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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:16-26 [options]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'SingleCellExperiment'
---
Backtrace:
    ▆
 1. └─base::library(SingleCellExperiment)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'anndataR.Rmd' failed with diagnostics:
there is no package called 'SingleCellExperiment'
--- failed re-building ‘anndataR.Rmd’

--- re-building ‘usage_python.Rmd’ using rmarkdown

  0%|          | 0.00/23.5M [00:00<?, ?B/s]
 25%|██▌       | 5.96M/23.5M [00:00<00:00, 61.0MB/s]
 71%|███████▏  | 16.8M/23.5M [00:00<00:00, 91.6MB/s]
100%|██████████| 23.5M/23.5M [00:00<00:00, 93.6MB/s]
sys:1: UserWarning: Some cells have zero counts
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/iFuaXLRe696ylP_bc1xvV/lib/python3.12/site-packages/scanpy/preprocessing/_simple.py:376: RuntimeWarning: invalid value encountered in log1p
  np.log1p(x, out=x)

Quitting from usage_python.Rmd:88-91 [convert_to_sce]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `check_requires()`:
! Converting AnnData to SingleCellExperiment requires the
  SingleCellExperiment package
ℹ To continue, install it using `install.packages("BiocManager");
  BiocManager::install("SingleCellExperiment")`
---
Backtrace:
    ▆
 1. └─adata$as_SingleCellExperiment()
 2.   └─anndataR:::as_SingleCellExperiment(...)
 3.     └─anndataR:::check_requires(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'usage_python.Rmd' failed with diagnostics:
Converting AnnData to SingleCellExperiment requires the
SingleCellExperiment package
ℹ To continue, install it using `install.packages("BiocManager");
  BiocManager::install("SingleCellExperiment")`
--- failed re-building ‘usage_python.Rmd’

--- re-building ‘usage_seurat.Rmd’ using rmarkdown
--- finished re-building ‘usage_seurat.Rmd’

--- re-building ‘usage_singlecellexperiment.Rmd’ using rmarkdown

Quitting from usage_singlecellexperiment.Rmd:42-47 [prep-h5ad-file]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'SingleCellExperiment'
---
Backtrace:
    ▆
 1. └─base::library(SingleCellExperiment)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'usage_singlecellexperiment.Rmd' failed with diagnostics:
there is no package called 'SingleCellExperiment'
--- failed re-building ‘usage_singlecellexperiment.Rmd’

SUMMARY: processing the following files failed:
  ‘anndataR.Rmd’ ‘usage_python.Rmd’ ‘usage_singlecellexperiment.Rmd’

Error: Vignette re-building failed.
Execution halted