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This page was generated on 2025-11-13 11:32 -0500 (Thu, 13 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4013 |
| 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 71/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| anndataR 1.1.0 (landing page) Robrecht Cannoodt
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | ||||||||
|
To the developers/maintainers of the anndataR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/anndataR.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: anndataR |
| Version: 1.1.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data anndataR |
| StartedAt: 2025-11-12 15:48:20 -0500 (Wed, 12 Nov 2025) |
| EndedAt: 2025-11-12 15:48:37 -0500 (Wed, 12 Nov 2025) |
| EllapsedTime: 17.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data anndataR
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* checking for file ‘anndataR/DESCRIPTION’ ... OK
* preparing ‘anndataR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘anndataR.Rmd’ using rmarkdown
Quitting from anndataR.Rmd:78-80 [read-in-memory]
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NULL
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Error: processing vignette 'anndataR.Rmd' failed with diagnostics:
HDF5AnnData requires the rhdf5 package
ℹ To continue, install it using `install.packages("BiocManager");
BiocManager::install("rhdf5")`
--- failed re-building ‘anndataR.Rmd’
--- re-building ‘usage_python.Rmd’ using rmarkdown
0%| | 0.00/23.5M [00:00<?, ?B/s]
17%|█▋ | 3.99M/23.5M [00:00<00:00, 37.6MB/s]
71%|███████ | 16.7M/23.5M [00:00<00:00, 91.3MB/s]
100%|██████████| 23.5M/23.5M [00:00<00:00, 89.8MB/s]
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/PqLW1mfYIRZozvVAwJJw5/lib/python3.11/site-packages/legacy_api_wrap/__init__.py:88: UserWarning: Some cells have zero counts
return fn(*args_all, **kw)
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/PqLW1mfYIRZozvVAwJJw5/lib/python3.11/site-packages/scanpy/preprocessing/_simple.py:391: RuntimeWarning: invalid value encountered in log1p
np.log1p(x, out=x)
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/PqLW1mfYIRZozvVAwJJw5/lib/python3.11/site-packages/mudata/_core/mudata.py:1598: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
self._update_attr("var", axis=0, join_common=join_common)
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/PqLW1mfYIRZozvVAwJJw5/lib/python3.11/site-packages/mudata/_core/mudata.py:1461: FutureWarning: From 0.4 .update() will not pull obs/var columns from individual modalities by default anymore. Set mudata.set_options(pull_on_update=False) to adopt the new behaviour, which will become the default. Use new pull_obs/pull_var and push_obs/push_var methods for more flexibility.
self._update_attr("obs", axis=1, join_common=join_common)
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/PqLW1mfYIRZozvVAwJJw5/bin/python: No module named pip
--- finished re-building ‘usage_python.Rmd’
--- re-building ‘usage_seurat.Rmd’ using rmarkdown
Quitting from usage_seurat.Rmd:48-51 [read-data]
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NULL
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Error: processing vignette 'usage_seurat.Rmd' failed with diagnostics:
HDF5AnnData requires the rhdf5 package
ℹ To continue, install it using `install.packages("BiocManager");
BiocManager::install("rhdf5")`
--- failed re-building ‘usage_seurat.Rmd’
--- re-building ‘usage_singlecellexperiment.Rmd’ using rmarkdown
Quitting from usage_singlecellexperiment.Rmd:51-54 [read-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
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Error: processing vignette 'usage_singlecellexperiment.Rmd' failed with diagnostics:
HDF5AnnData requires the rhdf5 package
ℹ To continue, install it using `install.packages("BiocManager");
BiocManager::install("rhdf5")`
--- failed re-building ‘usage_singlecellexperiment.Rmd’
SUMMARY: processing the following files failed:
‘anndataR.Rmd’ ‘usage_seurat.Rmd’ ‘usage_singlecellexperiment.Rmd’
Error: Vignette re-building failed.
Execution halted