtools 0.99.11 (landing page) Mariano Ruz Jurado
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the DOtools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DOtools.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: DOtools |
| Version: 0.99.11 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 DOtools |
| StartedAt: 2025-10-23 17:27:57 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 17:50:52 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 1375.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 DOtools
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* checking for file ‘DOtools/DESCRIPTION’ ... OK
* preparing ‘DOtools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DOtools.Rmd’ using rmarkdown
Downloading Python-3.14.0.tar.xz...
-> https://www.python.org/ftp/python/3.14.0/Python-3.14.0.tar.xz
Installing Python-3.14.0...
Installed Python-3.14.0 to /home/biocbuild/.pyenv/versions/3.14.0
Requirement already satisfied: pip in /var/cache/basilisk/1.21.5/zellkonverter/1.19.3/zellkonverterAnnDataEnv-0.12.3/lib/python3.14/site-packages (25.2)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools
Successfully installed setuptools-80.9.0 wheel-0.45.1
Collecting anndata==0.12.3
Downloading anndata-0.12.3-py3-none-any.whl.metadata (9.9 kB)
Collecting h5py==3.15.1
Downloading h5py-3.15.1-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (3.0 kB)
Collecting natsort==8.4.0
Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting numpy==2.3.4
Downloading numpy-2.3.4-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
Collecting pandas==2.3.3
Downloading pandas-2.3.3-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
Collecting scipy==1.16.2
Downloading scipy-1.16.2-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (62 kB)
Collecting array-api-compat>=1.7.1 (from anndata==0.12.3)
Using cached array_api_compat-1.12.0-py3-none-any.whl.metadata (2.5 kB)
Collecting legacy-api-wrap (from anndata==0.12.3)
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Collecting packaging>=24.2 (from anndata==0.12.3)
Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Collecting zarr!=3.0.*,>=2.18.7 (from anndata==0.12.3)
Downloading zarr-3.1.3-py3-none-any.whl.metadata (10 kB)
Collecting python-dateutil>=2.8.2 (from pandas==2.3.3)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas==2.3.3)
Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas==2.3.3)
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Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas==2.3.3)
Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Collecting donfig>=0.8 (from zarr!=3.0.*,>=2.18.7->anndata==0.12.3)
Using cached donfig-0.8.1.post1-py3-none-any.whl.metadata (5.0 kB)
Collecting numcodecs>=0.14 (from numcodecs[crc32c]>=0.14->zarr!=3.0.*,>=2.18.7->anndata==0.12.3)
Downloading numcodecs-0.16.3.tar.gz (6.3 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 typing-extensions>=4.9 (from zarr!=3.0.*,>=2.18.7->anndata==0.12.3)
Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
Collecting pyyaml (from donfig>=0.8->zarr!=3.0.*,>=2.18.7->anndata==0.12.3)
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Collecting crc32c>=2.7 (from numcodecs[crc32c]>=0.14->zarr!=3.0.*,>=2.18.7->anndata==0.12.3)
Downloading crc32c-2.8-cp314-cp314-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (7.8 kB)
Downloading anndata-0.12.3-py3-none-any.whl (169 kB)
Downloading h5py-3.15.1-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (5.1 MB)
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Using cached natsort-8.4.0-py3-none-any.whl (38 kB)
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Downloading pandas-2.3.3-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (12.3 MB)
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Building wheels for collected packages: numcodecs
Building wheel for numcodecs (pyproject.toml): started
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Building wheel for numcodecs (pyproject.toml): still running...
Building wheel for numcodecs (pyproject.toml): finished with status 'done'
Created wheel for numcodecs: filename=numcodecs-0.16.3-cp314-cp314-linux_x86_64.whl size=8596602 sha256=a7b84cd6ce961579c9233c67efdd1862acb52421a2667f4ecb13c67c49108813
Stored in directory: /home/biocbuild/.cache/pip/wheels/96/38/61/11fa8ba44fa0ffd4ed17fe04113c95bf4e0f0cc8feba449107
Successfully built numcodecs
Installing collected packages: pytz, tzdata, typing-extensions, six, pyyaml, packaging, numpy, natsort, legacy-api-wrap, crc32c, array-api-compat, scipy, python-dateutil, numcodecs, h5py, donfig, pandas, zarr, anndata
Successfully installed anndata-0.12.3 array-api-compat-1.12.0 crc32c-2.8 donfig-0.8.1.post1 h5py-3.15.1 legacy-api-wrap-1.4.1 natsort-8.4.0 numcodecs-0.16.3 numpy-2.3.4 packaging-25.0 pandas-2.3.3 python-dateutil-2.9.0.post0 pytz-2025.2 pyyaml-6.0.3 scipy-1.16.2 six-1.17.0 typing-extensions-4.15.0 tzdata-2025.2 zarr-3.1.3
Quitting from DOtools.Rmd:279-286 [annotation]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `lock()`:
! Cannot open lock file: Permission denied
---
Backtrace:
▆
1. └─DOtools::DO.CellTypist(...)
2. └─basilisk::basiliskRun(...)
3. └─basilisk::basiliskStart(...)
4. └─basilisk::obtainEnvironmentPath(env)
5. └─dir.expiry::lockDirectory(envdir, exclusive = !file.exists(envpath))
6. └─filelock::lock(plock, exclusive = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'DOtools.Rmd' failed with diagnostics:
Cannot open lock file: Permission denied
--- failed re-building ‘DOtools.Rmd’
SUMMARY: processing the following file failed:
‘DOtools.Rmd’
Error: Vignette re-building failed.
Execution halted