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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:90-92 [read-as-Seurat]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `check_requires()`:
! Converting AnnData to Seurat requires the Seurat package
ℹ To continue, install it using `install.packages("Seurat")`
---
Backtrace:
    ▆
 1. └─anndataR::read_h5ad(h5ad_path, as = "Seurat")
 2.   └─hdf5_adata$as_Seurat(...)
 3.     └─anndataR:::as_Seurat(...)
 4.       └─anndataR:::check_requires("Converting AnnData to Seurat", c("Seurat", "SeuratObject"))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘usage_python.Rmd’ using rmarkdown
Installed 42 packages in 411ms

  0%|          | 0.00/23.5M [00:00<?, ?B/s]
 28%|██▊       | 6.70M/23.5M [00:00<00:00, 70.1MB/s]
 61%|██████▏   | 14.4M/23.5M [00:00<00:00, 76.5MB/s]
100%|██████████| 23.5M/23.5M [00:00<00:00, 87.1MB/s]
sys:1: UserWarning: Some cells have zero counts
/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/O-WPa9VhIrB6dMOd2QMVz/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:95-98 [convert_to_seurat]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `check_requires()`:
! Converting AnnData to Seurat requires the Seurat package
ℹ To continue, install it using `install.packages("Seurat")`
---
Backtrace:
    ▆
 1. └─adata$as_Seurat()
 2.   └─anndataR:::as_Seurat(...)
 3.     └─anndataR:::check_requires("Converting AnnData to Seurat", c("Seurat", "SeuratObject"))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Quitting from usage_seurat.Rmd:39-44 [prep-file]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'Seurat' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
---
Backtrace:
    ▆
 1. └─base::library(Seurat)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'usage_seurat.Rmd' failed with diagnostics:
package or namespace load failed for 'Seurat' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
--- failed re-building ‘usage_seurat.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted